diff --git a/.github/styler.R b/.github/styler.R
new file mode 100755
index 000000000..c5c0cb5d8
--- /dev/null
+++ b/.github/styler.R
@@ -0,0 +1,36 @@
+#!/usr/bin/env Rscript
+
+library("argparse")
+library("styler")
+
+parser <- ArgumentParser(description = "Call styler")
+parser$add_argument("dir",
+    metavar = "DIR", type = "character",
+    help = "File to parse"
+)
+parser$add_argument("--dry",
+    choices = c("off", "on"), default = "on"
+)
+args <- parser$parse_args()
+
+file_info <- file.info(args$dir)
+is_directory <- file_info$isdir
+
+if (is_directory) {
+    captured_output <- capture.output({
+        result <- style_dir(args$dir, indent_by = 4, dry = args$dry, recursive = TRUE)
+    })
+} else {
+    captured_output <- capture.output({
+        result <- style_file(args$dir, indent_by = 4, dry = args$dry)
+    })
+}
+
+n <- nrow(subset(result, changed == TRUE))
+if (n > 0) {
+    if (args$dry == "off") {
+        print(paste("Changed", n, "files"))
+    } else {
+        stop(paste("Linting failed for", n, "files"))
+    }
+}
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index f1595b9e1..819936bd5 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -7,7 +7,7 @@ on:
     types: [run-all-tool-tests-command]
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_23.1
+  GALAXY_BRANCH: release_24.0
   MAX_CHUNKS: 40
 jobs:
   setup:
@@ -23,11 +23,11 @@ jobs:
       chunk-list: ${{ steps.discover.outputs.chunk-list }}
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
     - name: Add reaction
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v2
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
@@ -43,11 +43,11 @@ jobs:
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -56,7 +56,7 @@ jobs:
     # are not available as wheels, pip will build a wheel for them, which can be cached.
     - name: Install wheel
       run: pip install wheel
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -74,6 +74,42 @@ jobs:
       run: |
         echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})'
 
+  lint:
+    name: Check for missing containers
+    needs: setup
+    if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.11']
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v4
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+    - name: Planemo lint
+      uses: galaxyproject/planemo-ci-action@v1
+      id: lint
+      with:
+        mode: lint
+        repository-list: ${{ needs.setup.outputs.repository-list }}
+        tool-list: ${{ needs.setup.outputs.tool-list }}
+        additional-planemo-options: --biocontainers -s stdio,tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata,urls,readme,shed_yaml,repository_dependencies,tool_dependencies_actions,tool_dependencies_sha256sum,tool_dependencies_xsd,expansion
+    - uses: actions/upload-artifact@v4
+      if: ${{ failure() }}
+      with:
+        name: 'Tool linting output'
+        path: lint_report.txt
+
   test:
     name: Test tools
     # This job runs on Linux
@@ -84,7 +120,7 @@ jobs:
       fail-fast: false
       matrix:
         chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }}
-        python-version: ['3.7']
+        python-version: ['3.11']
     services:
       postgres:
         image: postgres:11
@@ -97,37 +133,23 @@ jobs:
     steps:
     # checkout the repository
     # and use it as the current working directory
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Get number of CPU cores
-      uses: SimenB/github-actions-cpu-cores@v1
+      uses: SimenB/github-actions-cpu-cores@v2
       id: cpu-cores
     - name: Clean dotnet folder for space
       run: rm -Rf /usr/share/dotnet
-    # TODO this is only temporary and only for OpenMS
-    - name: create test data
-      run: |
-           echo '${{ needs.setup.outputs.repository-list }}' > repository_list.txt
-           while read repo
-           do
-               if [ -x $repo/test-data.sh ]; then
-                   cd $repo
-                   ./test-data.sh
-               fi
-           done < repository_list.txt
-    # TODO without this planemo task aborts with `System.IO.IOException: No space left on device` 
-    #        sudo swapoff -a
-    #        sudo rm -f /swapfile
     - name: Planemo test
       uses: galaxyproject/planemo-ci-action@v1
       id: test
@@ -141,7 +163,7 @@ jobs:
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
         test_timeout: 900
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -156,18 +178,18 @@ jobs:
     needs: [setup, test]
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     # This job runs on Linux
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         path: artifacts
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -178,10 +200,11 @@ jobs:
       with:
         mode: combine
         html-report: true
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'All tool test results'
         path: upload
+    - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY
     - name: Create URL to the run output
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
       id: vars
@@ -189,7 +212,7 @@ jobs:
 
     - name: Create comment
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v2
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 7925c5d30..8f73177b9 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -2,7 +2,6 @@ name: Galaxy Tool Linting and Tests for push and PR
 on:
   pull_request:
     paths-ignore:
-      - '.github/**'
       - 'deprecated/**'
       - 'docs/**'
       - '*'
@@ -11,15 +10,14 @@ on:
       - main
       - master
     paths-ignore:
-      - '.github/**'
       - 'deprecated/**'
       - 'docs/**'
       - '*'
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_23.1
+  GALAXY_BRANCH: release_24.0
   MAX_CHUNKS: 4
-  MAX_FILE_SIZE: 2M
+  MAX_FILE_SIZE: 1M
 concurrency:
   # Group runs by PR, but keep runs on the default branch separate
   # because we do not want to cancel ToolShed uploads
@@ -45,7 +43,7 @@ jobs:
       commit-range: ${{ steps.discover.outputs.commit-range }}
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
     - name: Print github context properties
       run: |
@@ -59,17 +57,17 @@ jobs:
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" >> $GITHUB_OUTPUT
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
     - name: Cache .planemo
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-planemo
       with:
         path: ~/.planemo
@@ -80,7 +78,7 @@ jobs:
       run: pip install wheel
     - name: Install flake8
       run: pip install flake8 flake8-import-order
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -111,28 +109,38 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
+
+    - name: Set fail level for pull request
+      if: ${{ github.event_name == 'pull_request' }}
+      run:
+        echo "FAIL_LEVEL=warn" >> "$GITHUB_ENV"
+    - name: Set fail level for merge
+      if: ${{ github.event_name != 'pull_request' }}
+      run:
+        echo "FAIL_LEVEL=error" >> "$GITHUB_ENV"
     - name: Planemo lint
       uses: galaxyproject/planemo-ci-action@v1
       id: lint
       with:
         mode: lint
+        fail-level: ${{ env.FAIL_LEVEL }}
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
@@ -142,21 +150,21 @@ jobs:
   flake8:
     name: Lint Python scripts
     needs: setup
-    if: ${{ needs.setup.outputs.repository-list != '' }}
+    if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -165,7 +173,7 @@ jobs:
       run: pip install flake8 flake8-import-order
     - name: Flake8
       run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --output-file pylint_report.txt --tee
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'Python linting output'
@@ -181,50 +189,30 @@ jobs:
         os: [ubuntu-20.04]
         r-version: ['release']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - uses: r-lib/actions/setup-r@v2
       with:
         r-version: ${{ matrix.r-version }}
     - name: Cache R packages
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ env.R_LIBS_USER }}
         key: r_cache_${{ matrix.os }}_${{ matrix.r-version }}
-    - name: Install non-R lintr dependencies
-      run: sudo apt-get install libcurl4-openssl-dev
-    - name: Install lintr
-      run: |
-        install.packages('remotes')
-        remotes::install_cran("lintr")
-      shell: Rscript {0}
-    - name: Save repositories to file
-      run: echo '${{ needs.setup.outputs.repository-list }}' > repository_list.txt
+    - name: Install packages
+      uses: r-lib/actions/setup-r-dependencies@v2
+      with:
+        packages: |
+          any::argparse 
+          any::styler
     - name: lintr
       run: |
-        library(lintr)
-        linters <- linters_with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL, object_name_linter = NULL)
-        con <- file("repository_list.txt", "r")
-        status <- 0
-        while (TRUE) {
-          repo <- readLines(con, n = 1)
-          if (length(repo) == 0) {
-             break
-          }
-          lnt <- lint_dir(repo, relative_path=T, linters=linters)
-          if (length(lnt) > 0) {
-            status <- 1
-            for (l in lnt) {
-              rel_path <- paste(repo, l$filename, sep="/")
-              write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message, paste("(", l$line, ")")), stderr())
-              write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message, paste("(", l$line, ")")), "rlint_report.txt", append=TRUE)
-            }
-          }
-        }
-        quit(status = status)
-      shell: Rscript {0}
-    - uses: actions/upload-artifact@v3
+        set -eo pipefail
+        echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' -n 1 ./.github/styler.R --dry off
+        git status
+        git diff --exit-code | tee rlint_report.txt
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'R linting output'
@@ -236,7 +224,7 @@ jobs:
     if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Check file sizes
@@ -251,7 +239,7 @@ jobs:
           cat file_size_report.txt
           exit 1
         fi
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'File size report'
@@ -268,7 +256,7 @@ jobs:
       fail-fast: false
       matrix:
         chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }}
-        python-version: ['3.7']
+        python-version: ['3.11']
     services:
       postgres:
         image: postgres:11
@@ -279,20 +267,20 @@ jobs:
         ports:
           - 5432:5432
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Cache .planemo
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-planemo
       with:
         path: ~/.planemo
@@ -308,11 +296,8 @@ jobs:
                    ./test-data.sh
                fi
            done < repository_list.txt
-    # TODO without this planemo task aborts with `System.IO.IOException: No space left on device` 
-    #        sudo swapoff -a
-    #        sudo rm -f /swapfile
     - name: Get number of CPU cores
-      uses: SimenB/github-actions-cpu-cores@v1
+      uses: SimenB/github-actions-cpu-cores@v2
       id: cpu-cores
     - name: Clean dotnet folder for space
       run: rm -Rf /usr/share/dotnet
@@ -328,8 +313,8 @@ jobs:
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
-        test_timeout: 900
-    - uses: actions/upload-artifact@v3
+        test_timeout: 1800
+    - uses: actions/upload-artifact@v4
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -346,16 +331,16 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         path: artifacts
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -366,10 +351,12 @@ jobs:
       with:
         mode: combine
         html-report: true
-    - uses: actions/upload-artifact@v3
+        markdown-report: true
+    - uses: actions/upload-artifact@v4
       with:
         name: 'All tool test results'
         path: upload
+    - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY
     - name: Check outputs
       uses: galaxyproject/planemo-ci-action@v1
       id: check
@@ -385,21 +372,21 @@ jobs:
   # deploy the tools to the toolsheds (first TTS for testing)
   deploy:
     name: Deploy
-    needs: [setup, lint, flake8, lintr, combine_outputs]
+    needs: [setup, lint, combine_outputs]
     if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'galaxyproteomics' }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -423,7 +410,7 @@ jobs:
   deploy-report:
     name: Report deploy status
     needs: [deploy]
-    if: ${{ always() && needs.deploy.result != 'success' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'galaxyproject' }}
+    if: ${{ always() && needs.deploy.result != 'success' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'galaxyproteomics' }}
     runs-on: ubuntu-latest
     steps:
     # report to the PR if deployment failed
@@ -433,7 +420,7 @@ jobs:
       with:
         sha: ${{ github.event.after }}
     - name: Create comment
-      uses: peter-evans/create-or-update-comment@v2
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         issue-number: ${{ steps.getpr.outputs.number }}
diff --git a/.github/workflows/pr_without_tool_change.yaml b/.github/workflows/pr_without_tool_change.yaml
index 4e9cad6bf..edff41005 100644
--- a/.github/workflows/pr_without_tool_change.yaml
+++ b/.github/workflows/pr_without_tool_change.yaml
@@ -1,13 +1,11 @@
-name: Galaxy Tool Linting and Tests for push and PR
+name: Fallback
 # Fallback workflow that provides a succeeding "Check workflow success" job
 # as this is a requirement for being able to merge a PR
 # see https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/defining-the-mergeability-of-pull-requests/troubleshooting-required-status-checks#handling-skipped-but-required-checks
 on:
   pull_request:
 concurrency:
-  # Group runs by PR, but keep runs on the default branch separate
-  # because we do not want to cancel ToolShed uploads
-  group: pr-${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && github.run_number || github.ref }}
+  group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 jobs:
   determine-success:
diff --git a/tools/diann/diann.xml b/tools/diann/diann.xml
index b648c60bf..5a915500f 100644
--- a/tools/diann/diann.xml
+++ b/tools/diann/diann.xml
@@ -2,10 +2,10 @@
     <description>is a software for DIA/SWATH data processing</description>
     <macros>
         <token name="@TOOL_VERSION@">1.8.1</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">3</token>
     </macros>
     <requirements>
-        <container type="docker">biocontainers/diann:v@TOOL_VERSION@_cv1</container>
+        <container type="docker">biocontainers/diann:@TOOL_VERSION@_cv2</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         mkdir ./input_data &&
@@ -29,13 +29,17 @@
             #set $fasta_file_str += '--fasta ' + str($fasta_file) + ' '
         #end for
 
+        #if $input.spectral_lib_options.lib
+            ln -s '$input.spectral_lib_options.lib' './input_data/report-lib.predicted.speclib' &&
+        #end if
+
         diann
             #if $input.f != 'None'
             '$infiles_str'
             #end if
             --dir ./
             #if $input.spectral_lib_options.lib
-            --lib '$input.spectral_lib_options.lib'
+            --lib './input_data/report-lib.predicted.speclib'
             #else
             --lib
             #end if
@@ -60,12 +64,12 @@
             $input.spectral_lib_options.out_measured_rt
             $input.spectral_lib_options.predictor
             $input.spectral_lib_options.reannotate
-            #if $input.spectral_lib_options.ref
-            --ref '$input.spectral_lib_options.ref'
-            #end if
+            ##if $input.spectral_lib_options.ref
+            ##--ref '$input.spectral_lib_options.ref'
+            ###end if
 
             ## FASTA database options
-            #if $fasta_file_str != 'None'
+            #if $fasta_file_str != '--fasta None '
             '$fasta_file_str'
             #end if
             #if $input.fasta_db_options.fasta_filter
@@ -84,7 +88,7 @@
             #if $algo_options.mass_acc_ms1
             --mass-acc-ms1 '$algo_options.mass_acc_ms1'
             #end if
-            $algo_options.quick_mass_acc
+            ##$algo_options.quick_mass_acc
             $algo_options.reanalyse
             $algo_options.mbr_fix_settings
             $algo_options.relaxed_prot_inf
@@ -135,9 +139,9 @@
 
             ## Channel options
             ## ToDo: no_decoy_channel as condition?
-            #if $channel_options.channels
-            --channels '$channel_options.channels'
-            #end if
+            ##if $channel_options.channels
+            ##--channels '$channel_options.channels'
+            ###end if
             #if $channel_options.decoy_channel
             --decoy-channel '$channel_options.decoy_channel'
             #end if
@@ -191,14 +195,14 @@
             $other_options.full_unimod
             $other_options.gen_fr_restriction
             $other_options.global_mass_cal
-            $other_options.il_eq
+            ##$other_options.il_eq
             $other_options.individual_mass_acc
             $other_options.individual_reports
             $other_options.individual_windows
             $other_options.no_isotopes
             $other_options.regular_swath
             $other_options.scanning_swath
-            $other_options.semi
+            ##$other_options.semi
             $other_options.species_genes
             $other_options.tims_skip_errors
 
@@ -239,17 +243,17 @@
             <section name="spectral_lib_options" title="Spectral library">
                 <param name="gen_spec_lib" type="boolean" truevalue="--gen-spec-lib" falsevalue="" checked="false" label="Generate a spectral library" help="Instructs DIA-NN to generate a spectral library"/>
                 <param name="predictor" type="boolean" truevalue="--predictor" falsevalue="" checked="false" label="Perform deep learning-based prediction of spectra, retention times and ion mobility values" help="Instructs DIA-NN to perform deep learning-based prediction of spectra, retention times and ion mobility values"/>
-                <param name="lib" type="data" format="csv,tsv,xls,txt,binary,speclib,sptxt,msp" optional="true" label="Spectral library" help="Specify a spectral library"/>
+<!--                Removed sptxt,msp as input format > experimental feature-->
+                <param name="lib" type="data" format="csv,tsv,xls,txt,binary,speclib" optional="true" label="Spectral library" help="Specify a spectral library"/>
                 <param name="library_headers" type="text" optional="true" label="Library headers" help="Specifies column names in the spectral library to be used, in the order described in Spectral library formats [name 1],[name 2],.... Use '*' instead of the column name if DIA-NN already recognizes its name"/>
                 <param name="no_lib_filter" type="boolean" truevalue="--no-lib-filter" falsevalue="" checked="false" label="Use the input library 'as is'" help="The input library will be used 'as is' without discarding fragments that might be harmful for the analysis; use with caution"/>
                 <param name="learn_lib" type="data" format="tsv" optional="true" label="Training library" help="Specifies a 'training library' for the legacy predictor"/>
                 <param name="out_measured_rt" type="boolean" truevalue="--out-measured-rt" falsevalue="" checked="false" label="Save raw empirical retention times in the spectral library" help="Instructs DIA-NN to save raw empirical retention times in the spectral library being generated, instead of saving RTs aligned to a particular scale"/>
                 <param name="reannotate" type="boolean" truevalue="--reannotate" falsevalue="" checked="false" label="Reannotate the spectral library with protein information from the FASTA database" help="Reannotate the spectral library with protein information from the FASTA database, using the specified digest specificity"/>
-                <param name="ref" type="text" optional="true" label="Reference run" help="(Experimental) Specify a special (small) spectral library which will be used exclusively for calibration - this function can speed up calibration in library-free searches"/>
+<!--                <param name="ref" type="text" optional="true" label="Reference run" help="(Experimental) Specify a special (small) spectral library which will be used exclusively for calibration - this function can speed up calibration in library-free searches"/>-->
             </section>
             <section name="fasta_db_options" title="FASTA database">
-                <!-- ToDo fasta: use multiple fasta commands to specify multiple databases -->
-                <param name="fasta" type="data" format="fasta" multiple="true" label="Sequence database" help="Specify a sequence database in FASTA format"/>
+                <param name="fasta" type="data" format="fasta" optional="true" multiple="true" label="Sequence database" help="Specify a sequence database in FASTA format"/>
                 <param name="fasta_filter" type="data" format="txt" optional="true" label="Fasta filter" help="Only consider peptides matching the stripped sequences specified in the text file provided, when processing a sequence database"/>
                 <param name="fasta_search" type="boolean" truevalue="--fasta-search" falsevalue="" checked="false" label="Perform in silico digest of the sequence database" help="Instructs DIA-NN to perform an in silico digest of the sequence database"/>
             </section>
@@ -259,7 +263,7 @@
             <param name="mass_acc" type="float" min="0" optional="true" label="MS2 mass accuracy" help="Sets the MS2 mass accuracy to N ppm"/>
             <param name="mass_acc_cal" type="float" min="0" optional="true" label="Mass accuracy during calibration phase" help="Sets the mass accuracy used during the calibration phase of the search to N ppm"/>
             <param name="mass_acc_ms1" type="float" min="0" optional="true" label="MS1 mass accuracy" help="Sets the MS1 mass accuracy to N ppm"/>
-            <param name="quick_mass_acc" type="boolean" truevalue="--quick-mass-acc" falsevalue="" checked="false" label="(Experimental) Use a fast heuristical algorithm for MS2 mass accuracy" help="When choosing the MS2 mass accuracy setting automatically, DIA-NN will use a fast heuristical algorithm instead of IDs number optimisation"/>
+<!--            <param name="quick_mass_acc" type="boolean" truevalue="&#45;&#45;quick-mass-acc" falsevalue="" checked="false" label="(Experimental) Use a fast heuristical algorithm for MS2 mass accuracy" help="When choosing the MS2 mass accuracy setting automatically, DIA-NN will use a fast heuristical algorithm instead of IDs number optimisation"/>-->
             <!-- ToDo mbr_fix_settings: what does 'Unrelated runs' mean? -->
             <param name="reanalyse" type="boolean" truevalue="--reanalyse" falsevalue="" checked="false" label="Enable MBR" help="Enables MBR"/>
             <param name="mbr_fix_settings" type="boolean" truevalue="--mbr-fix-settings" falsevalue="" checked="false" label="Use the same settings for all runs during the second MBR pass" help="When using the 'Unrelated runs' option in combination with MBR, the same settings will be used to process all runs during the second MBR pass"/>
@@ -286,7 +290,7 @@
             <param name="cross_run_norm" type="select" label="Cross-run normalisation" help="Normalisation strategy. --global-norm/Global: Instructs DIA-NN to use simple global normalisation instead of RT-dependent normalisation. RT-dependent: Instructs DIA-NN to use RT-dependent normalisation. --sig-norm/RT and signal-dep. (experimental): Instructs DIA-NN to use RT and signal dependent normalisation (experimental). --no-norm/Off: disables cross-run normalisation. Normalised quantities reported along with the raw quantities. Default:  RT-dependent">
                 <option value="--global-norm">Global</option>
                 <option value="" selected="True">RT-dependent</option>
-                <option value="--sig-norm">RT and signal-dep. (experimental)</option>
+<!--                <option value="&#45;&#45;sig-norm">RT and signal-dep. (experimental)</option>-->
                 <option value="--no-norm">Off</option>
             </param>
             <param name="lib_gen_strategy" type="select" label="Library generationm strategy" help="Enables an intelligent algorithm which determines how to extract spectra, when creating a spectral library from DIA data. This is highly recommended and should almost always be enabled">
@@ -360,7 +364,7 @@
             <param name="target_fr" type="integer" min="0" optional="true" label="Number of fragment ions for spectral library" help="Fragment ions beyond this number will only be included in the spectral library being created (from DIA data) if they have high-quality chromatograms. Default value is 6"/>
         </section>
         <section name="channel_options" title="Channel">
-            <param name="channels" type="text" optional="true" label="(Experimental) List multiplexing channels" help="Lists multiplexing channels, wherein each channel declaration has the form [channel] = [label group],[channel name],[sites],[mass1:mass2:...], wherein [sites] has the same syntax as for --var-mod and if N sites are listed, N masses are listed at the end of the channel declaration. Examples: '--channels SILAC,L,KR,0:0; SILAC,H,KR,8.014199:10.008269' - declares standard light/heavy SILAC labels, '--channels mTRAQ,0,nK,0:0; mTRAQ,4,nK,4.0070994:4.0070994;mTRAQ,8,nK,8.0141988132:8.0141988132' - declares mTRAQ. The spectral library will be automatically split into multiple channels, for precursors bearing the [label group] modification. To add the latter to a label-free spectral library, can use --lib-fixed-mod, e.g. --fixed-mod SILAC,0.0,KR,label --lib-fixed-mod SILAC. The --channels command must be used in conjunction with --peak-translation."/>
+<!--            <param name="channels" type="text" optional="true" label="(Experimental) List multiplexing channels" help="Lists multiplexing channels, wherein each channel declaration has the form [channel] = [label group],[channel name],[sites],[mass1:mass2:...], wherein [sites] has the same syntax as for &#45;&#45;var-mod and if N sites are listed, N masses are listed at the end of the channel declaration. Examples: '&#45;&#45;channels SILAC,L,KR,0:0; SILAC,H,KR,8.014199:10.008269' - declares standard light/heavy SILAC labels, '&#45;&#45;channels mTRAQ,0,nK,0:0; mTRAQ,4,nK,4.0070994:4.0070994;mTRAQ,8,nK,8.0141988132:8.0141988132' - declares mTRAQ. The spectral library will be automatically split into multiple channels, for precursors bearing the [label group] modification. To add the latter to a label-free spectral library, can use &#45;&#45;lib-fixed-mod, e.g. &#45;&#45;fixed-mod SILAC,0.0,KR,label &#45;&#45;lib-fixed-mod SILAC. The &#45;&#45;channels command must be used in conjunction with &#45;&#45;peak-translation."/>-->
             <param name="decoy_channel" type="text" optional="true" label="Decoy channel" help="Specifies the decoy channel masses (same syntax as for --channels)"/>
             <param name="no_decoy_channel" type="boolean" truevalue="--no-decoy-channel" falsevalue="" checked="false" label="Disable the use of a decoy channel" help="Disables the use of a decoy channel for channel q-value calculation"/>
         </section>
@@ -381,7 +385,7 @@
             <param name="full_unimod" type="boolean" truevalue="--full-unimod" falsevalue="" checked="false" label="Full UniMod modification database" help="Loads the complete UniMod modification database and disables the automatic conversion of modification names to the UniMod format"/>
             <param name="gen_fr_restriction" type="boolean" truevalue="--gen-fr-restriction" falsevalue="" checked="false" label="Generate fragment exclusion information" help="Annotates the library with fragment exclusion information, based on the runs being analysed (fragments least affected by interferences are selected for quantification, why the rest are excluded)"/>
             <param name="global_mass_cal" type="boolean" truevalue="--global-mass-cal" falsevalue="" checked="false" label="Disable RT-dependent mass calibration" help="Disables RT-dependent mass calibration"/>
-            <param name="il_eq" type="boolean" truevalue="--il-eq" falsevalue="" checked="false" label="(Experimental) Isoleucine and leucine equivalent" help="When using the 'Reannotate' function, peptides will be matched to proteins while considering isoleucine and leucine equivalent"/>
+<!--            <param name="il_eq" type="boolean" truevalue="&#45;&#45;il-eq" falsevalue="" checked="false" label="(Experimental) Isoleucine and leucine equivalent" help="When using the 'Reannotate' function, peptides will be matched to proteins while considering isoleucine and leucine equivalent"/>-->
             <!-- ToDo individual_mass_acc: what does automatic mean? -->
             <param name="individual_mass_acc" type="boolean" truevalue="--individual-mass-acc" falsevalue="" checked="false" label="Independent mass accuracies" help="Mass accuracies, if set to automatic, will be determined independently for different runs"/>
             <param name="individual_reports" type="boolean" truevalue="--individual-reports" falsevalue="" checked="false" label="Individual output reports" help="A separate output report will be created for each run"/>
@@ -390,7 +394,7 @@
             <param name="no_isotopes" type="boolean" truevalue="--no-isotopes" falsevalue="" checked="false" label="Do not extract chromatograms for heavy isotopologues" help="Do not extract chromatograms for heavy isotopologues"/>
             <param name="regular_swath" type="boolean" truevalue="--regular-swath" falsevalue="" checked="false" label="Analyse all runs as regular runs" help="All runs will be analysed as if they were not Scanning SWATH runs"/>
             <param name="scanning_swath" type="boolean" truevalue="--scanning-swath" falsevalue="" checked="false" label="Analyse all runs as Scanning SWATH runs" help="All runs will be analysed as if they were Scanning SWATH runs"/>
-            <param name="semi" type="boolean" truevalue="--semi" falsevalue="" checked="false" label="(Experimental) Match a peptide to a protein with one specific and one non-specific cut" help="When using the 'Reannotate' function, a peptide will be matched to a protein also if it could be obtained with one specific and one non-specific cut (at either of the termini)"/>
+<!--            <param name="semi" type="boolean" truevalue="&#45;&#45;semi" falsevalue="" checked="false" label="(Experimental) Match a peptide to a protein with one specific and one non-specific cut" help="When using the 'Reannotate' function, a peptide will be matched to a protein also if it could be obtained with one specific and one non-specific cut (at either of the termini)"/>-->
             <param name="species_genes" type="boolean" truevalue="--species-genes" falsevalue="" checked="false" label="Add the organism identifier to the gene names" help="Instructs DIA-NN to add the organism identifier to the gene names - useful for distinguishing genes from different species, when analysing mixed samples. Works with UniProt sequence databases."/>
             <param name="tims_skip_errors" type="boolean" truevalue="--tims-skip-errors" falsevalue="" checked="false" label="Ignore errors when loading dia-PASEF data" help="DIA-NN will ignore errors when loading dia-PASEF data"/>
         </section>
@@ -464,6 +468,24 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- test for spec library -->
+        <test expect_num_outputs="1">
+            <section name="input">
+                <param name="f" value="small-peakpicking-cwt-allMS.mzML" />
+                <section name="spectral_lib_options">
+                    <param name="lib" value="report-lib.predicted.speclib"/>
+                </section>
+                <section name="fasta_db_options">
+                    <param name="fasta" value="bsa.fasta,bsa2.fasta"/>
+                    <param name="fasta_search" value="True"/>
+                </section>
+            </section>
+            <output name="output_report" file="report.tsv">
+                <assert_contents>
+                    <has_text text="PG.Normalised"/>
+                </assert_contents>
+            </output>
+        </test>
         <!-- test for Bruker data -->
 <!--        <test expect_num_outputs="2">-->
 <!--            <section name="input">-->
@@ -517,7 +539,7 @@
 
             *Spectral library formats*
 
-            DIA-NN supports comma-separated (.csv) or tab-separated (.tsv, .xls or .txt), .speclib (compact format used by DIA-NN), .sptxt (SpectraST, experimental) and .msp (NIST, experimental) library files. Important: the library must not contain non-fragmented precursor ions as 'fragments': each fragment ion must actually be produced by the peptide backbone fragmentation.
+            DIA-NN supports comma-separated (.csv) or tab-separated (.tsv, .xls or .txt), .speclib (compact format used by DIA-NN), .sptxt (SpectraST, experimental [not in Galaxy]) and .msp (NIST, experimental [not in Galaxy]) library files. Important: the library must not contain non-fragmented precursor ions as 'fragments': each fragment ion must actually be produced by the peptide backbone fragmentation.
 
             *Library-free search*
 
diff --git a/tools/eggnog_mapper/eggnog_macros.xml b/tools/eggnog_mapper/eggnog_macros.xml
index aa3623e89..56ae1e870 100644
--- a/tools/eggnog_mapper/eggnog_macros.xml
+++ b/tools/eggnog_mapper/eggnog_macros.xml
@@ -23,6 +23,11 @@
             <requirement type="package" version="@TOOL_VERSION@">eggnog-mapper</requirement>
         </requirements>
     </xml>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">eggnog-mapper-v2</xref>
+        </xrefs>
+    </xml>
     <xml name="version_command">
         <version_command>emapper.py --version</version_command>
     </xml>
diff --git a/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper.xml b/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper.xml
index e06a09a6a..9bad295e0 100644
--- a/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper.xml
+++ b/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper.xml
@@ -4,6 +4,7 @@
         <import>eggnog_macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <expand macro="biotools"/>
     <expand macro="version_command"/>
     <command detect_errors="aggressive"><![CDATA[
         @MERGE_ANNOTATIONS@
diff --git a/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper_annotate.xml b/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper_annotate.xml
index 14cc122fc..48f86d2d0 100644
--- a/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper_annotate.xml
+++ b/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper_annotate.xml
@@ -4,6 +4,7 @@
         <import>eggnog_macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <expand macro="biotools"/>
     <expand macro="version_command"/>
     <command detect_errors="aggressive"><![CDATA[
         @MERGE_ANNOTATIONS@
diff --git a/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper_search.xml b/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper_search.xml
index e1dc76c9e..36706a031 100644
--- a/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper_search.xml
+++ b/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper_search.xml
@@ -4,6 +4,7 @@
         <import>eggnog_macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <expand macro="biotools"/>
     <expand macro="version_command"/>
     <command detect_errors="aggressive"><![CDATA[
         emapper.py
diff --git a/tools/flashlfq/.shed.yml b/tools/flashlfq/.shed.yml
index 2875ee682..9a386badc 100644
--- a/tools/flashlfq/.shed.yml
+++ b/tools/flashlfq/.shed.yml
@@ -5,4 +5,4 @@ long_description: FlashLFQ is an ultrafast label-free quantification algorithm f
   mass-spectrometry proteomics
 name: flashlfq
 owner: galaxyp
-remote_repository_url: ' https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq'
+remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq
diff --git a/tools/flashlfq/flashlfq.xml b/tools/flashlfq/flashlfq.xml
index efa02eeff..9a06c48b3 100644
--- a/tools/flashlfq/flashlfq.xml
+++ b/tools/flashlfq/flashlfq.xml
@@ -1,5 +1,8 @@
 <tool id="flashlfq" name="FlashLFQ" version="1.0.3.1">
     <description>ultrafast label-free quantification for mass-spectrometry proteomics</description>
+    <xrefs>
+        <xref type="bio.tools">flashlfq</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="1.0.3">flashlfq</requirement>
     </requirements>
diff --git a/tools/maxquant/.shed.yml b/tools/maxquant/.shed.yml
index d93742c56..e9a70f494 100644
--- a/tools/maxquant/.shed.yml
+++ b/tools/maxquant/.shed.yml
@@ -3,7 +3,7 @@ name: maxquant
 categories:
 - Proteomics
 description: wrapper for MaxQuant
-homepage_url: 'https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant'
+homepage_url: https://www.maxquant.org/
 long_description: |
   MaxQuant is a quantitative proteomics software package
   designed for analyzing large mass-spectrometric data sets.
diff --git a/tools/maxquant/macros.xml b/tools/maxquant/macros.xml
index ebab76400..d3bce09bc 100644
--- a/tools/maxquant/macros.xml
+++ b/tools/maxquant/macros.xml
@@ -88,6 +88,11 @@
                     - [iodoTMT6plex-Cys130,'',0,0,0,0,True]
                     - [iodoTMT6plex-Cys131,'',0,0,0,0,True]
     </token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">maxquant</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">maxquant</requirement>
@@ -910,8 +915,7 @@
                     <param name="cp1" type="float" label="correction factor +1%" value="0.0"/>
                     <param name="cp2" type="float" label="correction factor +2%" value="0.0"/>
                     <param type="boolean" name="tmtlike" checked="false"
-                           label="TMT-like"
-                           truevalue="True" falsevalue="False"/>
+                           label="TMT-like" truevalue="true" falsevalue="false"/>
                 </repeat>
             </when>
         </conditional>
diff --git a/tools/maxquant/maxquant.xml b/tools/maxquant/maxquant.xml
index b9dc27725..135e8bf36 100755
--- a/tools/maxquant/maxquant.xml
+++ b/tools/maxquant/maxquant.xml
@@ -2,6 +2,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <expand macro="required_files"/>
     <command detect_errors="exit_code"><![CDATA[
diff --git a/tools/maxquant/maxquant_mqpar.xml b/tools/maxquant/maxquant_mqpar.xml
index 34eb7c6fa..265588234 100644
--- a/tools/maxquant/maxquant_mqpar.xml
+++ b/tools/maxquant/maxquant_mqpar.xml
@@ -2,6 +2,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <expand macro="required_files"/>
     <command detect_errors="exit_code"><![CDATA[
@@ -131,7 +132,7 @@
     <expand macro="outputs"/>
 
     <tests>
-        <test>
+        <test expect_num_outputs="19">
             <param name="ftype" value=".mzxml" />
             <param name="infiles" value="BSA_min_22,BSA_min_21.mzXML" />
             <param name="fasta_files" value="bsa.fasta" />
diff --git a/tools/metagene_annotator/.shed.yml b/tools/metagene_annotator/.shed.yml
index 0137fe19d..ae2c8a1b7 100644
--- a/tools/metagene_annotator/.shed.yml
+++ b/tools/metagene_annotator/.shed.yml
@@ -25,3 +25,4 @@ name: metagene_annotator
 owner: galaxyp
 remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator
 type: unrestricted
+homepage_url: http://metagene.nig.ac.jp/
\ No newline at end of file
diff --git a/tools/metagene_annotator/convert_mga.py b/tools/metagene_annotator/convert_mga.py
index 68c377139..527ba8774 100755
--- a/tools/metagene_annotator/convert_mga.py
+++ b/tools/metagene_annotator/convert_mga.py
@@ -35,7 +35,7 @@ def __main__():
             'complete/partial', 'gene score', 'used model',
             'rbs start', 'rbs end', 'rbs score']))
 
-    gc_rbs_pat = '# gc = (-?[0-9]*[.]?[0-9]+), rbs = (-?[0-9]*[.]?[0-9]+)' 
+    gc_rbs_pat = '# gc = (-?[0-9]*[.]?[0-9]+), rbs = (-?[0-9]*[.]?[0-9]+)'
     seq_count = 0
     gene_count = 0
     for i, line in enumerate(input_rdr):
@@ -46,12 +46,12 @@ def __main__():
             try:
                 m = re.match(gc_rbs_pat, line.strip())
                 seq_gc, seq_rbs = m.groups()
-            except:
+            except ValueError:
                 seq_gc = seq_rbs = ''
         elif line.startswith('# self:'):
             seq_type = re.sub('# self:', '', line.rstrip())
         elif line.startswith('# '):
-            seq_name = re.sub('# (\S+).*$', '\\1', line.rstrip())
+            seq_name = re.sub(r'# (\S+).*$', '\\1', line.rstrip())
             seq_count += 1
         else:
             fields = line.split('\t')
diff --git a/tools/metagene_annotator/metagene_annotator.xml b/tools/metagene_annotator/metagene_annotator.xml
index 4ec2de6f4..16480d7a6 100644
--- a/tools/metagene_annotator/metagene_annotator.xml
+++ b/tools/metagene_annotator/metagene_annotator.xml
@@ -1,8 +1,15 @@
-<tool id="metagene_annotator" name="MetaGeneAnnotator" version="1.0.0">
+<tool id="metagene_annotator" name="MetaGeneAnnotator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>gene-finding program for prokaryote and phage (used by sixgill)</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">metageneannotator</xref>
+    </xrefs>
     <requirements>
-        <requirement type="package">metagene_annotator</requirement>
-        <requirement type="package">python</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">metagene_annotator</requirement>
+        <requirement type="package" version="3.10">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #set $output_list = str($output_formats).split(',')
@@ -50,7 +57,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="inputs" value="metasequences.fasta" ftype="fasta"/>
             <param name="multiple_species" value="True"/>
             <param name="output_formats" value="txt"/>
@@ -61,7 +68,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="inputs" value="metasequences.fasta" ftype="fasta"/>
             <param name="multiple_species" value="False"/>
             <param name="output_formats" value="txt"/>
diff --git a/tools/metanovo/metanovo.xml b/tools/metanovo/metanovo.xml
index 994916a4f..5f0e9a10c 100644
--- a/tools/metanovo/metanovo.xml
+++ b/tools/metanovo/metanovo.xml
@@ -2,15 +2,18 @@
   <description>
     Produce targeted databases for mass spectrometry analysis.
   </description>
-  <requirements>
-    <requirement type="package" version="@TOOL_VERSION@">metanovo</requirement>
-  </requirements>
   <macros>
     <token name="@TOOL_VERSION@">1.9.4</token>
     <token name="@VERSION_SUFFIX@">4</token>
     <token name="@SUBSTITUTION_RX@">[^\w\-\.]</token>
     <import>macros_modifications.xml</import>
   </macros>
+  <xrefs>
+    <xref type="bio.tools">metanovo</xref>
+  </xrefs>
+  <requirements>
+    <requirement type="package" version="@TOOL_VERSION@">metanovo</requirement>
+  </requirements>
   <command>
     <![CDATA[
       #import re
@@ -152,35 +155,35 @@ novor_mass_analyzer=Trap
       <param name="CHUNKSIZE" label="Size to split fasta for parallel processing" value="100000" type="integer" optional="true"/>
     </section>
     <section name="metanovo_parameters" expanded="False" title="MetaNovo Parameters">
-      <param name="mn_specificity" argument="-mn_specificity" label="Enzyme Specificity" type="select">
+      <param argument="-mn_specificity" label="Enzyme Specificity" type="select">
         <option selected="true" value="specific">specific</option>
         <option value="semi-specific">semi-specific</option>
         <option value="unspecific">unspecific</option>
       </param>
-      <param name="mn_enzymes" argument="-mn_enzymes" label="Enzyme Rule" type="select">
+      <param argument="-mn_enzymes" label="Enzyme Rule" type="select">
         <option value="Trypsin">Trypsin</option>
         <option selected="true" value="Trypsin, no P rule">Trypsin, no P rule</option>
         <option value="Whole protein">Whole protein</option>
       </param>
-      <param name="mn_max_missed_cleavages" argument="-mn_max_missed_cleavages" label="Number of enzymatic missed cleavages" value="2" type="integer" optional="true"/>
+      <param argument="-mn_max_missed_cleavages" label="Number of enzymatic missed cleavages" value="2" type="integer" optional="true"/>
     </section>
     <section name="spectrum_matching_parameters" expanded="False" title="Spectrum Matching Parameters">
-      <param name="prec_tol" argument="-prec_tol" label="Precursor ion mass tolerance" value="10.0" type="float" optional="true"/>
-      <param name="prec_ppm" argument="-prec_ppm" label="Precursor ion tolerance unit" type="select">
+      <param argument="-prec_tol" label="Precursor ion mass tolerance" value="10.0" type="float" optional="true"/>
+      <param argument="-prec_ppm" label="Precursor ion tolerance unit" type="select">
         <option value="0">Da</option>
         <option selected="true" value="1">ppm</option>
       </param>
-      <param name="frag_tol" argument="-frag_tol" label="Fragment ion mass tolerance" value="0.05" type="float" optional="true"/>
-      <param name="frag_ppm" argument="-frag_ppm" label="Fragment ion tolerance unit" type="select">
+      <param argument="-frag_tol" label="Fragment ion mass tolerance" value="0.05" type="float" optional="true"/>
+      <param argument="-frag_ppm" label="Fragment ion tolerance unit" type="select">
         <option selected="true" value="0">Da</option>
         <option value="1">ppm</option>
       </param>
-      <param name="digestion" argument="-digestion" label="Digestion" type="select">
+      <param argument="-digestion" label="Digestion" type="select">
         <option selected="true" value="0">Enzyme</option>
         <option value="1">Unspecific</option>
         <option value="2">Whole Protein</option>
       </param>
-      <param name="enzyme" argument="-enzyme" label="Enzyme" type="select" multiple="true">
+      <param argument="-enzyme" label="Enzyme" type="select" multiple="true">
         <option value="Trypsin">Trypsin</option>
         <option selected="true" value="Trypsin (no P rule)">Trypsin (no P rule)</option>
         <option value="Arg-C">Arg-C</option>
@@ -199,108 +202,108 @@ novor_mass_analyzer=Trap
         <option value="Thermolysin">Thermolysin</option>
         <option value="LysargiNase">LysargiNase</option>
       </param>
-      <param name="specificity" argument="-specificity" label="Specificity" type="select">
+      <param argument="-specificity" label="Specificity" type="select">
           <option selected="true" value="0">Specific</option>
           <option value="1">Semi-Specific</option>
           <option value="2">N-term Specific</option>
           <option value="3">C-term Specific</option>
       </param>
-      <param name="mc" argument="-mc" label="Number of allowed missed cleavages" value="2" type="text" optional="true" help="If more than one enzyme was used, please provide the missed cleavages for every enzyme in the same order, with a comma separated list, e.g. &quot;2, 1&quot;."/>
-      <param name="fixed_mods" argument="-fixed_mods" label="Fixed modifications as comma separated list" type="select" multiple="true">
+      <param argument="-mc" label="Number of allowed missed cleavages" value="2" type="text" optional="true" help="If more than one enzyme was used, please provide the missed cleavages for every enzyme in the same order, with a comma separated list, e.g. &quot;2, 1&quot;."/>
+      <param argument="-fixed_mods" label="Fixed modifications as comma separated list" type="select" multiple="true">
         <expand macro="fixed_modifications"/>
       </param>
-      <param name="variable_mods" argument="-variable_mods" label="Variable modifications as comma separated list" type="select" multiple="true">
+      <param argument="-variable_mods" label="Variable modifications as comma separated list" type="select" multiple="true">
         <expand macro="variable_modifications"/>
       </param>
-      <param name="min_charge" argument="-min_charge" label="Minimal charge to search for" value="2" type="integer" optional="true"/>
-      <param name="max_charge" argument="-max_charge" label="Maximal charge to search for" value="4" type="integer" optional="true"/>
-      <param name="fi" argument="-fi" label="Type of forward ion searched" value="b" type="text" optional="true"/>
-      <param name="ri" argument="-ri" label="Type of rewind ion searched" value="y" type="text" optional="true"/>
-      <param name="min_isotope" argument="-min_isotope" label="Minimum precursor isotope" value="0" type="integer" optional="true"/>
-      <param name="max_isotope" argument="-max_isotope" label="Maximum precursor isotope" value="1" type="integer" optional="true"/>
+      <param argument="-min_charge" label="Minimal charge to search for" value="2" type="integer" optional="true"/>
+      <param argument="-max_charge" label="Maximal charge to search for" value="4" type="integer" optional="true"/>
+      <param argument="-fi" label="Type of forward ion searched" value="b" type="text" optional="true"/>
+      <param argument="-ri" label="Type of rewind ion searched" value="y" type="text" optional="true"/>
+      <param argument="-min_isotope" label="Minimum precursor isotope" value="0" type="integer" optional="true"/>
+      <param argument="-max_isotope" label="Maximum precursor isotope" value="1" type="integer" optional="true"/>
     </section>
     <section name="spectrum_annotation" expanded="False" title="Spectrum Annotation">
-      <param name="annotation_level" argument="-annotation_level" label="The intensity threshold to consider for annotation" value="0.75" type="float" optional="true" help="Using percentiles, 0.75 means that the 25% most intense peaks will be annotated."/>
-      <param name="annotation_high_resolution" argument="-annotation_high_resolution" label="If true the most accurate peak will be selected within the m/z tolerance." truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-annotation_level" label="The intensity threshold to consider for annotation" value="0.75" type="float" optional="true" help="Using percentiles, 0.75 means that the 25% most intense peaks will be annotated."/>
+      <param argument="-annotation_high_resolution" label="If true the most accurate peak will be selected within the m/z tolerance." truevalue="1" falsevalue="0" type="boolean" checked="true"/>
     </section>
     <section name="sequence_matching" expanded="False" title="Sequence Matching">
-      <param name="sequence_index_type" argument="-sequence_index_type" label="sequence_index_type (deprecated)" value="0" type="integer" optional="true"/>
-      <param name="sequence_matching_type" argument="-sequence_matching_type" label="The peptide to protein sequence matching type" type="select">
+      <param argument="-sequence_index_type" label="sequence_index_type (deprecated)" value="0" type="integer" optional="true"/>
+      <param argument="-sequence_matching_type" label="The peptide to protein sequence matching type" type="select">
           <option value="0">Character Sequence</option>
           <option value="1">Amino Acids</option>
           <option selected="true" value="2">Indistinguishable Amino Acids</option>
       </param>
-      <param name="sequence_matching_x" argument="-sequence_matching_x" label="The maximal share of Xs in a sequence, 0.25 means 25% of X's" value="0.25" type="float" optional="true"/>
+      <param argument="-sequence_matching_x" label="The maximal share of Xs in a sequence, 0.25 means 25% of X's" value="0.25" type="float" optional="true"/>
     </section>
     <section name="import_filters" expanded="False" title="Import Filters">
-      <param name="import_peptide_length_min" argument="-import_peptide_length_min" label="The minimal peptide length to consider when importing identification files" value="8" type="integer" optional="true"/>
-      <param name="import_peptide_length_max" argument="-import_peptide_length_max" label="The maximal peptide length to consider when importing identification files" value="30" type="integer" optional="true"/>
-      <param name="import_precursor_mz_ppm" argument="-import_precurosor_mz_ppm [sic]" label="Maximal precursor ion deviation unit" type="select">
+      <param argument="-import_peptide_length_min" label="The minimal peptide length to consider when importing identification files" value="8" type="integer" optional="true"/>
+      <param argument="-import_peptide_length_max" label="The maximal peptide length to consider when importing identification files" value="30" type="integer" optional="true"/>
+      <param argument="-import_precursor_mz_ppm" label="Maximal precursor ion deviation unit" type="select">
         <option selected="true" value="0">Da</option>
         <option value="1">ppm</option>
       </param>
-      <param name="exclude_unknown_ptms" argument="-exclude_unknown_ptms" label="Peptides presenting unrecognized PTMs will be excluded" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-exclude_unknown_ptms" label="Peptides presenting unrecognized PTMs will be excluded" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
     </section>
     <section name="ptm_localization" expanded="False" title="PTM Localization">
-      <param name="ptm_score" argument="-ptm_score" label="The PTM probabilistic score to use for modification localization" type="select">
+      <param argument="-ptm_score" label="The PTM probabilistic score to use for modification localization" type="select">
         <option value="0">A-score</option>
         <option selected="true" value="1">PhosphoRS</option>
         <option value="2">None</option>
       </param>
-      <param name="score_neutral_losses" argument="-score_neutral_losses" label="Include neutral losses in spectrum annotation of the PTM score" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
-      <param name="ptm_sequence_matching_type" argument="-ptm_sequence_matching_type" label="The modification to peptide sequence matching type" type="select">
+      <param argument="-score_neutral_losses" label="Include neutral losses in spectrum annotation of the PTM score" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
+      <param argument="-ptm_sequence_matching_type" label="The modification to peptide sequence matching type" type="select">
           <option value="0">Character Sequence</option>
           <option selected="true" value="1">Amino Acids</option>
           <option value="2">Indistinguishable Amino Acids</option>
       </param>
-      <param name="ptm_alignment" argument="-ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
     </section>
     <section name="gene_annotation" expanded="False" title="Gene Annotation">
-      <param name="useGeneMapping" argument="-useGeneMapping" label="Use and save gene mappings along with the project" truevalue="1" falsevalue="0" type="boolean" checked="true"  help="UniProt databases only"/>
-      <param name="updateGeneMapping" argument="-updateGeneMapping" label="Update gene mappings automatically from Ensembl" truevalue="1" falsevalue="0" type="boolean" checked="true" help="UniProt databases only"/>
+      <param argument="-useGeneMapping" label="Use and save gene mappings along with the project" truevalue="1" falsevalue="0" type="boolean" checked="true"  help="UniProt databases only"/>
+      <param argument="-updateGeneMapping" label="Update gene mappings automatically from Ensembl" truevalue="1" falsevalue="0" type="boolean" checked="true" help="UniProt databases only"/>
     </section>
     <section name="protein_inference" expanded="False" title="Protein Inference">
-      <param name="simplify_groups" argument="-simplify_groups" label="Simplify protein groups" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
-      <param name="simplify_score" argument="-simplify_score" label="Simplify protein groups based on the PeptideShaker target/decoy score" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
-      <param name="simplify_enzymaticity" argument="-simplify_enzymaticity" label="Simplify protein groups based on the peptide enzymaticity" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
-      <param name="simplify_evidence" argument="-simplify_evidence" label="Simplify protein groups based on the UniProt protein evidence" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
-      <param name="simplify_uncharacterized" argument="-simplify_uncharacterized" label="Simplify protein groups based on the protein characterization" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-simplify_groups" label="Simplify protein groups" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-simplify_score" label="Simplify protein groups based on the PeptideShaker target/decoy score" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-simplify_enzymaticity" label="Simplify protein groups based on the peptide enzymaticity" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-simplify_evidence" label="Simplify protein groups based on the UniProt protein evidence" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-simplify_uncharacterized" label="Simplify protein groups based on the protein characterization" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
     </section>
     <section name="validation_levels" expanded="False" title="Validation Levels">
-      <param name="psm_fdr" argument="-psm_fdr" label="FDR at the PSM level in percent" value="1" type="integer" optional="true"/>
-      <param name="peptide_fdr" argument="-peptide_fdr" label="FDR at the peptide level in percent" value="1" type="integer" optional="true"/>
-      <param name="protein_fdr" argument="-protein_fdr" label="FDR at the protein level in percent" value="1" type="integer" optional="true"/>
-      <param name="group_psms" argument="-group_psms" label="Group PSMs by charge for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
-      <param name="group_peptides" argument="-group_peptides" label="Group peptides by modification status for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
-      <param name="merge_subgroups" argument="-group_peptides" label="Merge small PSM and peptide groups for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-psm_fdr" label="FDR at the PSM level in percent" value="1" type="integer" optional="true"/>
+      <param argument="-peptide_fdr" label="FDR at the peptide level in percent" value="1" type="integer" optional="true"/>
+      <param argument="-protein_fdr" label="FDR at the protein level in percent" value="1" type="integer" optional="true"/>
+      <param argument="-group_psms" label="Group PSMs by charge for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-group_peptides" label="Group peptides by modification status for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-merge_subgroups" label="Merge small PSM and peptide groups for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
     </section>
     <section name="fraction_analysis" expanded="False" title="Fraction Analysis">
-      <param name="protein_fraction_mw_confidence" argument="-protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="95.0" type="float" optional="true"/>
+      <param argument="-protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="95.0" type="float" optional="true"/>
     </section>
     <section name="directag" expanded="False" title="DirecTag">
-      <param name="directag_tic_cutoff" argument="-directag_tic_cutoff" label="TIC cutoff in percent" value="85" type="integer" optional="true"/>
-      <param name="directag_max_peak_count" argument="-directag_max_peak_count" label="Max peak count" value="400" type="integer" optional="true"/>
-      <param name="directag_intensity_classes" argument="-directag_intensity_classes" label="Number of intensity classes" value="3" type="integer" optional="true"/>
-      <param name="directag_adjust_precursor" argument="-directag_adjust_precursor" label="Adjust precursor" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
-      <param name="directag_min_adjustment" argument="-directag_min_adjustment" label="Minimum precursor adjustment" value="-2.5" type="float" optional="true"/>
-      <param name="directag_max_adjustment" argument="-directag_max_adjustment" label="Maximum precursor adjustment" value="2.5" type="float" optional="true"/>
-      <param name="directag_adjustment_step" argument="-directag_adjustment_step" label="Precursor adjustment step" value="0.1" type="float" optional="true"/>
-      <param name="directag_charge_states" argument="-directag_charge_states" label="Number of charge states considered" value="3" type="integer" optional="true"/>
-      <param name="directag_ms_charge_state" argument="-directag_ms_charge_state" label="Use charge state from M spectrum" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
-      <param name="directag_duplicate_spectra" argument="-directag_duplicate_spectra" label="Duplicate spectra per charge" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
-      <param name="directag_deisotoping" argument="-directag_deisotoping" label="Deisotoping mode" type="select">
+      <param argument="-directag_tic_cutoff" label="TIC cutoff in percent" value="85" type="integer" optional="true"/>
+      <param argument="-directag_max_peak_count" label="Max peak count" value="400" type="integer" optional="true"/>
+      <param argument="-directag_intensity_classes" label="Number of intensity classes" value="3" type="integer" optional="true"/>
+      <param argument="-directag_adjust_precursor" label="Adjust precursor" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
+      <param argument="-directag_min_adjustment" label="Minimum precursor adjustment" value="-2.5" type="float" optional="true"/>
+      <param argument="-directag_max_adjustment" label="Maximum precursor adjustment" value="2.5" type="float" optional="true"/>
+      <param argument="-directag_adjustment_step" label="Precursor adjustment step" value="0.1" type="float" optional="true"/>
+      <param argument="-directag_charge_states" label="Number of charge states considered" value="3" type="integer" optional="true"/>
+      <param argument="-directag_ms_charge_state" label="Use charge state from M spectrum" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
+      <param argument="-directag_duplicate_spectra" label="Duplicate spectra per charge" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-directag_deisotoping" label="Deisotoping mode" type="select">
         <option selected="true" value="0">No deisotoping</option>
         <option value="1">Precursor only</option>
         <option value="2">Precursor and candidate</option>
       </param>
-      <param name="directag_isotope_tolerance" argument="-directag_isotope_tolerance" label="Isotope mz tolerance" value="0.25" type="float" optional="true"/>
-      <param name="directag_complement_tolerance" argument="-directag_complement_tolerance" label="Complement mz tolerance" value="0.5" type="float" optional="true"/>
-      <param name="directag_tag_length" argument="-directag_tag_length" label="Tag length" value="4" type="integer" optional="true"/>
-      <param name="directag_max_var_mods" argument="-directag_max_var_mods" label="Maximum variable modifications per sequence" value="2" type="integer" optional="true"/>
-      <param name="directag_max_tag_count" argument="-directag_max_tag_count" label="Maximum tag count" value="5" type="integer" optional="true"/>
-      <param name="directag_intensity_weight" argument="-directag_intensity_weight" label="Intensity score weight" value="1.0" type="float" optional="true"/>
-      <param name="directag_fidelity_weight" argument="-directag_fidelity_weight" label="Fidelity score weight" value="1.0" type="float" optional="true"/>
-      <param name="directag_complement_weight" argument="-directag_complement_weight" label="Complement score weight" value="1.0" type="float" optional="true"/>
+      <param argument="-directag_isotope_tolerance" label="Isotope mz tolerance" value="0.25" type="float" optional="true"/>
+      <param argument="-directag_complement_tolerance" label="Complement mz tolerance" value="0.5" type="float" optional="true"/>
+      <param argument="-directag_tag_length" label="Tag length" value="4" type="integer" optional="true"/>
+      <param argument="-directag_max_var_mods" label="Maximum variable modifications per sequence" value="2" type="integer" optional="true"/>
+      <param argument="-directag_max_tag_count" label="Maximum tag count" value="5" type="integer" optional="true"/>
+      <param argument="-directag_intensity_weight" label="Intensity score weight" value="1.0" type="float" optional="true"/>
+      <param argument="-directag_fidelity_weight" label="Fidelity score weight" value="1.0" type="float" optional="true"/>
+      <param argument="-directag_complement_weight" label="Complement score weight" value="1.0" type="float" optional="true"/>
     </section>
   </inputs>
   <outputs>
diff --git a/tools/metaquantome/macros.xml b/tools/metaquantome/macros.xml
index 45887340c..d1926abb1 100644
--- a/tools/metaquantome/macros.xml
+++ b/tools/metaquantome/macros.xml
@@ -1,32 +1,37 @@
 <macros>
     <token name="@TOOL_VERSION@">2.0.2</token>
     <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">metaQuantome</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
-          <requirement type="package" version="@TOOL_VERSION@">metaquantome</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">metaquantome</requirement>
             <yield/>
         </requirements>
     </xml>
     <xml name="db">
-      <param argument="db_tar" type="data" label="Database Archive File"/>
+        <param argument="db_tar" type="data" label="Database Archive File"/>
     </xml>
     <xml name="ONTOLOGY_ARGS">
-      <conditional name="ontology_args">
-        <param name="ontology" type="select" label="Ontology">
-          <option value="go">Gene Ontology (GO terms)</option>
-          <option value="ec">Enzyme Commission (EC) numbers</option>
-          <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
-        </param>
-        <when value="go">
-          <param argument="--slim_down" type="boolean" label="Use slim GO"/>
-        </when>
-        <when value="ec">
-          <!-- do nothing -->
-        </when>
-        <when value="cog">
-          <!-- do nothing -->
-        </when>
-      </conditional>
+        <conditional name="ontology_args">
+            <param name="ontology" type="select" label="Ontology">
+                <option value="go">Gene Ontology (GO terms)</option>
+                <option value="ec">Enzyme Commission (EC) numbers</option>
+                <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
+            </param>
+            <when value="go">
+                <param argument="--slim_down" type="boolean" label="Use slim GO"/>
+            </when>
+            <when value="ec">
+                <!-- do nothing -->
+            </when>
+            <when value="cog">
+                <!-- do nothing -->
+            </when>
+        </conditional>
     </xml>
     <token name="@COMMON_PARAMS@"><![CDATA[
             --samps '$samps'
@@ -40,12 +45,12 @@
     ]]>
     </token>
     <xml name="SAMPS">
-      <param name="samps" type="data" format="tabular" label="Samples file"
-        help="must be created by 'metaQuantome: create samples file'"/>
+        <param name="samps" type="data" format="tabular" label="Samples file" help="must be created by 'metaQuantome: create samples file'"/>
     </xml>
     <xml name="citations">
         <citations>
-            <yield />
+            <citation type="doi">10.1021/ACS.JPROTEOME.0C00960</citation>
+            <yield/>
         </citations>
     </xml>
 </macros>
diff --git a/tools/metaquantome/metaquantome_db.xml b/tools/metaquantome/metaquantome_db.xml
index edc8e412a..b176812dc 100644
--- a/tools/metaquantome/metaquantome_db.xml
+++ b/tools/metaquantome/metaquantome_db.xml
@@ -3,7 +3,8 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p data &&
         #set $database_list = str($databases).split(',')
@@ -14,26 +15,25 @@
         tar --create --file '$outfile' data
     ]]></command>
     <inputs>
-        <param name="databases" type="select" multiple="True" display="checkboxes"
-          label="Databases to Download">
-          <option value="ncbi" selected="true">NCBI Taxonomy Database</option>
-          <option value="go" selected="true">Gene Ontology Database</option>
-          <option value="ec" selected="true">Enzyme Commission (EC) database</option>
+        <param name="databases" type="select" multiple="True" display="checkboxes" label="Databases to Download">
+            <option value="ncbi" selected="true">NCBI Taxonomy Database</option>
+            <option value="go" selected="true">Gene Ontology Database</option>
+            <option value="ec" selected="true">Enzyme Commission (EC) database</option>
         </param>
     </inputs>
     <outputs>
         <data format="tar" name="outfile" label="metaquantome databases"/>
     </outputs>
     <tests>
-      <test>
-        <param name="databases" value="go"/>
-        <output name="outfile">
-          <assert_contents>
-            <has_text text="ontology: go"/>
-            <has_text text="ontology: go/subsets/goslim_metagenomics"/>
-          </assert_contents>
-        </output>
-      </test>
+        <test>
+            <param name="databases" value="go"/>
+            <output name="outfile">
+                <assert_contents>
+                    <has_text text="ontology: go"/>
+                    <has_text text="ontology: go/subsets/goslim_metagenomics"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[
@@ -69,5 +69,5 @@ Questions, Comments, Problems, Kudos
 
 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
 ]]></help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>
diff --git a/tools/metaquantome/metaquantome_expand.xml b/tools/metaquantome/metaquantome_expand.xml
index a348a5921..b705e3f7f 100644
--- a/tools/metaquantome/metaquantome_expand.xml
+++ b/tools/metaquantome/metaquantome_expand.xml
@@ -1,58 +1,54 @@
 <tool id="metaquantome_expand" name="metaQuantome: expand" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
-  <description>a set of functional or taxonomy annotations</description>
-  <macros>
-    <import>macros.xml</import>
-    <xml name="FUNC_FILE">
-      <param argument="--func_file" type="data" format="tabular" label="Functional file"
-          help="Tabular file with a peptide sequence column and a functional assignment column with GO terms, EC number, or COG."/>
-      <param argument="--pep_colname_func" type="text" label="Functional file: peptide column name" value="peptide"
-          help="The column name within the function file that corresponds to the peptide sequences">
-          <validator type="empty_field"/>
-      </param>
-    </xml>
-    <xml name="FUNC_COLNAME">
-      <param argument="--func_colname" type="text" label="Functional column name"
-          help="The column name within the function file with the functional terms">
-          <validator type="empty_field"/>
-      </param>
-    </xml>
-    <xml name="TAX_FILE">
-      <param argument="--tax_file" type="data" format="tabular" label="Taxonomy assignments file"/>
-      <param argument="--pep_colname_tax" type="text" label="Taxonomy file: peptide column name" value="peptide"
-          help="The column name within the taxonomy file that corresponds to the peptide sequences">
-          <validator type="empty_field"/>
-      </param>
-    </xml>
-    <xml name="TAX_COLNAME">
-      <param argument="--tax_colname" type="text" label="Taxonomy column name">
-          <help>
+    <description>a set of functional or taxonomy annotations</description>
+    <macros>
+        <import>macros.xml</import>
+        <xml name="FUNC_FILE">
+            <param argument="--func_file" type="data" format="tabular" label="Functional file" help="Tabular file with a peptide sequence column and a functional assignment column with GO terms, EC number, or COG."/>
+            <param argument="--pep_colname_func" type="text" label="Functional file: peptide column name" value="peptide" help="The column name within the function file that corresponds to the peptide sequences">
+                <validator type="empty_field"/>
+            </param>
+        </xml>
+        <xml name="FUNC_COLNAME">
+            <param argument="--func_colname" type="text" label="Functional column name" help="The column name within the function file with the functional terms">
+                <validator type="empty_field"/>
+            </param>
+        </xml>
+        <xml name="TAX_FILE">
+            <param argument="--tax_file" type="data" format="tabular" label="Taxonomy assignments file"/>
+            <param argument="--pep_colname_tax" type="text" label="Taxonomy file: peptide column name" value="peptide" help="The column name within the taxonomy file that corresponds to the peptide sequences">
+                <validator type="empty_field"/>
+            </param>
+        </xml>
+        <xml name="TAX_COLNAME">
+            <param argument="--tax_colname" type="text" label="Taxonomy column name">
+                <help>
               Name of column in taxonomy annotation file that contains
               the lowest common ancestor (LCA) annotation. The annotations must
               be either NCBI taxids (strongly preferred) or taxonomy
               names.
           </help>
-          <validator type="empty_field"/>
-      </param>
-    </xml>
-    <xml name="FT_TAR_RANK">
-      <param argument="--ft_tar_rank" type="select" label="rank at which to group taxonomy">
-        <option value="species">species</option>
-        <option value="genus" selected="true">genus</option>
-        <option value="family">family</option>
-        <option value="order">order</option>
-        <option value="class">class</option>
-        <option value="phylum">phylum</option>
-        <option value="kingdom">kingdom</option>
-      </param>
-    </xml>
-    <token name="@FUNC_FILE@">
+                <validator type="empty_field"/>
+            </param>
+        </xml>
+        <xml name="FT_TAR_RANK">
+            <param argument="--ft_tar_rank" type="select" label="rank at which to group taxonomy">
+                <option value="species">species</option>
+                <option value="genus" selected="true">genus</option>
+                <option value="family">family</option>
+                <option value="order">order</option>
+                <option value="class">class</option>
+                <option value="phylum">phylum</option>
+                <option value="kingdom">kingdom</option>
+            </param>
+        </xml>
+        <token name="@FUNC_FILE@">
       --func_file='$mode_args.func_file'
       --pep_colname_func='$mode_args.pep_colname_func'
     </token>
-    <token name="@FUNC_COLNAME@">
+        <token name="@FUNC_COLNAME@">
       --func_colname='$mode_args.func_colname'
     </token>
-    <token name="@ONTOLOGY@">
+        <token name="@ONTOLOGY@">
       --ontology='$mode_args.ontology_args.ontology'
       #if $mode_args.ontology_args.ontology == 'go'
           #if $mode_args.ontology_args.slim_down
@@ -60,19 +56,20 @@
           #end if
       #end if
     </token>
-    <token name="@TAX_FILE@">
+        <token name="@TAX_FILE@">
       --tax_file='$mode_args.tax_file'
       --pep_colname_tax='$mode_args.pep_colname_tax'
     </token>
-    <token name="@TAX_COLNAME@">
+        <token name="@TAX_COLNAME@">
       --tax_colname='$mode_args.tax_colname'
     </token>
-    <token name="@FT_TAR_RANK@">
+        <token name="@FT_TAR_RANK@">
       --ft_tar_rank='$mode_args.ft_tar_rank'
     </token>
-  </macros>
-  <expand macro="requirements" />
-  <command detect_errors="exit_code"><![CDATA[
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
     tar -xf '$db_tar' &&
     metaquantome expand
     --data_dir ./data
@@ -97,63 +94,60 @@
     #end if
     --outfile='$outfile'
   ]]></command>
-  <inputs>
-    <param name="db_tar" type="data" format="tar" label="Database Archive File"
-      help="must be created by 'metaQuantome: download'"/>
-    <expand macro="SAMPS"/>
-      <conditional name="mode_args">
-        <param argument="--mode" type="select" label="Mode">
-          <option value="f">Functional analysis</option>
-          <option value="t">Taxonomic analysis</option>
-          <option value="ft">Functional-taxonomic interaction analysis</option>
+    <inputs>
+        <param name="db_tar" type="data" format="tar" label="Database Archive File" help="must be created by 'metaQuantome: download'"/>
+        <expand macro="SAMPS"/>
+        <conditional name="mode_args">
+            <param argument="--mode" type="select" label="Mode">
+                <option value="f">Functional analysis</option>
+                <option value="t">Taxonomic analysis</option>
+                <option value="ft">Functional-taxonomic interaction analysis</option>
+            </param>
+            <when value="f">
+                <expand macro="FUNC_FILE"/>
+                <expand macro="ONTOLOGY_ARGS"/>
+                <expand macro="FUNC_COLNAME"/>
+            </when>
+            <when value="t">
+                <expand macro="TAX_FILE"/>
+                <expand macro="TAX_COLNAME"/>
+            </when>
+            <when value="ft">
+                <expand macro="FUNC_FILE"/>
+                <expand macro="FUNC_COLNAME"/>
+                <expand macro="ONTOLOGY_ARGS"/>
+                <expand macro="TAX_FILE"/>
+                <expand macro="TAX_COLNAME"/>
+                <expand macro="FT_TAR_RANK"/>
+            </when>
+        </conditional>
+        <param argument="--int_file" type="data" format="tabular" label="Intensity file" help=""/>
+        <param argument="--pep_colname_int" type="text" value="peptide" label="Intensity file: peptide column name" help="The column name within the intensity file that corresponds to the peptide sequences">
+            <validator type="empty_field"/>
         </param>
-        <when value="f">
-          <expand macro="FUNC_FILE"/>
-          <expand macro="ONTOLOGY_ARGS"/>
-          <expand macro="FUNC_COLNAME"/>
-        </when>
-        <when value="t">
-          <expand macro="TAX_FILE"/>
-          <expand macro="TAX_COLNAME"/>
-        </when>
-        <when value="ft">
-          <expand macro="FUNC_FILE"/>
-          <expand macro="FUNC_COLNAME"/>
-          <expand macro="ONTOLOGY_ARGS"/>
-          <expand macro="TAX_FILE"/>
-          <expand macro="TAX_COLNAME"/>
-          <expand macro="FT_TAR_RANK"/>
-        </when>
-      </conditional>
-      <param argument="--int_file" type="data" format="tabular" label="Intensity file"
-        help=""/>
-      <param argument="--pep_colname_int" type="text" value="peptide" label="Intensity file: peptide column name"
-        help="The column name within the intensity file that corresponds to the peptide sequences">
-        <validator type="empty_field"/>
-      </param>
-  </inputs>
-  <outputs>
-      <data format="tabular" name="outfile" label="${tool.name} on ${on_string} expanded"/>
-  </outputs>
-  <tests>
-    <test>
-       <param name="db_tar" value="ec.tar" ftype="tar"/>
-       <param name="samps" value="samples_basic.tab" ftype="tabular"/>
-       <param name="int_file" value="int_ttest.tab" ftype="tabular"/>
-       <param name="pep_colname_int" value="peptide" />
-       <param name="func_file" value="multiple_func.tab" />
-       <param name="pep_colname_func" value="peptide" />
-       <param name="func_colname" value="ec"/>
-       <param name="mode" value="f" />
-       <param name="ontology" value="ec" />
-       <output name="outfile">
-         <assert_contents>
-           <has_text text="1.2.7.10"/>
-         </assert_contents>
-       </output>
-    </test>
-  </tests>
-  <help>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outfile" label="${tool.name} on ${on_string} expanded"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="db_tar" value="ec.tar" ftype="tar"/>
+            <param name="samps" value="samples_basic.tab" ftype="tabular"/>
+            <param name="int_file" value="int_ttest.tab" ftype="tabular"/>
+            <param name="pep_colname_int" value="peptide"/>
+            <param name="func_file" value="multiple_func.tab"/>
+            <param name="pep_colname_func" value="peptide"/>
+            <param name="func_colname" value="ec"/>
+            <param name="mode" value="f"/>
+            <param name="ontology" value="ec"/>
+            <output name="outfile">
+                <assert_contents>
+                    <has_text text="1.2.7.10"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
 <![CDATA[
 metaQuantome expand
 ===================
@@ -230,5 +224,5 @@ Questions, Comments, Problems, Kudos
 
 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
 ]]></help>
-  <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>
diff --git a/tools/metaquantome/metaquantome_filter.xml b/tools/metaquantome/metaquantome_filter.xml
index 04d880fdd..92410b8f5 100755
--- a/tools/metaquantome/metaquantome_filter.xml
+++ b/tools/metaquantome/metaquantome_filter.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         metaquantome filter
diff --git a/tools/metaquantome/metaquantome_sample.xml b/tools/metaquantome/metaquantome_sample.xml
index 9d3dc8f8a..0212545e4 100644
--- a/tools/metaquantome/metaquantome_sample.xml
+++ b/tools/metaquantome/metaquantome_sample.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <command detect_errors="exit_code"><![CDATA[
         #set $samp_header = 'group\tcolnames'
         echo -e '${samp_header}' > samp_file.tab;
diff --git a/tools/metaquantome/metaquantome_stat.xml b/tools/metaquantome/metaquantome_stat.xml
index 749cc8257..5b4e5fa03 100755
--- a/tools/metaquantome/metaquantome_stat.xml
+++ b/tools/metaquantome/metaquantome_stat.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         metaquantome stat
diff --git a/tools/metaquantome/metaquantome_viz.xml b/tools/metaquantome/metaquantome_viz.xml
index 7bbbe108f..88e81d64e 100644
--- a/tools/metaquantome/metaquantome_viz.xml
+++ b/tools/metaquantome/metaquantome_viz.xml
@@ -3,79 +3,72 @@
     <macros>
         <import>macros.xml</import>
         <xml name="barcol">
-          <param argument="--barcol" type="select" label="Color for the bar fill">
-            <option value="1">Blue</option>
-            <option value="2">Orange</option>
-            <option value="3">Yellow</option>
-            <option value="4">Red</option>
-            <option value="5">Violet</option>
-            <option value="6">Black</option>
-              <help>
+            <param argument="--barcol" type="select" label="Color for the bar fill">
+                <option value="1">Blue</option>
+                <option value="2">Orange</option>
+                <option value="3">Yellow</option>
+                <option value="4">Red</option>
+                <option value="5">Violet</option>
+                <option value="6">Black</option>
+                <help>
                 These same colors are also used in the heatmap and PCA plot,
                 so the colors can be tweaked to match. Note that these colors
                 are coded as 1 through 6 in the command line tool.
               </help>
-          </param>
+            </param>
         </xml>
         <xml name="common_bar_params">
-          <param argument="--meancol" type="text" label="Mean intensity column name"
-                  help="Mean intensity column name for desired experimental condition">
-                  <validator type="empty_field"/>
-          </param>
-          <param argument="--nterms" type="integer"
-            value="5" min="1" optional="true"
-            label="Number of terms to display"
-            help="leave blank for all terms"/>
+            <param argument="--meancol" type="text" label="Mean intensity column name" help="Mean intensity column name for desired experimental condition">
+                <validator type="empty_field"/>
+            </param>
+            <param argument="--nterms" type="integer" value="5" min="1" optional="true" label="Number of terms to display" help="leave blank for all terms"/>
         </xml>
         <xml name="common_volc_params">
-          <param argument="--fc_name" type="text" label="Name of the fold change column in the stat dataframe">
-                  <validator type="empty_field"/>
-          </param>
-          <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe">
-                  <validator type="empty_field"/>
-          </param>
-          <param argument="--textannot" type="text" optional="true" label="Name of the annotation column"
-              help="Provides text annotatation for the plot.  Optional. If missing, no text will be plotted."/>
-          <param argument="--flip_fc" type="boolean" truevalue="--flip_fc" falsevalue="" checked="false"
-              label="Flip the fold change (i.e., multiply log fold change by -1)"/>
+            <param argument="--fc_name" type="text" label="Name of the fold change column in the stat dataframe">
+                <validator type="empty_field"/>
+            </param>
+            <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe">
+                <validator type="empty_field"/>
+            </param>
+            <param argument="--textannot" type="text" optional="true" label="Name of the annotation column" help="Provides text annotatation for the plot.  Optional. If missing, no text will be plotted."/>
+            <param argument="--flip_fc" type="boolean" truevalue="--flip_fc" falsevalue="" checked="false" label="Flip the fold change (i.e., multiply log fold change by -1)"/>
         </xml>
         <xml name="common_heatmap_params">
-          <conditional name="heatmap">
-            <param argument="--filter_to_sig" type="boolean" checked="false"
-              label="Only plot significant term" help="Necessitates use of results from `test`"/>
-            <when value="true">
-              <param argument="--alpha" type="float"
-              value="0.05" min="0.0" max="1.0"
-              label="The q-value significance level"/>
-              <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe">
-                <validator type="empty_field"/>
-              </param>
-            </when>
-            <when value="false">
-              <!-- do nothing -->
-            </when>
-          </conditional>
-          <param argument="--feature_cluster_size" value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the feature dendrogram tree."/>
-          <param argument="--sample_cluster_size"  value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the sample dendrogram tree."/>
+            <conditional name="heatmap">
+                <param argument="--filter_to_sig" type="select" label="Only plot significant term" help="Necessitates use of results from `test`">
+                    <option value="true">Only plot significant term</option>
+                    <option value="false">Plot all terms</option>
+                </param>
+                <when value="true">
+                    <param argument="--alpha" type="float" value="0.05" min="0.0" max="1.0" label="The q-value significance level"/>
+                    <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe">
+                        <validator type="empty_field"/>
+                    </param>
+                </when>
+                <when value="false">
+                    <!-- do nothing -->
+                </when>
+            </conditional>
+            <param argument="--feature_cluster_size" value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the feature dendrogram tree."/>
+            <param argument="--sample_cluster_size" value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the sample dendrogram tree."/>
         </xml>
         <xml name="pca_calcsep">
-          <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false"
-              label="Calculate separation between groups and include in title?"/>
+            <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false" label="Calculate separation between groups and include in title?"/>
         </xml>
         <xml name="target_onto">
-          <param argument="--target_onto" type="select" optional="false"
-            label="GO category to restrict to">
-            <help>
+            <param argument="--target_onto" type="select" optional="false" label="GO category to restrict to">
+                <help>
               Only the values from this category
               of GO terms will be displayed.
             </help>
-            <option value="bp">Biological Process</option>
-            <option value="mf">Molecular Function</option>
-            <option value="cc">Cellular Component</option>
-          </param>
+                <option value="bp">Biological Process</option>
+                <option value="mf">Molecular Function</option>
+                <option value="cc">Cellular Component</option>
+            </param>
         </xml>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 	#import re
 	#set $safename = re.sub('[^\w\-_\.]', '_', $infile.element_identifier)
@@ -172,294 +165,274 @@
 
     ]]></command>
     <inputs>
-      <param argument="--infile" type="data"
-        format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/>
-      <expand macro="SAMPS"/>
-      <conditional name="mode_args">
-        <param argument="--mode" type="select" label="Mode">
-            <option value="f">Functional analysis</option>
-            <option value="t">Taxonomic analysis</option>
-            <option value="ft">Functional-taxonomic interaction analysis</option>
-        </param>
-        <when value="f">
-          <param name="ontology" type="select" label="Ontology">
-            <option value="go">Gene Ontology (GO terms)</option>
-            <option value="ec">Enzyme Commission (EC) numbers</option>
-            <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
-          </param>
-          <conditional name="plot">
-            <param argument="--plottype" type="select" label="Plot type">
-              <option value="bar">Bar Chart (bar)</option>
-              <option value="volcano">Volcano Plot (volcano)</option>
-              <option value="heatmap">Heatmap (heatmap)</option>
-              <option value="pca">Principal Components Analysis (pca)</option>
+        <param argument="--infile" type="data" format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/>
+        <expand macro="SAMPS"/>
+        <conditional name="mode_args">
+            <param argument="--mode" type="select" label="Mode">
+                <option value="f">Functional analysis</option>
+                <option value="t">Taxonomic analysis</option>
+                <option value="ft">Functional-taxonomic interaction analysis</option>
             </param>
-            <when value="bar">
-              <expand macro="common_bar_params"/>
-              <expand macro="target_onto"/>
-              <expand macro="barcol"/>
-            </when>
-            <when value="volcano">
-              <expand macro="common_volc_params"/>
-              <param argument="--gosplit" type="boolean" truevalue="--gosplit" falsevalue="" checked="false"
-                  label="Make one plot for each of BiologicalProcess, CellularComponent, and MolecularFunction GO term categories."/>
-            </when>
-            <when value="heatmap">
-              <expand macro="common_heatmap_params"/>
-            </when>
-            <when value="pca">
-              <expand macro="pca_calcsep"/>
-            </when>
-          </conditional>
-        </when>
-        <when value="t">
-          <conditional name="plot">
-            <param argument="--plottype" type="select" label="Plot type">
-              <option value="bar">Bar Chart (bar)</option>
-              <option value="volcano">Volcano Plot (volcano)</option>
-              <option value="heatmap">Heatmap (heatmap)</option>
-              <option value="pca">Principal Components Analysis (pca)</option>
-            </param>
-            <when value="bar">
-              <param argument="--target_rank" type="select"
-                label="Taxonomic rank to restrict to in the plot"
-                      help="possibilities are taken from the input dataset.">
-                  <options from_dataset="infile">
-                    <column name="value" index="2"/>
-                    <filter type="unique_value" name="unique_taxon" column="2"/>
-                    <!-- <filter type="remove_value" value="rank" column="2"/> -->
-                  </options>
-              </param>
-              <expand macro="common_bar_params"/>
-              <expand macro="barcol"/>
-            </when>
-            <when value="volcano">
-              <expand macro="common_volc_params"/>
-            </when>
-            <when value="heatmap">
-              <expand macro="common_heatmap_params"/>
-            </when>
-            <when value="pca">
-              <expand macro="pca_calcsep"/>
-            </when>
-          </conditional>
-        </when>
-        <when value="ft">
-          <conditional name="plot">
-            <param argument="--plottype" type="select" label="Plot type">
-              <option value="ft_dist" selected="true">Functional Taxonomic Distribution (ft_dist)</option>
-            </param>
-            <when value="ft_dist">
-              <param argument="--meancol" type="text" label="Mean intensity column name"
-                      help="Mean intensity column name for desired experimental condition">
-                      <validator type="empty_field"/>
-              </param>
-              <conditional name="margin">
-                <param argument="--whichway" type="select" label="which distribution">
-                  <option value="f_dist">functional distribution for a taxon (f_dist)</option>
-                  <option value="t_dist">taxonomic distribution for a function (t_dist)</option>
+            <when value="f">
+                <param name="ontology" type="select" label="Ontology">
+                    <option value="go">Gene Ontology (GO terms)</option>
+                    <option value="ec">Enzyme Commission (EC) numbers</option>
+                    <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
                 </param>
-                <when value="f_dist">
-                  <conditional name="term">
-                    <param name="id_or_name" type="select" label="">
-                      <option value="id" selected="true">Taxon ID</option>
-                      <option value="name">Taxon name</option>
+                <conditional name="plot">
+                    <param argument="--plottype" type="select" label="Plot type">
+                        <option value="bar">Bar Chart (bar)</option>
+                        <option value="volcano">Volcano Plot (volcano)</option>
+                        <option value="heatmap">Heatmap (heatmap)</option>
+                        <option value="pca">Principal Components Analysis (pca)</option>
                     </param>
-                    <when value="id">
-                        <param argument="--id" type="select" label="Taxon id">
-                            <options from_dataset="infile">
-                              <column name="value" index="3"/>
-                              <filter type="unique_value" column="3"/>
-                              <!-- <filter type="remove_value" value="tax_id"/> -->
-                            </options>
-                        </param>
+                    <when value="bar">
+                        <expand macro="common_bar_params"/>
+                        <expand macro="target_onto"/>
+                        <expand macro="barcol"/>
                     </when>
-                    <when value="name">
-                      <param argument="--name" type="select" label="Taxon name">
-                          <options from_dataset="infile">
-                            <column name="value" index="4"/>
-                            <filter type="unique_value" column="4"/>
-                            <!-- <filter type="remove_value" value="taxon_name"/> -->
-                          </options>
-                      </param>
+                    <when value="volcano">
+                        <expand macro="common_volc_params"/>
+                        <param argument="--gosplit" type="boolean" truevalue="--gosplit" falsevalue="" checked="false" label="Make one plot for each of BiologicalProcess, CellularComponent, and MolecularFunction GO term categories."/>
                     </when>
-                  </conditional>
-                  <expand macro="target_onto"/>
-                </when>
-                <when value="t_dist">
-                  <conditional name="term">
-                    <param name="id_or_name" type="select" label="">
-                      <option value="id" selected="true">Functional term ID</option>
-                      <option value="name">Functional term name</option>
+                    <when value="heatmap">
+                        <expand macro="common_heatmap_params"/>
+                    </when>
+                    <when value="pca">
+                        <expand macro="pca_calcsep"/>
+                    </when>
+                </conditional>
+            </when>
+            <when value="t">
+                <conditional name="plot">
+                    <param argument="--plottype" type="select" label="Plot type">
+                        <option value="bar">Bar Chart (bar)</option>
+                        <option value="volcano">Volcano Plot (volcano)</option>
+                        <option value="heatmap">Heatmap (heatmap)</option>
+                        <option value="pca">Principal Components Analysis (pca)</option>
                     </param>
-                    <when value="id">
-                        <param argument="--id" type="select" label="Functional term id">
+                    <when value="bar">
+                        <param argument="--target_rank" type="select" label="Taxonomic rank to restrict to in the plot" help="possibilities are taken from the input dataset.">
                             <options from_dataset="infile">
-                              <column name="value" index="0"/>
-                              <filter type="unique_value" column="0"/>
-                              <!-- <filter type="remove_value" value="go_id"/> -->
+                                <column name="value" index="2"/>
+                                <filter type="unique_value" name="unique_taxon" column="2"/>
+                                <!-- <filter type="remove_value" value="rank" column="2"/> -->
                             </options>
                         </param>
+                        <expand macro="common_bar_params"/>
+                        <expand macro="barcol"/>
                     </when>
-                    <when value="name">
-                      <param argument="--name" type="select" label="Functional term name">
-                          <options from_dataset="infile">
-                            <column name="value" index="1"/>
-                            <filter type="unique_value" column="1"/>
-                            <!-- <filter type="remove_value" value="name"/> -->
-                          </options>
-                      </param>
+                    <when value="volcano">
+                        <expand macro="common_volc_params"/>
                     </when>
-                  </conditional>
-                  <param argument="--target_rank" type="select"
-                    label="Taxonomic rank to restrict to in the plot"
-                    help="possibilities are taken from the input dataset.">
-                    <options from_dataset="infile">
-                      <column name="value" index="5"/>
-                      <filter type="unique_value" name="unique_taxon" column="5"/>
-                      <!-- <filter type="remove_value" value="rank" column="5"/> -->
-                    </options>
-                  </param>
-                </when>
-              </conditional>
-              <expand macro="barcol"/>
+                    <when value="heatmap">
+                        <expand macro="common_heatmap_params"/>
+                    </when>
+                    <when value="pca">
+                        <expand macro="pca_calcsep"/>
+                    </when>
+                </conditional>
             </when>
-          </conditional>
-        </when>
-      </conditional>
-      <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/>
-      <param argument="--height" type="float" value="" optional="true" label="Image height in inches"/>
+            <when value="ft">
+                <conditional name="plot">
+                    <param argument="--plottype" type="select" label="Plot type">
+                        <option value="ft_dist" selected="true">Functional Taxonomic Distribution (ft_dist)</option>
+                    </param>
+                    <when value="ft_dist">
+                        <param argument="--meancol" type="text" label="Mean intensity column name" help="Mean intensity column name for desired experimental condition">
+                            <validator type="empty_field"/>
+                        </param>
+                        <conditional name="margin">
+                            <param argument="--whichway" type="select" label="which distribution">
+                                <option value="f_dist">functional distribution for a taxon (f_dist)</option>
+                                <option value="t_dist">taxonomic distribution for a function (t_dist)</option>
+                            </param>
+                            <when value="f_dist">
+                                <conditional name="term">
+                                    <param name="id_or_name" type="select" label="">
+                                        <option value="id" selected="true">Taxon ID</option>
+                                        <option value="name">Taxon name</option>
+                                    </param>
+                                    <when value="id">
+                                        <param argument="--id" type="select" label="Taxon id">
+                                            <options from_dataset="infile">
+                                                <column name="value" index="3"/>
+                                                <filter type="unique_value" column="3"/>
+                                                <!-- <filter type="remove_value" value="tax_id"/> -->
+                                            </options>
+                                        </param>
+                                    </when>
+                                    <when value="name">
+                                        <param argument="--name" type="select" label="Taxon name">
+                                            <options from_dataset="infile">
+                                                <column name="value" index="4"/>
+                                                <filter type="unique_value" column="4"/>
+                                                <!-- <filter type="remove_value" value="taxon_name"/> -->
+                                            </options>
+                                        </param>
+                                    </when>
+                                </conditional>
+                                <expand macro="target_onto"/>
+                            </when>
+                            <when value="t_dist">
+                                <conditional name="term">
+                                    <param name="id_or_name" type="select" label="">
+                                        <option value="id" selected="true">Functional term ID</option>
+                                        <option value="name">Functional term name</option>
+                                    </param>
+                                    <when value="id">
+                                        <param argument="--id" type="select" label="Functional term id">
+                                            <options from_dataset="infile">
+                                                <column name="value" index="0"/>
+                                                <filter type="unique_value" column="0"/>
+                                                <!-- <filter type="remove_value" value="go_id"/> -->
+                                            </options>
+                                        </param>
+                                    </when>
+                                    <when value="name">
+                                        <param argument="--name" type="select" label="Functional term name">
+                                            <options from_dataset="infile">
+                                                <column name="value" index="1"/>
+                                                <filter type="unique_value" column="1"/>
+                                                <!-- <filter type="remove_value" value="name"/> -->
+                                            </options>
+                                        </param>
+                                    </when>
+                                </conditional>
+                                <param argument="--target_rank" type="select" label="Taxonomic rank to restrict to in the plot" help="possibilities are taken from the input dataset.">
+                                    <options from_dataset="infile">
+                                        <column name="value" index="5"/>
+                                        <filter type="unique_value" name="unique_taxon" column="5"/>
+                                        <!-- <filter type="remove_value" value="rank" column="5"/> -->
+                                    </options>
+                                </param>
+                            </when>
+                        </conditional>
+                        <expand macro="barcol"/>
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+        <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/>
+        <param argument="--height" type="float" value="" optional="true" label="Image height in inches"/>
     </inputs>
     <outputs>
-      <data format="html" name="wrapped_outfile"
-          label="${tool.name} on ${on_string} ${mode_args.plot.plottype}.html"
-          from_work_dir="wrapped_outfile.html"/>
-      <data format="tabular" name="plotdata"
-        label="${tool.name} on ${on_string} ${mode_args.plot.plottype}: plot data"
-        from_work_dir="plotdata.tab">
-        <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter>
-      </data>
-      
-      <data format="tabular" name="heatmap_feature_cluster"
-        label="${mode_args.plot.plottype}: feature cluster data"
-        from_work_dir="feature_cluster_data.txt">
-        <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
-      </data>
-      <data format="tabular" name="heatmap_sample_cluster"
-        label="${mode_args.plot.plottype}: sample cluster data"
-        from_work_dir="sample_cluster_data.txt">
-        <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
-      </data>
-      
-      <data format="tabular" name="pca_sample_cluster"
-        label="${mode_args.plot.plottype}: sample cluster data"
-        from_work_dir="PC_Data.txt">
-        <filter>mode_args['plot']['plottype'] in ["pca"]</filter>
-      </data>
-      
+        <data format="html" name="wrapped_outfile" label="${tool.name} on ${on_string} ${mode_args.plot.plottype}.html" from_work_dir="wrapped_outfile.html"/>
+        <data format="tabular" name="plotdata" label="${tool.name} on ${on_string} ${mode_args.plot.plottype}: plot data" from_work_dir="plotdata.tab">
+            <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter>
+        </data>
+        <data format="tabular" name="heatmap_feature_cluster" label="${mode_args.plot.plottype}: feature cluster data" from_work_dir="feature_cluster_data.txt">
+            <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
+        </data>
+        <data format="tabular" name="heatmap_sample_cluster" label="${mode_args.plot.plottype}: Heatmap sample cluster data" from_work_dir="sample_cluster_data.txt">
+            <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
+        </data>
+        <data format="tabular" name="pca_sample_cluster" label="${mode_args.plot.plottype}: PCA sample cluster data" from_work_dir="PC_Data.txt">
+            <filter>mode_args['plot']['plottype'] in ["pca"]</filter>
+        </data>
     </outputs>
     <tests>
         <test expect_num_outputs="2">
-             <param name="infile" value="tax_filt_out.tab" ftype="tabular"/>
-             <param name="mode" value="t" />
-             <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
-             <param name="plottype" value="bar" />
-             <param name="target_rank" value="genus" />
-             <param name="meancol" value="NS_mean" />
-             <output name="wrapped_outfile">
+            <param name="infile" value="tax_filt_out.tab" ftype="tabular"/>
+            <param name="mode" value="t"/>
+            <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
+            <param name="plottype" value="bar"/>
+            <param name="target_rank" value="genus"/>
+            <param name="meancol" value="NS_mean"/>
+            <output name="wrapped_outfile">
                 <assert_contents>
-                    <has_text text="To download the image" />
+                    <has_text text="To download the image"/>
                 </assert_contents>
             </output>
         </test>
         <test expect_num_outputs="2">
-             <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
-             <param name="mode" value="t" />
-             <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
-             <param name="plottype" value="volcano" />
-             <param name="target_rank" value="genus" />
-             <param name="fc_name" value="log2fc_NS_over_WS" />
-             <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
-             <param name="textannot" value="taxon_name" />
-             <output name="wrapped_outfile">
+            <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
+            <param name="mode" value="t"/>
+            <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
+            <param name="plottype" value="volcano"/>
+            <param name="target_rank" value="genus"/>
+            <param name="fc_name" value="log2fc_NS_over_WS"/>
+            <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
+            <param name="textannot" value="taxon_name"/>
+            <output name="wrapped_outfile">
                 <assert_contents>
-                    <has_text text="To download the image" />
+                    <has_text text="To download the image"/>
                 </assert_contents>
             </output>
         </test>
         <test expect_num_outputs="3">
             <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
-            <param name="mode" value="t" />
+            <param name="mode" value="t"/>
             <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
-            <param name="plottype" value="heatmap" />
-            <param name="filter_to_sig" />
-            <param name="alpha" value="0.05" />
-            <param name="fc_corr_p" value="corrected_p_NS_over_WS" />
-            <param name="feature_cluster_size" value="2" />
-            <param name="sample_cluster_size" value="2" />
+            <param name="plottype" value="heatmap"/>
+            <param name="filter_to_sig"/>
+            <param name="alpha" value="0.05"/>
+            <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
+            <param name="feature_cluster_size" value="2"/>
+            <param name="sample_cluster_size" value="2"/>
             <output name="wrapped_outfile">
-              <assert_contents>
-                  <has_text text="To download the image" />
-              </assert_contents>
+                <assert_contents>
+                    <has_text text="To download the image"/>
+                </assert_contents>
             </output>
             <output name="heatmap_feature_cluster">
-              <assert_contents>
-                  <has_text text="481" />
-              </assert_contents>
+                <assert_contents>
+                    <has_text text="481"/>
+                </assert_contents>
             </output>
         </test>
         <test expect_num_outputs="2">
-             <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
-             <param name="mode" value="t" />
-             <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
-             <param name="plottype" value="pca" />
-             <output name="wrapped_outfile">
+            <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
+            <param name="mode" value="t"/>
+            <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
+            <param name="plottype" value="pca"/>
+            <output name="wrapped_outfile">
                 <assert_contents>
-                    <has_text text="To download the image" />
+                    <has_text text="To download the image"/>
                 </assert_contents>
-              </output>
+            </output>
         </test>
         <test expect_num_outputs="2">
-             <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
-             <param name="mode" value="f" />
-             <param name="ontology" value="go" />
-             <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
-             <param name="plottype" value="bar" />
-             <param name="meancol" value="NS_mean" />
-             <param name="target_onto" value="bp"/>
-             <output name="wrapped_outfile">
+            <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
+            <param name="mode" value="f"/>
+            <param name="ontology" value="go"/>
+            <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
+            <param name="plottype" value="bar"/>
+            <param name="meancol" value="NS_mean"/>
+            <param name="target_onto" value="bp"/>
+            <output name="wrapped_outfile">
                 <assert_contents>
-                    <has_text text="To download the image" />
+                    <has_text text="To download the image"/>
                 </assert_contents>
             </output>
         </test>
         <test expect_num_outputs="2">
-             <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
-             <param name="mode" value="f" />
-             <param name="ontology" value="go"/>
-             <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
-             <param name="plottype" value="volcano" />
-             <param name="fc_name" value="log2fc_NS_over_WS" />
-             <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
-             <output name="wrapped_outfile">
+            <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
+            <param name="mode" value="f"/>
+            <param name="ontology" value="go"/>
+            <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
+            <param name="plottype" value="volcano"/>
+            <param name="fc_name" value="log2fc_NS_over_WS"/>
+            <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
+            <output name="wrapped_outfile">
                 <assert_contents>
-                    <has_text text="To download the image" />
+                    <has_text text="To download the image"/>
                 </assert_contents>
             </output>
         </test>
         <test expect_num_outputs="1">
-             <param name="infile" value="tf_filt_out.tab" ftype="tabular"/>
-             <param name="mode" value="ft" />
-             <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
-             <param name="plottype" value="ft_dist" />
-             <param name="meancol" value="NS_mean" />
-             <param name="whichway" value="f_dist" />
-             <param name="id_or_name" value="id" />
-             <param name="id" value="1301" />
-             <param name="target_onto" value="bp" />
-             <output name="wrapped_outfile">
+            <param name="infile" value="tf_filt_out.tab" ftype="tabular"/>
+            <param name="mode" value="ft"/>
+            <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
+            <param name="plottype" value="ft_dist"/>
+            <param name="meancol" value="NS_mean"/>
+            <param name="whichway" value="f_dist"/>
+            <param name="id_or_name" value="id"/>
+            <param name="id" value="1301"/>
+            <param name="target_onto" value="bp"/>
+            <output name="wrapped_outfile">
                 <assert_contents>
-                    <has_text text="To download the image" />
+                    <has_text text="To download the image"/>
                 </assert_contents>
             </output>
         </test>
@@ -483,5 +456,5 @@ Questions, Comments, Problems, Kudos
 
 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
     ]]></help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>
diff --git a/tools/msconvert/.shed.yml b/tools/msconvert/.shed.yml
index 70041d931..92c963613 100644
--- a/tools/msconvert/.shed.yml
+++ b/tools/msconvert/.shed.yml
@@ -12,4 +12,4 @@ long_description: |
   Main web site: http://www.proteowizard.org
 remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert
 type: unrestricted
-
+homepage_url: http://proteowizard.sourceforge.net/tools.shtml
diff --git a/tools/msconvert/msconvert.xml b/tools/msconvert/msconvert.xml
index 054709b77..17f7f8b5a 100644
--- a/tools/msconvert/msconvert.xml
+++ b/tools/msconvert/msconvert.xml
@@ -1,25 +1,34 @@
-<tool id="msconvert" name="msconvert" version="@VERSION@.2">
-  <description>Convert and/or filter mass spectrometry files</description>
-  <macros>
-      <import>msconvert_macros.xml</import>
-  </macros>
-  <requirements>
-      <container type="docker">chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@</container>
-  </requirements>
-  <stdio>
-    <regex match="Error writing run" source="stderr" level="fatal" description="Could not convert. Check stderr." />
-  </stdio>
-  <expand macro="msconvertCommand" />
-  <inputs>
-      <param format="mzml,mzxml,mz5,mgf,ms2,thermo.raw,raw,wiff,wiff.tar,agilentbrukeryep.d.tar,agilentmasshunter.d.tar,brukerbaf.d.tar,brukertdf.d.tar,watersmasslynx.raw.tar" name="input" type="data" label="Input unrefined MS data" />
-      <expand macro="msconvertInputParameters" />
-  </inputs>
-  <expand macro="msconvertOutput" />
-  <tests>
-      <expand macro="msconvert_tests" />
-  </tests>
-  <help>
-      <expand macro="msconvert_help" />
-  </help>
-  <expand macro="citations" />
+<tool id="msconvert" name="msconvert" version="@VERSION@.3">
+    <description>Convert and/or filter mass spectrometry files</description>
+    <macros>
+        <import>msconvert_macros.xml</import>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">msconvert</xref>
+    </xrefs>
+    <requirements>
+        <container type="docker">chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@</container>
+    </requirements>
+    <stdio>
+        <regex match="Error writing run" source="stderr" level="fatal" description="Could not convert. Check stderr." />
+    </stdio>
+    <expand macro="msconvertCommand" />
+    <inputs>
+        <param format="mzml,mzxml,mz5,mgf,ms2,thermo.raw,raw,wiff,wiff.tar,agilentbrukeryep.d.tar,agilentmasshunter.d.tar,brukerbaf.d.tar,brukertdf.d.tar,watersmasslynx.raw.tar" name="input" type="data" label="Input unrefined MS data" />
+        <expand macro="msconvertInputParameters" />
+    </inputs>
+    <expand macro="msconvertOutput" />
+    <tests>
+        <expand macro="msconvert_tests" />
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. Additional options such as filtering and/or precursor recalculation are available.
+
+You can view the original documentation here_.
+
+.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
+]]></help>
+    <expand macro="citations" />
 </tool>
diff --git a/tools/msconvert/msconvert_macros.xml b/tools/msconvert/msconvert_macros.xml
index a5dcc490c..d48494c90 100644
--- a/tools/msconvert/msconvert_macros.xml
+++ b/tools/msconvert/msconvert_macros.xml
@@ -221,7 +221,7 @@
         && mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'
       #else
         ## make mzML and mzXML extensions lower case (the Galaxy data type is ) otherwise detetion of the file
-        ## TODO this won't be necessay from Galaxy 21.01 https://github.com/galaxyproject/galaxy/pull/10803
+        ## this won't be necessay from Galaxy 21.01 https://github.com/galaxyproject/galaxy/pull/10803
         #if $output_type == 'mzML' or $output_type == 'mzXML'
           && find outputs/ -name "*.$output_type" | xargs -I "FILE" sh -c 'mv FILE outputs/\$(basename FILE .$output_type).#echo str($output_type).lower()
           ## a newline is needed after `#echo ...` therefore the `;'` on the next line
@@ -251,7 +251,10 @@
 
     <section name="data_processing" title="Data Processing Filters">
         <conditional name="peak_picking">
-            <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
+            <param type="select" name="pick_peaks" label="Apply peak picking?">
+                <option value="true">Yes</option>
+                <option value="false">No</option>
+            </param>
             <when value="false" />
             <when value="true">
                 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
@@ -268,7 +271,10 @@
       </conditional>
 
       <conditional name="precursor_refinement">
-        <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
+        <param type="select" name="use_mzrefinement" label="Apply m/z refinement with identification data?">
+            <option value="true">Yes</option>
+            <option value="false" selected="true">No</option>
+        </param>
         <when value="false"></when>
         <when value="true">
           <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
@@ -337,7 +343,10 @@
       </repeat>
 
       <conditional name="filter_mz_windows">
-        <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
+        <param name="do_mzwindow_filter" type="select" label="Filter m/z Window" help="">
+            <option value="true">Yes</option>
+            <option value="false">No</option>
+        </param>
         <when value="false" />
         <when value="true">
           <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
@@ -346,7 +355,10 @@
       </conditional>
 
       <conditional name="etd_filtering">
-        <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />
+        <param type="select" name="do_etd_filtering" label="Filter out ETD precursor peaks?">
+            <option value="true">Yes</option>
+            <option value="false">No</option>
+        </param>
         <when value="false" />
         <when value="true">
           <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
@@ -374,7 +386,10 @@
       </conditional>
 
       <conditional name="ms2denoise">
-        <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter"  />
+        <param name="denoise" type="select" label="De-noise MS2 with moving window filter">
+            <option value="true">Yes</option>
+            <option value="false">No</option>
+        </param>
         <when value="true">
           <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
           <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
@@ -386,7 +401,10 @@
       <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
 
       <conditional name="demultiplex">
-        <param name="demultiplex_on" type="boolean" label="Demultiplex overlapping or MSX spectra" help="Separates overlapping or MSX multiplexed spectra into several demultiplexed spectra by inferring from adjacent multiplexed spectra. Optionally handles variable fill times (for Thermo)" />
+        <param name="demultiplex_on" type="select" label="Demultiplex overlapping or MSX spectra" help="Separates overlapping or MSX multiplexed spectra into several demultiplexed spectra by inferring from adjacent multiplexed spectra. Optionally handles variable fill times (for Thermo)">
+            <option value="true">Yes</option>
+            <option value="false">No</option>
+        </param>
         <when value="true">
           <param name="massError" type="float" label="Demultiplex Mass Tolerance" value="10" />
           <param name="massErrorUnits" type="select" label="Units for Demultiplex Mass Tolerance">
@@ -397,13 +415,13 @@
           <param name="nnlsEps" type="float" label="Epsilon value for convergence criterion of NNLS solver" value="1e-10"/>
           <param name="demuxBlockExtra" type="float" label="DemuxBlockExtra" help="Multiplier to expand or reduce the # of spectra considered when demultiplexing. If 0, a fully determined system of equations is built. If > 1.0, the number of rows included in the system is extended DemuxBlockExtra * (# scans in 1 duty cycle)" value="0"/>
           <param name="variableFill" type="boolean" truevalue="true" falsevalue="false" label="Allow fill times to vary for each scan window"/>
-          <param name="noSumNormalize" type="boolean" truevalue="false" falsevalue="true" checked="True" label="Normalize sums" help="After demultiplex solve, scale the sum of the intensities contributed from each of the input windows to match the non-demultiplexed intensity"/>
+          <param name="noSumNormalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No sum normalization?" help="After demultiplex solve, scale the sum of the intensities contributed from each of the input windows to match the non-demultiplexed intensity"/>
           <param name="optimization" type="select" label="Optimization" help="Optimizations can be applied when experimental design is known">
             <option value="none" selected="true">None</option>
             <option value="overlap_only">Overlap only</option>
           </param>
           <param name="interpolateRT" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Interpolate scan time"/>
-          <param name="noWeighting" type="boolean" truevalue="false" falsevalue="true" checked="True" label="Weight nearby spectra higher" help="If true, weight the spectra nearby to the input spectrum more heavily in the solve than the outer ones. Weighting is only applied if interpolateRetentionTime is false"/>
+          <param name="noWeighting" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No Weight nearby spectra higher" help="If true, weight the spectra nearby to the input spectrum more heavily in the solve than the outer ones. Weighting is only applied if interpolateRetentionTime is false"/>
           <param name="minWindowSize" type="float" label="Minimum window size" value="0.2"/>
         </when>
         <when value="false" />
@@ -443,7 +461,10 @@
       <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
 
       <conditional name="filter_ms_levels">
-        <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" />
+        <param name="do_ms_level_filter" type="select" label="Filter MS Levels">
+            <option value="true">Yes</option>
+            <option value="false">No</option>
+        </param>
         <when value="false" />
         <when value="true">
           <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
@@ -471,7 +492,10 @@
       <param argument="--combineIonMobilitySpectra" type="boolean" truevalue="--combineIonMobilitySpectra" falsevalue="" label="Combine ion mobility spectra" help="When false, each mobility scan is written as a separate spectrum. When true, each retention time point will have a single merged scan. For Bruker TIMS spectra, the ion mobilities will be preserved in a separate binaryDataArray, and for TIMS PASEF MS2s, each precursor will be merged separately." />
 
       <conditional name="scan_summing">
-        <param name="do_scan_summing" type="boolean" truevalue="true" falsevalue="false" label="Sum adjacent scans" help="Sums MS2 sub-scans whose precursors are similar in the m/z, scan time, and/or ion mobility dimensions. It is useful for some Waters DDA data and Bruker PASEF data, where sub-scans should be summed together to increase the SNR" />
+        <param name="do_scan_summing" type="select" label="Sum adjacent scans" help="Sums MS2 sub-scans whose precursors are similar in the m/z, scan time, and/or ion mobility dimensions. It is useful for some Waters DDA data and Bruker PASEF data, where sub-scans should be summed together to increase the SNR">
+            <option value="true">Yes</option>
+            <option value="false">No</option>
+        </param>
         <when value="false" />
         <when value="true">
           <param name="precursorTol" type="float" label="Precursor m/z tolerance" value="0.05" min="0" optional="true" help="Spectra with precursor m/z values with a difference less than this tolerance are summed together." />
@@ -486,7 +510,10 @@
       <param argument="--ignoreUnknownInstrumentError" type="boolean" truevalue="--ignoreUnknownInstrumentError" falsevalue=""  label="Ignore unknown instrument error" help="If true, if an instrument cannot be determined from a vendor file, it will not be an error" />
 
       <conditional name="multi_run_output">
-        <param name="do_multi_run_output" type="boolean" truevalue="true" falsevalue="false" label="Output multiple runs per file" help="Some input types can store multiple runs (samples) in a single file (e.g. WIFF). Each run must be written to a separate output file, so check this option if you want to output all runs for a file (each file will create a dataset collection)" />
+        <param name="do_multi_run_output" type="select" label="Output multiple runs per file" help="Some input types can store multiple runs (samples) in a single file (e.g. WIFF). Each run must be written to a separate output file, so check this option if you want to output all runs for a file (each file will create a dataset collection)">
+            <option value="true">Yes</option>
+            <option value="false">No</option>
+        </param>
         <when value="false">
           <param argument="--runIndexSet" type="integer" label="Select a single run for multi-run sources" value="0" min="0" help="For multi-run sources (e.g. WIFF), select only the specified run index (first run is index 0)" />
         </when>
@@ -535,7 +562,7 @@
       <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv">
         <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
       </data>
-      <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}">
+      <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type} collection">
         <filter>general_options['multi_run_output']['do_multi_run_output'] == True</filter>
         <discover_datasets pattern="__name_and_ext__" directory="outputs" />
       </collection>
@@ -544,7 +571,7 @@
 
 
   <xml name="msconvert_tests">
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -553,7 +580,7 @@
       <param name="pick_peaks_ms_levels" value="1-" />
       <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small.RAW" ftype="thermo.raw" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -562,7 +589,7 @@
       <param name="pick_peaks_ms_levels" value="1-" />
       <output name="output" file="small-peakpicking-vendor-allMS.mzML" ftype="mzml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="ThyroglobMRM000003.d.tar" ftype="brukertdf.d.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -570,19 +597,19 @@
       <param name="do_scan_summing" value="true" />
       <output name="output" file="ThyroglobMRM000003.mzML" ftype="mzml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="MassLynxTest.raw.tar" ftype="watersmasslynx.raw.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
       <output name="output" file="MassLynxTest.mzML" ftype="mzml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="AgilentMassHunterTest.d.tar" ftype="agilentmasshunter.d.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzXML" />
       <output name="output" file="AgilentMassHunterTest.mzXML" ftype="mzxml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="BrukerBafTest.d.tar" ftype="brukerbaf.d.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -591,7 +618,7 @@
       <param name="pick_peaks_ms_levels" value="1-" />
       <output name="output" file="BrukerBafTest.mzML" ftype="mzml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -599,7 +626,7 @@
       <param name="runIndexSet" value="0" />
       <output name="output" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzXML" />
@@ -610,7 +637,7 @@
       <param name="srmAsSpectra" value="true" />
       <output name="output" file="SciexTest-HPINalone-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzXML" />
@@ -621,7 +648,7 @@
       <param name="srmAsSpectra" value="true" />
       <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -633,7 +660,7 @@
         <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" />
       </output_collection>
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -645,7 +672,7 @@
     </test>
 
     <!-- this data file only has profile MS1, so the result is the same -->
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -654,7 +681,7 @@
       <param name="pick_peaks_ms_levels" value="1" />
       <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mz5" />
@@ -662,7 +689,7 @@
       <param name="intensity_encoding" value="64" />
       <output name="output" file="small-zlib-64.mz5" compare="sim_size" ftype="mz5" delta="150000" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzXML" />
@@ -690,7 +717,7 @@
       <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
     </test>-->
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -698,7 +725,7 @@
       <output name="output" file="small-numpressLP.mzML" ftype="mzml" lines_diff="114" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -706,7 +733,7 @@
       <output name="output" file="small-numpressLS.mzML" ftype="mzml" lines_diff="114" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -714,7 +741,7 @@
       <output name="output" file="small-numpressL.mzML" ftype="mzml" lines_diff="114" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -722,7 +749,7 @@
       <output name="output" file="small-numpressP.mzML" ftype="mzml" lines_diff="114" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -730,7 +757,7 @@
       <output name="output" file="small-numpressS.mzML" ftype="mzml" lines_diff="114" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="Rpal_01.mz5" ftype="mz5" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -743,7 +770,7 @@
       <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" ftype="tsv" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -756,7 +783,7 @@
       <param name="maxKnownCharge" value="8" />
       <output name="output" file="small-chargeStatePredictor.mzML" ftype="mzml" lines_diff="114" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -771,7 +798,7 @@
       <param name="defaultMaxCharge" value="5" />
       <output name="output" file="small-turbocharger.mzML" ftype="mzml" lines_diff="114" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" ftype="mz5" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -785,7 +812,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -798,7 +825,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-threshold.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -808,7 +835,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-mzWindow.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -819,7 +846,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-denoise.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -827,7 +854,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-deisotope.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -835,7 +862,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-activation.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -848,7 +875,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-index-filter.mzML" lines_diff="32" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -856,7 +883,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-strip-it.mzML" lines_diff="100" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -866,7 +893,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -874,7 +901,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-polarity-filter.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -882,7 +909,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -902,16 +929,6 @@
       <output name="output" file="small-deisotope-poisson.mzML" />
     </test>-->
   </xml>
-  <xml name="msconvert_help">
-**What it does**
-
-Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. Additional options such as filtering and/or precursor recalculation are available.
-
-You can view the original documentation here_.
-
-.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
-  </xml>
-
   <xml name="citations">
     <citations>
         <citation type="doi">10.1093/bioinformatics/btn323</citation>
diff --git a/tools/msstats/msstats.xml b/tools/msstats/msstats.xml
index 01d1848f0..4d4d12c55 100644
--- a/tools/msstats/msstats.xml
+++ b/tools/msstats/msstats.xml
@@ -23,6 +23,9 @@
         </xml>
         
     </macros>
+    <xrefs>
+        <xref type="bio.tools">msstatstmt</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">bioconductor-msstats</requirement>
     </requirements>
@@ -1020,7 +1023,7 @@ The MSstats Galaxy tool (version @TOOL_VERSION@) allows the detection of differe
 
 **Input data**
 
-- Data in tabular or csv format, either in the 10-column MSstats format or the outputs of spectral processing tools such as `MaxQuant <http://coxdocs.org/doku.php?id=maxquant:start/>`_, `OpenSWATH <http://openswath.org/en/latest/>`_
+- Data in tabular or csv format, either in the 10-column MSstats format or the outputs of spectral processing tools such as `MaxQuant <https://cox-labs.github.io/coxdocs/maxquant_instructions.html>`_, `OpenSWATH <http://openswath.org/en/latest/>`_
 
     - MSstats format: tabular file with 10 column either manually curated or other sources such as Swath2stats tool which is implemented in Pyprophet export in Galaxy. For manual curation: Names of headers are fixed but not case sensitive: 
     
diff --git a/tools/mz_to_sqlite/.shed.yml b/tools/mz_to_sqlite/.shed.yml
index 64cf99c73..00b70a580 100644
--- a/tools/mz_to_sqlite/.shed.yml
+++ b/tools/mz_to_sqlite/.shed.yml
@@ -7,3 +7,4 @@ long_description: |
   Extract proteomics files: mzIdentML, mzML, MGF, fasta, uniprot_xml into a SQLite DB
 remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite
 type: unrestricted
+homepage_url: https://github.com/galaxyproteomics/mzToSQLite
diff --git a/tools/mz_to_sqlite/mz_to_sqlite.xml b/tools/mz_to_sqlite/mz_to_sqlite.xml
index 1ea4a157e..e284aa77e 100644
--- a/tools/mz_to_sqlite/mz_to_sqlite.xml
+++ b/tools/mz_to_sqlite/mz_to_sqlite.xml
@@ -1,5 +1,8 @@
 <tool id="mz_to_sqlite" name="mz to sqlite" version="2.1.1+galaxy0">
     <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description>
+    <xrefs>
+      <xref type="bio.tools">mztosqlite</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="2.1.1">mztosqlite</requirement>
     </requirements>
@@ -49,5 +52,17 @@ mz_to_sqlite
 
 ]]>
     </help>
-    <citations></citations>
+    <citations>
+        <citation type="bibtex">
+            @misc{
+                mzToSQLite, 
+                author = {GalaxyP}, 
+                year = {2021}, 
+                title = {mzToSQLite}, 
+                publisher = {GitHub}, 
+                journal = {GitHub repository}, 
+                url = {https://github.com/galaxyproteomics/mzToSQLite},
+            }
+        </citation>
+    </citations>
 </tool>
diff --git a/tools/openms/.shed.yml b/tools/openms/.shed.yml
index 8bdf2421e..cdb1c42a2 100644
--- a/tools/openms/.shed.yml
+++ b/tools/openms/.shed.yml
@@ -12,7 +12,6 @@ categories:
 - Proteomics
 exclude:
 - aux/
-- generate.sh
 auto_tool_repositories:
   name_template: "openms_{{ tool_id }}"
   description_template: "Wrapper for the OpenMS suite tool: {{ tool_name }}"
diff --git a/tools/openms/AccurateMassSearch.xml b/tools/openms/AccurateMassSearch.xml
index be9b4ab35..4f7d59a47 100644
--- a/tools/openms/AccurateMassSearch.xml
+++ b/tools/openms/AccurateMassSearch.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Metabolite Identification]-->
 <tool id="AccurateMassSearch" name="AccurateMassSearch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Match MS signals to molecules from a database by mass.</description>
+  <description>Match MS signals to molecules from a database by mass</description>
   <macros>
     <token name="@EXECUTABLE@">AccurateMassSearch</token>
     <import>macros.xml</import>
@@ -15,35 +14,35 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_annotation &&
 #end if
 #if $positive_adducts:
   mkdir positive_adducts &&
-  ln -s '$positive_adducts' 'positive_adducts/${re.sub("[^\w\-_]", "_", $positive_adducts.element_identifier)}.$gxy2omsext($positive_adducts.ext)' &&
+  cp '$positive_adducts' 'positive_adducts/${re.sub("[^\w\-_]", "_", $positive_adducts.element_identifier)}.$gxy2omsext($positive_adducts.ext)' &&
 #end if
 #if $negative_adducts:
   mkdir negative_adducts &&
-  ln -s '$negative_adducts' 'negative_adducts/${re.sub("[^\w\-_]", "_", $negative_adducts.element_identifier)}.$gxy2omsext($negative_adducts.ext)' &&
+  cp '$negative_adducts' 'negative_adducts/${re.sub("[^\w\-_]", "_", $negative_adducts.element_identifier)}.$gxy2omsext($negative_adducts.ext)' &&
 #end if
 #if $db.mapping_cond.mapping:
   mkdir db.mapping_cond.mapping &&
   #if $db.mapping_cond.mapping_select == "no"
   mkdir ${' '.join(["'db.mapping_cond.mapping/%s'" % (i) for i, f in enumerate($db.mapping_cond.mapping) if f])} && 
-  ${' '.join(["ln -s '%s' 'db.mapping_cond.mapping/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.mapping_cond.mapping) if f])}
+  ${' '.join(["cp '%s' 'db.mapping_cond.mapping/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.mapping_cond.mapping) if f])}
   #else
-  ln -s '$db.mapping_cond.mapping' 'db.mapping_cond.mapping/${re.sub("[^\w\-_]", "_", $db.mapping_cond.mapping.element_identifier)}.$gxy2omsext($db.mapping_cond.mapping.ext)' &&
+  cp '$db.mapping_cond.mapping' 'db.mapping_cond.mapping/${re.sub("[^\w\-_]", "_", $db.mapping_cond.mapping.element_identifier)}.$gxy2omsext($db.mapping_cond.mapping.ext)' &&
   #end if
 #end if
 #if $db.struct_cond.struct:
   mkdir db.struct_cond.struct &&
   #if $db.struct_cond.struct_select == "no"
   mkdir ${' '.join(["'db.struct_cond.struct/%s'" % (i) for i, f in enumerate($db.struct_cond.struct) if f])} && 
-  ${' '.join(["ln -s '%s' 'db.struct_cond.struct/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.struct_cond.struct) if f])}
+  ${' '.join(["cp '%s' 'db.struct_cond.struct/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.struct_cond.struct) if f])}
   #else
-  ln -s '$db.struct_cond.struct' 'db.struct_cond.struct/${re.sub("[^\w\-_]", "_", $db.struct_cond.struct.element_identifier)}.$gxy2omsext($db.struct_cond.struct.ext)' &&
+  cp '$db.struct_cond.struct' 'db.struct_cond.struct/${re.sub("[^\w\-_]", "_", $db.struct_cond.struct.element_identifier)}.$gxy2omsext($db.struct_cond.struct.ext)' &&
   #end if
 #end if
 
@@ -102,8 +101,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="featureXML or consensusXML file" help=" select consensusxml,featurexml data sets(s)"/>
-    <param name="out_annotation_type" type="select" optional="false" label="File type of output out_annotation (A copy of the input file, annotated with matching hits from the database.)">
+    <param argument="-in" type="data" format="consensusxml,featurexml" label="featureXML or consensusXML file" help=" select consensusxml,featurexml data sets(s)"/>
+    <param name="out_annotation_type" type="select" label="File type of output out_annotation (A copy of the input file, annotated with matching hits from the database.)">
       <option value="featureXML">featurexml</option>
       <option value="consensusXML">consensusxml</option>
       <option value="oms">sqlite (oms)</option>
@@ -120,7 +119,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="mapping" argument="-db:mapping" type="data" format="tabular" multiple="true" optional="true" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
         </when>
         <when value="yes">
-          <param name="mapping" argument="-db:mapping" type="data" format="tabular" multiple="false" optional="true" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
+          <param name="mapping" argument="-db:mapping" type="data" format="tabular" optional="true" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
         </when>
       </conditional>
       <conditional name="struct_cond">
@@ -132,18 +131,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="struct" argument="-db:struct" type="data" format="tabular" multiple="true" optional="true" label="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
         </when>
         <when value="yes">
-          <param name="struct" argument="-db:struct" type="data" format="tabular" multiple="false" optional="true" label="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
+          <param name="struct" argument="-db:struct" type="data" format="tabular" optional="true" label="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
         </when>
       </conditional>
     </section>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="mass_error_value" argument="-algorithm:mass_error_value" type="float" optional="true" value="5.0" label="Tolerance allowed for accurate mass search" help=""/>
-      <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="true" label="Unit of mass error (ppm or Da)" help="">
+      <param name="mass_error_value" argument="-algorithm:mass_error_value" type="float" value="5.0" label="Tolerance allowed for accurate mass search" help=""/>
+      <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" label="Unit of mass error (ppm or Da)" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_error_unit"/>
       </param>
-      <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="true" label="Positive or negative ionization mode" help="If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error">
+      <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" label="Positive or negative ionization mode" help="If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error">
         <option value="positive" selected="true">positive</option>
         <option value="negative">negative</option>
         <option value="auto">auto</option>
@@ -152,7 +151,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="isotopic_similarity" argument="-algorithm:isotopic_similarity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces)" help=""/>
       <param name="use_feature_adducts" argument="-algorithm:use_feature_adducts" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to filter AMS candidates mismatching available feature adduct annotation" help=""/>
       <param name="keep_unidentified_masses" argument="-algorithm:keep_unidentified_masses" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Keep features that did not yield any DB hit" help=""/>
-      <param name="id_format" argument="-algorithm:id_format" type="select" optional="true" label="Use legacy (ProteinID/PeptideID based storage of metabolomics data) with mzTab-v1.0.0 as output format or novel Identification Data (ID) with mzTab-v2.0.0-M as output format (ID and its MzTab-M output is currently only support for featureXML files)" help="">
+      <param name="id_format" argument="-algorithm:id_format" type="select" label="Use legacy (ProteinID/PeptideID based storage of metabolomics data) with mzTab-v1.0.0 as output format or novel Identification Data (ID) with mzTab-v2.0.0-M as output format (ID and its MzTab-M output is currently only support for featureXML files)" help="">
         <option value="legacy" selected="true">legacy</option>
         <option value="ID">ID</option>
         <expand macro="list_string_san" name="id_format"/>
@@ -163,7 +162,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -185,14 +184,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_AccurateMassSearch_1 -->
+  <tests>
+    <!-- TOPP_AccurateMassSearch_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/>
-      <output name="out" file="AccurateMassSearch_1_output.tmp.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="out" value="AccurateMassSearch_1_output.csv" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
       <param name="positive_adducts" value="CHEMISTRY/PositiveAdducts.tsv" ftype="tabular"/>
       <param name="negative_adducts" value="CHEMISTRY/NegativeAdducts.tsv" ftype="tabular"/>
       <section name="db">
@@ -221,17 +221,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_AccurateMassSearch_2 -->
+    <!-- TOPP_AccurateMassSearch_2 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
-      <output name="out" file="AccurateMassSearch_2_output.tmp.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="out" value="AccurateMassSearch_2_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
       <param name="out_annotation_type" value="featureXML"/>
-      <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_annotation" value="AccurateMassSearch_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
       <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
       <section name="db">
@@ -260,17 +263,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_AccurateMassSearch_3 -->
+    <!-- TOPP_AccurateMassSearch_3 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
-      <output name="out" file="AccurateMassSearch_3_output.tmp.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="out" value="AccurateMassSearch_3_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
       <param name="out_annotation_type" value="featureXML"/>
-      <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_annotation" value="AccurateMassSearch_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
       <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
       <section name="db">
@@ -299,17 +305,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_AccurateMassSearch_5 -->
+    <!-- TOPP_AccurateMassSearch_5 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
-      <output name="out" file="AccurateMassSearch_5_output.tmp.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="out" value="AccurateMassSearch_5_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
       <param name="out_annotation_type" value="oms"/>
-      <output name="out_annotation" file="AccurateMassSearch_5_output.tmp.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
+      <output name="out_annotation" value="AccurateMassSearch_5_output.tmp.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
       <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
       <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
       <section name="db">
@@ -338,17 +347,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_AccurateMassSearch_6 -->
+    <!-- TOPP_AccurateMassSearch_6 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
-      <output name="out" file="AccurateMassSearch_6_output.tmp.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="out" value="AccurateMassSearch_6_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
       <param name="out_annotation_type" value="featureXML"/>
-      <output name="out_annotation" file="AccurateMassSearch_6_output.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_annotation" value="AccurateMassSearch_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
       <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
       <section name="db">
@@ -377,11 +389,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Match MS signals to molecules from a database by mass.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_AccurateMassSearch.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_AccurateMassSearch.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/AssayGeneratorMetabo.xml b/tools/openms/AssayGeneratorMetabo.xml
index 2f5cd2c0b..0257cf7ca 100644
--- a/tools/openms/AssayGeneratorMetabo.xml
+++ b/tools/openms/AssayGeneratorMetabo.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="AssayGeneratorMetabo" name="AssayGeneratorMetabo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Assay library generation from DDA data (Metabolomics)</description>
   <macros>
@@ -14,23 +13,19 @@
 #import re
 
 ## Preprocessing
-#if $sirius_executable:
-  mkdir sirius_executable &&
-  ln -s '$sirius_executable' 'sirius_executable/${re.sub("[^\w\-_]", "_", $sirius_executable.element_identifier)}.$gxy2omsext($sirius_executable.ext)' &&
-#end if
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir in_id_cond.in_id &&
 #if $in_id_cond.in_id_select == "no"
 mkdir ${' '.join(["'in_id_cond.in_id/%s'" % (i) for i, f in enumerate($in_id_cond.in_id) if f])} && 
-${' '.join(["ln -s '%s' 'in_id_cond.in_id/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_id_cond.in_id) if f])}
+${' '.join(["cp '%s' 'in_id_cond.in_id/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_id_cond.in_id) if f])}
 #else
-ln -s '$in_id_cond.in_id' 'in_id_cond.in_id/${re.sub("[^\w\-_]", "_", $in_id_cond.in_id.element_identifier)}.$gxy2omsext($in_id_cond.in_id.ext)' &&
+cp '$in_id_cond.in_id' 'in_id_cond.in_id/${re.sub("[^\w\-_]", "_", $in_id_cond.in_id.element_identifier)}.$gxy2omsext($in_id_cond.in_id.ext)' &&
 #end if
 mkdir out &&
 
@@ -40,10 +35,6 @@ set -o pipefail &&
 @EXECUTABLE@ -write_ctd ./ &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
-#if $sirius_executable:
-  -sirius_executable
-  'sirius_executable/${re.sub("[^\w\-_]", "_", $sirius_executable.element_identifier)}.$gxy2omsext($sirius_executable.ext)'
-#end if
 -in
 #if $in_cond.in_select == "no"
 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
@@ -66,20 +57,19 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
 #end if]]></command>
   <configfiles>
     <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"out_workspace_directory": "__SIRIUS_WORKSPACE__", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+    <configfile name="hardcoded_json"><![CDATA[{"sirius_executable": "\$(which sirius)", "out_workspace_directory": "__SIRIUS_WORKSPACE__", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-sirius_executable" type="data" format="txt" optional="true" label="The Sirius executable" help="Provide a full or relative path, or make sure it can be found in your PATH environment select txt data sets(s)"/>
     <conditional name="in_cond">
       <param name="in_select" type="select" label="Run tool in batch mode for -in">
         <option value="no">No: process all datasets jointly</option>
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" multiple="true" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/>
       </when>
     </conditional>
     <conditional name="in_id_cond">
@@ -88,139 +78,146 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in_id" type="data" format="featurexml" multiple="true" optional="false" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/>
+        <param argument="-in_id" type="data" format="featurexml" multiple="true" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in_id" type="data" format="featurexml" multiple="false" optional="false" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/>
+        <param argument="-in_id" type="data" format="featurexml" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/>
       </when>
     </conditional>
-    <param name="out_type" type="select" optional="false" label="File type of output out (Assay library output file)">
+    <param name="out_type" type="select" label="File type of output out (Assay library output file)">
       <option value="tsv">tabular (tsv)</option>
       <option value="traML">traml</option>
       <option value="pqp">pqp</option>
     </param>
-    <param argument="-fragment_annotation" type="select" optional="true" label="Fragment annotation method" help="">
+    <param argument="-fragment_annotation" type="select" label="Fragment annotation method" help="">
       <option value="none">none</option>
       <option value="sirius" selected="true">sirius</option>
       <expand macro="list_string_san" name="fragment_annotation"/>
     </param>
-    <param argument="-ambiguity_resolution_mz_tolerance" type="float" optional="true" value="10.0" label="Mz tolerance for the resolution of identification ambiguity over multiple files" help=""/>
-    <param argument="-ambiguity_resolution_rt_tolerance" type="float" optional="true" value="10.0" label="RT tolerance in seconds for the resolution of identification ambiguity over multiple files" help=""/>
-    <param argument="-total_occurrence_filter" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="Filter compound based on total occurrence in analysed samples" help=""/>
-    <param argument="-fragment_annotation_score_threshold" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Filters annotations based on the explained intensity of the peaks in a spectrum" help=""/>
+    <param argument="-ambiguity_resolution_mz_tolerance" type="float" value="10.0" label="Mz tolerance for the resolution of identification ambiguity over multiple files" help=""/>
+    <param argument="-ambiguity_resolution_rt_tolerance" type="float" value="10.0" label="RT tolerance in seconds for the resolution of identification ambiguity over multiple files" help=""/>
+    <param argument="-total_occurrence_filter" type="float" min="0.0" max="1.0" value="0.1" label="Filter compound based on total occurrence in analysed samples" help=""/>
+    <param argument="-fragment_annotation_score_threshold" type="float" min="0.0" max="1.0" value="0.8" label="Filters annotations based on the explained intensity of the peaks in a spectrum" help=""/>
     <param argument="-decoy_generation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decoys will be generated using the fragmentation tree re-rooting approach" help="This option does only work in combination with the fragment annotation via Sirius"/>
-    <param argument="-decoy_generation_method" type="select" optional="true" label="Uses different methods for decoy generation" help="Basis for the method is the fragmentation-tree re-rooting approach ('original'). This approach can be extended by using 'resolve_overlap', which will resolve overlapping fragments of the highest intensity fragments chosen, by adding -CH2 mass to the overlapping fragments. 'Add_shift' will add a -CH2 mass shift to the target fragments and use them as additional decoys if fragmentation-tree re-rooting failed. 'Both' combines the extended methods (resolve_overlap, add_shift)">
+    <param argument="-decoy_generation_method" type="select" label="Uses different methods for decoy generation" help="Basis for the method is the fragmentation-tree re-rooting approach ('original'). This approach can be extended by using 'resolve_overlap', which will resolve overlapping fragments of the highest intensity fragments chosen, by adding -CH2 mass to the overlapping fragments. 'Add_shift' will add a -CH2 mass shift to the target fragments and use them as additional decoys if fragmentation-tree re-rooting failed. 'Both' combines the extended methods (resolve_overlap, add_shift)">
       <option value="original" selected="true">original</option>
       <option value="resolve_overlap">resolve_overlap</option>
       <option value="add_shift">add_shift</option>
       <option value="both">both</option>
       <expand macro="list_string_san" name="decoy_generation_method"/>
     </param>
-    <param argument="-method" type="select" optional="true" label="Spectrum with the highest precursor intensity or a consensus spectrum is used for assay library construction (if no fragment annotation is used)" help="">
+    <param argument="-method" type="select" label="Spectrum with the highest precursor intensity or a consensus spectrum is used for assay library construction (if no fragment annotation is used)" help="">
       <option value="highest_intensity" selected="true">highest_intensity</option>
       <option value="consensus_spectrum">consensus_spectrum</option>
       <expand macro="list_string_san" name="method"/>
     </param>
     <param argument="-use_exact_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use exact mass for precursor and fragment annotations" help=""/>
     <param argument="-exclude_ms2_precursor" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Excludes precursor in ms2 from transition list" help=""/>
-    <param argument="-precursor_mz_distance" type="float" optional="true" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" help=""/>
-    <param argument="-consensus_spectrum_precursor_rt_tolerance" type="float" optional="true" value="5.0" label="Tolerance window (left and right) for precursor selection [seconds], for consensus spectrum generation (only available without fragment annotation)" help=""/>
+    <param argument="-precursor_mz_distance" type="float" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" help=""/>
+    <param argument="-consensus_spectrum_precursor_rt_tolerance" type="float" value="5.0" label="Tolerance window (left and right) for precursor selection [seconds], for consensus spectrum generation (only available without fragment annotation)" help=""/>
     <param argument="-use_known_unknowns" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use features without identification information" help=""/>
-    <param argument="-min_transitions" type="integer" optional="true" value="3" label="Minimal number of transitions" help=""/>
-    <param argument="-max_transitions" type="integer" optional="true" value="6" label="Maximal number of transitions" help=""/>
-    <param argument="-cosine_similarity_threshold" type="float" optional="true" value="0.98" label="Threshold for cosine similarity of MS2 spectra from the same precursor used in consensus spectrum creation" help=""/>
-    <param argument="-transition_threshold" type="float" optional="true" value="5.0" label="Further transitions need at least x% of the maximum intensity (default 5%)" help=""/>
+    <param argument="-min_transitions" type="integer" value="3" label="Minimal number of transitions" help=""/>
+    <param argument="-max_transitions" type="integer" value="6" label="Maximal number of transitions" help=""/>
+    <param argument="-cosine_similarity_threshold" type="float" value="0.98" label="Threshold for cosine similarity of MS2 spectra from the same precursor used in consensus spectrum creation" help=""/>
+    <param argument="-transition_threshold" type="float" value="5.0" label="Further transitions need at least x% of the maximum intensity (default 5%)" help=""/>
     <section name="deisotoping" title="deisotoping" help="" expanded="false">
       <param name="use_deisotoper" argument="-deisotoping:use_deisotoper" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use Deisotoper (if no fragment annotation is used)" help=""/>
-      <param name="fragment_tolerance" argument="-deisotoping:fragment_tolerance" type="float" optional="true" value="1.0" label="Tolerance used to match isotopic peaks" help=""/>
-      <param name="fragment_unit" argument="-deisotoping:fragment_unit" type="select" optional="true" label="Unit of the fragment tolerance" help="">
+      <param name="fragment_tolerance" argument="-deisotoping:fragment_tolerance" type="float" value="1.0" label="Tolerance used to match isotopic peaks" help=""/>
+      <param name="fragment_unit" argument="-deisotoping:fragment_unit" type="select" label="Unit of the fragment tolerance" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="fragment_unit"/>
       </param>
-      <param name="min_charge" argument="-deisotoping:min_charge" type="integer" optional="true" min="1" value="1" label="The minimum charge considered" help=""/>
-      <param name="max_charge" argument="-deisotoping:max_charge" type="integer" optional="true" min="1" value="1" label="The maximum charge considered" help=""/>
-      <param name="min_isopeaks" argument="-deisotoping:min_isopeaks" type="integer" optional="true" min="2" value="2" label="The minimum number of isotopic peaks (at least 2) required for an isotopic cluste" help=""/>
-      <param name="max_isopeaks" argument="-deisotoping:max_isopeaks" type="integer" optional="true" min="3" value="3" label="The maximum number of isotopic peaks (at least 2) considered for an isotopic cluste" help=""/>
+      <param name="min_charge" argument="-deisotoping:min_charge" type="integer" min="1" value="1" label="The minimum charge considered" help=""/>
+      <param name="max_charge" argument="-deisotoping:max_charge" type="integer" min="1" value="1" label="The maximum charge considered" help=""/>
+      <param name="min_isopeaks" argument="-deisotoping:min_isopeaks" type="integer" min="2" value="2" label="The minimum number of isotopic peaks (at least 2) required for an isotopic cluste" help=""/>
+      <param name="max_isopeaks" argument="-deisotoping:max_isopeaks" type="integer" min="3" value="3" label="The maximum number of isotopic peaks (at least 2) considered for an isotopic cluste" help=""/>
       <param name="keep_only_deisotoped" argument="-deisotoping:keep_only_deisotoped" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only monoisotopic peaks of fragments with isotopic pattern are retained" help=""/>
       <param name="annotate_charge" argument="-deisotoping:annotate_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Annotate the charge to the peaks" help=""/>
     </section>
     <section name="preprocessing" title="" help="" expanded="false">
-      <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" optional="true" min="1" value="1" label="Number of mass traces each feature has to have to be included" help="To use this parameter, setting the feature_only flag is necessary"/>
-      <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" optional="true" value="10.0" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/>
-      <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" optional="true" label="Unit of the precursor_mz_tolerance" help="">
+      <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" min="1" value="1" label="Number of mass traces each feature has to have to be included" help="To use this parameter, setting the feature_only flag is necessary"/>
+      <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" value="10.0" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/>
+      <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" label="Unit of the precursor_mz_tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="precursor_mz_tolerance_unit"/>
       </param>
-      <param name="precursor_rt_tolerance" argument="-preprocessing:precursor_rt_tolerance" type="float" optional="true" value="5.0" label="Tolerance window (left and right) for precursor selection [seconds]" help=""/>
-      <param name="isotope_pattern_iterations" argument="-preprocessing:isotope_pattern_iterations" type="integer" optional="true" value="3" label="Number of iterations that should be performed to extract the C13 isotope pattern" help="If no peak is found (C13 distance) the function will abort. Be careful with noisy data - since this can lead to wrong isotope patterns"/>
+      <param name="precursor_rt_tolerance" argument="-preprocessing:precursor_rt_tolerance" type="float" value="5.0" label="Tolerance window (left and right) for precursor selection [seconds]" help=""/>
+      <param name="isotope_pattern_iterations" argument="-preprocessing:isotope_pattern_iterations" type="integer" value="3" label="Number of iterations that should be performed to extract the C13 isotope pattern" help="If no peak is found (C13 distance) the function will abort. Be careful with noisy data - since this can lead to wrong isotope patterns"/>
       <param name="feature_only" argument="-preprocessing:feature_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Uses the feature information from in_featureinfo to reduce the search space to MS2 associated with a feature" help=""/>
       <param name="no_masstrace_info_isotope_pattern" argument="-preprocessing:no_masstrace_info_isotope_pattern" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if the masstrace information from a feature should be discarded and the isotope_pattern_iterations should be used instead" help=""/>
     </section>
     <section name="project" title="" help="" expanded="false">
-      <param name="processors" argument="-project:processors" type="integer" optional="true" value="1" label="Number of cpu cores to use" help="If not specified SIRIUS uses all available cores"/>
+      <param name="maxmz" argument="-project:maxmz" type="integer" value="-1" label="Just consider compounds with a precursor mz lower or equal" help="this maximum mz. All other compounds in the input file. are ignored"/>
+      <param name="processors" argument="-project:processors" type="integer" value="1" label="Number of cpu cores to use" help="If not specified SIRIUS uses all available cores"/>
+      <param name="loglevel" argument="-project:loglevel" type="text" optional="true" value="" label="Set logging level of the Jobs SIRIUS will execute" help="Valid values: SEVERE, WARNING, INFO, FINER, ALL. Default: WARNING">
+        <expand macro="list_string_san" name="loglevel"/>
+      </param>
       <param name="ignore_formula" argument="-project:ignore_formula" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Ignore given molecular formula in internal .ms format, while processing" help=""/>
       <param name="q" argument="-project:q" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress shell output" help=""/>
     </section>
     <section name="sirius" title="" help="" expanded="false">
-      <param name="ppm_max" argument="-sirius:ppm_max" type="float" optional="true" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses [ppm]" help=""/>
-      <param name="ppm_max_ms2" argument="-sirius:ppm_max_ms2" type="float" optional="true" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses in MS2 [ppm].If not specified, the same value as for the MS1 is used" help=""/>
-      <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" optional="true" min="0" value="0" label="Time out in seconds per fragmentation tree computations" help="0 for an infinite amount of time"/>
-      <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" optional="true" min="0" value="100" label="Maximal computation time in seconds for a single compound" help="0 for an infinite amount of time"/>
+      <param name="ppm_max" argument="-sirius:ppm_max" type="float" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses [ppm]" help=""/>
+      <param name="ppm_max_ms2" argument="-sirius:ppm_max_ms2" type="float" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses in MS2 [ppm].If not specified, the same value as for the MS1 is used" help=""/>
+      <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" min="0" value="100" label="Time out in seconds per fragmentation tree computations" help="0 for an infinite amount of time"/>
+      <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" min="0" value="100" label="Maximal computation time in seconds for a single compound" help="0 for an infinite amount of time"/>
       <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable recalibration of input spectra" help=""/>
-      <param name="profile" argument="-sirius:profile" type="select" optional="true" label="Name of the configuration profile" help="">
-        <option value="default">default</option>
-        <option value="qtof" selected="true">qtof</option>
+      <param name="profile" argument="-sirius:profile" type="select" label="Name of the configuration profile" help="">
+        <option value="default" selected="true">default</option>
+        <option value="qtof">qtof</option>
         <option value="orbitrap">orbitrap</option>
         <option value="fticr">fticr</option>
         <expand macro="list_string_san" name="profile"/>
       </param>
-      <param name="formula" argument="-sirius:formula" type="text" optional="true" value="" label="Specify the neutral molecular formula of the measured compound to compute its tree or a list of candidate formulas the method should discriminate" help="Omit this option if you want to consider all possible molecular formulas">
-        <expand macro="list_string_san" name="formula"/>
+      <param name="formulas" argument="-sirius:formulas" type="text" optional="true" value="" label="Specify the neutral molecular formula of the measured compound to compute its tree or a list of candidate formulas the method should discriminate" help="Omit this option if you want to consider all possible molecular formulas">
+        <expand macro="list_string_san" name="formulas"/>
       </param>
       <param name="ions_enforced" argument="-sirius:ions_enforced" type="text" optional="true" value="" label="The iontype/adduct of the MS/MS data" help="Example: [M+H]+, . [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a . comma separated list of adducts">
         <expand macro="list_string_san" name="ions_enforced"/>
       </param>
-      <param name="candidates" argument="-sirius:candidates" type="integer" optional="true" min="1" value="5" label="The number of formula candidates in the SIRIUS output" help=""/>
-      <param name="candidates_per_ion" argument="-sirius:candidates_per_ion" type="integer" optional="true" value="-1" label="Minimum number of candidates in the output for each ionization" help="Set to force output of results for each possible ionization, even if not part of highest ranked results. -1 omits parameter in Sirius"/>
-      <param name="elements_considered" argument="-sirius:elements_considered" type="text" optional="true" value="" label="Set the allowed elements for rare element detection" help="Write SBrClBSe to allow the elements S,Br,Cl,B and Se">
+      <param name="candidates" argument="-sirius:candidates" type="integer" min="0" value="10" label="The number of formula candidates in the SIRIUS output" help=""/>
+      <param name="candidates_per_ion" argument="-sirius:candidates_per_ion" type="integer" value="1" label="Minimum number of candidates in the output for each ionization" help="Set to force output of results for each possible ionization, even if not part of highest ranked results"/>
+      <param name="elements_considered" argument="-sirius:elements_considered" type="text" value="SBrClBSe" label="Set the allowed elements for rare element detection" help="Write SBrClBSe to allow the elements S,Br,Cl,B and Se">
         <expand macro="list_string_san" name="elements_considered"/>
       </param>
-      <param name="elements_enforced" argument="-sirius:elements_enforced" type="text" optional="true" value="" label="Enforce elements for molecular formula determination" help="Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the minimal and maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1-2]. When one number is given then it is interpreted as upper bound. Default is CHNOP">
+      <param name="elements_enforced" argument="-sirius:elements_enforced" type="text" value="CHNOP" label="Enforce elements for molecular formula determination" help="Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the minimal and maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1-2]. When one number is given then it is interpreted as upper bound">
         <expand macro="list_string_san" name="elements_enforced"/>
       </param>
       <param name="no_isotope_score" argument="-sirius:no_isotope_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable isotope pattern score" help=""/>
       <param name="no_isotope_filter" argument="-sirius:no_isotope_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable molecular formula filte" help="When filtering is enabled, molecular formulas are excluded if their theoretical isotope pattern does not match the theoretical one, even if their MS/MS pattern has high score"/>
-      <param name="ions_considered" argument="-sirius:ions_considered" type="text" optional="true" value="" label="the iontype/adduct of the MS/MS data" help="Example: [M+H]+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a comma separated list of adducts">
+      <param name="ions_considered" argument="-sirius:ions_considered" type="text" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-" label="the iontype/adduct of the MS/MS data" help="Example: [M+H]+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a comma separated list of adducts">
         <expand macro="list_string_san" name="ions_considered"/>
       </param>
-      <param name="db" argument="-sirius:db" type="text" optional="true" value="" label="Search formulas in the Union of the given databases db-name1,db-name2,db-name3" help="If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE">
+      <param name="db" argument="-sirius:db" type="text" value="none" label="Search formulas in the Union of the given databases db-name1,db-name2,db-name3" help="If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE">
         <expand macro="list_string_san" name="db"/>
       </param>
+      <param name="solver" argument="-sirius:solver" type="text" value="CLP" label="For GUROBI and CPLEX environment variables need to be configured" help="(see SIRIUS manual: https://boecker-lab.github.io/docs.sirius.github.io/install/)">
+        <expand macro="list_string_san" name="solver"/>
+      </param>
     </section>
     <section name="fingerid" title="" help="" expanded="false">
-      <param name="candidates" argument="-fingerid:candidates" type="integer" optional="true" min="1" value="10" label="Number of molecular structure candidates in the output" help=""/>
-      <param name="db" argument="-fingerid:db" type="text" optional="true" value="BIO" label="Search formulas in the Union of the given databases db-name1,db-name2,db-name3" help="If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE">
+      <param name="db" argument="-fingerid:db" type="text" optional="true" value="" label="Search structures in the Union of the given databases db-name1,db-name2,db-name3" help="If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE">
         <expand macro="list_string_san" name="db"/>
       </param>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-ambiguity_resolution_mz_tolerance_unit" type="select" optional="true" label="Unit of the ambiguity_resolution_mz_tolerance" help="">
+      <param argument="-ambiguity_resolution_mz_tolerance_unit" type="select" label="Unit of the ambiguity_resolution_mz_tolerance" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="ambiguity_resolution_mz_tolerance_unit"/>
       </param>
-      <param argument="-precursor_recalibration_window" type="float" optional="true" value="0.01" label="Tolerance window for precursor selection (Annotation of precursor mz and intensity)" help=""/>
-      <param argument="-precursor_recalibration_window_unit" type="select" optional="true" label="Unit of the precursor_mz_tolerance_annotation" help="">
+      <param argument="-precursor_recalibration_window" type="float" value="0.01" label="Tolerance window for precursor selection (Annotation of precursor mz and intensity)" help=""/>
+      <param argument="-precursor_recalibration_window_unit" type="select" label="Unit of the precursor_mz_tolerance_annotation" help="">
         <option value="Da" selected="true">Da</option>
         <option value="ppm">ppm</option>
         <expand macro="list_string_san" name="precursor_recalibration_window_unit"/>
       </param>
-      <param argument="-min_fragment_mz" type="float" optional="true" value="0.0" label="Minimal m/z of a fragment ion choosen as a transition" help=""/>
-      <param argument="-max_fragment_mz" type="float" optional="true" value="2000.0" label="Maximal m/z of a fragment ion choosen as a transition" help=""/>
+      <param argument="-min_fragment_mz" type="float" value="0.0" label="Minimal m/z of a fragment ion choosen as a transition" help=""/>
+      <param argument="-max_fragment_mz" type="float" value="2000.0" label="Maximal m/z of a fragment ion choosen as a transition" help=""/>
+      <param argument="-read_sirius_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Read and print the standard output and error of the Sirius executable, even if it succeeds" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -239,7 +236,8 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_AssayGeneratorMetabo_1 -->
+  <tests>
+    <!-- TOPP_AssayGeneratorMetabo_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
@@ -247,6 +245,7 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <param name="precursor_recalibration_window_unit" value="Da"/>
         <param name="min_fragment_mz" value="0.0"/>
         <param name="max_fragment_mz" value="2000.0"/>
+        <param name="read_sirius_stdout" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
@@ -257,7 +256,7 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
       </conditional>
       <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ffm_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="AssayGeneratorMetabo_ffm_output.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="fragment_annotation" value="none"/>
       <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
       <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
@@ -296,31 +295,33 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <param name="no_masstrace_info_isotope_pattern" value="false"/>
       </section>
       <section name="project">
+        <param name="maxmz" value="-1"/>
         <param name="processors" value="1"/>
+        <param name="loglevel" value=""/>
         <param name="ignore_formula" value="false"/>
         <param name="q" value="false"/>
       </section>
       <section name="sirius">
         <param name="ppm_max" value="10.0"/>
         <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
+        <param name="tree_timeout" value="100"/>
         <param name="compound_timeout" value="100"/>
         <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
+        <param name="profile" value="default"/>
+        <param name="formulas" value=""/>
         <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
+        <param name="candidates" value="10"/>
+        <param name="candidates_per_ion" value="1"/>
+        <param name="elements_considered" value="SBrClBSe"/>
+        <param name="elements_enforced" value="CHNOP"/>
         <param name="no_isotope_score" value="false"/>
         <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
+        <param name="ions_considered" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-"/>
+        <param name="db" value="none"/>
+        <param name="solver" value="CLP"/>
       </section>
       <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
+        <param name="db" value=""/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -328,8 +329,11 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_AssayGeneratorMetabo_2 -->
+    <!-- TOPP_AssayGeneratorMetabo_2 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
@@ -337,6 +341,7 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <param name="precursor_recalibration_window_unit" value="Da"/>
         <param name="min_fragment_mz" value="0.0"/>
         <param name="max_fragment_mz" value="2000.0"/>
+        <param name="read_sirius_stdout" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
@@ -347,7 +352,7 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
       </conditional>
       <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="AssayGeneratorMetabo_ams_output.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="fragment_annotation" value="none"/>
       <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
       <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
@@ -386,31 +391,33 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <param name="no_masstrace_info_isotope_pattern" value="false"/>
       </section>
       <section name="project">
+        <param name="maxmz" value="-1"/>
         <param name="processors" value="1"/>
+        <param name="loglevel" value=""/>
         <param name="ignore_formula" value="false"/>
         <param name="q" value="false"/>
       </section>
       <section name="sirius">
         <param name="ppm_max" value="10.0"/>
         <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
+        <param name="tree_timeout" value="100"/>
         <param name="compound_timeout" value="100"/>
         <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
+        <param name="profile" value="default"/>
+        <param name="formulas" value=""/>
         <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
+        <param name="candidates" value="10"/>
+        <param name="candidates_per_ion" value="1"/>
+        <param name="elements_considered" value="SBrClBSe"/>
+        <param name="elements_enforced" value="CHNOP"/>
         <param name="no_isotope_score" value="false"/>
         <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
+        <param name="ions_considered" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-"/>
+        <param name="db" value="none"/>
+        <param name="solver" value="CLP"/>
       </section>
       <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
+        <param name="db" value=""/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -418,8 +425,11 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_AssayGeneratorMetabo_3 -->
+    <!-- TOPP_AssayGeneratorMetabo_3 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
@@ -427,6 +437,7 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <param name="precursor_recalibration_window_unit" value="Da"/>
         <param name="min_fragment_mz" value="0.0"/>
         <param name="max_fragment_mz" value="2000.0"/>
+        <param name="read_sirius_stdout" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
@@ -437,7 +448,7 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
       </conditional>
       <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ffm_output_consensus.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="AssayGeneratorMetabo_ffm_output_consensus.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="fragment_annotation" value="none"/>
       <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
       <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
@@ -476,31 +487,33 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <param name="no_masstrace_info_isotope_pattern" value="false"/>
       </section>
       <section name="project">
+        <param name="maxmz" value="-1"/>
         <param name="processors" value="1"/>
+        <param name="loglevel" value=""/>
         <param name="ignore_formula" value="false"/>
         <param name="q" value="false"/>
       </section>
       <section name="sirius">
         <param name="ppm_max" value="10.0"/>
         <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
+        <param name="tree_timeout" value="100"/>
         <param name="compound_timeout" value="100"/>
         <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
+        <param name="profile" value="default"/>
+        <param name="formulas" value=""/>
         <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
+        <param name="candidates" value="10"/>
+        <param name="candidates_per_ion" value="1"/>
+        <param name="elements_considered" value="SBrClBSe"/>
+        <param name="elements_enforced" value="CHNOP"/>
         <param name="no_isotope_score" value="false"/>
         <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
+        <param name="ions_considered" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-"/>
+        <param name="db" value="none"/>
+        <param name="solver" value="CLP"/>
       </section>
       <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
+        <param name="db" value=""/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -508,8 +521,11 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_AssayGeneratorMetabo_4 -->
+    <!-- TOPP_AssayGeneratorMetabo_4 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
@@ -517,6 +533,7 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <param name="precursor_recalibration_window_unit" value="Da"/>
         <param name="min_fragment_mz" value="0.0"/>
         <param name="max_fragment_mz" value="2000.0"/>
+        <param name="read_sirius_stdout" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
@@ -527,7 +544,7 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
       </conditional>
       <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_output_consensus.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="AssayGeneratorMetabo_ams_output_consensus.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="fragment_annotation" value="none"/>
       <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
       <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
@@ -566,31 +583,33 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <param name="no_masstrace_info_isotope_pattern" value="false"/>
       </section>
       <section name="project">
+        <param name="maxmz" value="-1"/>
         <param name="processors" value="1"/>
+        <param name="loglevel" value=""/>
         <param name="ignore_formula" value="false"/>
         <param name="q" value="false"/>
       </section>
       <section name="sirius">
         <param name="ppm_max" value="10.0"/>
         <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
+        <param name="tree_timeout" value="100"/>
         <param name="compound_timeout" value="100"/>
         <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
+        <param name="profile" value="default"/>
+        <param name="formulas" value=""/>
         <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
+        <param name="candidates" value="10"/>
+        <param name="candidates_per_ion" value="1"/>
+        <param name="elements_considered" value="SBrClBSe"/>
+        <param name="elements_enforced" value="CHNOP"/>
         <param name="no_isotope_score" value="false"/>
         <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
+        <param name="ions_considered" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-"/>
+        <param name="db" value="none"/>
+        <param name="solver" value="CLP"/>
       </section>
       <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
+        <param name="db" value=""/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -598,8 +617,11 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_AssayGeneratorMetabo_5 -->
+    <!-- TOPP_AssayGeneratorMetabo_5 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
@@ -607,6 +629,7 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <param name="precursor_recalibration_window_unit" value="Da"/>
         <param name="min_fragment_mz" value="0.0"/>
         <param name="max_fragment_mz" value="2000.0"/>
+        <param name="read_sirius_stdout" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
@@ -617,7 +640,7 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
       </conditional>
       <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="fragment_annotation" value="none"/>
       <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
       <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
@@ -656,1123 +679,48 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <param name="no_masstrace_info_isotope_pattern" value="false"/>
       </section>
       <section name="project">
+        <param name="maxmz" value="-1"/>
         <param name="processors" value="1"/>
+        <param name="loglevel" value=""/>
         <param name="ignore_formula" value="false"/>
         <param name="q" value="false"/>
       </section>
       <section name="sirius">
         <param name="ppm_max" value="10.0"/>
         <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- UTILS_AssayGeneratorMetabo_7 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_recalibration_window" value="0.01"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <conditional name="in_cond">
-        <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      </conditional>
-      <conditional name="in_id_cond">
-        <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
-      </conditional>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_sirius_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
-      <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
-      <param name="total_occurrence_filter" value="0.1"/>
-      <param name="fragment_annotation_score_threshold" value="0.8"/>
-      <param name="decoy_generation" value="false"/>
-      <param name="decoy_generation_method" value="original"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="2"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
+        <param name="tree_timeout" value="100"/>
         <param name="compound_timeout" value="100"/>
         <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
+        <param name="profile" value="default"/>
+        <param name="formulas" value=""/>
         <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
-      </section>
-      <section name="fingerid">
         <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- UTILS_AssayGeneratorMetabo_8 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_recalibration_window" value="0.01"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <conditional name="in_cond">
-        <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      </conditional>
-      <conditional name="in_id_cond">
-        <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
-      </conditional>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_sirius_ukn_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
-      <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
-      <param name="total_occurrence_filter" value="0.1"/>
-      <param name="fragment_annotation_score_threshold" value="0.8"/>
-      <param name="decoy_generation" value="false"/>
-      <param name="decoy_generation_method" value="original"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="true"/>
-      <param name="min_transitions" value="2"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
+        <param name="candidates_per_ion" value="1"/>
+        <param name="elements_considered" value="SBrClBSe"/>
+        <param name="elements_enforced" value="CHNOP"/>
         <param name="no_isotope_score" value="false"/>
         <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value="ALL"/>
+        <param name="ions_considered" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-"/>
+        <param name="db" value="none"/>
+        <param name="solver" value="CLP"/>
       </section>
       <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- UTILS_AssayGeneratorMetabo_9 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_recalibration_window" value="0.01"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <conditional name="in_cond">
-        <param name="in" value="AssayGeneratorMetabo_intsort_input.mzML"/>
-      </conditional>
-      <conditional name="in_id_cond">
-        <param name="in_id" value="AssayGeneratorMetabo_intsort_input.featureXML"/>
-      </conditional>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_sirius_intsort_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
-      <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
-      <param name="total_occurrence_filter" value="0.1"/>
-      <param name="fragment_annotation_score_threshold" value="0.8"/>
-      <param name="decoy_generation" value="false"/>
-      <param name="decoy_generation_method" value="original"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="2"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
         <param name="db" value=""/>
       </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- UTILS_AssayGeneratorMetabo_10 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_recalibration_window" value="0.01"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="100.0"/>
-        <param name="max_fragment_mz" value="900.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <conditional name="in_cond">
-        <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      </conditional>
-      <conditional name="in_id_cond">
-        <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
-      </conditional>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
-      <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
-      <param name="total_occurrence_filter" value="0.1"/>
-      <param name="fragment_annotation_score_threshold" value="0.8"/>
-      <param name="decoy_generation" value="false"/>
-      <param name="decoy_generation_method" value="original"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="2"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- UTILS_AssayGeneratorMetabo_11 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_recalibration_window" value="0.01"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="100.0"/>
-        <param name="max_fragment_mz" value="900.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <conditional name="in_cond">
-        <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      </conditional>
-      <conditional name="in_id_cond">
-        <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
-      </conditional>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_decoy_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
-      <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
-      <param name="total_occurrence_filter" value="0.1"/>
-      <param name="fragment_annotation_score_threshold" value="0.8"/>
-      <param name="decoy_generation" value="true"/>
-      <param name="decoy_generation_method" value="original"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="3"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- UTILS_AssayGeneratorMetabo_12 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_recalibration_window" value="0.01"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="100.0"/>
-        <param name="max_fragment_mz" value="900.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <conditional name="in_cond">
-        <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
-      </conditional>
-      <conditional name="in_id_cond">
-        <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML"/>
-      </conditional>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_decoy_generation_output_original.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
-      <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
-      <param name="total_occurrence_filter" value="0.1"/>
-      <param name="fragment_annotation_score_threshold" value="0.8"/>
-      <param name="decoy_generation" value="true"/>
-      <param name="decoy_generation_method" value="original"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- UTILS_AssayGeneratorMetabo_13 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_recalibration_window" value="0.01"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="100.0"/>
-        <param name="max_fragment_mz" value="900.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <conditional name="in_cond">
-        <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
-      </conditional>
-      <conditional name="in_id_cond">
-        <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML"/>
-      </conditional>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_decoy_generation_output_resolve_overlap.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
-      <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
-      <param name="total_occurrence_filter" value="0.1"/>
-      <param name="fragment_annotation_score_threshold" value="0.8"/>
-      <param name="decoy_generation" value="true"/>
-      <param name="decoy_generation_method" value="resolve_overlap"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- UTILS_AssayGeneratorMetabo_14 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_recalibration_window" value="0.01"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="100.0"/>
-        <param name="max_fragment_mz" value="900.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <conditional name="in_cond">
-        <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
-      </conditional>
-      <conditional name="in_id_cond">
-        <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML"/>
-      </conditional>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_decoy_generation_output_add_shift.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
-      <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
-      <param name="total_occurrence_filter" value="0.1"/>
-      <param name="fragment_annotation_score_threshold" value="0.8"/>
-      <param name="decoy_generation" value="true"/>
-      <param name="decoy_generation_method" value="add_shift"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- UTILS_AssayGeneratorMetabo_15 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_recalibration_window" value="0.01"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="100.0"/>
-        <param name="max_fragment_mz" value="900.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <conditional name="in_cond">
-        <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
-      </conditional>
-      <conditional name="in_id_cond">
-        <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML"/>
-      </conditional>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_decoy_generation_output_both.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
-      <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
-      <param name="total_occurrence_filter" value="0.1"/>
-      <param name="fragment_annotation_score_threshold" value="0.8"/>
-      <param name="decoy_generation" value="true"/>
-      <param name="decoy_generation_method" value="both"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- UTILS_AssayGeneratorMetabo_16 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_recalibration_window" value="0.01"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="100.0"/>
-        <param name="max_fragment_mz" value="900.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <conditional name="in_cond">
-        <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
-      </conditional>
-      <conditional name="in_id_cond">
-        <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input_multids.featureXML"/>
-      </conditional>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_decoy_generation_output_both_multids.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
-      <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
-      <param name="total_occurrence_filter" value="0.1"/>
-      <param name="fragment_annotation_score_threshold" value="0.8"/>
-      <param name="decoy_generation" value="true"/>
-      <param name="decoy_generation_method" value="both"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- UTILS_AssayGeneratorMetabo_17 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="ambiguity_resolution_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_recalibration_window" value="0.01"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <conditional name="in_cond">
-        <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML,AssayGeneratorMetabo_decoy_generation_input_2.mzML,AssayGeneratorMetabo_decoy_generation_input_3.mzML"/>
-      </conditional>
-      <conditional name="in_id_cond">
-        <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML,AssayGeneratorMetabo_decoy_generation_input_1.featureXML,AssayGeneratorMetabo_decoy_generation_input_2.featureXML"/>
-      </conditional>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_decoy_generation_linking_output_both.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
-      <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
-      <param name="total_occurrence_filter" value="0.8"/>
-      <param name="fragment_annotation_score_threshold" value="0.8"/>
-      <param name="decoy_generation" value="true"/>
-      <param name="decoy_generation_method" value="both"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="6"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- UTILS_AssayGeneratorMetabo_18 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="ambiguity_resolution_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_recalibration_window" value="0.01"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <conditional name="in_cond">
-        <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML,AssayGeneratorMetabo_decoy_generation_input_2.mzML,AssayGeneratorMetabo_decoy_generation_input_3.mzML"/>
-      </conditional>
-      <conditional name="in_id_cond">
-        <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML,AssayGeneratorMetabo_decoy_generation_input_1.featureXML,AssayGeneratorMetabo_decoy_generation_input_2.featureXML"/>
-      </conditional>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_decoy_generation_linking_moladd_output_both.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
-      <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
-      <param name="total_occurrence_filter" value="0.1"/>
-      <param name="fragment_annotation_score_threshold" value="0.8"/>
-      <param name="decoy_generation" value="true"/>
-      <param name="decoy_generation_method" value="both"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="6"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Assay library generation from DDA data (Metabolomics)
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_AssayGeneratorMetabo.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_AssayGeneratorMetabo.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/BaselineFilter.xml b/tools/openms/BaselineFilter.xml
index d00766974..334e7a5e5 100644
--- a/tools/openms/BaselineFilter.xml
+++ b/tools/openms/BaselineFilter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="BaselineFilter" name="BaselineFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Removes the baseline from profile spectra using a top-hat filter.</description>
+  <description>Removes the baseline from profile spectra using a top-hat filter</description>
   <macros>
     <token name="@EXECUTABLE@">BaselineFilter</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,14 +38,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
-    <param argument="-struc_elem_length" type="float" optional="true" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/>
-    <param argument="-struc_elem_unit" type="select" optional="true" label="Unit of 'struc_elem_length' paramete" help="">
+    <param argument="-in" type="data" format="mzml" label="input raw data file" help=" select mzml data sets(s)"/>
+    <param argument="-struc_elem_length" type="float" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/>
+    <param argument="-struc_elem_unit" type="select" label="Unit of 'struc_elem_length' paramete" help="">
       <option value="Thomson" selected="true">Thomson</option>
       <option value="DataPoints">DataPoints</option>
       <expand macro="list_string_san" name="struc_elem_unit"/>
     </param>
-    <param argument="-method" type="select" optional="true" label="The name of the morphological filter to be applied" help="If you are unsure, use the default">
+    <param argument="-method" type="select" label="The name of the morphological filter to be applied" help="If you are unsure, use the default">
       <option value="identity">identity</option>
       <option value="erosion">erosion</option>
       <option value="dilation">dilation</option>
@@ -61,7 +60,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -75,14 +74,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_BaselineFilter_1 -->
+  <tests>
+    <!-- TOPP_BaselineFilter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="BaselineFilter_input.mzML"/>
-      <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="BaselineFilter_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="struc_elem_length" value="1.5"/>
       <param name="struc_elem_unit" value="Thomson"/>
       <param name="method" value="tophat"/>
@@ -92,11 +92,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Removes the baseline from profile spectra using a top-hat filter.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_BaselineFilter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_BaselineFilter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/CVInspector.xml b/tools/openms/CVInspector.xml
index d67b75b6f..7c49058a2 100644
--- a/tools/openms/CVInspector.xml
+++ b/tools/openms/CVInspector.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [[for Developers]]-->
 <tool id="CVInspector" name="CVInspector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>A tool for visualization and validation of PSI mapping and CV files.</description>
+  <description>A tool for visualization and validation of PSI mapping and CV files</description>
   <macros>
     <token name="@EXECUTABLE@">CVInspector</token>
     <import>macros.xml</import>
@@ -17,12 +16,12 @@
 mkdir cv_files_cond.cv_files &&
 #if $cv_files_cond.cv_files_select == "no"
 mkdir ${' '.join(["'cv_files_cond.cv_files/%s'" % (i) for i, f in enumerate($cv_files_cond.cv_files) if f])} && 
-${' '.join(["ln -s '%s' 'cv_files_cond.cv_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_files_cond.cv_files) if f])}
+${' '.join(["cp '%s' 'cv_files_cond.cv_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_files_cond.cv_files) if f])}
 #else
-ln -s '$cv_files_cond.cv_files' 'cv_files_cond.cv_files/${re.sub("[^\w\-_]", "_", $cv_files_cond.cv_files.element_identifier)}.$gxy2omsext($cv_files_cond.cv_files.ext)' &&
+cp '$cv_files_cond.cv_files' 'cv_files_cond.cv_files/${re.sub("[^\w\-_]", "_", $cv_files_cond.cv_files.element_identifier)}.$gxy2omsext($cv_files_cond.cv_files.ext)' &&
 #end if
 mkdir mapping_file &&
-ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
+cp '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir html &&
 #end if
@@ -67,24 +66,24 @@ ${' '.join(["'cv_files_cond.cv_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.el
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-cv_files" type="data" format="obo" multiple="true" optional="false" label="List of ontology files in OBO format" help=" select obo data sets(s)"/>
+        <param argument="-cv_files" type="data" format="obo" multiple="true" label="List of ontology files in OBO format" help=" select obo data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-cv_files" type="data" format="obo" multiple="false" optional="false" label="List of ontology files in OBO format" help=" select obo data sets(s)"/>
+        <param argument="-cv_files" type="data" format="obo" label="List of ontology files in OBO format" help=" select obo data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-cv_names" type="text" optional="false" value="" label="List of identifiers (one for each ontology file)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-cv_names" type="text" value="" label="List of identifiers (one for each ontology file)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="cv_names"/>
       <expand macro="list_string_san" name="cv_names"/>
     </param>
-    <param argument="-mapping_file" type="data" format="xml" optional="false" label="Mapping file in CVMapping (XML) format" help=" select xml data sets(s)"/>
-    <param argument="-ignore_cv" type="text" optional="true" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-mapping_file" type="data" format="xml" label="Mapping file in CVMapping (XML) format" help=" select xml data sets(s)"/>
+    <param argument="-ignore_cv" type="text" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="ignore_cv"/>
       <expand macro="list_string_san" name="ignore_cv"/>
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -104,19 +103,20 @@ ${' '.join(["'cv_files_cond.cv_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.el
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- test with https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo listed here https://www.psidev.info/groups/controlled-vocabularies, mapping file from share/OpenMS/MAPPING/ms-mapping.xml -->
-  <test expect_num_outputs="1">
-    <param name="adv_opts|test" value="true"/>
-    <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/>
-    <param name="cv_names" value="XLMOD"/>
-    <param name="mapping_file" value="MAPPING/ms-mapping.xml"/>
-    <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/>
-    <output name="html" ftype="html" value="CVInspector.html"/>
-  </test>
-</tests>
+  <tests>
+    <!-- test with https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo listed here https://www.psidev.info/groups/controlled-vocabularies, mapping file from share/OpenMS/MAPPING/ms-mapping.xml -->
+    <test expect_num_outputs="1">
+      <param name="adv_opts|test" value="true"/>
+      <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/>
+      <param name="cv_names" value="XLMOD"/>
+      <param name="mapping_file" value="MAPPING/ms-mapping.xml"/>
+      <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/>
+      <output name="html" ftype="html" value="CVInspector.html"/>
+    </test>
+  </tests>
   <help><![CDATA[A tool for visualization and validation of PSI mapping and CV files.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_CVInspector.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_CVInspector.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/ClusterMassTraces.xml b/tools/openms/ClusterMassTraces.xml
index 2831211d9..1f9931452 100644
--- a/tools/openms/ClusterMassTraces.xml
+++ b/tools/openms/ClusterMassTraces.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Misc / Helpers]-->
 <tool id="ClusterMassTraces" name="ClusterMassTraces" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Creates pseudo spectra.</description>
+  <description>Creates pseudo spectra</description>
   <macros>
     <token name="@EXECUTABLE@">ClusterMassTraces</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,16 +38,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml" optional="false" label="Mass traces" help=" select consensusxml data sets(s)"/>
-    <param argument="-min_pearson_correlation" type="float" optional="true" value="0.7" label="Minimal pearson correlation score" help=""/>
-    <param argument="-min_peak_nr" type="integer" optional="true" value="1" label="Minimal peak nr to output pseudo spectra" help=""/>
-    <param argument="-max_lag" type="integer" optional="true" value="1" label="Maximal lag" help=""/>
-    <param argument="-max_rt_apex_difference" type="float" optional="true" value="5.0" label="Maximal difference of the apex in retention time" help=""/>
-    <param argument="-max_intensity_cutoff" type="float" optional="true" value="0.0" label="Maximal intensity to be added to a spectrum" help=""/>
-    <param argument="-add_precursor" type="float" optional="true" value="0.0" label="Add a precursor mass" help=""/>
+    <param argument="-in" type="data" format="consensusxml" label="Mass traces" help=" select consensusxml data sets(s)"/>
+    <param argument="-min_pearson_correlation" type="float" value="0.7" label="Minimal pearson correlation score" help=""/>
+    <param argument="-min_peak_nr" type="integer" value="1" label="Minimal peak nr to output pseudo spectra" help=""/>
+    <param argument="-max_lag" type="integer" value="1" label="Maximal lag" help=""/>
+    <param argument="-max_rt_apex_difference" type="float" value="5.0" label="Maximal difference of the apex in retention time" help=""/>
+    <param argument="-max_intensity_cutoff" type="float" value="0.0" label="Maximal intensity to be added to a spectrum" help=""/>
+    <param argument="-add_precursor" type="float" value="0.0" label="Add a precursor mass" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -62,15 +61,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
-    <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- test with arbitarily chosen consensusXML -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
+      <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/>
+    </test>
+  </tests>
   <help><![CDATA[Creates pseudo spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_ClusterMassTraces.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ClusterMassTraces.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/ClusterMassTracesByPrecursor.xml b/tools/openms/ClusterMassTracesByPrecursor.xml
index e90aca239..3d1976c85 100644
--- a/tools/openms/ClusterMassTracesByPrecursor.xml
+++ b/tools/openms/ClusterMassTracesByPrecursor.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="ClusterMassTracesByPrecursor" name="ClusterMassTracesByPrecursor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile.</description>
+  <description>Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile</description>
   <macros>
     <token name="@EXECUTABLE@">ClusterMassTracesByPrecursor</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in_ms1 &&
-ln -s '$in_ms1' 'in_ms1/${re.sub("[^\w\-_]", "_", $in_ms1.element_identifier)}.$gxy2omsext($in_ms1.ext)' &&
+cp '$in_ms1' 'in_ms1/${re.sub("[^\w\-_]", "_", $in_ms1.element_identifier)}.$gxy2omsext($in_ms1.ext)' &&
 mkdir in_swath &&
-ln -s '$in_swath' 'in_swath/${re.sub("[^\w\-_]", "_", $in_swath.element_identifier)}.$gxy2omsext($in_swath.ext)' &&
+cp '$in_swath' 'in_swath/${re.sub("[^\w\-_]", "_", $in_swath.element_identifier)}.$gxy2omsext($in_swath.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -43,18 +42,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in_ms1" type="data" format="consensusxml" optional="false" label="MS1 mass traces" help=" select consensusxml data sets(s)"/>
-    <param argument="-in_swath" type="data" format="consensusxml" optional="false" label="MS2 / SWATH mass traces" help=" select consensusxml data sets(s)"/>
+    <param argument="-in_ms1" type="data" format="consensusxml" label="MS1 mass traces" help=" select consensusxml data sets(s)"/>
+    <param argument="-in_swath" type="data" format="consensusxml" label="MS2 / SWATH mass traces" help=" select consensusxml data sets(s)"/>
     <param argument="-assign_unassigned_to_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assign unassigned MS2 fragments to all precursors (only for ms1_centrif)" help=""/>
-    <param argument="-min_pearson_correlation" type="float" optional="true" value="0.7" label="Minimal pearson correlation score to match elution profiles to each othe" help=""/>
-    <param argument="-max_lag" type="integer" optional="true" value="1" label="Maximal lag" help="(e.g. by how many spectra the peak may be shifted at most). This parameter will depend on your chromatographic setup but a number between 1 and 3 is usually sensible"/>
-    <param argument="-min_nr_ions" type="integer" optional="true" value="3" label="Minimal number of ions to report a spectrum" help=""/>
-    <param argument="-max_rt_apex_difference" type="float" optional="true" value="5.0" label="Maximal difference of the apex in retention time (in seconds)" help="This is a hard parameter, all profiles further away will not be considered at all"/>
-    <param argument="-swath_lower" type="float" optional="true" value="0.0" label="Swath lower isolation window" help=""/>
-    <param argument="-swath_upper" type="float" optional="true" value="0.0" label="Swath upper isolation window" help=""/>
+    <param argument="-min_pearson_correlation" type="float" value="0.7" label="Minimal pearson correlation score to match elution profiles to each othe" help=""/>
+    <param argument="-max_lag" type="integer" value="1" label="Maximal lag" help="(e.g. by how many spectra the peak may be shifted at most). This parameter will depend on your chromatographic setup but a number between 1 and 3 is usually sensible"/>
+    <param argument="-min_nr_ions" type="integer" value="3" label="Minimal number of ions to report a spectrum" help=""/>
+    <param argument="-max_rt_apex_difference" type="float" value="5.0" label="Maximal difference of the apex in retention time (in seconds)" help="This is a hard parameter, all profiles further away will not be considered at all"/>
+    <param argument="-swath_lower" type="float" value="0.0" label="Swath lower isolation window" help=""/>
+    <param argument="-swath_upper" type="float" value="0.0" label="Swath upper isolation window" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -68,16 +67,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in_ms1" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
-    <param name="in_swath" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
-    <output name="out" ftype="mzml" value="ClusterMassTracesByPrecursor.mzml"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- test with arbitarily chosen consensusXML -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in_ms1" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
+      <param name="in_swath" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
+      <output name="out" ftype="mzml" value="ClusterMassTracesByPrecursor.mzml"/>
+    </test>
+  </tests>
   <help><![CDATA[Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_ClusterMassTracesByPrecursor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ClusterMassTracesByPrecursor.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/CometAdapter.xml b/tools/openms/CometAdapter.xml
index f4b74c592..87d95f443 100644
--- a/tools/openms/CometAdapter.xml
+++ b/tools/openms/CometAdapter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
 <tool id="CometAdapter" name="CometAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Annotates MS/MS spectra using Comet.</description>
+  <description>Annotates MS/MS spectra using Comet</description>
   <macros>
     <token name="@EXECUTABLE@">CometAdapter</token>
     <import>macros.xml</import>
@@ -15,16 +14,16 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 mkdir database &&
-ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
 #if "pin_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir pin_out &&
 #end if
 #if $default_params_file:
   mkdir default_params_file &&
-  ln -s '$default_params_file' 'default_params_file/${re.sub("[^\w\-_]", "_", $default_params_file.element_identifier)}.$gxy2omsext($default_params_file.ext)' &&
+  cp '$default_params_file' 'default_params_file/${re.sub("[^\w\-_]", "_", $default_params_file.element_identifier)}.$gxy2omsext($default_params_file.ext)' &&
 #end if
 
 ## Main program call
@@ -64,17 +63,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"comet_executable": "comet", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
-    <param argument="-database" type="data" format="fasta" optional="false" label="FASTA file" help=" select fasta data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Input file" help=" select mzml data sets(s)"/>
+    <param argument="-database" type="data" format="fasta" label="FASTA file" help=" select fasta data sets(s)"/>
     <param argument="-default_params_file" type="data" format="txt" optional="true" label="Default Comet params file" help="All parameters of this take precedence. A template file can be generated using 'comet.exe -p' select txt data sets(s)"/>
-    <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (Comet parameter: peptide_mass_tolerance)" help="See also precursor_error_units to set the unit"/>
-    <param argument="-precursor_error_units" type="select" optional="true" label="Unit of precursor monoisotopic mass tolerance for parameter precursor_mass_tolerance (Comet parameter: peptide_mass_units)" help="">
+    <param argument="-precursor_mass_tolerance" type="float" value="10.0" label="Precursor monoisotopic mass tolerance (Comet parameter: peptide_mass_tolerance)" help="See also precursor_error_units to set the unit"/>
+    <param argument="-precursor_error_units" type="select" label="Unit of precursor monoisotopic mass tolerance for parameter precursor_mass_tolerance (Comet parameter: peptide_mass_units)" help="">
       <option value="amu">amu</option>
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
       <expand macro="list_string_san" name="precursor_error_units"/>
     </param>
-    <param argument="-isotope_error" type="select" optional="true" label="This parameter controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement" help="Use -8/-4/0/4/8 only for SILAC">
+    <param argument="-isotope_error" type="select" label="This parameter controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement" help="Use -8/-4/0/4/8 only for SILAC">
       <option value="off" selected="true">off</option>
       <option value="0/1">0/1</option>
       <option value="0/1/2">0/1/2</option>
@@ -83,54 +82,55 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="-1/0/1/2/3">-1/0/1/2/3</option>
       <expand macro="list_string_san" name="isotope_error"/>
     </param>
-    <param argument="-fragment_mass_tolerance" type="float" optional="true" min="0.0001" value="0.01" label="This is half the bin size, which is used to segment the MS/MS spectrum" help="Thus, the value should be a bit higher than for other search engines, since the bin might not be centered around the peak apex (see 'fragment_bin_offset').CAUTION: Low tolerances have heavy impact on RAM usage (since Comet uses a lot of bins in this case). Consider using use_sparse_matrix and/or spectrum_batch_size"/>
-    <param argument="-fragment_error_units" type="select" optional="true" label="Fragment monoisotopic mass error units" help="">
+    <param argument="-fragment_mass_tolerance" type="float" min="0.0001" value="0.01" label="This is half the bin size, which is used to segment the MS/MS spectrum" help="Thus, the value should be a bit higher than for other search engines, since the bin might not be centered around the peak apex (see 'fragment_bin_offset').CAUTION: Low tolerances have heavy impact on RAM usage (since Comet uses a lot of bins in this case). Consider using use_sparse_matrix and/or spectrum_batch_size"/>
+    <param argument="-fragment_error_units" type="select" label="Fragment monoisotopic mass error units" help="">
       <option value="Da" selected="true">Da</option>
       <expand macro="list_string_san" name="fragment_error_units"/>
     </param>
-    <param argument="-fragment_bin_offset" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Offset of fragment bins" help="Recommended by Comet: low-res: 0.4, high-res: 0.0"/>
-    <param argument="-instrument" type="select" optional="true" label="Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only" help="">
+    <param argument="-fragment_bin_offset" type="float" min="0.0" max="1.0" value="0.0" label="Offset of fragment bins" help="Recommended by Comet: low-res: 0.4, high-res: 0.0"/>
+    <param argument="-instrument" type="select" label="Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only" help="">
       <option value="low_res">low_res</option>
       <option value="high_res" selected="true">high_res</option>
       <expand macro="list_string_san" name="instrument"/>
     </param>
-    <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
-      <option value="CNBr">CNBr</option>
-      <option value="Lys-C">Lys-C</option>
+    <param argument="-enzyme" type="select" label="The enzyme used for peptide digestion" help="">
+      <option value="Asp-N">Asp-N</option>
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
       <option value="Trypsin" selected="true">Trypsin</option>
       <option value="Arg-C">Arg-C</option>
-      <option value="Chymotrypsin">Chymotrypsin</option>
-      <option value="Asp-N">Asp-N</option>
+      <option value="no cleavage">no cleavage</option>
       <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="CNBr">CNBr</option>
+      <option value="Lys-C">Lys-C</option>
       <option value="Lys-N">Lys-N</option>
       <option value="PepsinA">PepsinA</option>
       <option value="Trypsin/P">Trypsin/P</option>
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
       <expand macro="list_string_san" name="enzyme"/>
     </param>
-    <param argument="-num_enzyme_termini" type="select" optional="true" label="Specify the termini where the cleavage rule has to match" help="">
+    <param argument="-num_enzyme_termini" type="select" label="Specify the termini where the cleavage rule has to match" help="">
       <option value="semi">semi</option>
       <option value="fully" selected="true">fully</option>
       <option value="C-term unspecific">C-term unspecific</option>
       <option value="N-term unspecific">N-term unspecific</option>
       <expand macro="list_string_san" name="num_enzyme_termini"/>
     </param>
-    <param argument="-missed_cleavages" type="integer" optional="true" min="0" max="5" value="1" label="Number of possible cleavage sites missed by the enzyme" help="It has no effect if enzyme is unspecific cleavage"/>
-    <param argument="-min_peptide_length" type="integer" optional="true" min="5" max="63" value="5" label="Minimum peptide length to conside" help=""/>
-    <param argument="-max_peptide_length" type="integer" optional="true" min="5" max="63" value="63" label="Maximum peptide length to conside" help=""/>
-    <param argument="-num_hits" type="integer" optional="true" value="1" label="Number of peptide hits in output file" help=""/>
-    <param argument="-precursor_charge" type="text" optional="true" value="0:0" label="Precursor charge range to search (if spectrum is not annotated with a charge or if override_charge!=keep any known): 0:[num] == search all charges, 2:6 == from +2 to +6, 3:3 == +3" help="">
+    <param argument="-missed_cleavages" type="integer" min="0" max="5" value="1" label="Number of possible cleavage sites missed by the enzyme" help="It has no effect if enzyme is unspecific cleavage"/>
+    <param argument="-min_peptide_length" type="integer" min="5" max="63" value="5" label="Minimum peptide length to conside" help=""/>
+    <param argument="-max_peptide_length" type="integer" min="5" max="63" value="63" label="Maximum peptide length to conside" help=""/>
+    <param argument="-num_hits" type="integer" value="1" label="Number of peptide hits (PSMs) per spectrum in output file" help=""/>
+    <param argument="-precursor_charge" type="text" value="0:0" label="Precursor charge range to search (if spectrum is not annotated with a charge or if override_charge!=keep any known): 0:[num] == search all charges, 2:6 == from +2 to +6, 3:3 == +3" help="">
       <expand macro="list_string_san" name="precursor_charge"/>
     </param>
-    <param argument="-override_charge" type="select" optional="true" label="_keep any known_: keep any precursor charge state (from input), _ignore known_: ignore known precursor charge state and use precursor_charge parameter, _ignore outside range_: ignore precursor charges outside precursor_charge range, _keep known search unknown_: keep any known precursor charge state" help="For unknown charge states, search as singly charged if there is no signal above the precursor m/z or use the precursor_charge range">
+    <param argument="-override_charge" type="select" label="_keep any known_: keep any precursor charge state (from input), _ignore known_: ignore known precursor charge state and use precursor_charge parameter, _ignore outside range_: ignore precursor charges outside precursor_charge range, _keep known search unknown_: keep any known precursor charge state" help="For unknown charge states, search as singly charged if there is no signal above the precursor m/z or use the precursor_charge range">
       <option value="keep any known">keep any known</option>
       <option value="ignore known">ignore known</option>
       <option value="ignore outside range">ignore outside range</option>
       <option value="keep known search unknown" selected="true">keep known search unknown</option>
       <expand macro="list_string_san" name="override_charge"/>
     </param>
-    <param argument="-ms_level" type="integer" optional="true" min="2" max="3" value="2" label="MS level to analyze, valid are levels 2 (default) or 3" help=""/>
-    <param argument="-activation_method" type="select" optional="true" label="If not ALL, only searches spectra of the given method" help="">
+    <param argument="-ms_level" type="integer" min="2" max="3" value="2" label="MS level to analyze, valid are levels 2 (default) or 3" help=""/>
+    <param argument="-activation_method" type="select" label="If not ALL, only searches spectra of the given method" help="">
       <option value="ALL" selected="true">ALL</option>
       <option value="CID">CID</option>
       <option value="ECD">ECD</option>
@@ -140,9 +140,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="IRMPD">IRMPD</option>
       <expand macro="list_string_san" name="activation_method"/>
     </param>
-    <param argument="-max_fragment_charge" type="integer" optional="true" min="1" max="5" value="3" label="Set maximum fragment charge state to analyze as long as still lower than precursor charge - 1" help="(Allowed max 5)"/>
+    <param argument="-max_fragment_charge" type="integer" min="1" max="5" value="3" label="Set maximum fragment charge state to analyze as long as still lower than precursor charge - 1" help="(Allowed max 5)"/>
     <param argument="-clip_nterm_methionine" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, also considers the peptide sequence w/o N-term methionine separately and applies appropriate N-term mods to it" help=""/>
-    <param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
+    <param argument="-fixed_modifications" type="select" multiple="true" optional="false" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
       <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
       <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
       <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -152,6 +152,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="2-succinyl (C)">2-succinyl (C)</option>
       <option value="2HPG (R)">2HPG (R)</option>
       <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+      <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+      <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+      <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+      <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
       <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
       <option value="3sulfo (N-term)">3sulfo (N-term)</option>
       <option value="4-ONE (C)">4-ONE (C)</option>
@@ -241,6 +245,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
       <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
       <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+      <option value="Andro-H2O (C)">Andro-H2O (C)</option>
       <option value="Archaeol (C)">Archaeol (C)</option>
       <option value="Arg (N-term)">Arg (N-term)</option>
       <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -344,6 +349,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
       <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
       <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+      <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
       <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
       <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
       <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -376,7 +382,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="BITC (N-term)">BITC (N-term)</option>
       <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
       <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-      <option value="Bodipy (C)">Bodipy (C)</option>
       <option value="Brij35 (N-term)">Brij35 (N-term)</option>
       <option value="Brij58 (N-term)">Brij58 (N-term)</option>
       <option value="Bromo (F)">Bromo (F)</option>
@@ -808,9 +813,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Dehydrated (T)">Dehydrated (T)</option>
       <option value="Dehydrated (Y)">Dehydrated (Y)</option>
       <option value="Dehydro (C)">Dehydro (C)</option>
+      <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
       <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-      <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
       <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
       <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -820,7 +825,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
       <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
       <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-      <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
       <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
       <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -832,6 +836,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
       <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
       <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+      <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
       <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
       <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -1404,7 +1409,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Ethanolyl (C)">Ethanolyl (C)</option>
       <option value="Ethanolyl (K)">Ethanolyl (K)</option>
       <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-      <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
       <option value="Ethyl (C-term)">Ethyl (C-term)</option>
       <option value="Ethyl (D)">Ethyl (D)</option>
       <option value="Ethyl (E)">Ethyl (E)</option>
@@ -1498,6 +1502,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
       <option value="Glu (E)">Glu (E)</option>
       <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+      <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
       <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
       <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
       <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -1512,7 +1517,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
       <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
       <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
       <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -1536,6 +1540,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gly (K)">Gly (K)</option>
       <option value="Gly (S)">Gly (S)</option>
       <option value="Gly (T)">Gly (T)</option>
+      <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
       <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
       <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
       <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -1926,6 +1931,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
       <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
       <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+      <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
       <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
       <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
       <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -1937,6 +1943,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
       <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
       <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+      <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+      <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+      <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
       <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
       <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
       <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -1992,6 +2001,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
       <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
       <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+      <option value="His+O(2) (H)">His+O(2) (H)</option>
       <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
       <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
       <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -2129,11 +2139,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+      <option value="Kdo (S)">Kdo (S)</option>
+      <option value="Kdo (T)">Kdo (T)</option>
       <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
       <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
       <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
       <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
       <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+      <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
       <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
       <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
       <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -2218,13 +2231,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
       <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
       <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+      <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
       <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
       <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
       <option value="Lipoyl (K)">Lipoyl (K)</option>
       <option value="LRGG (K)">LRGG (K)</option>
       <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
       <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+      <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
       <option value="Lys (N-term)">Lys (N-term)</option>
+      <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
       <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
       <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
       <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -2259,6 +2275,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Malonyl (C)">Malonyl (C)</option>
       <option value="Malonyl (K)">Malonyl (K)</option>
       <option value="Malonyl (S)">Malonyl (S)</option>
+      <option value="MBS+peptide (C)">MBS+peptide (C)</option>
       <option value="MDCC (C)">MDCC (C)</option>
       <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
       <option value="Menadione (C)">Menadione (C)</option>
@@ -2270,6 +2287,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="MesitylOxide (H)">MesitylOxide (H)</option>
       <option value="MesitylOxide (K)">MesitylOxide (K)</option>
       <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+      <option value="Met+O(2) (H)">Met+O(2) (H)</option>
       <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
       <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
       <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -2453,7 +2471,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
       <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
       <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-      <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
       <option value="NP40 (N-term)">NP40 (N-term)</option>
       <option value="NQIGG (K)">NQIGG (K)</option>
       <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -2541,6 +2558,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
       <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
       <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+      <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+      <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+      <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+      <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
       <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
       <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
       <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -2555,6 +2576,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phospho (Y)">Phospho (Y)</option>
       <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
       <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+      <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
       <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
       <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
       <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -2586,6 +2608,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
       <option value="Piperidine (K)">Piperidine (K)</option>
       <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+      <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
       <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
       <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
       <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -2663,18 +2686,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="QTGG (K)">QTGG (K)</option>
       <option value="Quinone (W)">Quinone (W)</option>
       <option value="Quinone (Y)">Quinone (Y)</option>
+      <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+      <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+      <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+      <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+      <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+      <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+      <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+      <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+      <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+      <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+      <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+      <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+      <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+      <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+      <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+      <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+      <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+      <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+      <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+      <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
       <option value="Retinylidene (K)">Retinylidene (K)</option>
       <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
       <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
       <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-      <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-      <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-      <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-      <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-      <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-      <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-      <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-      <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
       <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
       <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
       <option value="Saligenin (H)">Saligenin (H)</option>
@@ -2702,6 +2737,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="shTMT (K)">shTMT (K)</option>
       <option value="shTMT (N-term)">shTMT (N-term)</option>
       <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+      <option value="shTMTpro (K)">shTMTpro (K)</option>
+      <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+      <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
       <option value="SMA (K)">SMA (K)</option>
       <option value="SMA (N-term)">SMA (N-term)</option>
       <option value="spermidine (Q)">spermidine (Q)</option>
@@ -2877,7 +2915,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
       <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
       <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-      <option value="Ub-amide (C)">Ub-amide (C)</option>
       <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
       <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
       <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -3072,7 +3109,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="ZQG (K)">ZQG (K)</option>
       <expand macro="list_string_san" name="fixed_modifications"/>
     </param>
-    <param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
+    <param argument="-variable_modifications" type="select" multiple="true" optional="false" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
       <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
       <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
       <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -3082,6 +3119,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="2-succinyl (C)">2-succinyl (C)</option>
       <option value="2HPG (R)">2HPG (R)</option>
       <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+      <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+      <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+      <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+      <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
       <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
       <option value="3sulfo (N-term)">3sulfo (N-term)</option>
       <option value="4-ONE (C)">4-ONE (C)</option>
@@ -3171,6 +3212,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
       <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
       <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+      <option value="Andro-H2O (C)">Andro-H2O (C)</option>
       <option value="Archaeol (C)">Archaeol (C)</option>
       <option value="Arg (N-term)">Arg (N-term)</option>
       <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -3274,6 +3316,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
       <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
       <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+      <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
       <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
       <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
       <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -3306,7 +3349,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="BITC (N-term)">BITC (N-term)</option>
       <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
       <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-      <option value="Bodipy (C)">Bodipy (C)</option>
       <option value="Brij35 (N-term)">Brij35 (N-term)</option>
       <option value="Brij58 (N-term)">Brij58 (N-term)</option>
       <option value="Bromo (F)">Bromo (F)</option>
@@ -3738,9 +3780,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Dehydrated (T)">Dehydrated (T)</option>
       <option value="Dehydrated (Y)">Dehydrated (Y)</option>
       <option value="Dehydro (C)">Dehydro (C)</option>
+      <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
       <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-      <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
       <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
       <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -3750,7 +3792,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
       <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
       <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-      <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
       <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
       <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -3762,6 +3803,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
       <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
       <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+      <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
       <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
       <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -4334,7 +4376,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Ethanolyl (C)">Ethanolyl (C)</option>
       <option value="Ethanolyl (K)">Ethanolyl (K)</option>
       <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-      <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
       <option value="Ethyl (C-term)">Ethyl (C-term)</option>
       <option value="Ethyl (D)">Ethyl (D)</option>
       <option value="Ethyl (E)">Ethyl (E)</option>
@@ -4428,6 +4469,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
       <option value="Glu (E)">Glu (E)</option>
       <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+      <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
       <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
       <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
       <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -4442,7 +4484,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
       <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
       <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
       <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -4466,6 +4507,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gly (K)">Gly (K)</option>
       <option value="Gly (S)">Gly (S)</option>
       <option value="Gly (T)">Gly (T)</option>
+      <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
       <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
       <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
       <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -4856,6 +4898,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
       <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
       <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+      <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
       <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
       <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
       <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -4867,6 +4910,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
       <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
       <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+      <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+      <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+      <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
       <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
       <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
       <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -4922,6 +4968,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
       <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
       <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+      <option value="His+O(2) (H)">His+O(2) (H)</option>
       <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
       <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
       <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -5059,11 +5106,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+      <option value="Kdo (S)">Kdo (S)</option>
+      <option value="Kdo (T)">Kdo (T)</option>
       <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
       <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
       <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
       <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
       <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+      <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
       <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
       <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
       <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -5148,13 +5198,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
       <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
       <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+      <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
       <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
       <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
       <option value="Lipoyl (K)">Lipoyl (K)</option>
       <option value="LRGG (K)">LRGG (K)</option>
       <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
       <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+      <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
       <option value="Lys (N-term)">Lys (N-term)</option>
+      <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
       <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
       <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
       <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -5189,6 +5242,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Malonyl (C)">Malonyl (C)</option>
       <option value="Malonyl (K)">Malonyl (K)</option>
       <option value="Malonyl (S)">Malonyl (S)</option>
+      <option value="MBS+peptide (C)">MBS+peptide (C)</option>
       <option value="MDCC (C)">MDCC (C)</option>
       <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
       <option value="Menadione (C)">Menadione (C)</option>
@@ -5200,6 +5254,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="MesitylOxide (H)">MesitylOxide (H)</option>
       <option value="MesitylOxide (K)">MesitylOxide (K)</option>
       <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+      <option value="Met+O(2) (H)">Met+O(2) (H)</option>
       <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
       <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
       <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -5383,7 +5438,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
       <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
       <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-      <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
       <option value="NP40 (N-term)">NP40 (N-term)</option>
       <option value="NQIGG (K)">NQIGG (K)</option>
       <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -5471,6 +5525,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
       <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
       <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+      <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+      <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+      <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+      <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
       <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
       <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
       <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -5485,6 +5543,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phospho (Y)">Phospho (Y)</option>
       <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
       <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+      <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
       <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
       <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
       <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -5516,6 +5575,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
       <option value="Piperidine (K)">Piperidine (K)</option>
       <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+      <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
       <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
       <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
       <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -5593,18 +5653,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="QTGG (K)">QTGG (K)</option>
       <option value="Quinone (W)">Quinone (W)</option>
       <option value="Quinone (Y)">Quinone (Y)</option>
+      <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+      <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+      <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+      <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+      <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+      <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+      <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+      <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+      <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+      <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+      <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+      <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+      <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+      <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+      <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+      <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+      <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+      <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+      <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+      <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
       <option value="Retinylidene (K)">Retinylidene (K)</option>
       <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
       <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
       <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-      <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-      <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-      <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-      <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-      <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-      <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-      <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-      <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
       <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
       <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
       <option value="Saligenin (H)">Saligenin (H)</option>
@@ -5632,6 +5704,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="shTMT (K)">shTMT (K)</option>
       <option value="shTMT (N-term)">shTMT (N-term)</option>
       <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+      <option value="shTMTpro (K)">shTMTpro (K)</option>
+      <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+      <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
       <option value="SMA (K)">SMA (K)</option>
       <option value="SMA (N-term)">SMA (N-term)</option>
       <option value="spermidine (Q)">spermidine (Q)</option>
@@ -5807,7 +5882,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
       <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
       <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-      <option value="Ub-amide (C)">Ub-amide (C)</option>
       <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
       <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
       <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -6010,12 +6084,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
         <expand macro="list_string_san" name="decoy_string"/>
       </param>
-      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="true" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
+      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
         <option value="prefix" selected="true">prefix</option>
         <option value="suffix">suffix</option>
         <expand macro="list_string_san" name="decoy_string_position"/>
       </param>
-      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="true" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
+      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
         <option value="error">error</option>
         <option value="warn" selected="true">warn</option>
         <option value="silent">silent</option>
@@ -6024,19 +6098,29 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
       <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
       <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
-      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="true" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
+      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
         <option value="error" selected="true">error</option>
         <option value="warn">warn</option>
         <option value="remove">remove</option>
         <expand macro="list_string_san" name="unmatched_action"/>
       </param>
-      <param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
-      <param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
+      <param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
+      <param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
       <param name="IL_equivalent" argument="-PeptideIndexing:IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/>
+      <param name="allow_nterm_protein_cleavage" argument="-PeptideIndexing:allow_nterm_protein_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Allow the protein N-terminus amino acid to clip" help=""/>
       <section name="enzyme" title="" help="" expanded="false">
-        <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" optional="true" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
+        <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
           <option value="auto" selected="true">auto</option>
+          <option value="Arg-C">Arg-C</option>
+          <option value="Arg-C/P">Arg-C/P</option>
+          <option value="Asp-N">Asp-N</option>
+          <option value="Asp-N/B">Asp-N/B</option>
+          <option value="Asp-N_ambic">Asp-N_ambic</option>
           <option value="Trypsin">Trypsin</option>
+          <option value="Chymotrypsin">Chymotrypsin</option>
+          <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+          <option value="CNBr">CNBr</option>
+          <option value="Formic_acid">Formic_acid</option>
           <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
           <option value="Glu-C+P">Glu-C+P</option>
           <option value="PepsinA + P">PepsinA + P</option>
@@ -6044,34 +6128,25 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Clostripain/P">Clostripain/P</option>
           <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
           <option value="no cleavage">no cleavage</option>
+          <option value="unspecific cleavage">unspecific cleavage</option>
+          <option value="TrypChymo">TrypChymo</option>
+          <option value="Trypsin/P">Trypsin/P</option>
+          <option value="V8-DE">V8-DE</option>
+          <option value="V8-E">V8-E</option>
+          <option value="leukocyte elastase">leukocyte elastase</option>
           <option value="proline endopeptidase">proline endopeptidase</option>
           <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
           <option value="Alpha-lytic protease">Alpha-lytic protease</option>
           <option value="2-iodobenzoate">2-iodobenzoate</option>
           <option value="iodosobenzoate">iodosobenzoate</option>
           <option value="staphylococcal protease/D">staphylococcal protease/D</option>
-          <option value="Trypsin/P">Trypsin/P</option>
-          <option value="V8-DE">V8-DE</option>
-          <option value="V8-E">V8-E</option>
-          <option value="leukocyte elastase">leukocyte elastase</option>
-          <option value="PepsinA">PepsinA</option>
-          <option value="TrypChymo">TrypChymo</option>
-          <option value="Asp-N">Asp-N</option>
-          <option value="unspecific cleavage">unspecific cleavage</option>
-          <option value="Asp-N/B">Asp-N/B</option>
-          <option value="Asp-N_ambic">Asp-N_ambic</option>
-          <option value="Chymotrypsin">Chymotrypsin</option>
-          <option value="Chymotrypsin/P">Chymotrypsin/P</option>
-          <option value="CNBr">CNBr</option>
-          <option value="Arg-C/P">Arg-C/P</option>
+          <option value="Lys-C">Lys-C</option>
           <option value="Lys-N">Lys-N</option>
           <option value="Lys-C/P">Lys-C/P</option>
-          <option value="Formic_acid">Formic_acid</option>
-          <option value="Lys-C">Lys-C</option>
-          <option value="Arg-C">Arg-C</option>
+          <option value="PepsinA">PepsinA</option>
           <expand macro="list_string_san" name="name"/>
         </param>
-        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="true" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
+        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
           <option value="auto" selected="true">auto</option>
           <option value="full">full</option>
           <option value="semi">semi</option>
@@ -6089,44 +6164,45 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param argument="-use_Z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use Z ions for PSM" help=""/>
       <param argument="-use_NL_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use neutral loss (NH3, H2O) ions from b/y for PSM" help=""/>
       <param argument="-second_enzyme" type="select" optional="true" label="Additional enzyme used for peptide digestion" help="">
-        <option value="CNBr">CNBr</option>
-        <option value="Lys-C">Lys-C</option>
+        <option value="Asp-N">Asp-N</option>
+        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
         <option value="Trypsin">Trypsin</option>
         <option value="Arg-C">Arg-C</option>
-        <option value="Chymotrypsin">Chymotrypsin</option>
-        <option value="Asp-N">Asp-N</option>
+        <option value="no cleavage">no cleavage</option>
         <option value="unspecific cleavage">unspecific cleavage</option>
+        <option value="Chymotrypsin">Chymotrypsin</option>
+        <option value="CNBr">CNBr</option>
+        <option value="Lys-C">Lys-C</option>
         <option value="Lys-N">Lys-N</option>
         <option value="PepsinA">PepsinA</option>
         <option value="Trypsin/P">Trypsin/P</option>
-        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
         <expand macro="list_string_san" name="second_enzyme"/>
       </param>
-      <param argument="-digest_mass_range" type="text" optional="true" value="600:5000" label="MH+ peptide mass range to analyze" help="">
+      <param argument="-digest_mass_range" type="text" value="600:5000" label="MH+ peptide mass range to analyze" help="">
         <expand macro="list_string_san" name="digest_mass_range"/>
       </param>
-      <param argument="-max_precursor_charge" type="integer" optional="true" min="1" max="9" value="5" label="set maximum precursor charge state to analyze (allowed max 9)" help=""/>
-      <param argument="-spectrum_batch_size" type="integer" optional="true" min="0" value="20000" label="max" help="number of spectra to search at a time; use 0 to search the entire scan range in one batch"/>
-      <param argument="-mass_offsets" type="text" optional="true" value="0.0" label="One or more mass offsets to search (values subtracted from deconvoluted precursor mass)" help="Has to include 0.0 if you want the default mass to be searched (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param argument="-max_precursor_charge" type="integer" min="1" max="9" value="5" label="set maximum precursor charge state to analyze (allowed max 9)" help=""/>
+      <param argument="-spectrum_batch_size" type="integer" min="0" value="20000" label="max" help="number of spectra to search at a time; use 0 to search the entire scan range in one batch"/>
+      <param argument="-mass_offsets" type="text" value="0.0" label="One or more mass offsets to search (values subtracted from deconvoluted precursor mass)" help="Has to include 0.0 if you want the default mass to be searched (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_float_valsan" name="mass_offsets"/>
       </param>
-      <param argument="-minimum_peaks" type="integer" optional="true" value="10" label="Required minimum number of peaks in spectrum to search (default 10)" help=""/>
-      <param argument="-minimum_intensity" type="float" optional="true" min="0.0" value="0.0" label="Minimum intensity value to read in" help=""/>
-      <param argument="-remove_precursor_peak" type="select" optional="true" label="no = no removal, yes = remove all peaks around precursor m/z, charge_reduced = remove all charge reduced precursor peaks (for ETD/ECD)" help="phosphate_loss = remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks. See also remove_precursor_tolerance">
+      <param argument="-minimum_peaks" type="integer" value="10" label="Required minimum number of peaks in spectrum to search (default 10)" help=""/>
+      <param argument="-minimum_intensity" type="float" min="0.0" value="0.0" label="Minimum intensity value to read in" help=""/>
+      <param argument="-remove_precursor_peak" type="select" label="no = no removal, yes = remove all peaks around precursor m/z, charge_reduced = remove all charge reduced precursor peaks (for ETD/ECD)" help="phosphate_loss = remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks. See also remove_precursor_tolerance">
         <option value="no" selected="true">no</option>
         <option value="yes">yes</option>
         <option value="charge_reduced">charge_reduced</option>
         <option value="phosphate_loss">phosphate_loss</option>
         <expand macro="list_string_san" name="remove_precursor_peak"/>
       </param>
-      <param argument="-remove_precursor_tolerance" type="float" optional="true" value="1.5" label="one-sided tolerance for precursor removal in Thompson" help=""/>
-      <param argument="-clear_mz_range" type="text" optional="true" value="0:0" label="for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range, if not 0:0" help="">
+      <param argument="-remove_precursor_tolerance" type="float" value="1.5" label="one-sided tolerance for precursor removal in Thompson" help=""/>
+      <param argument="-clear_mz_range" type="text" value="0:0" label="for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range, if not 0:0" help="">
         <expand macro="list_string_san" name="clear_mz_range"/>
       </param>
-      <param argument="-max_variable_mods_in_peptide" type="integer" optional="true" value="5" label="Set a maximum number of variable modifications per peptide" help=""/>
+      <param argument="-max_variable_mods_in_peptide" type="integer" value="5" label="Set a maximum number of variable modifications per peptide" help=""/>
       <param argument="-require_variable_mod" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, requires at least one variable modification per peptide" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -6144,7 +6220,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_CometAdapter_1 -->
+  <tests>
+    <!-- TOPP_CometAdapter_1 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="use_A_ions" value="false"/>
@@ -6154,7 +6231,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="use_Y_ions" value="true"/>
         <param name="use_Z_ions" value="false"/>
         <param name="use_NL_ions" value="false"/>
-        <param name="second_enzyme"/>
         <param name="digest_mass_range" value="600:5000"/>
         <param name="max_precursor_charge" value="5"/>
         <param name="spectrum_batch_size" value="1000"/>
@@ -6170,9 +6246,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="spectra_comet.mzML"/>
-      <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="CometAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="database" value="proteins.fasta"/>
-      <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="pin_out" value="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="precursor_mass_tolerance" value="3.0"/>
       <param name="precursor_error_units" value="ppm"/>
       <param name="isotope_error" value="off"/>
@@ -6192,9 +6268,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="activation_method" value="ALL"/>
       <param name="max_fragment_charge" value="3"/>
       <param name="clip_nterm_methionine" value="false"/>
-      <param name="fixed_modifications"/>
-      <param name="variable_modifications"/>
-      <param name="binary_modifications" value=""/>
       <param name="reindex" value="true"/>
       <section name="PeptideIndexing">
         <param name="decoy_string" value=""/>
@@ -6207,6 +6280,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="aaa_max" value="3"/>
         <param name="mismatches_max" value="0"/>
         <param name="IL_equivalent" value="false"/>
+        <param name="allow_nterm_protein_cleavage" value="true"/>
         <section name="enzyme">
           <param name="name" value="auto"/>
           <param name="specificity" value="auto"/>
@@ -6218,6 +6292,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_CometAdapter_2 -->
     <test expect_num_outputs="3">
@@ -6229,7 +6306,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="use_Y_ions" value="true"/>
         <param name="use_Z_ions" value="false"/>
         <param name="use_NL_ions" value="false"/>
-        <param name="second_enzyme"/>
         <param name="digest_mass_range" value="600:5000"/>
         <param name="max_precursor_charge" value="5"/>
         <param name="spectrum_batch_size" value="1000"/>
@@ -6245,9 +6321,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="CometAdapter_2_prepared.mzML"/>
-      <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="CometAdapter_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="database" value="CometAdapter_2_in.fasta"/>
-      <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="pin_out" value="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="precursor_mass_tolerance" value="3.0"/>
       <param name="precursor_error_units" value="Da"/>
       <param name="isotope_error" value="off"/>
@@ -6267,9 +6343,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="activation_method" value="ALL"/>
       <param name="max_fragment_charge" value="3"/>
       <param name="clip_nterm_methionine" value="false"/>
-      <param name="fixed_modifications"/>
-      <param name="variable_modifications"/>
-      <param name="binary_modifications" value=""/>
       <param name="reindex" value="true"/>
       <section name="PeptideIndexing">
         <param name="decoy_string" value=""/>
@@ -6282,6 +6355,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="aaa_max" value="3"/>
         <param name="mismatches_max" value="0"/>
         <param name="IL_equivalent" value="false"/>
+        <param name="allow_nterm_protein_cleavage" value="true"/>
         <section name="enzyme">
           <param name="name" value="auto"/>
           <param name="specificity" value="auto"/>
@@ -6293,6 +6367,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_CometAdapter_3 -->
     <test expect_num_outputs="3">
@@ -6304,7 +6381,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="use_Y_ions" value="true"/>
         <param name="use_Z_ions" value="false"/>
         <param name="use_NL_ions" value="false"/>
-        <param name="second_enzyme"/>
         <param name="digest_mass_range" value="600:5000"/>
         <param name="max_precursor_charge" value="5"/>
         <param name="spectrum_batch_size" value="20000"/>
@@ -6320,9 +6396,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="CometAdapter_3.mzML"/>
-      <output name="out" file="CometAdapter_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="CometAdapter_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="database" value="CometAdapter_3.fasta"/>
-      <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="pin_out" value="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="precursor_mass_tolerance" value="5.0"/>
       <param name="precursor_error_units" value="ppm"/>
       <param name="isotope_error" value="off"/>
@@ -6344,7 +6420,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="clip_nterm_methionine" value="false"/>
       <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
       <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term),Phospho (S),Phospho (T),Phospho (Y)"/>
-      <param name="binary_modifications" value=""/>
       <param name="reindex" value="true"/>
       <section name="PeptideIndexing">
         <param name="decoy_string" value=""/>
@@ -6357,6 +6432,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="aaa_max" value="3"/>
         <param name="mismatches_max" value="0"/>
         <param name="IL_equivalent" value="false"/>
+        <param name="allow_nterm_protein_cleavage" value="true"/>
         <section name="enzyme">
           <param name="name" value="auto"/>
           <param name="specificity" value="auto"/>
@@ -6368,6 +6444,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_CometAdapter_4 -->
     <test expect_num_outputs="2">
@@ -6379,7 +6458,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="use_Y_ions" value="true"/>
         <param name="use_Z_ions" value="false"/>
         <param name="use_NL_ions" value="false"/>
-        <param name="second_enzyme"/>
         <param name="digest_mass_range" value="600:1200"/>
         <param name="max_precursor_charge" value="5"/>
         <param name="spectrum_batch_size" value="20000"/>
@@ -6395,7 +6473,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/>
-      <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="CometAdapter_4_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/>
       <param name="precursor_mass_tolerance" value="5.0"/>
       <param name="precursor_error_units" value="ppm"/>
@@ -6418,7 +6496,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="clip_nterm_methionine" value="false"/>
       <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
       <param name="variable_modifications" value="Met-loss (Protein N-term M)"/>
-      <param name="binary_modifications" value=""/>
       <param name="reindex" value="true"/>
       <section name="PeptideIndexing">
         <param name="decoy_string" value=""/>
@@ -6431,6 +6508,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="aaa_max" value="3"/>
         <param name="mismatches_max" value="0"/>
         <param name="IL_equivalent" value="false"/>
+        <param name="allow_nterm_protein_cleavage" value="true"/>
         <section name="enzyme">
           <param name="name" value="auto"/>
           <param name="specificity" value="auto"/>
@@ -6442,11 +6520,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Annotates MS/MS spectra using Comet.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_CometAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_CometAdapter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/CompNovo.xml b/tools/openms/CompNovo.xml
deleted file mode 100644
index 9102b3639..000000000
--- a/tools/openms/CompNovo.xml
+++ /dev/null
@@ -1,5984 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
-<tool id="CompNovo" name="CompNovo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Performs a de novo peptide identification using the CompNovo engine.</description>
-  <macros>
-    <token name="@EXECUTABLE@">CompNovo</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-mkdir out &&
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in
-'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
--out
-'out/output.${gxy2omsext("idxml")}'
-
-## Postprocessing
-&& mv 'out/output.${gxy2omsext("idxml")}' '$out'
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
-  </configfiles>
-  <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file in mzML format" help=" select mzml data sets(s)"/>
-    <section name="algorithm" title="Algorithm section" help="" expanded="false">
-      <param name="max_number_aa_per_decomp" argument="-algorithm:max_number_aa_per_decomp" type="integer" optional="true" value="4" label="maximal amino acid frequency per decomposition" help=""/>
-      <param name="tryptic_only" argument="-algorithm:tryptic_only" type="boolean" truevalue="true" falsevalue="false" checked="true" label="if set to true only tryptic peptides are reported" help=""/>
-      <param name="precursor_mass_tolerance" argument="-algorithm:precursor_mass_tolerance" type="float" optional="true" value="1.5" label="precursor mass tolerance" help=""/>
-      <param name="fragment_mass_tolerance" argument="-algorithm:fragment_mass_tolerance" type="float" optional="true" value="0.3" label="fragment mass tolerance" help=""/>
-      <param name="max_number_pivot" argument="-algorithm:max_number_pivot" type="integer" optional="true" value="9" label="maximal number of pivot ions to be used" help=""/>
-      <param name="max_subscore_number" argument="-algorithm:max_subscore_number" type="integer" optional="true" value="40" label="maximal number of solutions of a subsegment that are kept" help=""/>
-      <param name="decomp_weights_precision" argument="-algorithm:decomp_weights_precision" type="float" optional="true" value="0.01" label="precision used to calculate the decompositions, this only affects cache usage!" help=""/>
-      <param name="double_charged_iso_threshold" argument="-algorithm:double_charged_iso_threshold" type="float" optional="true" value="0.6" label="minimal isotope intensity correlation of doubly charged ions to be used to score the single scored ions" help=""/>
-      <param name="max_mz" argument="-algorithm:max_mz" type="float" optional="true" value="2000.0" label="maximal m/z value used to calculate isotope distributions" help=""/>
-      <param name="min_mz" argument="-algorithm:min_mz" type="float" optional="true" value="200.0" label="minimal m/z value used to calculate the isotope distributions" help=""/>
-      <param name="max_isotope_to_score" argument="-algorithm:max_isotope_to_score" type="integer" optional="true" value="3" label="max isotope peak to be considered in the scoring" help=""/>
-      <param name="max_decomp_weight" argument="-algorithm:max_decomp_weight" type="float" optional="true" value="450.0" label="maximal m/z difference used to calculate the decompositions" help=""/>
-      <param name="max_isotope" argument="-algorithm:max_isotope" type="integer" optional="true" value="3" label="max isotope used in the theoretical spectra to score" help=""/>
-      <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" value="1" label="maximal number of missed cleavages allowed per peptide" help=""/>
-      <param name="number_of_hits" argument="-algorithm:number_of_hits" type="integer" optional="true" value="100" label="maximal number of hits which are reported per spectrum" help=""/>
-      <param name="estimate_precursor_mz" argument="-algorithm:estimate_precursor_mz" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If set to true, the precursor charge will be estimated" help="e.g. from the precursor peaks of the ETD spectrum.. The input is believed otherwise"/>
-      <param name="number_of_prescoring_hits" argument="-algorithm:number_of_prescoring_hits" type="integer" optional="true" value="250" label="how many sequences are kept after first rough scoring for better scoring" help=""/>
-      <param name="fixed_modifications" argument="-algorithm:fixed_modifications" multiple="true" type="select" optional="true" label="fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
-        <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
-        <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
-        <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
-        <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
-        <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
-        <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
-        <option value="2-succinyl (C)">2-succinyl (C)</option>
-        <option value="2HPG (R)">2HPG (R)</option>
-        <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
-        <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
-        <option value="3sulfo (N-term)">3sulfo (N-term)</option>
-        <option value="4-ONE (C)">4-ONE (C)</option>
-        <option value="4-ONE (H)">4-ONE (H)</option>
-        <option value="4-ONE (K)">4-ONE (K)</option>
-        <option value="4-ONE+Delta:H(-2)O(-1) (C)">4-ONE+Delta:H(-2)O(-1) (C)</option>
-        <option value="4-ONE+Delta:H(-2)O(-1) (H)">4-ONE+Delta:H(-2)O(-1) (H)</option>
-        <option value="4-ONE+Delta:H(-2)O(-1) (K)">4-ONE+Delta:H(-2)O(-1) (K)</option>
-        <option value="4AcAllylGal (C)">4AcAllylGal (C)</option>
-        <option value="a-type-ion (C-term)">a-type-ion (C-term)</option>
-        <option value="AccQTag (K)">AccQTag (K)</option>
-        <option value="AccQTag (N-term)">AccQTag (N-term)</option>
-        <option value="Acetyl (C)">Acetyl (C)</option>
-        <option value="Acetyl (H)">Acetyl (H)</option>
-        <option value="Acetyl (K)">Acetyl (K)</option>
-        <option value="Acetyl (N-term)">Acetyl (N-term)</option>
-        <option value="Acetyl (Protein N-term)">Acetyl (Protein N-term)</option>
-        <option value="Acetyl (R)">Acetyl (R)</option>
-        <option value="Acetyl (S)">Acetyl (S)</option>
-        <option value="Acetyl (T)">Acetyl (T)</option>
-        <option value="Acetyl (Y)">Acetyl (Y)</option>
-        <option value="Acetyl:13C(2) (K)">Acetyl:13C(2) (K)</option>
-        <option value="Acetyl:13C(2) (Protein N-term)">Acetyl:13C(2) (Protein N-term)</option>
-        <option value="Acetyl:2H(3) (H)">Acetyl:2H(3) (H)</option>
-        <option value="Acetyl:2H(3) (K)">Acetyl:2H(3) (K)</option>
-        <option value="Acetyl:2H(3) (N-term)">Acetyl:2H(3) (N-term)</option>
-        <option value="Acetyl:2H(3) (Protein N-term)">Acetyl:2H(3) (Protein N-term)</option>
-        <option value="Acetyl:2H(3) (S)">Acetyl:2H(3) (S)</option>
-        <option value="Acetyl:2H(3) (T)">Acetyl:2H(3) (T)</option>
-        <option value="Acetyl:2H(3) (Y)">Acetyl:2H(3) (Y)</option>
-        <option value="Acetyldeoxyhypusine (K)">Acetyldeoxyhypusine (K)</option>
-        <option value="Acetylhypusine (K)">Acetylhypusine (K)</option>
-        <option value="ADP-Ribosyl (C)">ADP-Ribosyl (C)</option>
-        <option value="ADP-Ribosyl (D)">ADP-Ribosyl (D)</option>
-        <option value="ADP-Ribosyl (E)">ADP-Ribosyl (E)</option>
-        <option value="ADP-Ribosyl (K)">ADP-Ribosyl (K)</option>
-        <option value="ADP-Ribosyl (N)">ADP-Ribosyl (N)</option>
-        <option value="ADP-Ribosyl (R)">ADP-Ribosyl (R)</option>
-        <option value="ADP-Ribosyl (S)">ADP-Ribosyl (S)</option>
-        <option value="ADP-Ribosyl (T)">ADP-Ribosyl (T)</option>
-        <option value="AEBS (H)">AEBS (H)</option>
-        <option value="AEBS (K)">AEBS (K)</option>
-        <option value="AEBS (Protein N-term)">AEBS (Protein N-term)</option>
-        <option value="AEBS (S)">AEBS (S)</option>
-        <option value="AEBS (Y)">AEBS (Y)</option>
-        <option value="AEC-MAEC (S)">AEC-MAEC (S)</option>
-        <option value="AEC-MAEC (T)">AEC-MAEC (T)</option>
-        <option value="AEC-MAEC:2H(4) (S)">AEC-MAEC:2H(4) (S)</option>
-        <option value="AEC-MAEC:2H(4) (T)">AEC-MAEC:2H(4) (T)</option>
-        <option value="AFB1_Dialdehyde (K)">AFB1_Dialdehyde (K)</option>
-        <option value="AHA-Alkyne (M)">AHA-Alkyne (M)</option>
-        <option value="AHA-Alkyne-KDDDD (M)">AHA-Alkyne-KDDDD (M)</option>
-        <option value="AHA-SS (M)">AHA-SS (M)</option>
-        <option value="AHA-SS_CAM (M)">AHA-SS_CAM (M)</option>
-        <option value="Ahx2+Hsl (C-term)">Ahx2+Hsl (C-term)</option>
-        <option value="Ala-&gt;Arg (A)">Ala-&gt;Arg (A)</option>
-        <option value="Ala-&gt;Asn (A)">Ala-&gt;Asn (A)</option>
-        <option value="Ala-&gt;Asp (A)">Ala-&gt;Asp (A)</option>
-        <option value="Ala-&gt;Cys (A)">Ala-&gt;Cys (A)</option>
-        <option value="Ala-&gt;Gln (A)">Ala-&gt;Gln (A)</option>
-        <option value="Ala-&gt;Glu (A)">Ala-&gt;Glu (A)</option>
-        <option value="Ala-&gt;Gly (A)">Ala-&gt;Gly (A)</option>
-        <option value="Ala-&gt;His (A)">Ala-&gt;His (A)</option>
-        <option value="Ala-&gt;Lys (A)">Ala-&gt;Lys (A)</option>
-        <option value="Ala-&gt;Met (A)">Ala-&gt;Met (A)</option>
-        <option value="Ala-&gt;Phe (A)">Ala-&gt;Phe (A)</option>
-        <option value="Ala-&gt;Pro (A)">Ala-&gt;Pro (A)</option>
-        <option value="Ala-&gt;Ser (A)">Ala-&gt;Ser (A)</option>
-        <option value="Ala-&gt;Thr (A)">Ala-&gt;Thr (A)</option>
-        <option value="Ala-&gt;Trp (A)">Ala-&gt;Trp (A)</option>
-        <option value="Ala-&gt;Tyr (A)">Ala-&gt;Tyr (A)</option>
-        <option value="Ala-&gt;Val (A)">Ala-&gt;Val (A)</option>
-        <option value="Ala-&gt;Xle (A)">Ala-&gt;Xle (A)</option>
-        <option value="Amidated (C-term)">Amidated (C-term)</option>
-        <option value="Amidated (Protein C-term)">Amidated (Protein C-term)</option>
-        <option value="Amidine (K)">Amidine (K)</option>
-        <option value="Amidine (N-term)">Amidine (N-term)</option>
-        <option value="Amidino (C)">Amidino (C)</option>
-        <option value="Amino (Y)">Amino (Y)</option>
-        <option value="Ammonia-loss (N)">Ammonia-loss (N)</option>
-        <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
-        <option value="Ammonia-loss (Protein N-term S)">Ammonia-loss (Protein N-term S)</option>
-        <option value="Ammonia-loss (Protein N-term T)">Ammonia-loss (Protein N-term T)</option>
-        <option value="Ammonium (C-term)">Ammonium (C-term)</option>
-        <option value="Ammonium (D)">Ammonium (D)</option>
-        <option value="Ammonium (E)">Ammonium (E)</option>
-        <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
-        <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
-        <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
-        <option value="Archaeol (C)">Archaeol (C)</option>
-        <option value="Arg (N-term)">Arg (N-term)</option>
-        <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
-        <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
-        <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
-        <option value="Arg-&gt;Cys (R)">Arg-&gt;Cys (R)</option>
-        <option value="Arg-&gt;Gln (R)">Arg-&gt;Gln (R)</option>
-        <option value="Arg-&gt;Glu (R)">Arg-&gt;Glu (R)</option>
-        <option value="Arg-&gt;GluSA (R)">Arg-&gt;GluSA (R)</option>
-        <option value="Arg-&gt;Gly (R)">Arg-&gt;Gly (R)</option>
-        <option value="Arg-&gt;His (R)">Arg-&gt;His (R)</option>
-        <option value="Arg-&gt;Lys (R)">Arg-&gt;Lys (R)</option>
-        <option value="Arg-&gt;Met (R)">Arg-&gt;Met (R)</option>
-        <option value="Arg-&gt;Npo (R)">Arg-&gt;Npo (R)</option>
-        <option value="Arg-&gt;Orn (R)">Arg-&gt;Orn (R)</option>
-        <option value="Arg-&gt;Phe (R)">Arg-&gt;Phe (R)</option>
-        <option value="Arg-&gt;Pro (R)">Arg-&gt;Pro (R)</option>
-        <option value="Arg-&gt;Ser (R)">Arg-&gt;Ser (R)</option>
-        <option value="Arg-&gt;Thr (R)">Arg-&gt;Thr (R)</option>
-        <option value="Arg-&gt;Trp (R)">Arg-&gt;Trp (R)</option>
-        <option value="Arg-&gt;Tyr (R)">Arg-&gt;Tyr (R)</option>
-        <option value="Arg-&gt;Val (R)">Arg-&gt;Val (R)</option>
-        <option value="Arg-&gt;Xle (R)">Arg-&gt;Xle (R)</option>
-        <option value="Arg-loss (C-term R)">Arg-loss (C-term R)</option>
-        <option value="Arg2PG (R)">Arg2PG (R)</option>
-        <option value="Argbiotinhydrazide (R)">Argbiotinhydrazide (R)</option>
-        <option value="AROD (C)">AROD (C)</option>
-        <option value="Asn-&gt;Ala (N)">Asn-&gt;Ala (N)</option>
-        <option value="Asn-&gt;Arg (N)">Asn-&gt;Arg (N)</option>
-        <option value="Asn-&gt;Asp (N)">Asn-&gt;Asp (N)</option>
-        <option value="Asn-&gt;Cys (N)">Asn-&gt;Cys (N)</option>
-        <option value="Asn-&gt;Gln (N)">Asn-&gt;Gln (N)</option>
-        <option value="Asn-&gt;Glu (N)">Asn-&gt;Glu (N)</option>
-        <option value="Asn-&gt;Gly (N)">Asn-&gt;Gly (N)</option>
-        <option value="Asn-&gt;His (N)">Asn-&gt;His (N)</option>
-        <option value="Asn-&gt;Lys (N)">Asn-&gt;Lys (N)</option>
-        <option value="Asn-&gt;Met (N)">Asn-&gt;Met (N)</option>
-        <option value="Asn-&gt;Phe (N)">Asn-&gt;Phe (N)</option>
-        <option value="Asn-&gt;Pro (N)">Asn-&gt;Pro (N)</option>
-        <option value="Asn-&gt;Ser (N)">Asn-&gt;Ser (N)</option>
-        <option value="Asn-&gt;Thr (N)">Asn-&gt;Thr (N)</option>
-        <option value="Asn-&gt;Trp (N)">Asn-&gt;Trp (N)</option>
-        <option value="Asn-&gt;Tyr (N)">Asn-&gt;Tyr (N)</option>
-        <option value="Asn-&gt;Val (N)">Asn-&gt;Val (N)</option>
-        <option value="Asn-&gt;Xle (N)">Asn-&gt;Xle (N)</option>
-        <option value="Asp-&gt;Ala (D)">Asp-&gt;Ala (D)</option>
-        <option value="Asp-&gt;Arg (D)">Asp-&gt;Arg (D)</option>
-        <option value="Asp-&gt;Asn (D)">Asp-&gt;Asn (D)</option>
-        <option value="Asp-&gt;Cys (D)">Asp-&gt;Cys (D)</option>
-        <option value="Asp-&gt;Gln (D)">Asp-&gt;Gln (D)</option>
-        <option value="Asp-&gt;Glu (D)">Asp-&gt;Glu (D)</option>
-        <option value="Asp-&gt;Gly (D)">Asp-&gt;Gly (D)</option>
-        <option value="Asp-&gt;His (D)">Asp-&gt;His (D)</option>
-        <option value="Asp-&gt;Lys (D)">Asp-&gt;Lys (D)</option>
-        <option value="Asp-&gt;Met (D)">Asp-&gt;Met (D)</option>
-        <option value="Asp-&gt;Phe (D)">Asp-&gt;Phe (D)</option>
-        <option value="Asp-&gt;Pro (D)">Asp-&gt;Pro (D)</option>
-        <option value="Asp-&gt;Ser (D)">Asp-&gt;Ser (D)</option>
-        <option value="Asp-&gt;Thr (D)">Asp-&gt;Thr (D)</option>
-        <option value="Asp-&gt;Trp (D)">Asp-&gt;Trp (D)</option>
-        <option value="Asp-&gt;Tyr (D)">Asp-&gt;Tyr (D)</option>
-        <option value="Asp-&gt;Val (D)">Asp-&gt;Val (D)</option>
-        <option value="Asp-&gt;Xle (D)">Asp-&gt;Xle (D)</option>
-        <option value="Aspartylurea (H)">Aspartylurea (H)</option>
-        <option value="Atto495Maleimide (C)">Atto495Maleimide (C)</option>
-        <option value="AzidoF (F)">AzidoF (F)</option>
-        <option value="azole (C)">azole (C)</option>
-        <option value="azole (S)">azole (S)</option>
-        <option value="Bacillosamine (N)">Bacillosamine (N)</option>
-        <option value="BADGE (C)">BADGE (C)</option>
-        <option value="BDMAPP (H)">BDMAPP (H)</option>
-        <option value="BDMAPP (K)">BDMAPP (K)</option>
-        <option value="BDMAPP (Protein N-term)">BDMAPP (Protein N-term)</option>
-        <option value="BDMAPP (W)">BDMAPP (W)</option>
-        <option value="BDMAPP (Y)">BDMAPP (Y)</option>
-        <option value="BEMAD_C (C)">BEMAD_C (C)</option>
-        <option value="BEMAD_C:2H(6) (C)">BEMAD_C:2H(6) (C)</option>
-        <option value="BEMAD_ST (S)">BEMAD_ST (S)</option>
-        <option value="BEMAD_ST (T)">BEMAD_ST (T)</option>
-        <option value="BEMAD_ST:2H(6) (S)">BEMAD_ST:2H(6) (S)</option>
-        <option value="BEMAD_ST:2H(6) (T)">BEMAD_ST:2H(6) (T)</option>
-        <option value="Benzoyl (K)">Benzoyl (K)</option>
-        <option value="Benzoyl (N-term)">Benzoyl (N-term)</option>
-        <option value="benzylguanidine (K)">benzylguanidine (K)</option>
-        <option value="betaFNA (C)">betaFNA (C)</option>
-        <option value="betaFNA (K)">betaFNA (K)</option>
-        <option value="BHT (C)">BHT (C)</option>
-        <option value="BHT (H)">BHT (H)</option>
-        <option value="BHT (K)">BHT (K)</option>
-        <option value="BHTOH (C)">BHTOH (C)</option>
-        <option value="BHTOH (H)">BHTOH (H)</option>
-        <option value="BHTOH (K)">BHTOH (K)</option>
-        <option value="Biotin (K)">Biotin (K)</option>
-        <option value="Biotin (N-term)">Biotin (N-term)</option>
-        <option value="Biotin-HPDP (C)">Biotin-HPDP (C)</option>
-        <option value="Biotin-PEG-PRA (M)">Biotin-PEG-PRA (M)</option>
-        <option value="Biotin-PEO-Amine (D)">Biotin-PEO-Amine (D)</option>
-        <option value="Biotin-PEO-Amine (E)">Biotin-PEO-Amine (E)</option>
-        <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
-        <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
-        <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
-        <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
-        <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
-        <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
-        <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
-        <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
-        <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
-        <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
-        <option value="Biotin:Thermo-21328 (K)">Biotin:Thermo-21328 (K)</option>
-        <option value="Biotin:Thermo-21328 (N-term)">Biotin:Thermo-21328 (N-term)</option>
-        <option value="Biotin:Thermo-21330 (K)">Biotin:Thermo-21330 (K)</option>
-        <option value="Biotin:Thermo-21330 (N-term)">Biotin:Thermo-21330 (N-term)</option>
-        <option value="Biotin:Thermo-21345 (Q)">Biotin:Thermo-21345 (Q)</option>
-        <option value="Biotin:Thermo-21360 (X)">Biotin:Thermo-21360 (X)</option>
-        <option value="Biotin:Thermo-21901+2H2O (C)">Biotin:Thermo-21901+2H2O (C)</option>
-        <option value="Biotin:Thermo-21901+H2O (C)">Biotin:Thermo-21901+H2O (C)</option>
-        <option value="Biotin:Thermo-21911 (C)">Biotin:Thermo-21911 (C)</option>
-        <option value="Biotin:Thermo-33033 (X)">Biotin:Thermo-33033 (X)</option>
-        <option value="Biotin:Thermo-33033-H (X)">Biotin:Thermo-33033-H (X)</option>
-        <option value="Biotin:Thermo-88310 (K)">Biotin:Thermo-88310 (K)</option>
-        <option value="Biotin:Thermo-88317 (S)">Biotin:Thermo-88317 (S)</option>
-        <option value="Biotin:Thermo-88317 (Y)">Biotin:Thermo-88317 (Y)</option>
-        <option value="biotinAcrolein298 (C)">biotinAcrolein298 (C)</option>
-        <option value="biotinAcrolein298 (H)">biotinAcrolein298 (H)</option>
-        <option value="biotinAcrolein298 (K)">biotinAcrolein298 (K)</option>
-        <option value="biotinAcrolein298 (Protein N-term)">biotinAcrolein298 (Protein N-term)</option>
-        <option value="BisANS (K)">BisANS (K)</option>
-        <option value="bisANS-sulfonates (K)">bisANS-sulfonates (K)</option>
-        <option value="bisANS-sulfonates (S)">bisANS-sulfonates (S)</option>
-        <option value="bisANS-sulfonates (T)">bisANS-sulfonates (T)</option>
-        <option value="BITC (C)">BITC (C)</option>
-        <option value="BITC (K)">BITC (K)</option>
-        <option value="BITC (N-term)">BITC (N-term)</option>
-        <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
-        <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-        <option value="Bodipy (C)">Bodipy (C)</option>
-        <option value="Brij35 (N-term)">Brij35 (N-term)</option>
-        <option value="Brij58 (N-term)">Brij58 (N-term)</option>
-        <option value="Bromo (F)">Bromo (F)</option>
-        <option value="Bromo (H)">Bromo (H)</option>
-        <option value="Bromo (W)">Bromo (W)</option>
-        <option value="Bromo (Y)">Bromo (Y)</option>
-        <option value="Bromobimane (C)">Bromobimane (C)</option>
-        <option value="Butyryl (K)">Butyryl (K)</option>
-        <option value="C8-QAT (K)">C8-QAT (K)</option>
-        <option value="C8-QAT (N-term)">C8-QAT (N-term)</option>
-        <option value="CAF (N-term)">CAF (N-term)</option>
-        <option value="CAMthiopropanoyl (K)">CAMthiopropanoyl (K)</option>
-        <option value="CAMthiopropanoyl (Protein N-term)">CAMthiopropanoyl (Protein N-term)</option>
-        <option value="Can-FP-biotin (S)">Can-FP-biotin (S)</option>
-        <option value="Can-FP-biotin (T)">Can-FP-biotin (T)</option>
-        <option value="Can-FP-biotin (Y)">Can-FP-biotin (Y)</option>
-        <option value="Carbamidomethyl (C)">Carbamidomethyl (C)</option>
-        <option value="Carbamidomethyl (D)">Carbamidomethyl (D)</option>
-        <option value="Carbamidomethyl (E)">Carbamidomethyl (E)</option>
-        <option value="Carbamidomethyl (H)">Carbamidomethyl (H)</option>
-        <option value="Carbamidomethyl (K)">Carbamidomethyl (K)</option>
-        <option value="Carbamidomethyl (M)">Carbamidomethyl (M)</option>
-        <option value="Carbamidomethyl (N-term)">Carbamidomethyl (N-term)</option>
-        <option value="Carbamidomethyl (S)">Carbamidomethyl (S)</option>
-        <option value="Carbamidomethyl (T)">Carbamidomethyl (T)</option>
-        <option value="Carbamidomethyl (U)">Carbamidomethyl (U)</option>
-        <option value="Carbamidomethyl (Y)">Carbamidomethyl (Y)</option>
-        <option value="CarbamidomethylDTT (C)">CarbamidomethylDTT (C)</option>
-        <option value="Carbamyl (C)">Carbamyl (C)</option>
-        <option value="Carbamyl (K)">Carbamyl (K)</option>
-        <option value="Carbamyl (M)">Carbamyl (M)</option>
-        <option value="Carbamyl (N-term)">Carbamyl (N-term)</option>
-        <option value="Carbamyl (Protein N-term)">Carbamyl (Protein N-term)</option>
-        <option value="Carbamyl (R)">Carbamyl (R)</option>
-        <option value="Carbamyl (S)">Carbamyl (S)</option>
-        <option value="Carbamyl (T)">Carbamyl (T)</option>
-        <option value="Carbamyl (Y)">Carbamyl (Y)</option>
-        <option value="Carbofuran (S)">Carbofuran (S)</option>
-        <option value="Carbonyl (A)">Carbonyl (A)</option>
-        <option value="Carbonyl (E)">Carbonyl (E)</option>
-        <option value="Carbonyl (I)">Carbonyl (I)</option>
-        <option value="Carbonyl (L)">Carbonyl (L)</option>
-        <option value="Carbonyl (Q)">Carbonyl (Q)</option>
-        <option value="Carbonyl (R)">Carbonyl (R)</option>
-        <option value="Carbonyl (S)">Carbonyl (S)</option>
-        <option value="Carbonyl (V)">Carbonyl (V)</option>
-        <option value="Carboxy (D)">Carboxy (D)</option>
-        <option value="Carboxy (E)">Carboxy (E)</option>
-        <option value="Carboxy (K)">Carboxy (K)</option>
-        <option value="Carboxy (Protein N-term M)">Carboxy (Protein N-term M)</option>
-        <option value="Carboxy (W)">Carboxy (W)</option>
-        <option value="Carboxy-&gt;Thiocarboxy (Protein C-term G)">Carboxy-&gt;Thiocarboxy (Protein C-term G)</option>
-        <option value="Carboxyethyl (H)">Carboxyethyl (H)</option>
-        <option value="Carboxyethyl (K)">Carboxyethyl (K)</option>
-        <option value="Carboxyethylpyrrole (K)">Carboxyethylpyrrole (K)</option>
-        <option value="Carboxymethyl (C)">Carboxymethyl (C)</option>
-        <option value="Carboxymethyl (K)">Carboxymethyl (K)</option>
-        <option value="Carboxymethyl (N-term)">Carboxymethyl (N-term)</option>
-        <option value="Carboxymethyl (U)">Carboxymethyl (U)</option>
-        <option value="Carboxymethyl (W)">Carboxymethyl (W)</option>
-        <option value="Carboxymethyl:13C(2) (C)">Carboxymethyl:13C(2) (C)</option>
-        <option value="CarboxymethylDMAP (N-term)">CarboxymethylDMAP (N-term)</option>
-        <option value="CarboxymethylDTT (C)">CarboxymethylDTT (C)</option>
-        <option value="Cation:Ag (C-term)">Cation:Ag (C-term)</option>
-        <option value="Cation:Ag (D)">Cation:Ag (D)</option>
-        <option value="Cation:Ag (E)">Cation:Ag (E)</option>
-        <option value="Cation:Al[III] (C-term)">Cation:Al[III] (C-term)</option>
-        <option value="Cation:Al[III] (D)">Cation:Al[III] (D)</option>
-        <option value="Cation:Al[III] (E)">Cation:Al[III] (E)</option>
-        <option value="Cation:Ca[II] (C-term)">Cation:Ca[II] (C-term)</option>
-        <option value="Cation:Ca[II] (D)">Cation:Ca[II] (D)</option>
-        <option value="Cation:Ca[II] (E)">Cation:Ca[II] (E)</option>
-        <option value="Cation:Cu[I] (C-term)">Cation:Cu[I] (C-term)</option>
-        <option value="Cation:Cu[I] (D)">Cation:Cu[I] (D)</option>
-        <option value="Cation:Cu[I] (E)">Cation:Cu[I] (E)</option>
-        <option value="Cation:Cu[I] (H)">Cation:Cu[I] (H)</option>
-        <option value="Cation:Fe[II] (C-term)">Cation:Fe[II] (C-term)</option>
-        <option value="Cation:Fe[II] (D)">Cation:Fe[II] (D)</option>
-        <option value="Cation:Fe[II] (E)">Cation:Fe[II] (E)</option>
-        <option value="Cation:Fe[III] (C-term)">Cation:Fe[III] (C-term)</option>
-        <option value="Cation:Fe[III] (D)">Cation:Fe[III] (D)</option>
-        <option value="Cation:Fe[III] (E)">Cation:Fe[III] (E)</option>
-        <option value="Cation:K (C-term)">Cation:K (C-term)</option>
-        <option value="Cation:K (D)">Cation:K (D)</option>
-        <option value="Cation:K (E)">Cation:K (E)</option>
-        <option value="Cation:Li (C-term)">Cation:Li (C-term)</option>
-        <option value="Cation:Li (D)">Cation:Li (D)</option>
-        <option value="Cation:Li (E)">Cation:Li (E)</option>
-        <option value="Cation:Mg[II] (C-term)">Cation:Mg[II] (C-term)</option>
-        <option value="Cation:Mg[II] (D)">Cation:Mg[II] (D)</option>
-        <option value="Cation:Mg[II] (E)">Cation:Mg[II] (E)</option>
-        <option value="Cation:Na (C-term)">Cation:Na (C-term)</option>
-        <option value="Cation:Na (D)">Cation:Na (D)</option>
-        <option value="Cation:Na (E)">Cation:Na (E)</option>
-        <option value="Cation:Ni[II] (C-term)">Cation:Ni[II] (C-term)</option>
-        <option value="Cation:Ni[II] (D)">Cation:Ni[II] (D)</option>
-        <option value="Cation:Ni[II] (E)">Cation:Ni[II] (E)</option>
-        <option value="Cation:Zn[II] (C-term)">Cation:Zn[II] (C-term)</option>
-        <option value="Cation:Zn[II] (D)">Cation:Zn[II] (D)</option>
-        <option value="Cation:Zn[II] (E)">Cation:Zn[II] (E)</option>
-        <option value="Cation:Zn[II] (H)">Cation:Zn[II] (H)</option>
-        <option value="cGMP (C)">cGMP (C)</option>
-        <option value="cGMP (S)">cGMP (S)</option>
-        <option value="cGMP+RMP-loss (C)">cGMP+RMP-loss (C)</option>
-        <option value="cGMP+RMP-loss (S)">cGMP+RMP-loss (S)</option>
-        <option value="CHDH (D)">CHDH (D)</option>
-        <option value="Chlorination (W)">Chlorination (W)</option>
-        <option value="Chlorination (Y)">Chlorination (Y)</option>
-        <option value="Cholesterol (Protein C-term)">Cholesterol (Protein C-term)</option>
-        <option value="CIGG (K)">CIGG (K)</option>
-        <option value="CLIP_TRAQ_2 (K)">CLIP_TRAQ_2 (K)</option>
-        <option value="CLIP_TRAQ_2 (N-term)">CLIP_TRAQ_2 (N-term)</option>
-        <option value="CLIP_TRAQ_2 (Y)">CLIP_TRAQ_2 (Y)</option>
-        <option value="CLIP_TRAQ_3 (K)">CLIP_TRAQ_3 (K)</option>
-        <option value="CLIP_TRAQ_3 (N-term)">CLIP_TRAQ_3 (N-term)</option>
-        <option value="CLIP_TRAQ_3 (Y)">CLIP_TRAQ_3 (Y)</option>
-        <option value="CLIP_TRAQ_4 (K)">CLIP_TRAQ_4 (K)</option>
-        <option value="CLIP_TRAQ_4 (N-term)">CLIP_TRAQ_4 (N-term)</option>
-        <option value="CLIP_TRAQ_4 (Y)">CLIP_TRAQ_4 (Y)</option>
-        <option value="CoenzymeA (C)">CoenzymeA (C)</option>
-        <option value="Cresylphosphate (H)">Cresylphosphate (H)</option>
-        <option value="Cresylphosphate (K)">Cresylphosphate (K)</option>
-        <option value="Cresylphosphate (R)">Cresylphosphate (R)</option>
-        <option value="Cresylphosphate (S)">Cresylphosphate (S)</option>
-        <option value="Cresylphosphate (T)">Cresylphosphate (T)</option>
-        <option value="Cresylphosphate (Y)">Cresylphosphate (Y)</option>
-        <option value="CresylSaligeninPhosphate (H)">CresylSaligeninPhosphate (H)</option>
-        <option value="CresylSaligeninPhosphate (K)">CresylSaligeninPhosphate (K)</option>
-        <option value="CresylSaligeninPhosphate (R)">CresylSaligeninPhosphate (R)</option>
-        <option value="CresylSaligeninPhosphate (S)">CresylSaligeninPhosphate (S)</option>
-        <option value="CresylSaligeninPhosphate (T)">CresylSaligeninPhosphate (T)</option>
-        <option value="CresylSaligeninPhosphate (Y)">CresylSaligeninPhosphate (Y)</option>
-        <option value="Crotonaldehyde (C)">Crotonaldehyde (C)</option>
-        <option value="Crotonaldehyde (H)">Crotonaldehyde (H)</option>
-        <option value="Crotonaldehyde (K)">Crotonaldehyde (K)</option>
-        <option value="Crotonyl (K)">Crotonyl (K)</option>
-        <option value="CuSMo (C)">CuSMo (C)</option>
-        <option value="CUSTOM0 (A)">CUSTOM0 (A)</option>
-        <option value="CUSTOM0 (C)">CUSTOM0 (C)</option>
-        <option value="CUSTOM0 (C-term)">CUSTOM0 (C-term)</option>
-        <option value="CUSTOM0 (D)">CUSTOM0 (D)</option>
-        <option value="CUSTOM0 (E)">CUSTOM0 (E)</option>
-        <option value="CUSTOM0 (F)">CUSTOM0 (F)</option>
-        <option value="CUSTOM0 (G)">CUSTOM0 (G)</option>
-        <option value="CUSTOM0 (H)">CUSTOM0 (H)</option>
-        <option value="CUSTOM0 (I)">CUSTOM0 (I)</option>
-        <option value="CUSTOM0 (K)">CUSTOM0 (K)</option>
-        <option value="CUSTOM0 (L)">CUSTOM0 (L)</option>
-        <option value="CUSTOM0 (M)">CUSTOM0 (M)</option>
-        <option value="CUSTOM0 (N)">CUSTOM0 (N)</option>
-        <option value="CUSTOM0 (N-term)">CUSTOM0 (N-term)</option>
-        <option value="CUSTOM0 (P)">CUSTOM0 (P)</option>
-        <option value="CUSTOM0 (Q)">CUSTOM0 (Q)</option>
-        <option value="CUSTOM0 (R)">CUSTOM0 (R)</option>
-        <option value="CUSTOM0 (S)">CUSTOM0 (S)</option>
-        <option value="CUSTOM0 (T)">CUSTOM0 (T)</option>
-        <option value="CUSTOM0 (V)">CUSTOM0 (V)</option>
-        <option value="CUSTOM0 (W)">CUSTOM0 (W)</option>
-        <option value="CUSTOM0 (Y)">CUSTOM0 (Y)</option>
-        <option value="CUSTOM1 (A)">CUSTOM1 (A)</option>
-        <option value="CUSTOM1 (C)">CUSTOM1 (C)</option>
-        <option value="CUSTOM1 (C-term)">CUSTOM1 (C-term)</option>
-        <option value="CUSTOM1 (D)">CUSTOM1 (D)</option>
-        <option value="CUSTOM1 (E)">CUSTOM1 (E)</option>
-        <option value="CUSTOM1 (F)">CUSTOM1 (F)</option>
-        <option value="CUSTOM1 (G)">CUSTOM1 (G)</option>
-        <option value="CUSTOM1 (H)">CUSTOM1 (H)</option>
-        <option value="CUSTOM1 (I)">CUSTOM1 (I)</option>
-        <option value="CUSTOM1 (K)">CUSTOM1 (K)</option>
-        <option value="CUSTOM1 (L)">CUSTOM1 (L)</option>
-        <option value="CUSTOM1 (M)">CUSTOM1 (M)</option>
-        <option value="CUSTOM1 (N)">CUSTOM1 (N)</option>
-        <option value="CUSTOM1 (N-term)">CUSTOM1 (N-term)</option>
-        <option value="CUSTOM1 (P)">CUSTOM1 (P)</option>
-        <option value="CUSTOM1 (Q)">CUSTOM1 (Q)</option>
-        <option value="CUSTOM1 (R)">CUSTOM1 (R)</option>
-        <option value="CUSTOM1 (S)">CUSTOM1 (S)</option>
-        <option value="CUSTOM1 (T)">CUSTOM1 (T)</option>
-        <option value="CUSTOM1 (V)">CUSTOM1 (V)</option>
-        <option value="CUSTOM1 (W)">CUSTOM1 (W)</option>
-        <option value="CUSTOM1 (Y)">CUSTOM1 (Y)</option>
-        <option value="CUSTOM2 (A)">CUSTOM2 (A)</option>
-        <option value="CUSTOM2 (C)">CUSTOM2 (C)</option>
-        <option value="CUSTOM2 (C-term)">CUSTOM2 (C-term)</option>
-        <option value="CUSTOM2 (D)">CUSTOM2 (D)</option>
-        <option value="CUSTOM2 (E)">CUSTOM2 (E)</option>
-        <option value="CUSTOM2 (F)">CUSTOM2 (F)</option>
-        <option value="CUSTOM2 (G)">CUSTOM2 (G)</option>
-        <option value="CUSTOM2 (H)">CUSTOM2 (H)</option>
-        <option value="CUSTOM2 (I)">CUSTOM2 (I)</option>
-        <option value="CUSTOM2 (K)">CUSTOM2 (K)</option>
-        <option value="CUSTOM2 (L)">CUSTOM2 (L)</option>
-        <option value="CUSTOM2 (M)">CUSTOM2 (M)</option>
-        <option value="CUSTOM2 (N)">CUSTOM2 (N)</option>
-        <option value="CUSTOM2 (N-term)">CUSTOM2 (N-term)</option>
-        <option value="CUSTOM2 (P)">CUSTOM2 (P)</option>
-        <option value="CUSTOM2 (Q)">CUSTOM2 (Q)</option>
-        <option value="CUSTOM2 (R)">CUSTOM2 (R)</option>
-        <option value="CUSTOM2 (S)">CUSTOM2 (S)</option>
-        <option value="CUSTOM2 (T)">CUSTOM2 (T)</option>
-        <option value="CUSTOM2 (V)">CUSTOM2 (V)</option>
-        <option value="CUSTOM2 (W)">CUSTOM2 (W)</option>
-        <option value="CUSTOM2 (Y)">CUSTOM2 (Y)</option>
-        <option value="CUSTOM3 (A)">CUSTOM3 (A)</option>
-        <option value="CUSTOM3 (C)">CUSTOM3 (C)</option>
-        <option value="CUSTOM3 (C-term)">CUSTOM3 (C-term)</option>
-        <option value="CUSTOM3 (D)">CUSTOM3 (D)</option>
-        <option value="CUSTOM3 (E)">CUSTOM3 (E)</option>
-        <option value="CUSTOM3 (F)">CUSTOM3 (F)</option>
-        <option value="CUSTOM3 (G)">CUSTOM3 (G)</option>
-        <option value="CUSTOM3 (H)">CUSTOM3 (H)</option>
-        <option value="CUSTOM3 (I)">CUSTOM3 (I)</option>
-        <option value="CUSTOM3 (K)">CUSTOM3 (K)</option>
-        <option value="CUSTOM3 (L)">CUSTOM3 (L)</option>
-        <option value="CUSTOM3 (M)">CUSTOM3 (M)</option>
-        <option value="CUSTOM3 (N)">CUSTOM3 (N)</option>
-        <option value="CUSTOM3 (N-term)">CUSTOM3 (N-term)</option>
-        <option value="CUSTOM3 (P)">CUSTOM3 (P)</option>
-        <option value="CUSTOM3 (Q)">CUSTOM3 (Q)</option>
-        <option value="CUSTOM3 (R)">CUSTOM3 (R)</option>
-        <option value="CUSTOM3 (S)">CUSTOM3 (S)</option>
-        <option value="CUSTOM3 (T)">CUSTOM3 (T)</option>
-        <option value="CUSTOM3 (V)">CUSTOM3 (V)</option>
-        <option value="CUSTOM3 (W)">CUSTOM3 (W)</option>
-        <option value="CUSTOM3 (Y)">CUSTOM3 (Y)</option>
-        <option value="CUSTOM4 (A)">CUSTOM4 (A)</option>
-        <option value="CUSTOM4 (C)">CUSTOM4 (C)</option>
-        <option value="CUSTOM4 (C-term)">CUSTOM4 (C-term)</option>
-        <option value="CUSTOM4 (D)">CUSTOM4 (D)</option>
-        <option value="CUSTOM4 (E)">CUSTOM4 (E)</option>
-        <option value="CUSTOM4 (F)">CUSTOM4 (F)</option>
-        <option value="CUSTOM4 (G)">CUSTOM4 (G)</option>
-        <option value="CUSTOM4 (H)">CUSTOM4 (H)</option>
-        <option value="CUSTOM4 (I)">CUSTOM4 (I)</option>
-        <option value="CUSTOM4 (K)">CUSTOM4 (K)</option>
-        <option value="CUSTOM4 (L)">CUSTOM4 (L)</option>
-        <option value="CUSTOM4 (M)">CUSTOM4 (M)</option>
-        <option value="CUSTOM4 (N)">CUSTOM4 (N)</option>
-        <option value="CUSTOM4 (N-term)">CUSTOM4 (N-term)</option>
-        <option value="CUSTOM4 (P)">CUSTOM4 (P)</option>
-        <option value="CUSTOM4 (Q)">CUSTOM4 (Q)</option>
-        <option value="CUSTOM4 (R)">CUSTOM4 (R)</option>
-        <option value="CUSTOM4 (S)">CUSTOM4 (S)</option>
-        <option value="CUSTOM4 (T)">CUSTOM4 (T)</option>
-        <option value="CUSTOM4 (V)">CUSTOM4 (V)</option>
-        <option value="CUSTOM4 (W)">CUSTOM4 (W)</option>
-        <option value="CUSTOM4 (Y)">CUSTOM4 (Y)</option>
-        <option value="CUSTOM5 (A)">CUSTOM5 (A)</option>
-        <option value="CUSTOM5 (C)">CUSTOM5 (C)</option>
-        <option value="CUSTOM5 (C-term)">CUSTOM5 (C-term)</option>
-        <option value="CUSTOM5 (D)">CUSTOM5 (D)</option>
-        <option value="CUSTOM5 (E)">CUSTOM5 (E)</option>
-        <option value="CUSTOM5 (F)">CUSTOM5 (F)</option>
-        <option value="CUSTOM5 (G)">CUSTOM5 (G)</option>
-        <option value="CUSTOM5 (H)">CUSTOM5 (H)</option>
-        <option value="CUSTOM5 (I)">CUSTOM5 (I)</option>
-        <option value="CUSTOM5 (K)">CUSTOM5 (K)</option>
-        <option value="CUSTOM5 (L)">CUSTOM5 (L)</option>
-        <option value="CUSTOM5 (M)">CUSTOM5 (M)</option>
-        <option value="CUSTOM5 (N)">CUSTOM5 (N)</option>
-        <option value="CUSTOM5 (N-term)">CUSTOM5 (N-term)</option>
-        <option value="CUSTOM5 (P)">CUSTOM5 (P)</option>
-        <option value="CUSTOM5 (Q)">CUSTOM5 (Q)</option>
-        <option value="CUSTOM5 (R)">CUSTOM5 (R)</option>
-        <option value="CUSTOM5 (S)">CUSTOM5 (S)</option>
-        <option value="CUSTOM5 (T)">CUSTOM5 (T)</option>
-        <option value="CUSTOM5 (V)">CUSTOM5 (V)</option>
-        <option value="CUSTOM5 (W)">CUSTOM5 (W)</option>
-        <option value="CUSTOM5 (Y)">CUSTOM5 (Y)</option>
-        <option value="CUSTOM6 (A)">CUSTOM6 (A)</option>
-        <option value="CUSTOM6 (C)">CUSTOM6 (C)</option>
-        <option value="CUSTOM6 (C-term)">CUSTOM6 (C-term)</option>
-        <option value="CUSTOM6 (D)">CUSTOM6 (D)</option>
-        <option value="CUSTOM6 (E)">CUSTOM6 (E)</option>
-        <option value="CUSTOM6 (F)">CUSTOM6 (F)</option>
-        <option value="CUSTOM6 (G)">CUSTOM6 (G)</option>
-        <option value="CUSTOM6 (H)">CUSTOM6 (H)</option>
-        <option value="CUSTOM6 (I)">CUSTOM6 (I)</option>
-        <option value="CUSTOM6 (K)">CUSTOM6 (K)</option>
-        <option value="CUSTOM6 (L)">CUSTOM6 (L)</option>
-        <option value="CUSTOM6 (M)">CUSTOM6 (M)</option>
-        <option value="CUSTOM6 (N)">CUSTOM6 (N)</option>
-        <option value="CUSTOM6 (N-term)">CUSTOM6 (N-term)</option>
-        <option value="CUSTOM6 (P)">CUSTOM6 (P)</option>
-        <option value="CUSTOM6 (Q)">CUSTOM6 (Q)</option>
-        <option value="CUSTOM6 (R)">CUSTOM6 (R)</option>
-        <option value="CUSTOM6 (S)">CUSTOM6 (S)</option>
-        <option value="CUSTOM6 (T)">CUSTOM6 (T)</option>
-        <option value="CUSTOM6 (V)">CUSTOM6 (V)</option>
-        <option value="CUSTOM6 (W)">CUSTOM6 (W)</option>
-        <option value="CUSTOM6 (Y)">CUSTOM6 (Y)</option>
-        <option value="CUSTOM7 (A)">CUSTOM7 (A)</option>
-        <option value="CUSTOM7 (C)">CUSTOM7 (C)</option>
-        <option value="CUSTOM7 (C-term)">CUSTOM7 (C-term)</option>
-        <option value="CUSTOM7 (D)">CUSTOM7 (D)</option>
-        <option value="CUSTOM7 (E)">CUSTOM7 (E)</option>
-        <option value="CUSTOM7 (F)">CUSTOM7 (F)</option>
-        <option value="CUSTOM7 (G)">CUSTOM7 (G)</option>
-        <option value="CUSTOM7 (H)">CUSTOM7 (H)</option>
-        <option value="CUSTOM7 (I)">CUSTOM7 (I)</option>
-        <option value="CUSTOM7 (K)">CUSTOM7 (K)</option>
-        <option value="CUSTOM7 (L)">CUSTOM7 (L)</option>
-        <option value="CUSTOM7 (M)">CUSTOM7 (M)</option>
-        <option value="CUSTOM7 (N)">CUSTOM7 (N)</option>
-        <option value="CUSTOM7 (N-term)">CUSTOM7 (N-term)</option>
-        <option value="CUSTOM7 (P)">CUSTOM7 (P)</option>
-        <option value="CUSTOM7 (Q)">CUSTOM7 (Q)</option>
-        <option value="CUSTOM7 (R)">CUSTOM7 (R)</option>
-        <option value="CUSTOM7 (S)">CUSTOM7 (S)</option>
-        <option value="CUSTOM7 (T)">CUSTOM7 (T)</option>
-        <option value="CUSTOM7 (V)">CUSTOM7 (V)</option>
-        <option value="CUSTOM7 (W)">CUSTOM7 (W)</option>
-        <option value="CUSTOM7 (Y)">CUSTOM7 (Y)</option>
-        <option value="CUSTOM8 (A)">CUSTOM8 (A)</option>
-        <option value="CUSTOM8 (C)">CUSTOM8 (C)</option>
-        <option value="CUSTOM8 (C-term)">CUSTOM8 (C-term)</option>
-        <option value="CUSTOM8 (D)">CUSTOM8 (D)</option>
-        <option value="CUSTOM8 (E)">CUSTOM8 (E)</option>
-        <option value="CUSTOM8 (F)">CUSTOM8 (F)</option>
-        <option value="CUSTOM8 (G)">CUSTOM8 (G)</option>
-        <option value="CUSTOM8 (H)">CUSTOM8 (H)</option>
-        <option value="CUSTOM8 (I)">CUSTOM8 (I)</option>
-        <option value="CUSTOM8 (K)">CUSTOM8 (K)</option>
-        <option value="CUSTOM8 (L)">CUSTOM8 (L)</option>
-        <option value="CUSTOM8 (M)">CUSTOM8 (M)</option>
-        <option value="CUSTOM8 (N)">CUSTOM8 (N)</option>
-        <option value="CUSTOM8 (N-term)">CUSTOM8 (N-term)</option>
-        <option value="CUSTOM8 (P)">CUSTOM8 (P)</option>
-        <option value="CUSTOM8 (Q)">CUSTOM8 (Q)</option>
-        <option value="CUSTOM8 (R)">CUSTOM8 (R)</option>
-        <option value="CUSTOM8 (S)">CUSTOM8 (S)</option>
-        <option value="CUSTOM8 (T)">CUSTOM8 (T)</option>
-        <option value="CUSTOM8 (V)">CUSTOM8 (V)</option>
-        <option value="CUSTOM8 (W)">CUSTOM8 (W)</option>
-        <option value="CUSTOM8 (Y)">CUSTOM8 (Y)</option>
-        <option value="CUSTOM9 (A)">CUSTOM9 (A)</option>
-        <option value="CUSTOM9 (C)">CUSTOM9 (C)</option>
-        <option value="CUSTOM9 (C-term)">CUSTOM9 (C-term)</option>
-        <option value="CUSTOM9 (D)">CUSTOM9 (D)</option>
-        <option value="CUSTOM9 (E)">CUSTOM9 (E)</option>
-        <option value="CUSTOM9 (F)">CUSTOM9 (F)</option>
-        <option value="CUSTOM9 (G)">CUSTOM9 (G)</option>
-        <option value="CUSTOM9 (H)">CUSTOM9 (H)</option>
-        <option value="CUSTOM9 (I)">CUSTOM9 (I)</option>
-        <option value="CUSTOM9 (K)">CUSTOM9 (K)</option>
-        <option value="CUSTOM9 (L)">CUSTOM9 (L)</option>
-        <option value="CUSTOM9 (M)">CUSTOM9 (M)</option>
-        <option value="CUSTOM9 (N)">CUSTOM9 (N)</option>
-        <option value="CUSTOM9 (N-term)">CUSTOM9 (N-term)</option>
-        <option value="CUSTOM9 (P)">CUSTOM9 (P)</option>
-        <option value="CUSTOM9 (Q)">CUSTOM9 (Q)</option>
-        <option value="CUSTOM9 (R)">CUSTOM9 (R)</option>
-        <option value="CUSTOM9 (S)">CUSTOM9 (S)</option>
-        <option value="CUSTOM9 (T)">CUSTOM9 (T)</option>
-        <option value="CUSTOM9 (V)">CUSTOM9 (V)</option>
-        <option value="CUSTOM9 (W)">CUSTOM9 (W)</option>
-        <option value="CUSTOM9 (Y)">CUSTOM9 (Y)</option>
-        <option value="Cy3-maleimide (C)">Cy3-maleimide (C)</option>
-        <option value="Cy3b-maleimide (C)">Cy3b-maleimide (C)</option>
-        <option value="Cyano (C)">Cyano (C)</option>
-        <option value="CyDye-Cy3 (C)">CyDye-Cy3 (C)</option>
-        <option value="CyDye-Cy5 (C)">CyDye-Cy5 (C)</option>
-        <option value="Cys-&gt;Ala (C)">Cys-&gt;Ala (C)</option>
-        <option value="Cys-&gt;Arg (C)">Cys-&gt;Arg (C)</option>
-        <option value="Cys-&gt;Asn (C)">Cys-&gt;Asn (C)</option>
-        <option value="Cys-&gt;Asp (C)">Cys-&gt;Asp (C)</option>
-        <option value="Cys-&gt;CamSec (C)">Cys-&gt;CamSec (C)</option>
-        <option value="Cys-&gt;Dha (C)">Cys-&gt;Dha (C)</option>
-        <option value="Cys-&gt;ethylaminoAla (C)">Cys-&gt;ethylaminoAla (C)</option>
-        <option value="Cys-&gt;Gln (C)">Cys-&gt;Gln (C)</option>
-        <option value="Cys-&gt;Glu (C)">Cys-&gt;Glu (C)</option>
-        <option value="Cys-&gt;Gly (C)">Cys-&gt;Gly (C)</option>
-        <option value="Cys-&gt;His (C)">Cys-&gt;His (C)</option>
-        <option value="Cys-&gt;Lys (C)">Cys-&gt;Lys (C)</option>
-        <option value="Cys-&gt;Met (C)">Cys-&gt;Met (C)</option>
-        <option value="Cys-&gt;methylaminoAla (C)">Cys-&gt;methylaminoAla (C)</option>
-        <option value="Cys-&gt;Oxoalanine (C)">Cys-&gt;Oxoalanine (C)</option>
-        <option value="Cys-&gt;Phe (C)">Cys-&gt;Phe (C)</option>
-        <option value="Cys-&gt;Pro (C)">Cys-&gt;Pro (C)</option>
-        <option value="Cys-&gt;PyruvicAcid (Protein N-term C)">Cys-&gt;PyruvicAcid (Protein N-term C)</option>
-        <option value="Cys-&gt;SecNEM (C)">Cys-&gt;SecNEM (C)</option>
-        <option value="Cys-&gt;SecNEM:2H(5) (C)">Cys-&gt;SecNEM:2H(5) (C)</option>
-        <option value="Cys-&gt;Ser (C)">Cys-&gt;Ser (C)</option>
-        <option value="Cys-&gt;Thr (C)">Cys-&gt;Thr (C)</option>
-        <option value="Cys-&gt;Trp (C)">Cys-&gt;Trp (C)</option>
-        <option value="Cys-&gt;Tyr (C)">Cys-&gt;Tyr (C)</option>
-        <option value="Cys-&gt;Val (C)">Cys-&gt;Val (C)</option>
-        <option value="Cys-&gt;Xle (C)">Cys-&gt;Xle (C)</option>
-        <option value="Cysteinyl (C)">Cysteinyl (C)</option>
-        <option value="cysTMT (C)">cysTMT (C)</option>
-        <option value="cysTMT6plex (C)">cysTMT6plex (C)</option>
-        <option value="Cytopiloyne (C)">Cytopiloyne (C)</option>
-        <option value="Cytopiloyne (K)">Cytopiloyne (K)</option>
-        <option value="Cytopiloyne (N-term)">Cytopiloyne (N-term)</option>
-        <option value="Cytopiloyne (P)">Cytopiloyne (P)</option>
-        <option value="Cytopiloyne (R)">Cytopiloyne (R)</option>
-        <option value="Cytopiloyne (S)">Cytopiloyne (S)</option>
-        <option value="Cytopiloyne (Y)">Cytopiloyne (Y)</option>
-        <option value="Cytopiloyne+water (C)">Cytopiloyne+water (C)</option>
-        <option value="Cytopiloyne+water (K)">Cytopiloyne+water (K)</option>
-        <option value="Cytopiloyne+water (N-term)">Cytopiloyne+water (N-term)</option>
-        <option value="Cytopiloyne+water (R)">Cytopiloyne+water (R)</option>
-        <option value="Cytopiloyne+water (S)">Cytopiloyne+water (S)</option>
-        <option value="Cytopiloyne+water (T)">Cytopiloyne+water (T)</option>
-        <option value="Cytopiloyne+water (Y)">Cytopiloyne+water (Y)</option>
-        <option value="DAET (S)">DAET (S)</option>
-        <option value="DAET (T)">DAET (T)</option>
-        <option value="Dansyl (K)">Dansyl (K)</option>
-        <option value="Dansyl (N-term)">Dansyl (N-term)</option>
-        <option value="Dap-DSP (A)">Dap-DSP (A)</option>
-        <option value="Dap-DSP (E)">Dap-DSP (E)</option>
-        <option value="Dap-DSP (K)">Dap-DSP (K)</option>
-        <option value="Deamidated (N)">Deamidated (N)</option>
-        <option value="Deamidated (Protein N-term F)">Deamidated (Protein N-term F)</option>
-        <option value="Deamidated (Q)">Deamidated (Q)</option>
-        <option value="Deamidated (R)">Deamidated (R)</option>
-        <option value="Deamidated:18O(1) (N)">Deamidated:18O(1) (N)</option>
-        <option value="Deamidated:18O(1) (Q)">Deamidated:18O(1) (Q)</option>
-        <option value="Decanoyl (S)">Decanoyl (S)</option>
-        <option value="Decanoyl (T)">Decanoyl (T)</option>
-        <option value="Decarboxylation (D)">Decarboxylation (D)</option>
-        <option value="Decarboxylation (E)">Decarboxylation (E)</option>
-        <option value="DEDGFLYMVYASQETFG (K)">DEDGFLYMVYASQETFG (K)</option>
-        <option value="Dehydrated (D)">Dehydrated (D)</option>
-        <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
-        <option value="Dehydrated (Protein C-term N)">Dehydrated (Protein C-term N)</option>
-        <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
-        <option value="Dehydrated (S)">Dehydrated (S)</option>
-        <option value="Dehydrated (T)">Dehydrated (T)</option>
-        <option value="Dehydrated (Y)">Dehydrated (Y)</option>
-        <option value="Dehydro (C)">Dehydro (C)</option>
-        <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
-        <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-        <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
-        <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
-        <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
-        <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
-        <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
-        <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
-        <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
-        <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
-        <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
-        <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-        <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
-        <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
-        <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
-        <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
-        <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
-        <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
-        <option value="Delta:H(4)C(3) (K)">Delta:H(4)C(3) (K)</option>
-        <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
-        <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
-        <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
-        <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
-        <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
-        <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
-        <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
-        <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
-        <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
-        <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
-        <option value="Delta:H(6)C(3)O(1) (K)">Delta:H(6)C(3)O(1) (K)</option>
-        <option value="Delta:H(6)C(3)O(1) (Protein N-term)">Delta:H(6)C(3)O(1) (Protein N-term)</option>
-        <option value="Delta:H(6)C(6)O(1) (K)">Delta:H(6)C(6)O(1) (K)</option>
-        <option value="Delta:H(6)C(7)O(4) (R)">Delta:H(6)C(7)O(4) (R)</option>
-        <option value="Delta:H(8)C(6)O(1) (K)">Delta:H(8)C(6)O(1) (K)</option>
-        <option value="Delta:H(8)C(6)O(1) (Protein N-term)">Delta:H(8)C(6)O(1) (Protein N-term)</option>
-        <option value="Delta:H(8)C(6)O(2) (K)">Delta:H(8)C(6)O(2) (K)</option>
-        <option value="Delta:Hg(1) (C)">Delta:Hg(1) (C)</option>
-        <option value="Delta:O(4) (W)">Delta:O(4) (W)</option>
-        <option value="Delta:S(-1)Se(1) (C)">Delta:S(-1)Se(1) (C)</option>
-        <option value="Delta:S(-1)Se(1) (M)">Delta:S(-1)Se(1) (M)</option>
-        <option value="Delta:Se(1) (C)">Delta:Se(1) (C)</option>
-        <option value="Deoxy (D)">Deoxy (D)</option>
-        <option value="Deoxy (S)">Deoxy (S)</option>
-        <option value="Deoxy (T)">Deoxy (T)</option>
-        <option value="Deoxyhypusine (K)">Deoxyhypusine (K)</option>
-        <option value="Deoxyhypusine (Q)">Deoxyhypusine (Q)</option>
-        <option value="DeStreak (C)">DeStreak (C)</option>
-        <option value="Dethiomethyl (M)">Dethiomethyl (M)</option>
-        <option value="dHex (N)">dHex (N)</option>
-        <option value="dHex (S)">dHex (S)</option>
-        <option value="dHex (T)">dHex (T)</option>
-        <option value="dHex(1)Hex(1) (S)">dHex(1)Hex(1) (S)</option>
-        <option value="dHex(1)Hex(1) (T)">dHex(1)Hex(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexA(1)HexNAc(3) (S)">dHex(1)Hex(1)HexA(1)HexNAc(3) (S)</option>
-        <option value="dHex(1)Hex(1)HexA(1)HexNAc(3) (T)">dHex(1)Hex(1)HexA(1)HexNAc(3) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)Kdn(1) (S)">dHex(1)Hex(1)HexNAc(1)Kdn(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)Kdn(1) (T)">dHex(1)Hex(1)HexNAc(1)Kdn(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(1)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(1)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3) (S)">dHex(1)Hex(1)HexNAc(3) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3) (T)">dHex(1)Hex(1)HexNAc(3) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(4) (S)">dHex(1)Hex(1)HexNAc(4) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(4) (T)">dHex(1)Hex(1)HexNAc(4) (T)</option>
-        <option value="dHex(1)Hex(2) (S)">dHex(1)Hex(2) (S)</option>
-        <option value="dHex(1)Hex(2) (T)">dHex(1)Hex(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexA(1) (S)">dHex(1)Hex(2)HexA(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexA(1) (T)">dHex(1)Hex(2)HexA(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(1) (S)">dHex(1)Hex(2)HexA(1)HexNAc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(1) (T)">dHex(1)Hex(2)HexA(1)HexNAc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (S)">dHex(1)Hex(2)HexA(1)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (T)">dHex(1)Hex(2)HexA(1)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1) (S)">dHex(1)Hex(2)HexNAc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1) (T)">dHex(1)Hex(2)HexNAc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)Pent(1) (N)">dHex(1)Hex(2)HexNAc(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3) (N)">dHex(1)Hex(2)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3) (S)">dHex(1)Hex(2)HexNAc(3) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3) (T)">dHex(1)Hex(2)HexNAc(3) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4) (N)">dHex(1)Hex(2)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4) (S)">dHex(1)Hex(2)HexNAc(4) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4) (T)">dHex(1)Hex(2)HexNAc(4) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-        <option value="dHex(1)Hex(3) (S)">dHex(1)Hex(3) (S)</option>
-        <option value="dHex(1)Hex(3) (T)">dHex(1)Hex(3) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(2) (S)">dHex(1)Hex(3)HexA(1)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(2) (T)">dHex(1)Hex(3)HexA(1)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(2)HexNAc(2) (S)">dHex(1)Hex(3)HexA(2)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(2)HexNAc(2) (T)">dHex(1)Hex(3)HexA(2)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(1) (S)">dHex(1)Hex(3)HexNAc(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(1) (T)">dHex(1)Hex(3)HexNAc(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2) (N)">dHex(1)Hex(3)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2) (S)">dHex(1)Hex(3)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2) (T)">dHex(1)Hex(3)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)Pent(1) (N)">dHex(1)Hex(3)HexNAc(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3) (N)">dHex(1)Hex(3)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3) (S)">dHex(1)Hex(3)HexNAc(3) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3) (T)">dHex(1)Hex(3)HexNAc(3) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Pent(1) (N)">dHex(1)Hex(3)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Pent(2) (N)">dHex(1)Hex(3)HexNAc(3)Pent(2) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Pent(3) (N)">dHex(1)Hex(3)HexNAc(3)Pent(3) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4) (N)">dHex(1)Hex(3)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4) (S)">dHex(1)Hex(3)HexNAc(4) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4) (T)">dHex(1)Hex(3)HexNAc(4) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)Pent(1) (N)">dHex(1)Hex(3)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)Pent(2) (N)">dHex(1)Hex(3)HexNAc(4)Pent(2) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)Pent(3) (N)">dHex(1)Hex(3)HexNAc(4)Pent(3) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5) (N)">dHex(1)Hex(3)HexNAc(5) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5) (S)">dHex(1)Hex(3)HexNAc(5) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5) (T)">dHex(1)Hex(3)HexNAc(5) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(5)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(6) (N)">dHex(1)Hex(3)HexNAc(6) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(6) (S)">dHex(1)Hex(3)HexNAc(6) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(6) (T)">dHex(1)Hex(3)HexNAc(6) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4) (S)">dHex(1)Hex(4) (S)</option>
-        <option value="dHex(1)Hex(4) (T)">dHex(1)Hex(4) (T)</option>
-        <option value="dHex(1)Hex(4)HexA(1) (S)">dHex(1)Hex(4)HexA(1) (S)</option>
-        <option value="dHex(1)Hex(4)HexA(1) (T)">dHex(1)Hex(4)HexA(1) (T)</option>
-        <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (S)">dHex(1)Hex(4)HexA(1)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (T)">dHex(1)Hex(4)HexA(1)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(1)Pent(1) (N)">dHex(1)Hex(4)HexNAc(1)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(2) (N)">dHex(1)Hex(4)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(2) (S)">dHex(1)Hex(4)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(4)HexNAc(2) (T)">dHex(1)Hex(4)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(2)Pent(1) (N)">dHex(1)Hex(4)HexNAc(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3) (N)">dHex(1)Hex(4)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)Pent(1) (N)">dHex(1)Hex(4)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4) (N)">dHex(1)Hex(4)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4) (S)">dHex(1)Hex(4)HexNAc(4) (S)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4) (T)">dHex(1)Hex(4)HexNAc(4) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)Pent(1) (N)">dHex(1)Hex(4)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(5) (N)">dHex(1)Hex(4)HexNAc(5) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(5)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(5)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5) (S)">dHex(1)Hex(5) (S)</option>
-        <option value="dHex(1)Hex(5) (T)">dHex(1)Hex(5) (T)</option>
-        <option value="dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N)">dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(2) (N)">dHex(1)Hex(5)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(2)Pent(1) (N)">dHex(1)Hex(5)HexNAc(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3) (N)">dHex(1)Hex(5)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4) (N)">dHex(1)Hex(5)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N)">dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N)">dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)Pent(1) (N)">dHex(1)Hex(5)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)Sulf(2) (N)">dHex(1)Hex(5)HexNAc(4)Sulf(2) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(5) (N)">dHex(1)Hex(5)HexNAc(5) (N)</option>
-        <option value="dHex(1)Hex(6) (S)">dHex(1)Hex(6) (S)</option>
-        <option value="dHex(1)Hex(6) (T)">dHex(1)Hex(6) (T)</option>
-        <option value="dHex(1)Hex(6)HexNAc(2) (N)">dHex(1)Hex(6)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(6)HexNAc(3) (N)">dHex(1)Hex(6)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(6)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(6)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(6)HexNAc(4) (N)">dHex(1)Hex(6)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(2) (N)">dHex(1)Hex(7)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(3) (N)">dHex(1)Hex(7)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(3)Phos(1) (N)">dHex(1)Hex(7)HexNAc(3)Phos(1) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(4) (N)">dHex(1)Hex(7)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(8)HexNAc(2) (N)">dHex(1)Hex(8)HexNAc(2) (N)</option>
-        <option value="dHex(1)HexNAc(3) (S)">dHex(1)HexNAc(3) (S)</option>
-        <option value="dHex(1)HexNAc(3) (T)">dHex(1)HexNAc(3) (T)</option>
-        <option value="dHex(1)HexNAc(4) (S)">dHex(1)HexNAc(4) (S)</option>
-        <option value="dHex(1)HexNAc(4) (T)">dHex(1)HexNAc(4) (T)</option>
-        <option value="dHex(1)HexNAc(5) (S)">dHex(1)HexNAc(5) (S)</option>
-        <option value="dHex(1)HexNAc(5) (T)">dHex(1)HexNAc(5) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(1)Kdn(1) (S)">dHex(2)Hex(1)HexNAc(1)Kdn(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(1)Kdn(1) (T)">dHex(2)Hex(1)HexNAc(1)Kdn(1) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(2)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(2)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)NeuAc(1) (S)">dHex(2)Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)NeuAc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(3) (S)">dHex(2)Hex(1)HexNAc(3) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(3) (T)">dHex(2)Hex(1)HexNAc(3) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2) (S)">dHex(2)Hex(2) (S)</option>
-        <option value="dHex(2)Hex(2) (T)">dHex(2)Hex(2) (T)</option>
-        <option value="dHex(2)Hex(2)HexA(1) (S)">dHex(2)Hex(2)HexA(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexA(1) (T)">dHex(2)Hex(2)HexA(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexA(1)HexNAc(1) (S)">dHex(2)Hex(2)HexA(1)HexNAc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexA(1)HexNAc(1) (T)">dHex(2)Hex(2)HexA(1)HexNAc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(1) (S)">dHex(2)Hex(2)HexNAc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(1) (T)">dHex(2)Hex(2)HexNAc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2) (N)">dHex(2)Hex(2)HexNAc(2) (N)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2) (S)">dHex(2)Hex(2)HexNAc(2) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2) (T)">dHex(2)Hex(2)HexNAc(2) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(2)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(2)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(2)Sulf(2) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(2)Sulf(2) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3) (N)">dHex(2)Hex(2)HexNAc(3) (N)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3) (S)">dHex(2)Hex(2)HexNAc(3) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3) (T)">dHex(2)Hex(2)HexNAc(3) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)NeuAc(1) (S)">dHex(2)Hex(2)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(2)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)NeuGc(1) (S)">dHex(2)Hex(2)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)NeuGc(1) (T)">dHex(2)Hex(2)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(4) (S)">dHex(2)Hex(2)HexNAc(4) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(4) (T)">dHex(2)Hex(2)HexNAc(4) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(5) (S)">dHex(2)Hex(2)HexNAc(5) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(5) (T)">dHex(2)Hex(2)HexNAc(5) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3) (S)">dHex(2)Hex(3) (S)</option>
-        <option value="dHex(2)Hex(3) (T)">dHex(2)Hex(3) (T)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(1)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2) (N)">dHex(2)Hex(3)HexNAc(2) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2) (S)">dHex(2)Hex(3)HexNAc(2) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2) (T)">dHex(2)Hex(3)HexNAc(2) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(3)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(3)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3) (N)">dHex(2)Hex(3)HexNAc(3) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3) (S)">dHex(2)Hex(3)HexNAc(3) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3) (T)">dHex(2)Hex(3)HexNAc(3) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)Pent(1) (N)">dHex(2)Hex(3)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)Pent(2) (N)">dHex(2)Hex(3)HexNAc(3)Pent(2) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4) (N)">dHex(2)Hex(3)HexNAc(4) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4) (S)">dHex(2)Hex(3)HexNAc(4) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4) (T)">dHex(2)Hex(3)HexNAc(4) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4)Pent(1) (N)">dHex(2)Hex(3)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4)Pent(2) (N)">dHex(2)Hex(3)HexNAc(4)Pent(2) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(5) (N)">dHex(2)Hex(3)HexNAc(5) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(5) (S)">dHex(2)Hex(3)HexNAc(5) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(5) (T)">dHex(2)Hex(3)HexNAc(5) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(6) (N)">dHex(2)Hex(3)HexNAc(6) (N)</option>
-        <option value="dHex(2)Hex(4) (S)">dHex(2)Hex(4) (S)</option>
-        <option value="dHex(2)Hex(4) (T)">dHex(2)Hex(4) (T)</option>
-        <option value="dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(4)HexNAc(1) (S)">dHex(2)Hex(4)HexNAc(1) (S)</option>
-        <option value="dHex(2)Hex(4)HexNAc(1) (T)">dHex(2)Hex(4)HexNAc(1) (T)</option>
-        <option value="dHex(2)Hex(4)HexNAc(2) (N)">dHex(2)Hex(4)HexNAc(2) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(2) (S)">dHex(2)Hex(4)HexNAc(2) (S)</option>
-        <option value="dHex(2)Hex(4)HexNAc(2) (T)">dHex(2)Hex(4)HexNAc(2) (T)</option>
-        <option value="dHex(2)Hex(4)HexNAc(3) (N)">dHex(2)Hex(4)HexNAc(3) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(3)Pent(1) (N)">dHex(2)Hex(4)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4) (N)">dHex(2)Hex(4)HexNAc(4) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4) (S)">dHex(2)Hex(4)HexNAc(4) (S)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4) (T)">dHex(2)Hex(4)HexNAc(4) (T)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4)Pent(1) (N)">dHex(2)Hex(4)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(2)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(5) (N)">dHex(2)Hex(4)HexNAc(5) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(5) (S)">dHex(2)Hex(4)HexNAc(5) (S)</option>
-        <option value="dHex(2)Hex(4)HexNAc(5) (T)">dHex(2)Hex(4)HexNAc(5) (T)</option>
-        <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (S)">dHex(2)Hex(5)HexNAc(2)Me(1) (S)</option>
-        <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (T)">dHex(2)Hex(5)HexNAc(2)Me(1) (T)</option>
-        <option value="dHex(2)Hex(5)HexNAc(3)Pent(1) (N)">dHex(2)Hex(5)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(5)HexNAc(4) (N)">dHex(2)Hex(5)HexNAc(4) (N)</option>
-        <option value="dHex(2)HexNAc(2)Kdn(1) (S)">dHex(2)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(2)HexNAc(2)Kdn(1) (T)">dHex(2)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(2)HexNAc(5) (S)">dHex(2)HexNAc(5) (S)</option>
-        <option value="dHex(2)HexNAc(5) (T)">dHex(2)HexNAc(5) (T)</option>
-        <option value="dHex(2)HexNAc(7) (S)">dHex(2)HexNAc(7) (S)</option>
-        <option value="dHex(2)HexNAc(7) (T)">dHex(2)HexNAc(7) (T)</option>
-        <option value="dHex(3)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(3)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(3)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(3)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(3)Hex(1)HexNAc(3)Kdn(1) (S)">dHex(3)Hex(1)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(3)Hex(1)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(1)HexNAc(3)Kdn(1) (T)</option>
-        <option value="dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(2) (S)">dHex(3)Hex(2)HexNAc(2) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(2) (T)">dHex(3)Hex(2)HexNAc(2) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(3)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(3) (S)">dHex(3)Hex(2)HexNAc(3) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(3) (T)">dHex(3)Hex(2)HexNAc(3) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (S)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(4) (S)">dHex(3)Hex(2)HexNAc(4) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(4) (T)">dHex(3)Hex(2)HexNAc(4) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(1) (S)">dHex(3)Hex(3)HexNAc(1) (S)</option>
-        <option value="dHex(3)Hex(3)HexNAc(1) (T)">dHex(3)Hex(3)HexNAc(1) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(2) (S)">dHex(3)Hex(3)HexNAc(2) (S)</option>
-        <option value="dHex(3)Hex(3)HexNAc(2) (T)">dHex(3)Hex(3)HexNAc(2) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3) (S)">dHex(3)Hex(3)HexNAc(3) (S)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3) (T)">dHex(3)Hex(3)HexNAc(3) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3)Pent(1) (N)">dHex(3)Hex(3)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(3)Hex(3)HexNAc(4) (N)">dHex(3)Hex(3)HexNAc(4) (N)</option>
-        <option value="dHex(3)Hex(3)HexNAc(4)Pent(1) (N)">dHex(3)Hex(3)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(3)Hex(4)HexNAc(4) (N)">dHex(3)Hex(4)HexNAc(4) (N)</option>
-        <option value="dHex(3)Hex(4)HexNAc(4) (S)">dHex(3)Hex(4)HexNAc(4) (S)</option>
-        <option value="dHex(3)Hex(4)HexNAc(4) (T)">dHex(3)Hex(4)HexNAc(4) (T)</option>
-        <option value="dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(3)HexNAc(3)Kdn(1) (S)">dHex(3)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(3)HexNAc(3)Kdn(1) (T)">dHex(3)HexNAc(3)Kdn(1) (T)</option>
-        <option value="dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)">dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)</option>
-        <option value="dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)">dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)</option>
-        <option value="dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)">dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)">dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)</option>
-        <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(4)Hex(2)HexNAc(3) (S)">dHex(4)Hex(2)HexNAc(3) (S)</option>
-        <option value="dHex(4)Hex(2)HexNAc(3) (T)">dHex(4)Hex(2)HexNAc(3) (T)</option>
-        <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="dHex(4)Hex(3)HexNAc(3) (S)">dHex(4)Hex(3)HexNAc(3) (S)</option>
-        <option value="dHex(4)Hex(3)HexNAc(3) (T)">dHex(4)Hex(3)HexNAc(3) (T)</option>
-        <option value="dHex(4)HexNAc(3)Kdn(1) (S)">dHex(4)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(4)HexNAc(3)Kdn(1) (T)">dHex(4)HexNAc(3)Kdn(1) (T)</option>
-        <option value="DHP (C)">DHP (C)</option>
-        <option value="Diacylglycerol (C)">Diacylglycerol (C)</option>
-        <option value="DiART6plex (K)">DiART6plex (K)</option>
-        <option value="DiART6plex (N-term)">DiART6plex (N-term)</option>
-        <option value="DiART6plex (Protein N-term)">DiART6plex (Protein N-term)</option>
-        <option value="DiART6plex (Y)">DiART6plex (Y)</option>
-        <option value="DiART6plex115 (K)">DiART6plex115 (K)</option>
-        <option value="DiART6plex115 (N-term)">DiART6plex115 (N-term)</option>
-        <option value="DiART6plex115 (Protein N-term)">DiART6plex115 (Protein N-term)</option>
-        <option value="DiART6plex115 (Y)">DiART6plex115 (Y)</option>
-        <option value="DiART6plex116/119 (K)">DiART6plex116/119 (K)</option>
-        <option value="DiART6plex116/119 (N-term)">DiART6plex116/119 (N-term)</option>
-        <option value="DiART6plex116/119 (Protein N-term)">DiART6plex116/119 (Protein N-term)</option>
-        <option value="DiART6plex116/119 (Y)">DiART6plex116/119 (Y)</option>
-        <option value="DiART6plex117 (K)">DiART6plex117 (K)</option>
-        <option value="DiART6plex117 (N-term)">DiART6plex117 (N-term)</option>
-        <option value="DiART6plex117 (Protein N-term)">DiART6plex117 (Protein N-term)</option>
-        <option value="DiART6plex117 (Y)">DiART6plex117 (Y)</option>
-        <option value="DiART6plex118 (K)">DiART6plex118 (K)</option>
-        <option value="DiART6plex118 (N-term)">DiART6plex118 (N-term)</option>
-        <option value="DiART6plex118 (Protein N-term)">DiART6plex118 (Protein N-term)</option>
-        <option value="DiART6plex118 (Y)">DiART6plex118 (Y)</option>
-        <option value="Dibromo (Y)">Dibromo (Y)</option>
-        <option value="Dicarbamidomethyl (C)">Dicarbamidomethyl (C)</option>
-        <option value="Dicarbamidomethyl (H)">Dicarbamidomethyl (H)</option>
-        <option value="Dicarbamidomethyl (K)">Dicarbamidomethyl (K)</option>
-        <option value="Dicarbamidomethyl (N-term)">Dicarbamidomethyl (N-term)</option>
-        <option value="Dicarbamidomethyl (R)">Dicarbamidomethyl (R)</option>
-        <option value="dichlorination (C)">dichlorination (C)</option>
-        <option value="dichlorination (Y)">dichlorination (Y)</option>
-        <option value="Didehydro (C-term K)">Didehydro (C-term K)</option>
-        <option value="Didehydro (S)">Didehydro (S)</option>
-        <option value="Didehydro (T)">Didehydro (T)</option>
-        <option value="Didehydro (Y)">Didehydro (Y)</option>
-        <option value="Didehydroretinylidene (K)">Didehydroretinylidene (K)</option>
-        <option value="Diethyl (K)">Diethyl (K)</option>
-        <option value="Diethyl (N-term)">Diethyl (N-term)</option>
-        <option value="Diethylphosphate (C)">Diethylphosphate (C)</option>
-        <option value="Diethylphosphate (H)">Diethylphosphate (H)</option>
-        <option value="Diethylphosphate (K)">Diethylphosphate (K)</option>
-        <option value="Diethylphosphate (N-term)">Diethylphosphate (N-term)</option>
-        <option value="Diethylphosphate (S)">Diethylphosphate (S)</option>
-        <option value="Diethylphosphate (T)">Diethylphosphate (T)</option>
-        <option value="Diethylphosphate (Y)">Diethylphosphate (Y)</option>
-        <option value="Diethylphosphothione (C)">Diethylphosphothione (C)</option>
-        <option value="Diethylphosphothione (H)">Diethylphosphothione (H)</option>
-        <option value="Diethylphosphothione (K)">Diethylphosphothione (K)</option>
-        <option value="Diethylphosphothione (S)">Diethylphosphothione (S)</option>
-        <option value="Diethylphosphothione (T)">Diethylphosphothione (T)</option>
-        <option value="Diethylphosphothione (Y)">Diethylphosphothione (Y)</option>
-        <option value="Difuran (Y)">Difuran (Y)</option>
-        <option value="Dihydroxyimidazolidine (R)">Dihydroxyimidazolidine (R)</option>
-        <option value="Diiodo (H)">Diiodo (H)</option>
-        <option value="Diiodo (Y)">Diiodo (Y)</option>
-        <option value="Diironsubcluster (C)">Diironsubcluster (C)</option>
-        <option value="Diisopropylphosphate (K)">Diisopropylphosphate (K)</option>
-        <option value="Diisopropylphosphate (N-term)">Diisopropylphosphate (N-term)</option>
-        <option value="Diisopropylphosphate (S)">Diisopropylphosphate (S)</option>
-        <option value="Diisopropylphosphate (T)">Diisopropylphosphate (T)</option>
-        <option value="Diisopropylphosphate (Y)">Diisopropylphosphate (Y)</option>
-        <option value="DiLeu4plex (K)">DiLeu4plex (K)</option>
-        <option value="DiLeu4plex (N-term)">DiLeu4plex (N-term)</option>
-        <option value="DiLeu4plex (Y)">DiLeu4plex (Y)</option>
-        <option value="DiLeu4plex115 (K)">DiLeu4plex115 (K)</option>
-        <option value="DiLeu4plex115 (N-term)">DiLeu4plex115 (N-term)</option>
-        <option value="DiLeu4plex115 (Y)">DiLeu4plex115 (Y)</option>
-        <option value="DiLeu4plex117 (K)">DiLeu4plex117 (K)</option>
-        <option value="DiLeu4plex117 (N-term)">DiLeu4plex117 (N-term)</option>
-        <option value="DiLeu4plex117 (Y)">DiLeu4plex117 (Y)</option>
-        <option value="DiLeu4plex118 (K)">DiLeu4plex118 (K)</option>
-        <option value="DiLeu4plex118 (N-term)">DiLeu4plex118 (N-term)</option>
-        <option value="DiLeu4plex118 (Y)">DiLeu4plex118 (Y)</option>
-        <option value="Dimethyl (K)">Dimethyl (K)</option>
-        <option value="Dimethyl (N)">Dimethyl (N)</option>
-        <option value="Dimethyl (N-term)">Dimethyl (N-term)</option>
-        <option value="Dimethyl (Protein N-term P)">Dimethyl (Protein N-term P)</option>
-        <option value="Dimethyl (Protein N-term)">Dimethyl (Protein N-term)</option>
-        <option value="Dimethyl (R)">Dimethyl (R)</option>
-        <option value="Dimethyl:2H(2)13C (K)">Dimethyl:2H(2)13C (K)</option>
-        <option value="Dimethyl:2H(2)13C (N)">Dimethyl:2H(2)13C (N)</option>
-        <option value="Dimethyl:2H(2)13C (N-term)">Dimethyl:2H(2)13C (N-term)</option>
-        <option value="Dimethyl:2H(2)13C (Protein N-term P)">Dimethyl:2H(2)13C (Protein N-term P)</option>
-        <option value="Dimethyl:2H(2)13C (R)">Dimethyl:2H(2)13C (R)</option>
-        <option value="Dimethyl:2H(4) (K)">Dimethyl:2H(4) (K)</option>
-        <option value="Dimethyl:2H(4) (N-term)">Dimethyl:2H(4) (N-term)</option>
-        <option value="Dimethyl:2H(4) (Protein N-term)">Dimethyl:2H(4) (Protein N-term)</option>
-        <option value="Dimethyl:2H(4) (R)">Dimethyl:2H(4) (R)</option>
-        <option value="Dimethyl:2H(4)13C(2) (K)">Dimethyl:2H(4)13C(2) (K)</option>
-        <option value="Dimethyl:2H(4)13C(2) (N-term)">Dimethyl:2H(4)13C(2) (N-term)</option>
-        <option value="Dimethyl:2H(4)13C(2) (Protein N-term)">Dimethyl:2H(4)13C(2) (Protein N-term)</option>
-        <option value="Dimethyl:2H(4)13C(2) (R)">Dimethyl:2H(4)13C(2) (R)</option>
-        <option value="Dimethyl:2H(6) (K)">Dimethyl:2H(6) (K)</option>
-        <option value="Dimethyl:2H(6) (N-term)">Dimethyl:2H(6) (N-term)</option>
-        <option value="Dimethyl:2H(6) (R)">Dimethyl:2H(6) (R)</option>
-        <option value="Dimethyl:2H(6)13C(2) (K)">Dimethyl:2H(6)13C(2) (K)</option>
-        <option value="Dimethyl:2H(6)13C(2) (N-term)">Dimethyl:2H(6)13C(2) (N-term)</option>
-        <option value="Dimethyl:2H(6)13C(2) (Protein N-term)">Dimethyl:2H(6)13C(2) (Protein N-term)</option>
-        <option value="Dimethyl:2H(6)13C(2) (R)">Dimethyl:2H(6)13C(2) (R)</option>
-        <option value="DimethylamineGMBS (C)">DimethylamineGMBS (C)</option>
-        <option value="Dimethylaminoethyl (C)">Dimethylaminoethyl (C)</option>
-        <option value="DimethylArsino (C)">DimethylArsino (C)</option>
-        <option value="Dimethylphosphothione (C)">Dimethylphosphothione (C)</option>
-        <option value="Dimethylphosphothione (H)">Dimethylphosphothione (H)</option>
-        <option value="Dimethylphosphothione (K)">Dimethylphosphothione (K)</option>
-        <option value="Dimethylphosphothione (S)">Dimethylphosphothione (S)</option>
-        <option value="Dimethylphosphothione (T)">Dimethylphosphothione (T)</option>
-        <option value="Dimethylphosphothione (Y)">Dimethylphosphothione (Y)</option>
-        <option value="DimethylpyrroleAdduct (K)">DimethylpyrroleAdduct (K)</option>
-        <option value="Dioxidation (C)">Dioxidation (C)</option>
-        <option value="Dioxidation (E)">Dioxidation (E)</option>
-        <option value="Dioxidation (F)">Dioxidation (F)</option>
-        <option value="Dioxidation (I)">Dioxidation (I)</option>
-        <option value="Dioxidation (K)">Dioxidation (K)</option>
-        <option value="Dioxidation (L)">Dioxidation (L)</option>
-        <option value="Dioxidation (M)">Dioxidation (M)</option>
-        <option value="Dioxidation (P)">Dioxidation (P)</option>
-        <option value="Dioxidation (R)">Dioxidation (R)</option>
-        <option value="Dioxidation (U)">Dioxidation (U)</option>
-        <option value="Dioxidation (V)">Dioxidation (V)</option>
-        <option value="Dioxidation (W)">Dioxidation (W)</option>
-        <option value="Dioxidation (Y)">Dioxidation (Y)</option>
-        <option value="Diphthamide (H)">Diphthamide (H)</option>
-        <option value="Dipyridyl (C)">Dipyridyl (C)</option>
-        <option value="Dipyrrolylmethanemethyl (C)">Dipyrrolylmethanemethyl (C)</option>
-        <option value="DMPO (C)">DMPO (C)</option>
-        <option value="DMPO (H)">DMPO (H)</option>
-        <option value="DMPO (Y)">DMPO (Y)</option>
-        <option value="DNCB_hapten (C)">DNCB_hapten (C)</option>
-        <option value="DNCB_hapten (H)">DNCB_hapten (H)</option>
-        <option value="DNCB_hapten (K)">DNCB_hapten (K)</option>
-        <option value="DNCB_hapten (Y)">DNCB_hapten (Y)</option>
-        <option value="dNIC (K)">dNIC (K)</option>
-        <option value="dNIC (N-term)">dNIC (N-term)</option>
-        <option value="DNPS (C)">DNPS (C)</option>
-        <option value="DNPS (W)">DNPS (W)</option>
-        <option value="DTT (C)">DTT (C)</option>
-        <option value="DyLight-maleimide (C)">DyLight-maleimide (C)</option>
-        <option value="DYn-2 (C)">DYn-2 (C)</option>
-        <option value="EDEDTIDVFQQQTGG (K)">EDEDTIDVFQQQTGG (K)</option>
-        <option value="EDT-iodoacetyl-PEO-biotin (S)">EDT-iodoacetyl-PEO-biotin (S)</option>
-        <option value="EDT-iodoacetyl-PEO-biotin (T)">EDT-iodoacetyl-PEO-biotin (T)</option>
-        <option value="EDT-maleimide-PEO-biotin (S)">EDT-maleimide-PEO-biotin (S)</option>
-        <option value="EDT-maleimide-PEO-biotin (T)">EDT-maleimide-PEO-biotin (T)</option>
-        <option value="EEEDVIEVYQEQTGG (K)">EEEDVIEVYQEQTGG (K)</option>
-        <option value="EGCG1 (C)">EGCG1 (C)</option>
-        <option value="EGCG2 (C)">EGCG2 (C)</option>
-        <option value="EHD-diphenylpentanone (C)">EHD-diphenylpentanone (C)</option>
-        <option value="EHD-diphenylpentanone (M)">EHD-diphenylpentanone (M)</option>
-        <option value="EQAT (C)">EQAT (C)</option>
-        <option value="EQAT:2H(5) (C)">EQAT:2H(5) (C)</option>
-        <option value="EQIGG (K)">EQIGG (K)</option>
-        <option value="ESP (K)">ESP (K)</option>
-        <option value="ESP (N-term)">ESP (N-term)</option>
-        <option value="ESP:2H(10) (K)">ESP:2H(10) (K)</option>
-        <option value="ESP:2H(10) (N-term)">ESP:2H(10) (N-term)</option>
-        <option value="Ethanedithiol (S)">Ethanedithiol (S)</option>
-        <option value="Ethanedithiol (T)">Ethanedithiol (T)</option>
-        <option value="Ethanolamine (C)">Ethanolamine (C)</option>
-        <option value="Ethanolamine (C-term)">Ethanolamine (C-term)</option>
-        <option value="Ethanolamine (D)">Ethanolamine (D)</option>
-        <option value="Ethanolamine (E)">Ethanolamine (E)</option>
-        <option value="Ethanolyl (C)">Ethanolyl (C)</option>
-        <option value="Ethanolyl (K)">Ethanolyl (K)</option>
-        <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-        <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
-        <option value="Ethyl (C-term)">Ethyl (C-term)</option>
-        <option value="Ethyl (D)">Ethyl (D)</option>
-        <option value="Ethyl (E)">Ethyl (E)</option>
-        <option value="Ethyl (K)">Ethyl (K)</option>
-        <option value="Ethyl (N-term)">Ethyl (N-term)</option>
-        <option value="Ethyl (Protein N-term)">Ethyl (Protein N-term)</option>
-        <option value="Ethyl+Deamidated (N)">Ethyl+Deamidated (N)</option>
-        <option value="Ethyl+Deamidated (Q)">Ethyl+Deamidated (Q)</option>
-        <option value="ethylamino (S)">ethylamino (S)</option>
-        <option value="ethylamino (T)">ethylamino (T)</option>
-        <option value="Ethylphosphate (K)">Ethylphosphate (K)</option>
-        <option value="Ethylphosphate (N-term)">Ethylphosphate (N-term)</option>
-        <option value="Ethylphosphate (S)">Ethylphosphate (S)</option>
-        <option value="Ethylphosphate (T)">Ethylphosphate (T)</option>
-        <option value="Ethylphosphate (Y)">Ethylphosphate (Y)</option>
-        <option value="ethylsulfonylethyl (C)">ethylsulfonylethyl (C)</option>
-        <option value="ethylsulfonylethyl (H)">ethylsulfonylethyl (H)</option>
-        <option value="ethylsulfonylethyl (K)">ethylsulfonylethyl (K)</option>
-        <option value="ExacTagAmine (K)">ExacTagAmine (K)</option>
-        <option value="ExacTagThiol (C)">ExacTagThiol (C)</option>
-        <option value="FAD (C)">FAD (C)</option>
-        <option value="FAD (H)">FAD (H)</option>
-        <option value="FAD (Y)">FAD (Y)</option>
-        <option value="Farnesyl (C)">Farnesyl (C)</option>
-        <option value="Fluorescein (C)">Fluorescein (C)</option>
-        <option value="Fluorescein-tyramine (Y)">Fluorescein-tyramine (Y)</option>
-        <option value="Fluoro (A)">Fluoro (A)</option>
-        <option value="Fluoro (F)">Fluoro (F)</option>
-        <option value="Fluoro (W)">Fluoro (W)</option>
-        <option value="Fluoro (Y)">Fluoro (Y)</option>
-        <option value="FMN (S)">FMN (S)</option>
-        <option value="FMN (T)">FMN (T)</option>
-        <option value="FMNC (C)">FMNC (C)</option>
-        <option value="FMNH (C)">FMNH (C)</option>
-        <option value="FMNH (H)">FMNH (H)</option>
-        <option value="FNEM (C)">FNEM (C)</option>
-        <option value="Formyl (K)">Formyl (K)</option>
-        <option value="Formyl (N-term)">Formyl (N-term)</option>
-        <option value="Formyl (Protein N-term)">Formyl (Protein N-term)</option>
-        <option value="Formyl (S)">Formyl (S)</option>
-        <option value="Formyl (T)">Formyl (T)</option>
-        <option value="Formylasparagine (H)">Formylasparagine (H)</option>
-        <option value="FormylMet (Protein N-term)">FormylMet (Protein N-term)</option>
-        <option value="FP-Biotin (K)">FP-Biotin (K)</option>
-        <option value="FP-Biotin (S)">FP-Biotin (S)</option>
-        <option value="FP-Biotin (T)">FP-Biotin (T)</option>
-        <option value="FP-Biotin (Y)">FP-Biotin (Y)</option>
-        <option value="FTC (C)">FTC (C)</option>
-        <option value="FTC (K)">FTC (K)</option>
-        <option value="FTC (P)">FTC (P)</option>
-        <option value="FTC (R)">FTC (R)</option>
-        <option value="FTC (S)">FTC (S)</option>
-        <option value="Furan (Y)">Furan (Y)</option>
-        <option value="G-H1 (R)">G-H1 (R)</option>
-        <option value="Galactosyl (K)">Galactosyl (K)</option>
-        <option value="Galactosyl (N-term)">Galactosyl (N-term)</option>
-        <option value="GEE (Q)">GEE (Q)</option>
-        <option value="GeranylGeranyl (C)">GeranylGeranyl (C)</option>
-        <option value="GG (C)">GG (C)</option>
-        <option value="GG (K)">GG (K)</option>
-        <option value="GG (Protein N-term)">GG (Protein N-term)</option>
-        <option value="GG (S)">GG (S)</option>
-        <option value="GG (T)">GG (T)</option>
-        <option value="GGQ (K)">GGQ (K)</option>
-        <option value="GIST-Quat (K)">GIST-Quat (K)</option>
-        <option value="GIST-Quat (N-term)">GIST-Quat (N-term)</option>
-        <option value="GIST-Quat:2H(3) (K)">GIST-Quat:2H(3) (K)</option>
-        <option value="GIST-Quat:2H(3) (N-term)">GIST-Quat:2H(3) (N-term)</option>
-        <option value="GIST-Quat:2H(6) (K)">GIST-Quat:2H(6) (K)</option>
-        <option value="GIST-Quat:2H(6) (N-term)">GIST-Quat:2H(6) (N-term)</option>
-        <option value="GIST-Quat:2H(9) (K)">GIST-Quat:2H(9) (K)</option>
-        <option value="GIST-Quat:2H(9) (N-term)">GIST-Quat:2H(9) (N-term)</option>
-        <option value="Gln-&gt;Ala (Q)">Gln-&gt;Ala (Q)</option>
-        <option value="Gln-&gt;Arg (Q)">Gln-&gt;Arg (Q)</option>
-        <option value="Gln-&gt;Asn (Q)">Gln-&gt;Asn (Q)</option>
-        <option value="Gln-&gt;Asp (Q)">Gln-&gt;Asp (Q)</option>
-        <option value="Gln-&gt;Cys (Q)">Gln-&gt;Cys (Q)</option>
-        <option value="Gln-&gt;Glu (Q)">Gln-&gt;Glu (Q)</option>
-        <option value="Gln-&gt;Gly (Q)">Gln-&gt;Gly (Q)</option>
-        <option value="Gln-&gt;His (Q)">Gln-&gt;His (Q)</option>
-        <option value="Gln-&gt;Lys (Q)">Gln-&gt;Lys (Q)</option>
-        <option value="Gln-&gt;Met (Q)">Gln-&gt;Met (Q)</option>
-        <option value="Gln-&gt;Phe (Q)">Gln-&gt;Phe (Q)</option>
-        <option value="Gln-&gt;Pro (Q)">Gln-&gt;Pro (Q)</option>
-        <option value="Gln-&gt;pyro-Glu (N-term Q)">Gln-&gt;pyro-Glu (N-term Q)</option>
-        <option value="Gln-&gt;Ser (Q)">Gln-&gt;Ser (Q)</option>
-        <option value="Gln-&gt;Thr (Q)">Gln-&gt;Thr (Q)</option>
-        <option value="Gln-&gt;Trp (Q)">Gln-&gt;Trp (Q)</option>
-        <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
-        <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
-        <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
-        <option value="Glu (E)">Glu (E)</option>
-        <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
-        <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
-        <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
-        <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
-        <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
-        <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
-        <option value="Glu-&gt;Gln (E)">Glu-&gt;Gln (E)</option>
-        <option value="Glu-&gt;Gly (E)">Glu-&gt;Gly (E)</option>
-        <option value="Glu-&gt;His (E)">Glu-&gt;His (E)</option>
-        <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
-        <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
-        <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
-        <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
-        <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
-        <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
-        <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
-        <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
-        <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
-        <option value="Glu-&gt;Val (E)">Glu-&gt;Val (E)</option>
-        <option value="Glu-&gt;Xle (E)">Glu-&gt;Xle (E)</option>
-        <option value="glucosone (R)">glucosone (R)</option>
-        <option value="Glucosylgalactosyl (K)">Glucosylgalactosyl (K)</option>
-        <option value="Glucuronyl (Protein N-term)">Glucuronyl (Protein N-term)</option>
-        <option value="Glucuronyl (S)">Glucuronyl (S)</option>
-        <option value="Glucuronyl (T)">Glucuronyl (T)</option>
-        <option value="GluGlu (E)">GluGlu (E)</option>
-        <option value="GluGlu (Protein C-term)">GluGlu (Protein C-term)</option>
-        <option value="GluGluGlu (E)">GluGluGlu (E)</option>
-        <option value="GluGluGlu (Protein C-term)">GluGluGlu (Protein C-term)</option>
-        <option value="GluGluGluGlu (E)">GluGluGluGlu (E)</option>
-        <option value="GluGluGluGlu (Protein C-term)">GluGluGluGlu (Protein C-term)</option>
-        <option value="Gluratylation (K)">Gluratylation (K)</option>
-        <option value="Glutathione (C)">Glutathione (C)</option>
-        <option value="Gly (K)">Gly (K)</option>
-        <option value="Gly (S)">Gly (S)</option>
-        <option value="Gly (T)">Gly (T)</option>
-        <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
-        <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
-        <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
-        <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
-        <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
-        <option value="Gly-&gt;Gln (G)">Gly-&gt;Gln (G)</option>
-        <option value="Gly-&gt;Glu (G)">Gly-&gt;Glu (G)</option>
-        <option value="Gly-&gt;His (G)">Gly-&gt;His (G)</option>
-        <option value="Gly-&gt;Lys (G)">Gly-&gt;Lys (G)</option>
-        <option value="Gly-&gt;Met (G)">Gly-&gt;Met (G)</option>
-        <option value="Gly-&gt;Phe (G)">Gly-&gt;Phe (G)</option>
-        <option value="Gly-&gt;Pro (G)">Gly-&gt;Pro (G)</option>
-        <option value="Gly-&gt;Ser (G)">Gly-&gt;Ser (G)</option>
-        <option value="Gly-&gt;Thr (G)">Gly-&gt;Thr (G)</option>
-        <option value="Gly-&gt;Trp (G)">Gly-&gt;Trp (G)</option>
-        <option value="Gly-&gt;Tyr (G)">Gly-&gt;Tyr (G)</option>
-        <option value="Gly-&gt;Val (G)">Gly-&gt;Val (G)</option>
-        <option value="Gly-&gt;Xle (G)">Gly-&gt;Xle (G)</option>
-        <option value="Gly-loss+Amide (C-term G)">Gly-loss+Amide (C-term G)</option>
-        <option value="Glycerophospho (S)">Glycerophospho (S)</option>
-        <option value="GlycerylPE (E)">GlycerylPE (E)</option>
-        <option value="glycidamide (K)">glycidamide (K)</option>
-        <option value="glycidamide (N-term)">glycidamide (N-term)</option>
-        <option value="Glycosyl (P)">Glycosyl (P)</option>
-        <option value="glyoxalAGE (R)">glyoxalAGE (R)</option>
-        <option value="GNLLFLACYCIGG (K)">GNLLFLACYCIGG (K)</option>
-        <option value="GPIanchor (Protein C-term)">GPIanchor (Protein C-term)</option>
-        <option value="Guanidinyl (K)">Guanidinyl (K)</option>
-        <option value="Guanidinyl (N-term)">Guanidinyl (N-term)</option>
-        <option value="Haloxon (C)">Haloxon (C)</option>
-        <option value="Haloxon (H)">Haloxon (H)</option>
-        <option value="Haloxon (K)">Haloxon (K)</option>
-        <option value="Haloxon (S)">Haloxon (S)</option>
-        <option value="Haloxon (T)">Haloxon (T)</option>
-        <option value="Haloxon (Y)">Haloxon (Y)</option>
-        <option value="HCysteinyl (C)">HCysteinyl (C)</option>
-        <option value="HCysThiolactone (K)">HCysThiolactone (K)</option>
-        <option value="Heme (C)">Heme (C)</option>
-        <option value="Heme (H)">Heme (H)</option>
-        <option value="Hep (K)">Hep (K)</option>
-        <option value="Hep (N)">Hep (N)</option>
-        <option value="Hep (Q)">Hep (Q)</option>
-        <option value="Hep (R)">Hep (R)</option>
-        <option value="Hep (S)">Hep (S)</option>
-        <option value="Hep (T)">Hep (T)</option>
-        <option value="Hex (C)">Hex (C)</option>
-        <option value="Hex (K)">Hex (K)</option>
-        <option value="Hex (N)">Hex (N)</option>
-        <option value="Hex (N-term)">Hex (N-term)</option>
-        <option value="Hex (R)">Hex (R)</option>
-        <option value="Hex (S)">Hex (S)</option>
-        <option value="Hex (T)">Hex (T)</option>
-        <option value="Hex (W)">Hex (W)</option>
-        <option value="Hex (Y)">Hex (Y)</option>
-        <option value="Hex(1)HexA(1) (S)">Hex(1)HexA(1) (S)</option>
-        <option value="Hex(1)HexA(1) (T)">Hex(1)HexA(1) (T)</option>
-        <option value="Hex(1)HexA(1)HexNAc(1) (S)">Hex(1)HexA(1)HexNAc(1) (S)</option>
-        <option value="Hex(1)HexA(1)HexNAc(1) (T)">Hex(1)HexA(1)HexNAc(1) (T)</option>
-        <option value="Hex(1)HexA(1)HexNAc(2) (S)">Hex(1)HexA(1)HexNAc(2) (S)</option>
-        <option value="Hex(1)HexA(1)HexNAc(2) (T)">Hex(1)HexA(1)HexNAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(1) (N)">Hex(1)HexNAc(1) (N)</option>
-        <option value="Hex(1)HexNAc(1) (S)">Hex(1)HexNAc(1) (S)</option>
-        <option value="Hex(1)HexNAc(1) (T)">Hex(1)HexNAc(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1) (N)">Hex(1)HexNAc(1)dHex(1) (N)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1) (S)">Hex(1)HexNAc(1)dHex(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1) (T)">Hex(1)HexNAc(1)dHex(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1)Me(1) (S)">Hex(1)HexNAc(1)dHex(1)Me(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1)Me(1) (T)">Hex(1)HexNAc(1)dHex(1)Me(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1)Me(2) (S)">Hex(1)HexNAc(1)dHex(1)Me(2) (S)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1)Me(2) (T)">Hex(1)HexNAc(1)dHex(1)Me(2) (T)</option>
-        <option value="Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S)">Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T)">Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1) (N)">Hex(1)HexNAc(1)NeuAc(1) (N)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1) (S)">Hex(1)HexNAc(1)NeuAc(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1) (T)">Hex(1)HexNAc(1)NeuAc(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S)">Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T)">Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S)">Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T)">Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T)">Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2) (N)">Hex(1)HexNAc(1)NeuAc(2) (N)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2) (S)">Hex(1)HexNAc(1)NeuAc(2) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2) (T)">Hex(1)HexNAc(1)NeuAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S)">Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T)">Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S)">Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T)">Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(3) (S)">Hex(1)HexNAc(1)NeuAc(3) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(3) (T)">Hex(1)HexNAc(1)NeuAc(3) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(1) (S)">Hex(1)HexNAc(1)NeuGc(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(1) (T)">Hex(1)HexNAc(1)NeuGc(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(2) (S)">Hex(1)HexNAc(1)NeuGc(2) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(2) (T)">Hex(1)HexNAc(1)NeuGc(2) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(3) (S)">Hex(1)HexNAc(1)NeuGc(3) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(3) (T)">Hex(1)HexNAc(1)NeuGc(3) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(4) (S)">Hex(1)HexNAc(1)NeuGc(4) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(4) (T)">Hex(1)HexNAc(1)NeuGc(4) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(5) (S)">Hex(1)HexNAc(1)NeuGc(5) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(5) (T)">Hex(1)HexNAc(1)NeuGc(5) (T)</option>
-        <option value="Hex(1)HexNAc(1)Phos(1) (S)">Hex(1)HexNAc(1)Phos(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)Phos(1) (T)">Hex(1)HexNAc(1)Phos(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)Sulf(1) (S)">Hex(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)Sulf(1) (T)">Hex(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(2) (N)">Hex(1)HexNAc(2) (N)</option>
-        <option value="Hex(1)HexNAc(2) (S)">Hex(1)HexNAc(2) (S)</option>
-        <option value="Hex(1)HexNAc(2) (T)">Hex(1)HexNAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(2)dHex(1) (N)">Hex(1)HexNAc(2)dHex(1) (N)</option>
-        <option value="Hex(1)HexNAc(2)dHex(1) (S)">Hex(1)HexNAc(2)dHex(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)dHex(1) (T)">Hex(1)HexNAc(2)dHex(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)dHex(1)Pent(1) (N)">Hex(1)HexNAc(2)dHex(1)Pent(1) (N)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2) (N)">Hex(1)HexNAc(2)dHex(2) (N)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2) (S)">Hex(1)HexNAc(2)dHex(2) (S)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2) (T)">Hex(1)HexNAc(2)dHex(2) (T)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(1) (S)">Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(1) (T)">Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(2) (S)">Hex(1)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(2) (T)">Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T)">Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuGc(1) (S)">Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuGc(1) (T)">Hex(1)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)Pent(1) (N)">Hex(1)HexNAc(2)Pent(1) (N)</option>
-        <option value="Hex(1)HexNAc(2)Sulf(1) (S)">Hex(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)Sulf(1) (T)">Hex(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(3) (S)">Hex(1)HexNAc(3) (S)</option>
-        <option value="Hex(1)HexNAc(3) (T)">Hex(1)HexNAc(3) (T)</option>
-        <option value="Hex(1)HexNAc(3)NeuAc(1) (S)">Hex(1)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="Hex(1)HexNAc(3)NeuAc(1) (T)">Hex(1)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="Hex(1)HexNAc(3)NeuAc(2) (S)">Hex(1)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="Hex(1)HexNAc(3)NeuAc(2) (T)">Hex(1)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(3)NeuGc(1) (S)">Hex(1)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="Hex(1)HexNAc(3)NeuGc(1) (T)">Hex(1)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="Hex(1)HexNAc(3)Sulf(1) (S)">Hex(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(3)Sulf(1) (T)">Hex(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)</option>
-        <option value="Hex(1)NeuAc(1) (S)">Hex(1)NeuAc(1) (S)</option>
-        <option value="Hex(1)NeuAc(1) (T)">Hex(1)NeuAc(1) (T)</option>
-        <option value="Hex(1)NeuAc(1)Pent(1) (S)">Hex(1)NeuAc(1)Pent(1) (S)</option>
-        <option value="Hex(1)NeuAc(1)Pent(1) (T)">Hex(1)NeuAc(1)Pent(1) (T)</option>
-        <option value="Hex(1)NeuGc(1) (S)">Hex(1)NeuGc(1) (S)</option>
-        <option value="Hex(1)NeuGc(1) (T)">Hex(1)NeuGc(1) (T)</option>
-        <option value="Hex(1)Pent(1) (S)">Hex(1)Pent(1) (S)</option>
-        <option value="Hex(1)Pent(1) (T)">Hex(1)Pent(1) (T)</option>
-        <option value="Hex(1)Pent(2) (S)">Hex(1)Pent(2) (S)</option>
-        <option value="Hex(1)Pent(2) (T)">Hex(1)Pent(2) (T)</option>
-        <option value="Hex(1)Pent(2)Me(1) (S)">Hex(1)Pent(2)Me(1) (S)</option>
-        <option value="Hex(1)Pent(2)Me(1) (T)">Hex(1)Pent(2)Me(1) (T)</option>
-        <option value="Hex(1)Pent(3) (S)">Hex(1)Pent(3) (S)</option>
-        <option value="Hex(1)Pent(3) (T)">Hex(1)Pent(3) (T)</option>
-        <option value="Hex(1)Pent(3)Me(1) (S)">Hex(1)Pent(3)Me(1) (S)</option>
-        <option value="Hex(1)Pent(3)Me(1) (T)">Hex(1)Pent(3)Me(1) (T)</option>
-        <option value="Hex(10)HexNAc(1) (N)">Hex(10)HexNAc(1) (N)</option>
-        <option value="Hex(10)Phos(3) (S)">Hex(10)Phos(3) (S)</option>
-        <option value="Hex(10)Phos(3) (T)">Hex(10)Phos(3) (T)</option>
-        <option value="Hex(2) (K)">Hex(2) (K)</option>
-        <option value="Hex(2) (R)">Hex(2) (R)</option>
-        <option value="Hex(2) (S)">Hex(2) (S)</option>
-        <option value="Hex(2) (T)">Hex(2) (T)</option>
-        <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)Pent(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)Pent(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(1) (N)">Hex(2)HexNAc(1) (N)</option>
-        <option value="Hex(2)HexNAc(1) (S)">Hex(2)HexNAc(1) (S)</option>
-        <option value="Hex(2)HexNAc(1) (T)">Hex(2)HexNAc(1) (T)</option>
-        <option value="Hex(2)HexNAc(1)Me(1) (S)">Hex(2)HexNAc(1)Me(1) (S)</option>
-        <option value="Hex(2)HexNAc(1)Me(1) (T)">Hex(2)HexNAc(1)Me(1) (T)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(1) (S)">Hex(2)HexNAc(1)NeuGc(1) (S)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(1) (T)">Hex(2)HexNAc(1)NeuGc(1) (T)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(2) (S)">Hex(2)HexNAc(1)NeuGc(2) (S)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(2) (T)">Hex(2)HexNAc(1)NeuGc(2) (T)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(3) (S)">Hex(2)HexNAc(1)NeuGc(3) (S)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(3) (T)">Hex(2)HexNAc(1)NeuGc(3) (T)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(4) (S)">Hex(2)HexNAc(1)NeuGc(4) (S)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(4) (T)">Hex(2)HexNAc(1)NeuGc(4) (T)</option>
-        <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (S)">Hex(2)HexNAc(1)Pent(1)HexA(1) (S)</option>
-        <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (T)">Hex(2)HexNAc(1)Pent(1)HexA(1) (T)</option>
-        <option value="Hex(2)HexNAc(1)Sulf(1) (S)">Hex(2)HexNAc(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(1)Sulf(1) (T)">Hex(2)HexNAc(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(2) (N)">Hex(2)HexNAc(2) (N)</option>
-        <option value="Hex(2)HexNAc(2) (S)">Hex(2)HexNAc(2) (S)</option>
-        <option value="Hex(2)HexNAc(2) (T)">Hex(2)HexNAc(2) (T)</option>
-        <option value="Hex(2)HexNAc(2)dHex(1) (N)">Hex(2)HexNAc(2)dHex(1) (N)</option>
-        <option value="Hex(2)HexNAc(2)dHex(1) (S)">Hex(2)HexNAc(2)dHex(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)dHex(1) (T)">Hex(2)HexNAc(2)dHex(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1) (N)">Hex(2)HexNAc(2)NeuAc(1) (N)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1) (S)">Hex(2)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1) (T)">Hex(2)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(2) (S)">Hex(2)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(2) (T)">Hex(2)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuGc(1) (S)">Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuGc(1) (T)">Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)Pent(1) (N)">Hex(2)HexNAc(2)Pent(1) (N)</option>
-        <option value="Hex(2)HexNAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(3) (N)">Hex(2)HexNAc(3) (N)</option>
-        <option value="Hex(2)HexNAc(3) (S)">Hex(2)HexNAc(3) (S)</option>
-        <option value="Hex(2)HexNAc(3) (T)">Hex(2)HexNAc(3) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(2) (S)">Hex(2)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(2) (T)">Hex(2)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(3) (S)">Hex(2)HexNAc(3)NeuAc(3) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(3) (T)">Hex(2)HexNAc(3)NeuAc(3) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(1) (T)">Hex(2)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(2) (S)">Hex(2)HexNAc(3)NeuGc(2) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(2) (T)">Hex(2)HexNAc(3)NeuGc(2) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(3) (S)">Hex(2)HexNAc(3)NeuGc(3) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(3) (T)">Hex(2)HexNAc(3)NeuGc(3) (T)</option>
-        <option value="Hex(2)HexNAc(3)Sulf(1) (S)">Hex(2)HexNAc(3)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(3)Sulf(1) (T)">Hex(2)HexNAc(3)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(4) (N)">Hex(2)HexNAc(4) (N)</option>
-        <option value="Hex(2)HexNAc(4) (S)">Hex(2)HexNAc(4) (S)</option>
-        <option value="Hex(2)HexNAc(4) (T)">Hex(2)HexNAc(4) (T)</option>
-        <option value="Hex(2)HexNAc(4)NeuAc(1) (S)">Hex(2)HexNAc(4)NeuAc(1) (S)</option>
-        <option value="Hex(2)HexNAc(4)NeuAc(1) (T)">Hex(2)HexNAc(4)NeuAc(1) (T)</option>
-        <option value="Hex(2)HexNAc(5) (S)">Hex(2)HexNAc(5) (S)</option>
-        <option value="Hex(2)HexNAc(5) (T)">Hex(2)HexNAc(5) (T)</option>
-        <option value="Hex(2)NeuAc(1) (S)">Hex(2)NeuAc(1) (S)</option>
-        <option value="Hex(2)NeuAc(1) (T)">Hex(2)NeuAc(1) (T)</option>
-        <option value="Hex(2)Pent(2) (S)">Hex(2)Pent(2) (S)</option>
-        <option value="Hex(2)Pent(2) (T)">Hex(2)Pent(2) (T)</option>
-        <option value="Hex(2)Pent(2)Me(1) (S)">Hex(2)Pent(2)Me(1) (S)</option>
-        <option value="Hex(2)Pent(2)Me(1) (T)">Hex(2)Pent(2)Me(1) (T)</option>
-        <option value="Hex(2)Sulf(1) (S)">Hex(2)Sulf(1) (S)</option>
-        <option value="Hex(2)Sulf(1) (T)">Hex(2)Sulf(1) (T)</option>
-        <option value="Hex(3) (N)">Hex(3) (N)</option>
-        <option value="Hex(3) (S)">Hex(3) (S)</option>
-        <option value="Hex(3) (T)">Hex(3) (T)</option>
-        <option value="Hex(3)HexNAc(1) (N)">Hex(3)HexNAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(1) (S)">Hex(3)HexNAc(1) (S)</option>
-        <option value="Hex(3)HexNAc(1) (T)">Hex(3)HexNAc(1) (T)</option>
-        <option value="Hex(3)HexNAc(1)HexA(1) (S)">Hex(3)HexNAc(1)HexA(1) (S)</option>
-        <option value="Hex(3)HexNAc(1)HexA(1) (T)">Hex(3)HexNAc(1)HexA(1) (T)</option>
-        <option value="Hex(3)HexNAc(1)Me(1) (S)">Hex(3)HexNAc(1)Me(1) (S)</option>
-        <option value="Hex(3)HexNAc(1)Me(1) (T)">Hex(3)HexNAc(1)Me(1) (T)</option>
-        <option value="Hex(3)HexNAc(1)Pent(1) (N)">Hex(3)HexNAc(1)Pent(1) (N)</option>
-        <option value="Hex(3)HexNAc(2) (N)">Hex(3)HexNAc(2) (N)</option>
-        <option value="Hex(3)HexNAc(2) (S)">Hex(3)HexNAc(2) (S)</option>
-        <option value="Hex(3)HexNAc(2) (T)">Hex(3)HexNAc(2) (T)</option>
-        <option value="Hex(3)HexNAc(2)NeuAc(1) (N)">Hex(3)HexNAc(2)NeuAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(2)NeuAc(2) (S)">Hex(3)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="Hex(3)HexNAc(2)NeuAc(2) (T)">Hex(3)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="Hex(3)HexNAc(2)Pent(1) (N)">Hex(3)HexNAc(2)Pent(1) (N)</option>
-        <option value="Hex(3)HexNAc(2)Phos(1) (N)">Hex(3)HexNAc(2)Phos(1) (N)</option>
-        <option value="Hex(3)HexNAc(3) (N)">Hex(3)HexNAc(3) (N)</option>
-        <option value="Hex(3)HexNAc(3) (S)">Hex(3)HexNAc(3) (S)</option>
-        <option value="Hex(3)HexNAc(3) (T)">Hex(3)HexNAc(3) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(1) (S)">Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(1) (T)">Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(2) (S)">Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(2) (T)">Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(3) (S)">Hex(3)HexNAc(3)NeuAc(3) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(3) (T)">Hex(3)HexNAc(3)NeuAc(3) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuGc(1) (S)">Hex(3)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuGc(1) (T)">Hex(3)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)Pent(1) (N)">Hex(3)HexNAc(3)Pent(1) (N)</option>
-        <option value="Hex(3)HexNAc(3)Sulf(1) (N)">Hex(3)HexNAc(3)Sulf(1) (N)</option>
-        <option value="Hex(3)HexNAc(3)Sulf(1) (S)">Hex(3)HexNAc(3)Sulf(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)Sulf(1) (T)">Hex(3)HexNAc(3)Sulf(1) (T)</option>
-        <option value="Hex(3)HexNAc(4) (N)">Hex(3)HexNAc(4) (N)</option>
-        <option value="Hex(3)HexNAc(4) (S)">Hex(3)HexNAc(4) (S)</option>
-        <option value="Hex(3)HexNAc(4) (T)">Hex(3)HexNAc(4) (T)</option>
-        <option value="Hex(3)HexNAc(4)NeuAc(1) (N)">Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(4)NeuAc(2) (N)">Hex(3)HexNAc(4)NeuAc(2) (N)</option>
-        <option value="Hex(3)HexNAc(4)Pent(1) (N)">Hex(3)HexNAc(4)Pent(1) (N)</option>
-        <option value="Hex(3)HexNAc(4)Sulf(1) (N)">Hex(3)HexNAc(4)Sulf(1) (N)</option>
-        <option value="Hex(3)HexNAc(5) (N)">Hex(3)HexNAc(5) (N)</option>
-        <option value="Hex(3)HexNAc(5) (S)">Hex(3)HexNAc(5) (S)</option>
-        <option value="Hex(3)HexNAc(5) (T)">Hex(3)HexNAc(5) (T)</option>
-        <option value="Hex(3)HexNAc(5)NeuAc(1) (N)">Hex(3)HexNAc(5)NeuAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(5)Sulf(1) (N)">Hex(3)HexNAc(5)Sulf(1) (N)</option>
-        <option value="Hex(3)HexNAc(6) (N)">Hex(3)HexNAc(6) (N)</option>
-        <option value="Hex(3)HexNAc(6) (S)">Hex(3)HexNAc(6) (S)</option>
-        <option value="Hex(3)HexNAc(6) (T)">Hex(3)HexNAc(6) (T)</option>
-        <option value="Hex(3)HexNAc(6)NeuAc(1) (N)">Hex(3)HexNAc(6)NeuAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(6)Sulf(1) (N)">Hex(3)HexNAc(6)Sulf(1) (N)</option>
-        <option value="Hex(3)HexNAc(6)Sulf(2) (N)">Hex(3)HexNAc(6)Sulf(2) (N)</option>
-        <option value="Hex(3)HexNAc(7) (N)">Hex(3)HexNAc(7) (N)</option>
-        <option value="Hex(3)HexNAc(7)Sulf(1) (N)">Hex(3)HexNAc(7)Sulf(1) (N)</option>
-        <option value="Hex(4) (S)">Hex(4) (S)</option>
-        <option value="Hex(4) (T)">Hex(4) (T)</option>
-        <option value="Hex(4)HexA(1) (S)">Hex(4)HexA(1) (S)</option>
-        <option value="Hex(4)HexA(1) (T)">Hex(4)HexA(1) (T)</option>
-        <option value="Hex(4)HexA(1)HexNAc(1) (S)">Hex(4)HexA(1)HexNAc(1) (S)</option>
-        <option value="Hex(4)HexA(1)HexNAc(1) (T)">Hex(4)HexA(1)HexNAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(1) (N)">Hex(4)HexNAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(1) (S)">Hex(4)HexNAc(1) (S)</option>
-        <option value="Hex(4)HexNAc(1) (T)">Hex(4)HexNAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(2) (N)">Hex(4)HexNAc(2) (N)</option>
-        <option value="Hex(4)HexNAc(2)NeuAc(1) (N)">Hex(4)HexNAc(2)NeuAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(2)NeuAc(1) (S)">Hex(4)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="Hex(4)HexNAc(2)NeuAc(1) (T)">Hex(4)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(2)Pent(1) (N)">Hex(4)HexNAc(2)Pent(1) (N)</option>
-        <option value="Hex(4)HexNAc(3) (N)">Hex(4)HexNAc(3) (N)</option>
-        <option value="Hex(4)HexNAc(3) (S)">Hex(4)HexNAc(3) (S)</option>
-        <option value="Hex(4)HexNAc(3) (T)">Hex(4)HexNAc(3) (T)</option>
-        <option value="Hex(4)HexNAc(3)NeuAc(1) (N)">Hex(4)HexNAc(3)NeuAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(3)NeuAc(1) (S)">Hex(4)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="Hex(4)HexNAc(3)NeuAc(1) (T)">Hex(4)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(3)NeuAc(2) (N)">Hex(4)HexNAc(3)NeuAc(2) (N)</option>
-        <option value="Hex(4)HexNAc(3)NeuGc(1) (N)">Hex(4)HexNAc(3)NeuGc(1) (N)</option>
-        <option value="Hex(4)HexNAc(3)Pent(1) (N)">Hex(4)HexNAc(3)Pent(1) (N)</option>
-        <option value="Hex(4)HexNAc(4) (N)">Hex(4)HexNAc(4) (N)</option>
-        <option value="Hex(4)HexNAc(4) (S)">Hex(4)HexNAc(4) (S)</option>
-        <option value="Hex(4)HexNAc(4) (T)">Hex(4)HexNAc(4) (T)</option>
-        <option value="Hex(4)HexNAc(4)Me(2)Pent(1) (N)">Hex(4)HexNAc(4)Me(2)Pent(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1) (N)">Hex(4)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1) (S)">Hex(4)HexNAc(4)NeuAc(1) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1) (T)">Hex(4)HexNAc(4)NeuAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1) (N)">Hex(4)HexNAc(4)NeuGc(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1) (S)">Hex(4)HexNAc(4)NeuGc(1) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1) (T)">Hex(4)HexNAc(4)NeuGc(1) (T)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)</option>
-        <option value="Hex(4)HexNAc(4)Pent(1) (N)">Hex(4)HexNAc(4)Pent(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)Sulf(1) (N)">Hex(4)HexNAc(4)Sulf(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)Sulf(2) (S)">Hex(4)HexNAc(4)Sulf(2) (S)</option>
-        <option value="Hex(4)HexNAc(4)Sulf(2) (T)">Hex(4)HexNAc(4)Sulf(2) (T)</option>
-        <option value="Hex(4)HexNAc(5) (N)">Hex(4)HexNAc(5) (N)</option>
-        <option value="Hex(4)HexNAc(5)NeuAc(1) (N)">Hex(4)HexNAc(5)NeuAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(5)Sulf(1) (N)">Hex(4)HexNAc(5)Sulf(1) (N)</option>
-        <option value="Hex(4)HexNAc(6) (N)">Hex(4)HexNAc(6) (N)</option>
-        <option value="Hex(4)Phos(1) (S)">Hex(4)Phos(1) (S)</option>
-        <option value="Hex(4)Phos(1) (T)">Hex(4)Phos(1) (T)</option>
-        <option value="Hex(5) (S)">Hex(5) (S)</option>
-        <option value="Hex(5) (T)">Hex(5) (T)</option>
-        <option value="Hex(5)HexA(1) (S)">Hex(5)HexA(1) (S)</option>
-        <option value="Hex(5)HexA(1) (T)">Hex(5)HexA(1) (T)</option>
-        <option value="Hex(5)HexNAc(1) (N)">Hex(5)HexNAc(1) (N)</option>
-        <option value="Hex(5)HexNAc(1) (S)">Hex(5)HexNAc(1) (S)</option>
-        <option value="Hex(5)HexNAc(1) (T)">Hex(5)HexNAc(1) (T)</option>
-        <option value="Hex(5)HexNAc(2) (N)">Hex(5)HexNAc(2) (N)</option>
-        <option value="Hex(5)HexNAc(2)Phos(1) (N)">Hex(5)HexNAc(2)Phos(1) (N)</option>
-        <option value="Hex(5)HexNAc(3) (N)">Hex(5)HexNAc(3) (N)</option>
-        <option value="Hex(5)HexNAc(3)Pent(1) (N)">Hex(5)HexNAc(3)Pent(1) (N)</option>
-        <option value="Hex(5)HexNAc(4) (N)">Hex(5)HexNAc(4) (N)</option>
-        <option value="Hex(5)HexNAc(4) (S)">Hex(5)HexNAc(4) (S)</option>
-        <option value="Hex(5)HexNAc(4) (T)">Hex(5)HexNAc(4) (T)</option>
-        <option value="Hex(5)HexNAc(4)Me(2)Pent(1) (N)">Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(1) (N)">Hex(5)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(2) (N)">Hex(5)HexNAc(4)NeuAc(2) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuGc(1) (N)">Hex(5)HexNAc(4)NeuGc(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)Sulf(1) (N)">Hex(5)HexNAc(4)Sulf(1) (N)</option>
-        <option value="Hex(5)HexNAc(5) (N)">Hex(5)HexNAc(5) (N)</option>
-        <option value="Hex(5)HexNAc(5) (S)">Hex(5)HexNAc(5) (S)</option>
-        <option value="Hex(5)HexNAc(5) (T)">Hex(5)HexNAc(5) (T)</option>
-        <option value="Hex(5)Phos(1) (S)">Hex(5)Phos(1) (S)</option>
-        <option value="Hex(5)Phos(1) (T)">Hex(5)Phos(1) (T)</option>
-        <option value="Hex(5)Phos(3) (S)">Hex(5)Phos(3) (S)</option>
-        <option value="Hex(5)Phos(3) (T)">Hex(5)Phos(3) (T)</option>
-        <option value="Hex(6)HexNAc(1) (N)">Hex(6)HexNAc(1) (N)</option>
-        <option value="Hex(6)HexNAc(2) (N)">Hex(6)HexNAc(2) (N)</option>
-        <option value="Hex(6)HexNAc(2)Phos(1) (N)">Hex(6)HexNAc(2)Phos(1) (N)</option>
-        <option value="Hex(6)HexNAc(3) (N)">Hex(6)HexNAc(3) (N)</option>
-        <option value="Hex(6)HexNAc(3)Phos(1) (N)">Hex(6)HexNAc(3)Phos(1) (N)</option>
-        <option value="Hex(6)HexNAc(4) (N)">Hex(6)HexNAc(4) (N)</option>
-        <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
-        <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
-        <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
-        <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
-        <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
-        <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
-        <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
-        <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
-        <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
-        <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
-        <option value="Hex(7)HexNAc(2) (N)">Hex(7)HexNAc(2) (N)</option>
-        <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
-        <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
-        <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
-        <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
-        <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
-        <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
-        <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
-        <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
-        <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
-        <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
-        <option value="Hex(8)Phos(3) (T)">Hex(8)Phos(3) (T)</option>
-        <option value="Hex(9) (N)">Hex(9) (N)</option>
-        <option value="Hex(9)HexNAc(1) (N)">Hex(9)HexNAc(1) (N)</option>
-        <option value="Hex(9)HexNAc(2) (N)">Hex(9)HexNAc(2) (N)</option>
-        <option value="Hex(9)Phos(3) (S)">Hex(9)Phos(3) (S)</option>
-        <option value="Hex(9)Phos(3) (T)">Hex(9)Phos(3) (T)</option>
-        <option value="HexA(2)HexNAc(3) (S)">HexA(2)HexNAc(3) (S)</option>
-        <option value="HexA(2)HexNAc(3) (T)">HexA(2)HexNAc(3) (T)</option>
-        <option value="HexN (K)">HexN (K)</option>
-        <option value="HexN (N)">HexN (N)</option>
-        <option value="HexN (S)">HexN (S)</option>
-        <option value="HexN (T)">HexN (T)</option>
-        <option value="HexN (W)">HexN (W)</option>
-        <option value="HexNAc (C)">HexNAc (C)</option>
-        <option value="HexNAc (N)">HexNAc (N)</option>
-        <option value="HexNAc (S)">HexNAc (S)</option>
-        <option value="HexNAc (T)">HexNAc (T)</option>
-        <option value="HexNAc(1)dHex(1) (N)">HexNAc(1)dHex(1) (N)</option>
-        <option value="HexNAc(1)dHex(1) (S)">HexNAc(1)dHex(1) (S)</option>
-        <option value="HexNAc(1)dHex(1) (T)">HexNAc(1)dHex(1) (T)</option>
-        <option value="HexNAc(1)dHex(2) (N)">HexNAc(1)dHex(2) (N)</option>
-        <option value="HexNAc(1)Kdn(2) (S)">HexNAc(1)Kdn(2) (S)</option>
-        <option value="HexNAc(1)Kdn(2) (T)">HexNAc(1)Kdn(2) (T)</option>
-        <option value="HexNAc(1)NeuAc(1) (S)">HexNAc(1)NeuAc(1) (S)</option>
-        <option value="HexNAc(1)NeuAc(1) (T)">HexNAc(1)NeuAc(1) (T)</option>
-        <option value="HexNAc(1)NeuGc(1) (S)">HexNAc(1)NeuGc(1) (S)</option>
-        <option value="HexNAc(1)NeuGc(1) (T)">HexNAc(1)NeuGc(1) (T)</option>
-        <option value="HexNAc(1)NeuGc(2) (S)">HexNAc(1)NeuGc(2) (S)</option>
-        <option value="HexNAc(1)NeuGc(2) (T)">HexNAc(1)NeuGc(2) (T)</option>
-        <option value="HexNAc(2) (N)">HexNAc(2) (N)</option>
-        <option value="HexNAc(2) (S)">HexNAc(2) (S)</option>
-        <option value="HexNAc(2) (T)">HexNAc(2) (T)</option>
-        <option value="HexNAc(2)dHex(1) (N)">HexNAc(2)dHex(1) (N)</option>
-        <option value="HexNAc(2)dHex(2) (N)">HexNAc(2)dHex(2) (N)</option>
-        <option value="HexNAc(2)NeuAc(1) (S)">HexNAc(2)NeuAc(1) (S)</option>
-        <option value="HexNAc(2)NeuAc(1) (T)">HexNAc(2)NeuAc(1) (T)</option>
-        <option value="HexNAc(2)NeuAc(1)Sulf(1) (S)">HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="HexNAc(2)NeuAc(1)Sulf(1) (T)">HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="HexNAc(2)NeuGc(1) (S)">HexNAc(2)NeuGc(1) (S)</option>
-        <option value="HexNAc(2)NeuGc(1) (T)">HexNAc(2)NeuGc(1) (T)</option>
-        <option value="HexNAc(2)Sulf(1) (S)">HexNAc(2)Sulf(1) (S)</option>
-        <option value="HexNAc(2)Sulf(1) (T)">HexNAc(2)Sulf(1) (T)</option>
-        <option value="HexNAc(3) (S)">HexNAc(3) (S)</option>
-        <option value="HexNAc(3) (T)">HexNAc(3) (T)</option>
-        <option value="HexNAc(3)Sulf(1) (S)">HexNAc(3)Sulf(1) (S)</option>
-        <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
-        <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
-        <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
-        <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
-        <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
-        <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
-        <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
-        <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
-        <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
-        <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
-        <option value="His-&gt;Gln (H)">His-&gt;Gln (H)</option>
-        <option value="His-&gt;Glu (H)">His-&gt;Glu (H)</option>
-        <option value="His-&gt;Gly (H)">His-&gt;Gly (H)</option>
-        <option value="His-&gt;Lys (H)">His-&gt;Lys (H)</option>
-        <option value="His-&gt;Met (H)">His-&gt;Met (H)</option>
-        <option value="His-&gt;Phe (H)">His-&gt;Phe (H)</option>
-        <option value="His-&gt;Pro (H)">His-&gt;Pro (H)</option>
-        <option value="His-&gt;Ser (H)">His-&gt;Ser (H)</option>
-        <option value="His-&gt;Thr (H)">His-&gt;Thr (H)</option>
-        <option value="His-&gt;Trp (H)">His-&gt;Trp (H)</option>
-        <option value="His-&gt;Tyr (H)">His-&gt;Tyr (H)</option>
-        <option value="His-&gt;Val (H)">His-&gt;Val (H)</option>
-        <option value="His-&gt;Xle (H)">His-&gt;Xle (H)</option>
-        <option value="HMVK (C)">HMVK (C)</option>
-        <option value="HN2_mustard (C)">HN2_mustard (C)</option>
-        <option value="HN2_mustard (H)">HN2_mustard (H)</option>
-        <option value="HN2_mustard (K)">HN2_mustard (K)</option>
-        <option value="HN3_mustard (C)">HN3_mustard (C)</option>
-        <option value="HN3_mustard (H)">HN3_mustard (H)</option>
-        <option value="HN3_mustard (K)">HN3_mustard (K)</option>
-        <option value="HNE (A)">HNE (A)</option>
-        <option value="HNE (C)">HNE (C)</option>
-        <option value="HNE (H)">HNE (H)</option>
-        <option value="HNE (K)">HNE (K)</option>
-        <option value="HNE (L)">HNE (L)</option>
-        <option value="HNE+Delta:H(2) (C)">HNE+Delta:H(2) (C)</option>
-        <option value="HNE+Delta:H(2) (H)">HNE+Delta:H(2) (H)</option>
-        <option value="HNE+Delta:H(2) (K)">HNE+Delta:H(2) (K)</option>
-        <option value="HNE-BAHAH (C)">HNE-BAHAH (C)</option>
-        <option value="HNE-BAHAH (H)">HNE-BAHAH (H)</option>
-        <option value="HNE-BAHAH (K)">HNE-BAHAH (K)</option>
-        <option value="HNE-Delta:H(2)O (C)">HNE-Delta:H(2)O (C)</option>
-        <option value="HNE-Delta:H(2)O (H)">HNE-Delta:H(2)O (H)</option>
-        <option value="HNE-Delta:H(2)O (K)">HNE-Delta:H(2)O (K)</option>
-        <option value="Homocysteic_acid (M)">Homocysteic_acid (M)</option>
-        <option value="HPG (R)">HPG (R)</option>
-        <option value="Hydroxamic_acid (D)">Hydroxamic_acid (D)</option>
-        <option value="Hydroxamic_acid (E)">Hydroxamic_acid (E)</option>
-        <option value="Hydroxycinnamyl (C)">Hydroxycinnamyl (C)</option>
-        <option value="Hydroxyfarnesyl (C)">Hydroxyfarnesyl (C)</option>
-        <option value="Hydroxyheme (E)">Hydroxyheme (E)</option>
-        <option value="hydroxyisobutyryl (K)">hydroxyisobutyryl (K)</option>
-        <option value="Hydroxymethyl (N)">Hydroxymethyl (N)</option>
-        <option value="HydroxymethylOP (K)">HydroxymethylOP (K)</option>
-        <option value="Hydroxytrimethyl (K)">Hydroxytrimethyl (K)</option>
-        <option value="Hypusine (K)">Hypusine (K)</option>
-        <option value="IASD (C)">IASD (C)</option>
-        <option value="IBTP (C)">IBTP (C)</option>
-        <option value="ICAT-C (C)">ICAT-C (C)</option>
-        <option value="ICAT-C:13C(9) (C)">ICAT-C:13C(9) (C)</option>
-        <option value="ICAT-D (C)">ICAT-D (C)</option>
-        <option value="ICAT-D:2H(8) (C)">ICAT-D:2H(8) (C)</option>
-        <option value="ICAT-G (C)">ICAT-G (C)</option>
-        <option value="ICAT-G:2H(8) (C)">ICAT-G:2H(8) (C)</option>
-        <option value="ICAT-H (C)">ICAT-H (C)</option>
-        <option value="ICAT-H:13C(6) (C)">ICAT-H:13C(6) (C)</option>
-        <option value="ICDID (C)">ICDID (C)</option>
-        <option value="ICDID:2H(6) (C)">ICDID:2H(6) (C)</option>
-        <option value="ICPL (K)">ICPL (K)</option>
-        <option value="ICPL (N-term)">ICPL (N-term)</option>
-        <option value="ICPL (Protein N-term)">ICPL (Protein N-term)</option>
-        <option value="ICPL:13C(6) (K)">ICPL:13C(6) (K)</option>
-        <option value="ICPL:13C(6) (N-term)">ICPL:13C(6) (N-term)</option>
-        <option value="ICPL:13C(6) (Protein N-term)">ICPL:13C(6) (Protein N-term)</option>
-        <option value="ICPL:13C(6)2H(4) (K)">ICPL:13C(6)2H(4) (K)</option>
-        <option value="ICPL:13C(6)2H(4) (N-term)">ICPL:13C(6)2H(4) (N-term)</option>
-        <option value="ICPL:13C(6)2H(4) (Protein N-term)">ICPL:13C(6)2H(4) (Protein N-term)</option>
-        <option value="ICPL:2H(4) (K)">ICPL:2H(4) (K)</option>
-        <option value="ICPL:2H(4) (N-term)">ICPL:2H(4) (N-term)</option>
-        <option value="ICPL:2H(4) (Protein N-term)">ICPL:2H(4) (Protein N-term)</option>
-        <option value="IDEnT (C)">IDEnT (C)</option>
-        <option value="IED-Biotin (C)">IED-Biotin (C)</option>
-        <option value="IGBP (C)">IGBP (C)</option>
-        <option value="IGBP:13C(2) (C)">IGBP:13C(2) (C)</option>
-        <option value="IMEHex(2)NeuAc(1) (K)">IMEHex(2)NeuAc(1) (K)</option>
-        <option value="IMID (K)">IMID (K)</option>
-        <option value="IMID:2H(4) (K)">IMID:2H(4) (K)</option>
-        <option value="Iminobiotin (K)">Iminobiotin (K)</option>
-        <option value="Iminobiotin (N-term)">Iminobiotin (N-term)</option>
-        <option value="Iodo (H)">Iodo (H)</option>
-        <option value="Iodo (Y)">Iodo (Y)</option>
-        <option value="Iodoacetanilide (C)">Iodoacetanilide (C)</option>
-        <option value="Iodoacetanilide (K)">Iodoacetanilide (K)</option>
-        <option value="Iodoacetanilide (N-term)">Iodoacetanilide (N-term)</option>
-        <option value="Iodoacetanilide:13C(6) (C)">Iodoacetanilide:13C(6) (C)</option>
-        <option value="Iodoacetanilide:13C(6) (K)">Iodoacetanilide:13C(6) (K)</option>
-        <option value="Iodoacetanilide:13C(6) (N-term)">Iodoacetanilide:13C(6) (N-term)</option>
-        <option value="iodoTMT (C)">iodoTMT (C)</option>
-        <option value="iodoTMT (D)">iodoTMT (D)</option>
-        <option value="iodoTMT (E)">iodoTMT (E)</option>
-        <option value="iodoTMT (H)">iodoTMT (H)</option>
-        <option value="iodoTMT (K)">iodoTMT (K)</option>
-        <option value="iodoTMT6plex (C)">iodoTMT6plex (C)</option>
-        <option value="iodoTMT6plex (D)">iodoTMT6plex (D)</option>
-        <option value="iodoTMT6plex (E)">iodoTMT6plex (E)</option>
-        <option value="iodoTMT6plex (H)">iodoTMT6plex (H)</option>
-        <option value="iodoTMT6plex (K)">iodoTMT6plex (K)</option>
-        <option value="IodoU-AMP (F)">IodoU-AMP (F)</option>
-        <option value="IodoU-AMP (W)">IodoU-AMP (W)</option>
-        <option value="IodoU-AMP (Y)">IodoU-AMP (Y)</option>
-        <option value="ISD_z+2_ion (N-term)">ISD_z+2_ion (N-term)</option>
-        <option value="Isopropylphospho (S)">Isopropylphospho (S)</option>
-        <option value="Isopropylphospho (T)">Isopropylphospho (T)</option>
-        <option value="Isopropylphospho (Y)">Isopropylphospho (Y)</option>
-        <option value="iTRAQ4plex (C)">iTRAQ4plex (C)</option>
-        <option value="iTRAQ4plex (H)">iTRAQ4plex (H)</option>
-        <option value="iTRAQ4plex (K)">iTRAQ4plex (K)</option>
-        <option value="iTRAQ4plex (N-term)">iTRAQ4plex (N-term)</option>
-        <option value="iTRAQ4plex (Protein N-term)">iTRAQ4plex (Protein N-term)</option>
-        <option value="iTRAQ4plex (S)">iTRAQ4plex (S)</option>
-        <option value="iTRAQ4plex (T)">iTRAQ4plex (T)</option>
-        <option value="iTRAQ4plex (Y)">iTRAQ4plex (Y)</option>
-        <option value="iTRAQ4plex114 (C)">iTRAQ4plex114 (C)</option>
-        <option value="iTRAQ4plex114 (K)">iTRAQ4plex114 (K)</option>
-        <option value="iTRAQ4plex114 (N-term)">iTRAQ4plex114 (N-term)</option>
-        <option value="iTRAQ4plex114 (Y)">iTRAQ4plex114 (Y)</option>
-        <option value="iTRAQ4plex115 (C)">iTRAQ4plex115 (C)</option>
-        <option value="iTRAQ4plex115 (K)">iTRAQ4plex115 (K)</option>
-        <option value="iTRAQ4plex115 (N-term)">iTRAQ4plex115 (N-term)</option>
-        <option value="iTRAQ4plex115 (Y)">iTRAQ4plex115 (Y)</option>
-        <option value="iTRAQ8plex (C)">iTRAQ8plex (C)</option>
-        <option value="iTRAQ8plex (H)">iTRAQ8plex (H)</option>
-        <option value="iTRAQ8plex (K)">iTRAQ8plex (K)</option>
-        <option value="iTRAQ8plex (N-term)">iTRAQ8plex (N-term)</option>
-        <option value="iTRAQ8plex (Protein N-term)">iTRAQ8plex (Protein N-term)</option>
-        <option value="iTRAQ8plex (S)">iTRAQ8plex (S)</option>
-        <option value="iTRAQ8plex (T)">iTRAQ8plex (T)</option>
-        <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
-        <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
-        <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
-        <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
-        <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
-        <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
-        <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
-        <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
-        <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
-        <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
-        <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
-        <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
-        <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
-        <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
-        <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
-        <option value="Label:13C(5)15N(1) (E)">Label:13C(5)15N(1) (E)</option>
-        <option value="Label:13C(5)15N(1) (M)">Label:13C(5)15N(1) (M)</option>
-        <option value="Label:13C(5)15N(1) (P)">Label:13C(5)15N(1) (P)</option>
-        <option value="Label:13C(5)15N(1) (V)">Label:13C(5)15N(1) (V)</option>
-        <option value="Label:13C(6) (I)">Label:13C(6) (I)</option>
-        <option value="Label:13C(6) (K)">Label:13C(6) (K)</option>
-        <option value="Label:13C(6) (L)">Label:13C(6) (L)</option>
-        <option value="Label:13C(6) (R)">Label:13C(6) (R)</option>
-        <option value="Label:13C(6)+Acetyl (K)">Label:13C(6)+Acetyl (K)</option>
-        <option value="Label:13C(6)+Dimethyl (K)">Label:13C(6)+Dimethyl (K)</option>
-        <option value="Label:13C(6)+GG (K)">Label:13C(6)+GG (K)</option>
-        <option value="Label:13C(6)15N(1) (I)">Label:13C(6)15N(1) (I)</option>
-        <option value="Label:13C(6)15N(1) (L)">Label:13C(6)15N(1) (L)</option>
-        <option value="Label:13C(6)15N(2) (K)">Label:13C(6)15N(2) (K)</option>
-        <option value="Label:13C(6)15N(2)+Acetyl (K)">Label:13C(6)15N(2)+Acetyl (K)</option>
-        <option value="Label:13C(6)15N(2)+Dimethyl (K)">Label:13C(6)15N(2)+Dimethyl (K)</option>
-        <option value="Label:13C(6)15N(2)+GG (K)">Label:13C(6)15N(2)+GG (K)</option>
-        <option value="Label:13C(6)15N(4) (R)">Label:13C(6)15N(4) (R)</option>
-        <option value="Label:13C(6)15N(4)+Dimethyl (R)">Label:13C(6)15N(4)+Dimethyl (R)</option>
-        <option value="Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R)">Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R)</option>
-        <option value="Label:13C(6)15N(4)+Methyl (R)">Label:13C(6)15N(4)+Methyl (R)</option>
-        <option value="Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R)">Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R)</option>
-        <option value="Label:13C(9) (F)">Label:13C(9) (F)</option>
-        <option value="Label:13C(9) (Y)">Label:13C(9) (Y)</option>
-        <option value="Label:13C(9)+Phospho (Y)">Label:13C(9)+Phospho (Y)</option>
-        <option value="Label:13C(9)15N(1) (F)">Label:13C(9)15N(1) (F)</option>
-        <option value="Label:15N(1) (A)">Label:15N(1) (A)</option>
-        <option value="Label:15N(1) (C)">Label:15N(1) (C)</option>
-        <option value="Label:15N(1) (D)">Label:15N(1) (D)</option>
-        <option value="Label:15N(1) (E)">Label:15N(1) (E)</option>
-        <option value="Label:15N(1) (F)">Label:15N(1) (F)</option>
-        <option value="Label:15N(1) (G)">Label:15N(1) (G)</option>
-        <option value="Label:15N(1) (I)">Label:15N(1) (I)</option>
-        <option value="Label:15N(1) (L)">Label:15N(1) (L)</option>
-        <option value="Label:15N(1) (M)">Label:15N(1) (M)</option>
-        <option value="Label:15N(1) (P)">Label:15N(1) (P)</option>
-        <option value="Label:15N(1) (S)">Label:15N(1) (S)</option>
-        <option value="Label:15N(1) (T)">Label:15N(1) (T)</option>
-        <option value="Label:15N(1) (V)">Label:15N(1) (V)</option>
-        <option value="Label:15N(1) (Y)">Label:15N(1) (Y)</option>
-        <option value="Label:15N(2) (K)">Label:15N(2) (K)</option>
-        <option value="Label:15N(2) (N)">Label:15N(2) (N)</option>
-        <option value="Label:15N(2) (Q)">Label:15N(2) (Q)</option>
-        <option value="Label:15N(2) (W)">Label:15N(2) (W)</option>
-        <option value="Label:15N(2)2H(9) (K)">Label:15N(2)2H(9) (K)</option>
-        <option value="Label:15N(3) (H)">Label:15N(3) (H)</option>
-        <option value="Label:15N(4) (R)">Label:15N(4) (R)</option>
-        <option value="Label:18O(1) (C-term)">Label:18O(1) (C-term)</option>
-        <option value="Label:18O(1) (S)">Label:18O(1) (S)</option>
-        <option value="Label:18O(1) (T)">Label:18O(1) (T)</option>
-        <option value="Label:18O(1) (Y)">Label:18O(1) (Y)</option>
-        <option value="Label:18O(2) (C-term)">Label:18O(2) (C-term)</option>
-        <option value="Label:2H(10) (L)">Label:2H(10) (L)</option>
-        <option value="Label:2H(3) (L)">Label:2H(3) (L)</option>
-        <option value="Label:2H(3) (M)">Label:2H(3) (M)</option>
-        <option value="Label:2H(3)+Oxidation (M)">Label:2H(3)+Oxidation (M)</option>
-        <option value="Label:2H(4) (A)">Label:2H(4) (A)</option>
-        <option value="Label:2H(4) (F)">Label:2H(4) (F)</option>
-        <option value="Label:2H(4) (K)">Label:2H(4) (K)</option>
-        <option value="Label:2H(4) (U)">Label:2H(4) (U)</option>
-        <option value="Label:2H(4) (Y)">Label:2H(4) (Y)</option>
-        <option value="Label:2H(4)+Acetyl (K)">Label:2H(4)+Acetyl (K)</option>
-        <option value="Label:2H(4)+GG (K)">Label:2H(4)+GG (K)</option>
-        <option value="Label:2H(4)13C(1) (R)">Label:2H(4)13C(1) (R)</option>
-        <option value="Label:2H(6)15N(1) (P)">Label:2H(6)15N(1) (P)</option>
-        <option value="Label:2H(7)15N(4) (R)">Label:2H(7)15N(4) (R)</option>
-        <option value="Label:2H(9)13C(6)15N(2) (K)">Label:2H(9)13C(6)15N(2) (K)</option>
-        <option value="lapachenole (C)">lapachenole (C)</option>
-        <option value="Leu-&gt;MetOx (L)">Leu-&gt;MetOx (L)</option>
-        <option value="LG-anhydrolactam (K)">LG-anhydrolactam (K)</option>
-        <option value="LG-anhydrolactam (N-term)">LG-anhydrolactam (N-term)</option>
-        <option value="LG-anhyropyrrole (K)">LG-anhyropyrrole (K)</option>
-        <option value="LG-anhyropyrrole (N-term)">LG-anhyropyrrole (N-term)</option>
-        <option value="LG-Hlactam-K (K)">LG-Hlactam-K (K)</option>
-        <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
-        <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
-        <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
-        <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
-        <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
-        <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
-        <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
-        <option value="Lipoyl (K)">Lipoyl (K)</option>
-        <option value="LRGG (K)">LRGG (K)</option>
-        <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
-        <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
-        <option value="Lys (N-term)">Lys (N-term)</option>
-        <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
-        <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
-        <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
-        <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
-        <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
-        <option value="Lys-&gt;Asp (K)">Lys-&gt;Asp (K)</option>
-        <option value="Lys-&gt;CamCys (K)">Lys-&gt;CamCys (K)</option>
-        <option value="Lys-&gt;Cys (K)">Lys-&gt;Cys (K)</option>
-        <option value="Lys-&gt;Gln (K)">Lys-&gt;Gln (K)</option>
-        <option value="Lys-&gt;Glu (K)">Lys-&gt;Glu (K)</option>
-        <option value="Lys-&gt;Gly (K)">Lys-&gt;Gly (K)</option>
-        <option value="Lys-&gt;His (K)">Lys-&gt;His (K)</option>
-        <option value="Lys-&gt;Met (K)">Lys-&gt;Met (K)</option>
-        <option value="Lys-&gt;MetOx (K)">Lys-&gt;MetOx (K)</option>
-        <option value="Lys-&gt;Phe (K)">Lys-&gt;Phe (K)</option>
-        <option value="Lys-&gt;Pro (K)">Lys-&gt;Pro (K)</option>
-        <option value="Lys-&gt;Ser (K)">Lys-&gt;Ser (K)</option>
-        <option value="Lys-&gt;Thr (K)">Lys-&gt;Thr (K)</option>
-        <option value="Lys-&gt;Trp (K)">Lys-&gt;Trp (K)</option>
-        <option value="Lys-&gt;Tyr (K)">Lys-&gt;Tyr (K)</option>
-        <option value="Lys-&gt;Val (K)">Lys-&gt;Val (K)</option>
-        <option value="Lys-&gt;Xle (K)">Lys-&gt;Xle (K)</option>
-        <option value="Lys-loss (Protein C-term K)">Lys-loss (Protein C-term K)</option>
-        <option value="Lysbiotinhydrazide (K)">Lysbiotinhydrazide (K)</option>
-        <option value="maleimide (C)">maleimide (C)</option>
-        <option value="maleimide (K)">maleimide (K)</option>
-        <option value="Maleimide-PEO2-Biotin (C)">Maleimide-PEO2-Biotin (C)</option>
-        <option value="maleimide3 (C)">maleimide3 (C)</option>
-        <option value="maleimide3 (K)">maleimide3 (K)</option>
-        <option value="maleimide5 (C)">maleimide5 (C)</option>
-        <option value="maleimide5 (K)">maleimide5 (K)</option>
-        <option value="Malonyl (C)">Malonyl (C)</option>
-        <option value="Malonyl (K)">Malonyl (K)</option>
-        <option value="Malonyl (S)">Malonyl (S)</option>
-        <option value="MDCC (C)">MDCC (C)</option>
-        <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
-        <option value="Menadione (C)">Menadione (C)</option>
-        <option value="Menadione (K)">Menadione (K)</option>
-        <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
-        <option value="Menadione-HQ (K)">Menadione-HQ (K)</option>
-        <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
-        <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
-        <option value="MesitylOxide (H)">MesitylOxide (H)</option>
-        <option value="MesitylOxide (K)">MesitylOxide (K)</option>
-        <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
-        <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
-        <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
-        <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
-        <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
-        <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
-        <option value="Met-&gt;AspSA (M)">Met-&gt;AspSA (M)</option>
-        <option value="Met-&gt;Cys (M)">Met-&gt;Cys (M)</option>
-        <option value="Met-&gt;Gln (M)">Met-&gt;Gln (M)</option>
-        <option value="Met-&gt;Glu (M)">Met-&gt;Glu (M)</option>
-        <option value="Met-&gt;Gly (M)">Met-&gt;Gly (M)</option>
-        <option value="Met-&gt;His (M)">Met-&gt;His (M)</option>
-        <option value="Met-&gt;Hpg (M)">Met-&gt;Hpg (M)</option>
-        <option value="Met-&gt;Hse (C-term M)">Met-&gt;Hse (C-term M)</option>
-        <option value="Met-&gt;Hsl (C-term M)">Met-&gt;Hsl (C-term M)</option>
-        <option value="Met-&gt;Lys (M)">Met-&gt;Lys (M)</option>
-        <option value="Met-&gt;Phe (M)">Met-&gt;Phe (M)</option>
-        <option value="Met-&gt;Pro (M)">Met-&gt;Pro (M)</option>
-        <option value="Met-&gt;Ser (M)">Met-&gt;Ser (M)</option>
-        <option value="Met-&gt;Thr (M)">Met-&gt;Thr (M)</option>
-        <option value="Met-&gt;Trp (M)">Met-&gt;Trp (M)</option>
-        <option value="Met-&gt;Tyr (M)">Met-&gt;Tyr (M)</option>
-        <option value="Met-&gt;Val (M)">Met-&gt;Val (M)</option>
-        <option value="Met-&gt;Xle (M)">Met-&gt;Xle (M)</option>
-        <option value="Met-loss (Protein N-term M)">Met-loss (Protein N-term M)</option>
-        <option value="Met-loss+Acetyl (Protein N-term M)">Met-loss+Acetyl (Protein N-term M)</option>
-        <option value="Methamidophos-O (C)">Methamidophos-O (C)</option>
-        <option value="Methamidophos-O (H)">Methamidophos-O (H)</option>
-        <option value="Methamidophos-O (K)">Methamidophos-O (K)</option>
-        <option value="Methamidophos-O (S)">Methamidophos-O (S)</option>
-        <option value="Methamidophos-O (T)">Methamidophos-O (T)</option>
-        <option value="Methamidophos-O (Y)">Methamidophos-O (Y)</option>
-        <option value="Methamidophos-S (C)">Methamidophos-S (C)</option>
-        <option value="Methamidophos-S (H)">Methamidophos-S (H)</option>
-        <option value="Methamidophos-S (K)">Methamidophos-S (K)</option>
-        <option value="Methamidophos-S (S)">Methamidophos-S (S)</option>
-        <option value="Methamidophos-S (T)">Methamidophos-S (T)</option>
-        <option value="Methamidophos-S (Y)">Methamidophos-S (Y)</option>
-        <option value="Methyl (C)">Methyl (C)</option>
-        <option value="Methyl (C-term)">Methyl (C-term)</option>
-        <option value="Methyl (D)">Methyl (D)</option>
-        <option value="Methyl (E)">Methyl (E)</option>
-        <option value="Methyl (H)">Methyl (H)</option>
-        <option value="Methyl (I)">Methyl (I)</option>
-        <option value="Methyl (K)">Methyl (K)</option>
-        <option value="Methyl (L)">Methyl (L)</option>
-        <option value="Methyl (N)">Methyl (N)</option>
-        <option value="Methyl (N-term)">Methyl (N-term)</option>
-        <option value="Methyl (Protein N-term)">Methyl (Protein N-term)</option>
-        <option value="Methyl (Q)">Methyl (Q)</option>
-        <option value="Methyl (R)">Methyl (R)</option>
-        <option value="Methyl (S)">Methyl (S)</option>
-        <option value="Methyl (T)">Methyl (T)</option>
-        <option value="Methyl+Acetyl:2H(3) (K)">Methyl+Acetyl:2H(3) (K)</option>
-        <option value="Methyl+Deamidated (N)">Methyl+Deamidated (N)</option>
-        <option value="Methyl+Deamidated (Q)">Methyl+Deamidated (Q)</option>
-        <option value="Methyl-PEO12-Maleimide (C)">Methyl-PEO12-Maleimide (C)</option>
-        <option value="Methyl:2H(2) (K)">Methyl:2H(2) (K)</option>
-        <option value="Methyl:2H(2) (N-term)">Methyl:2H(2) (N-term)</option>
-        <option value="Methyl:2H(2)13C (C)">Methyl:2H(2)13C (C)</option>
-        <option value="Methyl:2H(2)13C (C-term)">Methyl:2H(2)13C (C-term)</option>
-        <option value="Methyl:2H(2)13C (D)">Methyl:2H(2)13C (D)</option>
-        <option value="Methyl:2H(2)13C (E)">Methyl:2H(2)13C (E)</option>
-        <option value="Methyl:2H(2)13C (H)">Methyl:2H(2)13C (H)</option>
-        <option value="Methyl:2H(2)13C (I)">Methyl:2H(2)13C (I)</option>
-        <option value="Methyl:2H(2)13C (K)">Methyl:2H(2)13C (K)</option>
-        <option value="Methyl:2H(2)13C (L)">Methyl:2H(2)13C (L)</option>
-        <option value="Methyl:2H(2)13C (N)">Methyl:2H(2)13C (N)</option>
-        <option value="Methyl:2H(2)13C (N-term)">Methyl:2H(2)13C (N-term)</option>
-        <option value="Methyl:2H(2)13C (Protein N-term)">Methyl:2H(2)13C (Protein N-term)</option>
-        <option value="Methyl:2H(2)13C (Q)">Methyl:2H(2)13C (Q)</option>
-        <option value="Methyl:2H(2)13C (R)">Methyl:2H(2)13C (R)</option>
-        <option value="Methyl:2H(2)13C (S)">Methyl:2H(2)13C (S)</option>
-        <option value="Methyl:2H(2)13C (T)">Methyl:2H(2)13C (T)</option>
-        <option value="Methyl:2H(3) (D)">Methyl:2H(3) (D)</option>
-        <option value="Methyl:2H(3) (E)">Methyl:2H(3) (E)</option>
-        <option value="Methyl:2H(3) (K)">Methyl:2H(3) (K)</option>
-        <option value="Methyl:2H(3) (R)">Methyl:2H(3) (R)</option>
-        <option value="Methyl:2H(3) (X)">Methyl:2H(3) (X)</option>
-        <option value="Methyl:2H(3)+Acetyl:2H(3) (K)">Methyl:2H(3)+Acetyl:2H(3) (K)</option>
-        <option value="Methyl:2H(3)13C(1) (K)">Methyl:2H(3)13C(1) (K)</option>
-        <option value="Methyl:2H(3)13C(1) (N-term)">Methyl:2H(3)13C(1) (N-term)</option>
-        <option value="Methyl:2H(3)13C(1) (R)">Methyl:2H(3)13C(1) (R)</option>
-        <option value="Methylamine (S)">Methylamine (S)</option>
-        <option value="Methylamine (T)">Methylamine (T)</option>
-        <option value="Methylmalonylation (S)">Methylmalonylation (S)</option>
-        <option value="methylol (K)">methylol (K)</option>
-        <option value="methylol (W)">methylol (W)</option>
-        <option value="methylol (Y)">methylol (Y)</option>
-        <option value="Methylphosphonate (S)">Methylphosphonate (S)</option>
-        <option value="Methylphosphonate (T)">Methylphosphonate (T)</option>
-        <option value="Methylphosphonate (Y)">Methylphosphonate (Y)</option>
-        <option value="Methylpyrroline (K)">Methylpyrroline (K)</option>
-        <option value="methylsulfonylethyl (C)">methylsulfonylethyl (C)</option>
-        <option value="methylsulfonylethyl (H)">methylsulfonylethyl (H)</option>
-        <option value="methylsulfonylethyl (K)">methylsulfonylethyl (K)</option>
-        <option value="Methylthio (C)">Methylthio (C)</option>
-        <option value="Methylthio (D)">Methylthio (D)</option>
-        <option value="Methylthio (K)">Methylthio (K)</option>
-        <option value="Methylthio (N)">Methylthio (N)</option>
-        <option value="Methylthio (N-term)">Methylthio (N-term)</option>
-        <option value="MG-H1 (R)">MG-H1 (R)</option>
-        <option value="Microcin (Protein C-term)">Microcin (Protein C-term)</option>
-        <option value="MicrocinC7 (Protein C-term)">MicrocinC7 (Protein C-term)</option>
-        <option value="MM-diphenylpentanone (C)">MM-diphenylpentanone (C)</option>
-        <option value="Molybdopterin (C)">Molybdopterin (C)</option>
-        <option value="MolybdopterinGD (C)">MolybdopterinGD (C)</option>
-        <option value="MolybdopterinGD (D)">MolybdopterinGD (D)</option>
-        <option value="MolybdopterinGD (U)">MolybdopterinGD (U)</option>
-        <option value="MolybdopterinGD+Delta:S(-1)Se(1) (C)">MolybdopterinGD+Delta:S(-1)Se(1) (C)</option>
-        <option value="monomethylphosphothione (C)">monomethylphosphothione (C)</option>
-        <option value="monomethylphosphothione (H)">monomethylphosphothione (H)</option>
-        <option value="monomethylphosphothione (K)">monomethylphosphothione (K)</option>
-        <option value="monomethylphosphothione (S)">monomethylphosphothione (S)</option>
-        <option value="monomethylphosphothione (T)">monomethylphosphothione (T)</option>
-        <option value="monomethylphosphothione (Y)">monomethylphosphothione (Y)</option>
-        <option value="mTRAQ (H)">mTRAQ (H)</option>
-        <option value="mTRAQ (K)">mTRAQ (K)</option>
-        <option value="mTRAQ (N-term)">mTRAQ (N-term)</option>
-        <option value="mTRAQ (S)">mTRAQ (S)</option>
-        <option value="mTRAQ (T)">mTRAQ (T)</option>
-        <option value="mTRAQ (Y)">mTRAQ (Y)</option>
-        <option value="mTRAQ:13C(3)15N(1) (H)">mTRAQ:13C(3)15N(1) (H)</option>
-        <option value="mTRAQ:13C(3)15N(1) (K)">mTRAQ:13C(3)15N(1) (K)</option>
-        <option value="mTRAQ:13C(3)15N(1) (N-term)">mTRAQ:13C(3)15N(1) (N-term)</option>
-        <option value="mTRAQ:13C(3)15N(1) (S)">mTRAQ:13C(3)15N(1) (S)</option>
-        <option value="mTRAQ:13C(3)15N(1) (T)">mTRAQ:13C(3)15N(1) (T)</option>
-        <option value="mTRAQ:13C(3)15N(1) (Y)">mTRAQ:13C(3)15N(1) (Y)</option>
-        <option value="mTRAQ:13C(6)15N(2) (H)">mTRAQ:13C(6)15N(2) (H)</option>
-        <option value="mTRAQ:13C(6)15N(2) (K)">mTRAQ:13C(6)15N(2) (K)</option>
-        <option value="mTRAQ:13C(6)15N(2) (N-term)">mTRAQ:13C(6)15N(2) (N-term)</option>
-        <option value="mTRAQ:13C(6)15N(2) (S)">mTRAQ:13C(6)15N(2) (S)</option>
-        <option value="mTRAQ:13C(6)15N(2) (T)">mTRAQ:13C(6)15N(2) (T)</option>
-        <option value="mTRAQ:13C(6)15N(2) (Y)">mTRAQ:13C(6)15N(2) (Y)</option>
-        <option value="MTSL (C)">MTSL (C)</option>
-        <option value="MurNAc (A)">MurNAc (A)</option>
-        <option value="Myristoleyl (Protein N-term G)">Myristoleyl (Protein N-term G)</option>
-        <option value="Myristoyl (C)">Myristoyl (C)</option>
-        <option value="Myristoyl (K)">Myristoyl (K)</option>
-        <option value="Myristoyl (N-term G)">Myristoyl (N-term G)</option>
-        <option value="Myristoyl+Delta:H(-4) (Protein N-term G)">Myristoyl+Delta:H(-4) (Protein N-term G)</option>
-        <option value="N-dimethylphosphate (S)">N-dimethylphosphate (S)</option>
-        <option value="NA-LNO2 (C)">NA-LNO2 (C)</option>
-        <option value="NA-LNO2 (H)">NA-LNO2 (H)</option>
-        <option value="NA-OA-NO2 (C)">NA-OA-NO2 (C)</option>
-        <option value="NA-OA-NO2 (H)">NA-OA-NO2 (H)</option>
-        <option value="NBS (W)">NBS (W)</option>
-        <option value="NBS:13C(6) (W)">NBS:13C(6) (W)</option>
-        <option value="NDA (K)">NDA (K)</option>
-        <option value="NDA (N-term)">NDA (N-term)</option>
-        <option value="NEIAA (C)">NEIAA (C)</option>
-        <option value="NEIAA (Y)">NEIAA (Y)</option>
-        <option value="NEIAA:2H(5) (C)">NEIAA:2H(5) (C)</option>
-        <option value="NEIAA:2H(5) (Y)">NEIAA:2H(5) (Y)</option>
-        <option value="NEM:2H(5) (C)">NEM:2H(5) (C)</option>
-        <option value="NEM:2H(5)+H2O (C)">NEM:2H(5)+H2O (C)</option>
-        <option value="NEMsulfur (C)">NEMsulfur (C)</option>
-        <option value="NEMsulfurWater (C)">NEMsulfurWater (C)</option>
-        <option value="Nethylmaleimide (C)">Nethylmaleimide (C)</option>
-        <option value="Nethylmaleimide+water (C)">Nethylmaleimide+water (C)</option>
-        <option value="Nethylmaleimide+water (K)">Nethylmaleimide+water (K)</option>
-        <option value="NeuAc (N)">NeuAc (N)</option>
-        <option value="NeuAc (S)">NeuAc (S)</option>
-        <option value="NeuAc (T)">NeuAc (T)</option>
-        <option value="NeuGc (N)">NeuGc (N)</option>
-        <option value="NeuGc (S)">NeuGc (S)</option>
-        <option value="NeuGc (T)">NeuGc (T)</option>
-        <option value="NHS-fluorescein (K)">NHS-fluorescein (K)</option>
-        <option value="NHS-LC-Biotin (K)">NHS-LC-Biotin (K)</option>
-        <option value="NHS-LC-Biotin (N-term)">NHS-LC-Biotin (N-term)</option>
-        <option value="NIC (K)">NIC (K)</option>
-        <option value="NIC (N-term)">NIC (N-term)</option>
-        <option value="NIPCAM (C)">NIPCAM (C)</option>
-        <option value="Nitrene (Y)">Nitrene (Y)</option>
-        <option value="Nitro (F)">Nitro (F)</option>
-        <option value="Nitro (W)">Nitro (W)</option>
-        <option value="Nitro (Y)">Nitro (Y)</option>
-        <option value="Nitrosyl (C)">Nitrosyl (C)</option>
-        <option value="Nitrosyl (Y)">Nitrosyl (Y)</option>
-        <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
-        <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
-        <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
-        <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
-        <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-        <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
-        <option value="NP40 (N-term)">NP40 (N-term)</option>
-        <option value="NQIGG (K)">NQIGG (K)</option>
-        <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
-        <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
-        <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
-        <option value="O-Et-N-diMePhospho (S)">O-Et-N-diMePhospho (S)</option>
-        <option value="O-Isopropylmethylphosphonate (S)">O-Isopropylmethylphosphonate (S)</option>
-        <option value="O-Isopropylmethylphosphonate (T)">O-Isopropylmethylphosphonate (T)</option>
-        <option value="O-Isopropylmethylphosphonate (Y)">O-Isopropylmethylphosphonate (Y)</option>
-        <option value="O-Methylphosphate (S)">O-Methylphosphate (S)</option>
-        <option value="O-Methylphosphate (T)">O-Methylphosphate (T)</option>
-        <option value="O-Methylphosphate (Y)">O-Methylphosphate (Y)</option>
-        <option value="O-pinacolylmethylphosphonate (H)">O-pinacolylmethylphosphonate (H)</option>
-        <option value="O-pinacolylmethylphosphonate (K)">O-pinacolylmethylphosphonate (K)</option>
-        <option value="O-pinacolylmethylphosphonate (S)">O-pinacolylmethylphosphonate (S)</option>
-        <option value="O-pinacolylmethylphosphonate (T)">O-pinacolylmethylphosphonate (T)</option>
-        <option value="O-pinacolylmethylphosphonate (Y)">O-pinacolylmethylphosphonate (Y)</option>
-        <option value="Octanoyl (C)">Octanoyl (C)</option>
-        <option value="Octanoyl (S)">Octanoyl (S)</option>
-        <option value="Octanoyl (T)">Octanoyl (T)</option>
-        <option value="OxArgBiotin (R)">OxArgBiotin (R)</option>
-        <option value="OxArgBiotinRed (R)">OxArgBiotinRed (R)</option>
-        <option value="Oxidation (C)">Oxidation (C)</option>
-        <option value="Oxidation (C-term G)">Oxidation (C-term G)</option>
-        <option value="Oxidation (D)">Oxidation (D)</option>
-        <option value="Oxidation (E)">Oxidation (E)</option>
-        <option value="Oxidation (F)">Oxidation (F)</option>
-        <option value="Oxidation (H)">Oxidation (H)</option>
-        <option value="Oxidation (I)">Oxidation (I)</option>
-        <option value="Oxidation (K)">Oxidation (K)</option>
-        <option value="Oxidation (L)">Oxidation (L)</option>
-        <option value="Oxidation (M)">Oxidation (M)</option>
-        <option value="Oxidation (N)">Oxidation (N)</option>
-        <option value="Oxidation (P)">Oxidation (P)</option>
-        <option value="Oxidation (Q)">Oxidation (Q)</option>
-        <option value="Oxidation (R)">Oxidation (R)</option>
-        <option value="Oxidation (S)">Oxidation (S)</option>
-        <option value="Oxidation (T)">Oxidation (T)</option>
-        <option value="Oxidation (U)">Oxidation (U)</option>
-        <option value="Oxidation (V)">Oxidation (V)</option>
-        <option value="Oxidation (W)">Oxidation (W)</option>
-        <option value="Oxidation (Y)">Oxidation (Y)</option>
-        <option value="Oxidation+NEM (C)">Oxidation+NEM (C)</option>
-        <option value="OxLysBiotin (K)">OxLysBiotin (K)</option>
-        <option value="OxLysBiotinRed (K)">OxLysBiotinRed (K)</option>
-        <option value="OxProBiotin (P)">OxProBiotin (P)</option>
-        <option value="OxProBiotinRed (P)">OxProBiotinRed (P)</option>
-        <option value="Palmitoleyl (C)">Palmitoleyl (C)</option>
-        <option value="Palmitoleyl (S)">Palmitoleyl (S)</option>
-        <option value="Palmitoleyl (T)">Palmitoleyl (T)</option>
-        <option value="Palmitoyl (C)">Palmitoyl (C)</option>
-        <option value="Palmitoyl (K)">Palmitoyl (K)</option>
-        <option value="Palmitoyl (Protein N-term)">Palmitoyl (Protein N-term)</option>
-        <option value="Palmitoyl (S)">Palmitoyl (S)</option>
-        <option value="Palmitoyl (T)">Palmitoyl (T)</option>
-        <option value="PEITC (C)">PEITC (C)</option>
-        <option value="PEITC (K)">PEITC (K)</option>
-        <option value="PEITC (N-term)">PEITC (N-term)</option>
-        <option value="Pent(1)HexNAc(1) (S)">Pent(1)HexNAc(1) (S)</option>
-        <option value="Pent(1)HexNAc(1) (T)">Pent(1)HexNAc(1) (T)</option>
-        <option value="Pent(2) (S)">Pent(2) (S)</option>
-        <option value="Pent(2) (T)">Pent(2) (T)</option>
-        <option value="Pentose (S)">Pentose (S)</option>
-        <option value="Pentose (T)">Pentose (T)</option>
-        <option value="Pentylamine (Q)">Pentylamine (Q)</option>
-        <option value="PEO-Iodoacetyl-LC-Biotin (C)">PEO-Iodoacetyl-LC-Biotin (C)</option>
-        <option value="PET (S)">PET (S)</option>
-        <option value="PET (T)">PET (T)</option>
-        <option value="Phe-&gt;Ala (F)">Phe-&gt;Ala (F)</option>
-        <option value="Phe-&gt;Arg (F)">Phe-&gt;Arg (F)</option>
-        <option value="Phe-&gt;Asn (F)">Phe-&gt;Asn (F)</option>
-        <option value="Phe-&gt;Asp (F)">Phe-&gt;Asp (F)</option>
-        <option value="Phe-&gt;CamCys (F)">Phe-&gt;CamCys (F)</option>
-        <option value="Phe-&gt;Cys (F)">Phe-&gt;Cys (F)</option>
-        <option value="Phe-&gt;Gln (F)">Phe-&gt;Gln (F)</option>
-        <option value="Phe-&gt;Glu (F)">Phe-&gt;Glu (F)</option>
-        <option value="Phe-&gt;Gly (F)">Phe-&gt;Gly (F)</option>
-        <option value="Phe-&gt;His (F)">Phe-&gt;His (F)</option>
-        <option value="Phe-&gt;Lys (F)">Phe-&gt;Lys (F)</option>
-        <option value="Phe-&gt;Met (F)">Phe-&gt;Met (F)</option>
-        <option value="Phe-&gt;Pro (F)">Phe-&gt;Pro (F)</option>
-        <option value="Phe-&gt;Ser (F)">Phe-&gt;Ser (F)</option>
-        <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
-        <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
-        <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
-        <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
-        <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
-        <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
-        <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
-        <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
-        <option value="Phospho (C)">Phospho (C)</option>
-        <option value="Phospho (D)">Phospho (D)</option>
-        <option value="Phospho (E)">Phospho (E)</option>
-        <option value="Phospho (H)">Phospho (H)</option>
-        <option value="Phospho (K)">Phospho (K)</option>
-        <option value="Phospho (R)">Phospho (R)</option>
-        <option value="Phospho (S)">Phospho (S)</option>
-        <option value="Phospho (T)">Phospho (T)</option>
-        <option value="Phospho (Y)">Phospho (Y)</option>
-        <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
-        <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
-        <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
-        <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
-        <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
-        <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
-        <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
-        <option value="Phosphogluconoylation (K)">Phosphogluconoylation (K)</option>
-        <option value="Phosphogluconoylation (N-term)">Phosphogluconoylation (N-term)</option>
-        <option value="Phosphoguanosine (H)">Phosphoguanosine (H)</option>
-        <option value="Phosphoguanosine (K)">Phosphoguanosine (K)</option>
-        <option value="PhosphoHex (S)">PhosphoHex (S)</option>
-        <option value="PhosphoHex (T)">PhosphoHex (T)</option>
-        <option value="PhosphoHex(2) (N)">PhosphoHex(2) (N)</option>
-        <option value="PhosphoHex(2) (S)">PhosphoHex(2) (S)</option>
-        <option value="PhosphoHex(2) (T)">PhosphoHex(2) (T)</option>
-        <option value="PhosphoHexNAc (S)">PhosphoHexNAc (S)</option>
-        <option value="PhosphoHexNAc (T)">PhosphoHexNAc (T)</option>
-        <option value="Phosphopantetheine (S)">Phosphopantetheine (S)</option>
-        <option value="Phosphopropargyl (S)">Phosphopropargyl (S)</option>
-        <option value="Phosphopropargyl (T)">Phosphopropargyl (T)</option>
-        <option value="Phosphopropargyl (Y)">Phosphopropargyl (Y)</option>
-        <option value="phosphoRibosyl (D)">phosphoRibosyl (D)</option>
-        <option value="phosphoRibosyl (E)">phosphoRibosyl (E)</option>
-        <option value="phosphoRibosyl (R)">phosphoRibosyl (R)</option>
-        <option value="PhosphoribosyldephosphoCoA (S)">PhosphoribosyldephosphoCoA (S)</option>
-        <option value="PhosphoUridine (H)">PhosphoUridine (H)</option>
-        <option value="PhosphoUridine (Y)">PhosphoUridine (Y)</option>
-        <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
-        <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
-        <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
-        <option value="Piperidine (K)">Piperidine (K)</option>
-        <option value="Piperidine (N-term)">Piperidine (N-term)</option>
-        <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
-        <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
-        <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
-        <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
-        <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
-        <option value="Pro-&gt;Gln (P)">Pro-&gt;Gln (P)</option>
-        <option value="Pro-&gt;Glu (P)">Pro-&gt;Glu (P)</option>
-        <option value="Pro-&gt;Gly (P)">Pro-&gt;Gly (P)</option>
-        <option value="Pro-&gt;HAVA (P)">Pro-&gt;HAVA (P)</option>
-        <option value="Pro-&gt;His (P)">Pro-&gt;His (P)</option>
-        <option value="Pro-&gt;Lys (P)">Pro-&gt;Lys (P)</option>
-        <option value="Pro-&gt;Met (P)">Pro-&gt;Met (P)</option>
-        <option value="Pro-&gt;Phe (P)">Pro-&gt;Phe (P)</option>
-        <option value="Pro-&gt;pyro-Glu (P)">Pro-&gt;pyro-Glu (P)</option>
-        <option value="Pro-&gt;Pyrrolidinone (P)">Pro-&gt;Pyrrolidinone (P)</option>
-        <option value="Pro-&gt;Pyrrolidone (P)">Pro-&gt;Pyrrolidone (P)</option>
-        <option value="Pro-&gt;Ser (P)">Pro-&gt;Ser (P)</option>
-        <option value="Pro-&gt;Thr (P)">Pro-&gt;Thr (P)</option>
-        <option value="Pro-&gt;Trp (P)">Pro-&gt;Trp (P)</option>
-        <option value="Pro-&gt;Tyr (P)">Pro-&gt;Tyr (P)</option>
-        <option value="Pro-&gt;Val (P)">Pro-&gt;Val (P)</option>
-        <option value="Pro-&gt;Xle (P)">Pro-&gt;Xle (P)</option>
-        <option value="probiotinhydrazide (P)">probiotinhydrazide (P)</option>
-        <option value="Propargylamine (C-term)">Propargylamine (C-term)</option>
-        <option value="Propargylamine (D)">Propargylamine (D)</option>
-        <option value="Propargylamine (E)">Propargylamine (E)</option>
-        <option value="Propionamide (C)">Propionamide (C)</option>
-        <option value="Propionamide (K)">Propionamide (K)</option>
-        <option value="Propionamide (N-term)">Propionamide (N-term)</option>
-        <option value="Propionamide:2H(3) (C)">Propionamide:2H(3) (C)</option>
-        <option value="Propionyl (K)">Propionyl (K)</option>
-        <option value="Propionyl (N-term)">Propionyl (N-term)</option>
-        <option value="Propionyl (Protein N-term)">Propionyl (Protein N-term)</option>
-        <option value="Propionyl (S)">Propionyl (S)</option>
-        <option value="Propionyl (T)">Propionyl (T)</option>
-        <option value="Propionyl:13C(3) (K)">Propionyl:13C(3) (K)</option>
-        <option value="Propionyl:13C(3) (N-term)">Propionyl:13C(3) (N-term)</option>
-        <option value="Propiophenone (C)">Propiophenone (C)</option>
-        <option value="Propiophenone (H)">Propiophenone (H)</option>
-        <option value="Propiophenone (K)">Propiophenone (K)</option>
-        <option value="Propiophenone (R)">Propiophenone (R)</option>
-        <option value="Propiophenone (S)">Propiophenone (S)</option>
-        <option value="Propiophenone (T)">Propiophenone (T)</option>
-        <option value="Propiophenone (W)">Propiophenone (W)</option>
-        <option value="Propyl (C-term)">Propyl (C-term)</option>
-        <option value="Propyl (D)">Propyl (D)</option>
-        <option value="Propyl (E)">Propyl (E)</option>
-        <option value="Propyl (K)">Propyl (K)</option>
-        <option value="Propyl (N-term)">Propyl (N-term)</option>
-        <option value="Propyl (Protein C-term)">Propyl (Protein C-term)</option>
-        <option value="Propyl:2H(6) (K)">Propyl:2H(6) (K)</option>
-        <option value="Propyl:2H(6) (N-term)">Propyl:2H(6) (N-term)</option>
-        <option value="PropylNAGthiazoline (C)">PropylNAGthiazoline (C)</option>
-        <option value="PS_Hapten (C)">PS_Hapten (C)</option>
-        <option value="PS_Hapten (H)">PS_Hapten (H)</option>
-        <option value="PS_Hapten (K)">PS_Hapten (K)</option>
-        <option value="pupylation (K)">pupylation (K)</option>
-        <option value="Puromycin (C-term)">Puromycin (C-term)</option>
-        <option value="PyMIC (N-term)">PyMIC (N-term)</option>
-        <option value="PyridoxalPhosphate (K)">PyridoxalPhosphate (K)</option>
-        <option value="PyridoxalPhosphateH2 (K)">PyridoxalPhosphateH2 (K)</option>
-        <option value="Pyridylacetyl (K)">Pyridylacetyl (K)</option>
-        <option value="Pyridylacetyl (N-term)">Pyridylacetyl (N-term)</option>
-        <option value="Pyridylethyl (C)">Pyridylethyl (C)</option>
-        <option value="Pyro-carbamidomethyl (N-term C)">Pyro-carbamidomethyl (N-term C)</option>
-        <option value="pyrophospho (S)">pyrophospho (S)</option>
-        <option value="pyrophospho (T)">pyrophospho (T)</option>
-        <option value="PyruvicAcidIminyl (K)">PyruvicAcidIminyl (K)</option>
-        <option value="PyruvicAcidIminyl (Protein N-term C)">PyruvicAcidIminyl (Protein N-term C)</option>
-        <option value="PyruvicAcidIminyl (Protein N-term V)">PyruvicAcidIminyl (Protein N-term V)</option>
-        <option value="QAT (C)">QAT (C)</option>
-        <option value="QAT:2H(3) (C)">QAT:2H(3) (C)</option>
-        <option value="QEQTGG (K)">QEQTGG (K)</option>
-        <option value="QQQTGG (K)">QQQTGG (K)</option>
-        <option value="QTGG (K)">QTGG (K)</option>
-        <option value="Quinone (W)">Quinone (W)</option>
-        <option value="Quinone (Y)">Quinone (Y)</option>
-        <option value="Retinylidene (K)">Retinylidene (K)</option>
-        <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
-        <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
-        <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-        <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-        <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-        <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-        <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-        <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-        <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-        <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-        <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
-        <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
-        <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
-        <option value="Saligenin (H)">Saligenin (H)</option>
-        <option value="Saligenin (K)">Saligenin (K)</option>
-        <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
-        <option value="Ser-&gt;Arg (S)">Ser-&gt;Arg (S)</option>
-        <option value="Ser-&gt;Asn (S)">Ser-&gt;Asn (S)</option>
-        <option value="Ser-&gt;Asp (S)">Ser-&gt;Asp (S)</option>
-        <option value="Ser-&gt;Cys (S)">Ser-&gt;Cys (S)</option>
-        <option value="Ser-&gt;Gln (S)">Ser-&gt;Gln (S)</option>
-        <option value="Ser-&gt;Glu (S)">Ser-&gt;Glu (S)</option>
-        <option value="Ser-&gt;Gly (S)">Ser-&gt;Gly (S)</option>
-        <option value="Ser-&gt;His (S)">Ser-&gt;His (S)</option>
-        <option value="Ser-&gt;LacticAcid (Protein N-term S)">Ser-&gt;LacticAcid (Protein N-term S)</option>
-        <option value="Ser-&gt;Lys (S)">Ser-&gt;Lys (S)</option>
-        <option value="Ser-&gt;Met (S)">Ser-&gt;Met (S)</option>
-        <option value="Ser-&gt;Phe (S)">Ser-&gt;Phe (S)</option>
-        <option value="Ser-&gt;Pro (S)">Ser-&gt;Pro (S)</option>
-        <option value="Ser-&gt;Thr (S)">Ser-&gt;Thr (S)</option>
-        <option value="Ser-&gt;Trp (S)">Ser-&gt;Trp (S)</option>
-        <option value="Ser-&gt;Tyr (S)">Ser-&gt;Tyr (S)</option>
-        <option value="Ser-&gt;Val (S)">Ser-&gt;Val (S)</option>
-        <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
-        <option value="serotonylation (Q)">serotonylation (Q)</option>
-        <option value="shTMT (K)">shTMT (K)</option>
-        <option value="shTMT (N-term)">shTMT (N-term)</option>
-        <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
-        <option value="SMA (K)">SMA (K)</option>
-        <option value="SMA (N-term)">SMA (N-term)</option>
-        <option value="spermidine (Q)">spermidine (Q)</option>
-        <option value="spermine (Q)">spermine (Q)</option>
-        <option value="SPITC (K)">SPITC (K)</option>
-        <option value="SPITC (N-term)">SPITC (N-term)</option>
-        <option value="SPITC:13C(6) (K)">SPITC:13C(6) (K)</option>
-        <option value="SPITC:13C(6) (N-term)">SPITC:13C(6) (N-term)</option>
-        <option value="Succinyl (K)">Succinyl (K)</option>
-        <option value="Succinyl (N-term)">Succinyl (N-term)</option>
-        <option value="Succinyl (Protein N-term)">Succinyl (Protein N-term)</option>
-        <option value="Succinyl:13C(4) (K)">Succinyl:13C(4) (K)</option>
-        <option value="Succinyl:13C(4) (N-term)">Succinyl:13C(4) (N-term)</option>
-        <option value="Succinyl:2H(4) (K)">Succinyl:2H(4) (K)</option>
-        <option value="Succinyl:2H(4) (N-term)">Succinyl:2H(4) (N-term)</option>
-        <option value="SulfanilicAcid (C-term)">SulfanilicAcid (C-term)</option>
-        <option value="SulfanilicAcid (D)">SulfanilicAcid (D)</option>
-        <option value="SulfanilicAcid (E)">SulfanilicAcid (E)</option>
-        <option value="SulfanilicAcid:13C(6) (C-term)">SulfanilicAcid:13C(6) (C-term)</option>
-        <option value="SulfanilicAcid:13C(6) (D)">SulfanilicAcid:13C(6) (D)</option>
-        <option value="SulfanilicAcid:13C(6) (E)">SulfanilicAcid:13C(6) (E)</option>
-        <option value="Sulfide (C)">Sulfide (C)</option>
-        <option value="Sulfide (D)">Sulfide (D)</option>
-        <option value="Sulfide (W)">Sulfide (W)</option>
-        <option value="Sulfo (C)">Sulfo (C)</option>
-        <option value="Sulfo (S)">Sulfo (S)</option>
-        <option value="Sulfo (T)">Sulfo (T)</option>
-        <option value="Sulfo (Y)">Sulfo (Y)</option>
-        <option value="sulfo+amino (Y)">sulfo+amino (Y)</option>
-        <option value="Sulfo-NHS-LC-LC-Biotin (K)">Sulfo-NHS-LC-LC-Biotin (K)</option>
-        <option value="Sulfo-NHS-LC-LC-Biotin (N-term)">Sulfo-NHS-LC-LC-Biotin (N-term)</option>
-        <option value="SulfoGMBS (C)">SulfoGMBS (C)</option>
-        <option value="SulfurDioxide (C)">SulfurDioxide (C)</option>
-        <option value="SUMO2135 (K)">SUMO2135 (K)</option>
-        <option value="SUMO3549 (K)">SUMO3549 (K)</option>
-        <option value="TAMRA-FP (S)">TAMRA-FP (S)</option>
-        <option value="TAMRA-FP (Y)">TAMRA-FP (Y)</option>
-        <option value="Thiadiazole (C)">Thiadiazole (C)</option>
-        <option value="Thiazolidine (C)">Thiazolidine (C)</option>
-        <option value="Thiazolidine (F)">Thiazolidine (F)</option>
-        <option value="Thiazolidine (H)">Thiazolidine (H)</option>
-        <option value="Thiazolidine (K)">Thiazolidine (K)</option>
-        <option value="Thiazolidine (Protein N-term)">Thiazolidine (Protein N-term)</option>
-        <option value="Thiazolidine (R)">Thiazolidine (R)</option>
-        <option value="Thiazolidine (W)">Thiazolidine (W)</option>
-        <option value="Thiazolidine (Y)">Thiazolidine (Y)</option>
-        <option value="thioacylPA (K)">thioacylPA (K)</option>
-        <option value="Thiophos-S-S-biotin (S)">Thiophos-S-S-biotin (S)</option>
-        <option value="Thiophos-S-S-biotin (T)">Thiophos-S-S-biotin (T)</option>
-        <option value="Thiophos-S-S-biotin (Y)">Thiophos-S-S-biotin (Y)</option>
-        <option value="Thiophospho (S)">Thiophospho (S)</option>
-        <option value="Thiophospho (T)">Thiophospho (T)</option>
-        <option value="Thiophospho (Y)">Thiophospho (Y)</option>
-        <option value="Thr-&gt;Ala (T)">Thr-&gt;Ala (T)</option>
-        <option value="Thr-&gt;Arg (T)">Thr-&gt;Arg (T)</option>
-        <option value="Thr-&gt;Asn (T)">Thr-&gt;Asn (T)</option>
-        <option value="Thr-&gt;Asp (T)">Thr-&gt;Asp (T)</option>
-        <option value="Thr-&gt;Cys (T)">Thr-&gt;Cys (T)</option>
-        <option value="Thr-&gt;Gln (T)">Thr-&gt;Gln (T)</option>
-        <option value="Thr-&gt;Glu (T)">Thr-&gt;Glu (T)</option>
-        <option value="Thr-&gt;Gly (T)">Thr-&gt;Gly (T)</option>
-        <option value="Thr-&gt;His (T)">Thr-&gt;His (T)</option>
-        <option value="Thr-&gt;Lys (T)">Thr-&gt;Lys (T)</option>
-        <option value="Thr-&gt;Met (T)">Thr-&gt;Met (T)</option>
-        <option value="Thr-&gt;Phe (T)">Thr-&gt;Phe (T)</option>
-        <option value="Thr-&gt;Pro (T)">Thr-&gt;Pro (T)</option>
-        <option value="Thr-&gt;Ser (T)">Thr-&gt;Ser (T)</option>
-        <option value="Thr-&gt;Trp (T)">Thr-&gt;Trp (T)</option>
-        <option value="Thr-&gt;Tyr (T)">Thr-&gt;Tyr (T)</option>
-        <option value="Thr-&gt;Val (T)">Thr-&gt;Val (T)</option>
-        <option value="Thr-&gt;Xle (T)">Thr-&gt;Xle (T)</option>
-        <option value="Thrbiotinhydrazide (T)">Thrbiotinhydrazide (T)</option>
-        <option value="Thyroxine (Y)">Thyroxine (Y)</option>
-        <option value="TMAB (K)">TMAB (K)</option>
-        <option value="TMAB (N-term)">TMAB (N-term)</option>
-        <option value="TMAB:2H(9) (K)">TMAB:2H(9) (K)</option>
-        <option value="TMAB:2H(9) (N-term)">TMAB:2H(9) (N-term)</option>
-        <option value="TMPP-Ac (K)">TMPP-Ac (K)</option>
-        <option value="TMPP-Ac (N-term)">TMPP-Ac (N-term)</option>
-        <option value="TMPP-Ac (Y)">TMPP-Ac (Y)</option>
-        <option value="TMPP-Ac:13C(9) (K)">TMPP-Ac:13C(9) (K)</option>
-        <option value="TMPP-Ac:13C(9) (N-term)">TMPP-Ac:13C(9) (N-term)</option>
-        <option value="TMPP-Ac:13C(9) (Y)">TMPP-Ac:13C(9) (Y)</option>
-        <option value="TMT (H)">TMT (H)</option>
-        <option value="TMT (K)">TMT (K)</option>
-        <option value="TMT (N-term)">TMT (N-term)</option>
-        <option value="TMT (Protein N-term)">TMT (Protein N-term)</option>
-        <option value="TMT (S)">TMT (S)</option>
-        <option value="TMT (T)">TMT (T)</option>
-        <option value="TMT2plex (H)">TMT2plex (H)</option>
-        <option value="TMT2plex (K)">TMT2plex (K)</option>
-        <option value="TMT2plex (N-term)">TMT2plex (N-term)</option>
-        <option value="TMT2plex (Protein N-term)">TMT2plex (Protein N-term)</option>
-        <option value="TMT2plex (S)">TMT2plex (S)</option>
-        <option value="TMT2plex (T)">TMT2plex (T)</option>
-        <option value="TMT6plex (H)">TMT6plex (H)</option>
-        <option value="TMT6plex (K)">TMT6plex (K)</option>
-        <option value="TMT6plex (N-term)">TMT6plex (N-term)</option>
-        <option value="TMT6plex (Protein N-term)">TMT6plex (Protein N-term)</option>
-        <option value="TMT6plex (S)">TMT6plex (S)</option>
-        <option value="TMT6plex (T)">TMT6plex (T)</option>
-        <option value="TMTpro (H)">TMTpro (H)</option>
-        <option value="TMTpro (K)">TMTpro (K)</option>
-        <option value="TMTpro (N-term)">TMTpro (N-term)</option>
-        <option value="TMTpro (Protein N-term)">TMTpro (Protein N-term)</option>
-        <option value="TMTpro (S)">TMTpro (S)</option>
-        <option value="TMTpro (T)">TMTpro (T)</option>
-        <option value="TMTpro_zero (H)">TMTpro_zero (H)</option>
-        <option value="TMTpro_zero (K)">TMTpro_zero (K)</option>
-        <option value="TMTpro_zero (N-term)">TMTpro_zero (N-term)</option>
-        <option value="TMTpro_zero (Protein N-term)">TMTpro_zero (Protein N-term)</option>
-        <option value="TMTpro_zero (S)">TMTpro_zero (S)</option>
-        <option value="TMTpro_zero (T)">TMTpro_zero (T)</option>
-        <option value="TNBS (K)">TNBS (K)</option>
-        <option value="TNBS (N-term)">TNBS (N-term)</option>
-        <option value="trifluoro (L)">trifluoro (L)</option>
-        <option value="Triiodo (Y)">Triiodo (Y)</option>
-        <option value="Triiodothyronine (Y)">Triiodothyronine (Y)</option>
-        <option value="Trimethyl (K)">Trimethyl (K)</option>
-        <option value="Trimethyl (Protein N-term A)">Trimethyl (Protein N-term A)</option>
-        <option value="Trimethyl (R)">Trimethyl (R)</option>
-        <option value="Trimethyl:13C(3)2H(9) (K)">Trimethyl:13C(3)2H(9) (K)</option>
-        <option value="Trimethyl:13C(3)2H(9) (R)">Trimethyl:13C(3)2H(9) (R)</option>
-        <option value="Trimethyl:2H(9) (K)">Trimethyl:2H(9) (K)</option>
-        <option value="Trimethyl:2H(9) (R)">Trimethyl:2H(9) (R)</option>
-        <option value="Trioxidation (C)">Trioxidation (C)</option>
-        <option value="Trioxidation (F)">Trioxidation (F)</option>
-        <option value="Trioxidation (W)">Trioxidation (W)</option>
-        <option value="Trioxidation (Y)">Trioxidation (Y)</option>
-        <option value="Tripalmitate (Protein N-term C)">Tripalmitate (Protein N-term C)</option>
-        <option value="Tris (N)">Tris (N)</option>
-        <option value="Triton (C-term)">Triton (C-term)</option>
-        <option value="Triton (N-term)">Triton (N-term)</option>
-        <option value="Trp-&gt;Ala (W)">Trp-&gt;Ala (W)</option>
-        <option value="Trp-&gt;Arg (W)">Trp-&gt;Arg (W)</option>
-        <option value="Trp-&gt;Asn (W)">Trp-&gt;Asn (W)</option>
-        <option value="Trp-&gt;Asp (W)">Trp-&gt;Asp (W)</option>
-        <option value="Trp-&gt;Cys (W)">Trp-&gt;Cys (W)</option>
-        <option value="Trp-&gt;Gln (W)">Trp-&gt;Gln (W)</option>
-        <option value="Trp-&gt;Glu (W)">Trp-&gt;Glu (W)</option>
-        <option value="Trp-&gt;Gly (W)">Trp-&gt;Gly (W)</option>
-        <option value="Trp-&gt;His (W)">Trp-&gt;His (W)</option>
-        <option value="Trp-&gt;Hydroxykynurenin (W)">Trp-&gt;Hydroxykynurenin (W)</option>
-        <option value="Trp-&gt;Kynurenin (W)">Trp-&gt;Kynurenin (W)</option>
-        <option value="Trp-&gt;Lys (W)">Trp-&gt;Lys (W)</option>
-        <option value="Trp-&gt;Met (W)">Trp-&gt;Met (W)</option>
-        <option value="Trp-&gt;Oxolactone (W)">Trp-&gt;Oxolactone (W)</option>
-        <option value="Trp-&gt;Phe (W)">Trp-&gt;Phe (W)</option>
-        <option value="Trp-&gt;Pro (W)">Trp-&gt;Pro (W)</option>
-        <option value="Trp-&gt;Ser (W)">Trp-&gt;Ser (W)</option>
-        <option value="Trp-&gt;Thr (W)">Trp-&gt;Thr (W)</option>
-        <option value="Trp-&gt;Tyr (W)">Trp-&gt;Tyr (W)</option>
-        <option value="Trp-&gt;Val (W)">Trp-&gt;Val (W)</option>
-        <option value="Trp-&gt;Xle (W)">Trp-&gt;Xle (W)</option>
-        <option value="Tween20 (N-term)">Tween20 (N-term)</option>
-        <option value="Tween80 (C-term)">Tween80 (C-term)</option>
-        <option value="Tyr-&gt;Ala (Y)">Tyr-&gt;Ala (Y)</option>
-        <option value="Tyr-&gt;Arg (Y)">Tyr-&gt;Arg (Y)</option>
-        <option value="Tyr-&gt;Asn (Y)">Tyr-&gt;Asn (Y)</option>
-        <option value="Tyr-&gt;Asp (Y)">Tyr-&gt;Asp (Y)</option>
-        <option value="Tyr-&gt;Cys (Y)">Tyr-&gt;Cys (Y)</option>
-        <option value="Tyr-&gt;Dha (Y)">Tyr-&gt;Dha (Y)</option>
-        <option value="Tyr-&gt;Gln (Y)">Tyr-&gt;Gln (Y)</option>
-        <option value="Tyr-&gt;Glu (Y)">Tyr-&gt;Glu (Y)</option>
-        <option value="Tyr-&gt;Gly (Y)">Tyr-&gt;Gly (Y)</option>
-        <option value="Tyr-&gt;His (Y)">Tyr-&gt;His (Y)</option>
-        <option value="Tyr-&gt;Lys (Y)">Tyr-&gt;Lys (Y)</option>
-        <option value="Tyr-&gt;Met (Y)">Tyr-&gt;Met (Y)</option>
-        <option value="Tyr-&gt;Phe (Y)">Tyr-&gt;Phe (Y)</option>
-        <option value="Tyr-&gt;Pro (Y)">Tyr-&gt;Pro (Y)</option>
-        <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
-        <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
-        <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
-        <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
-        <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-        <option value="Ub-amide (C)">Ub-amide (C)</option>
-        <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
-        <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
-        <option value="Ub-VME (C)">Ub-VME (C)</option>
-        <option value="UgiJoullie (D)">UgiJoullie (D)</option>
-        <option value="UgiJoullie (E)">UgiJoullie (E)</option>
-        <option value="UgiJoullieProGly (D)">UgiJoullieProGly (D)</option>
-        <option value="UgiJoullieProGly (E)">UgiJoullieProGly (E)</option>
-        <option value="UgiJoullieProGlyProGly (D)">UgiJoullieProGlyProGly (D)</option>
-        <option value="UgiJoullieProGlyProGly (E)">UgiJoullieProGlyProGly (E)</option>
-        <option value="Unknown:162 (C-term)">Unknown:162 (C-term)</option>
-        <option value="Unknown:162 (D)">Unknown:162 (D)</option>
-        <option value="Unknown:162 (E)">Unknown:162 (E)</option>
-        <option value="Unknown:162 (N-term)">Unknown:162 (N-term)</option>
-        <option value="Unknown:177 (C-term)">Unknown:177 (C-term)</option>
-        <option value="Unknown:177 (D)">Unknown:177 (D)</option>
-        <option value="Unknown:177 (E)">Unknown:177 (E)</option>
-        <option value="Unknown:177 (N-term)">Unknown:177 (N-term)</option>
-        <option value="Unknown:210 (C-term)">Unknown:210 (C-term)</option>
-        <option value="Unknown:210 (D)">Unknown:210 (D)</option>
-        <option value="Unknown:210 (E)">Unknown:210 (E)</option>
-        <option value="Unknown:210 (N-term)">Unknown:210 (N-term)</option>
-        <option value="Unknown:216 (C-term)">Unknown:216 (C-term)</option>
-        <option value="Unknown:216 (D)">Unknown:216 (D)</option>
-        <option value="Unknown:216 (E)">Unknown:216 (E)</option>
-        <option value="Unknown:216 (N-term)">Unknown:216 (N-term)</option>
-        <option value="Unknown:234 (C-term)">Unknown:234 (C-term)</option>
-        <option value="Unknown:234 (D)">Unknown:234 (D)</option>
-        <option value="Unknown:234 (E)">Unknown:234 (E)</option>
-        <option value="Unknown:234 (N-term)">Unknown:234 (N-term)</option>
-        <option value="Unknown:248 (C-term)">Unknown:248 (C-term)</option>
-        <option value="Unknown:248 (D)">Unknown:248 (D)</option>
-        <option value="Unknown:248 (E)">Unknown:248 (E)</option>
-        <option value="Unknown:248 (N-term)">Unknown:248 (N-term)</option>
-        <option value="Unknown:250 (C-term)">Unknown:250 (C-term)</option>
-        <option value="Unknown:250 (D)">Unknown:250 (D)</option>
-        <option value="Unknown:250 (E)">Unknown:250 (E)</option>
-        <option value="Unknown:250 (N-term)">Unknown:250 (N-term)</option>
-        <option value="Unknown:302 (C-term)">Unknown:302 (C-term)</option>
-        <option value="Unknown:302 (D)">Unknown:302 (D)</option>
-        <option value="Unknown:302 (E)">Unknown:302 (E)</option>
-        <option value="Unknown:302 (N-term)">Unknown:302 (N-term)</option>
-        <option value="Unknown:306 (C-term)">Unknown:306 (C-term)</option>
-        <option value="Unknown:306 (D)">Unknown:306 (D)</option>
-        <option value="Unknown:306 (E)">Unknown:306 (E)</option>
-        <option value="Unknown:306 (N-term)">Unknown:306 (N-term)</option>
-        <option value="Unknown:420 (C-term)">Unknown:420 (C-term)</option>
-        <option value="Unknown:420 (N-term)">Unknown:420 (N-term)</option>
-        <option value="Val-&gt;Ala (V)">Val-&gt;Ala (V)</option>
-        <option value="Val-&gt;Arg (V)">Val-&gt;Arg (V)</option>
-        <option value="Val-&gt;Asn (V)">Val-&gt;Asn (V)</option>
-        <option value="Val-&gt;Asp (V)">Val-&gt;Asp (V)</option>
-        <option value="Val-&gt;Cys (V)">Val-&gt;Cys (V)</option>
-        <option value="Val-&gt;Gln (V)">Val-&gt;Gln (V)</option>
-        <option value="Val-&gt;Glu (V)">Val-&gt;Glu (V)</option>
-        <option value="Val-&gt;Gly (V)">Val-&gt;Gly (V)</option>
-        <option value="Val-&gt;His (V)">Val-&gt;His (V)</option>
-        <option value="Val-&gt;Lys (V)">Val-&gt;Lys (V)</option>
-        <option value="Val-&gt;Met (V)">Val-&gt;Met (V)</option>
-        <option value="Val-&gt;Phe (V)">Val-&gt;Phe (V)</option>
-        <option value="Val-&gt;Pro (V)">Val-&gt;Pro (V)</option>
-        <option value="Val-&gt;Ser (V)">Val-&gt;Ser (V)</option>
-        <option value="Val-&gt;Thr (V)">Val-&gt;Thr (V)</option>
-        <option value="Val-&gt;Trp (V)">Val-&gt;Trp (V)</option>
-        <option value="Val-&gt;Tyr (V)">Val-&gt;Tyr (V)</option>
-        <option value="Val-&gt;Xle (V)">Val-&gt;Xle (V)</option>
-        <option value="VFQQQTGG (K)">VFQQQTGG (K)</option>
-        <option value="VIEVYQEQTGG (K)">VIEVYQEQTGG (K)</option>
-        <option value="Withaferin (C)">Withaferin (C)</option>
-        <option value="Xle-&gt;Ala (I)">Xle-&gt;Ala (I)</option>
-        <option value="Xle-&gt;Ala (L)">Xle-&gt;Ala (L)</option>
-        <option value="Xle-&gt;Arg (I)">Xle-&gt;Arg (I)</option>
-        <option value="Xle-&gt;Arg (L)">Xle-&gt;Arg (L)</option>
-        <option value="Xle-&gt;Asn (I)">Xle-&gt;Asn (I)</option>
-        <option value="Xle-&gt;Asn (L)">Xle-&gt;Asn (L)</option>
-        <option value="Xle-&gt;Asp (I)">Xle-&gt;Asp (I)</option>
-        <option value="Xle-&gt;Asp (L)">Xle-&gt;Asp (L)</option>
-        <option value="Xle-&gt;Cys (I)">Xle-&gt;Cys (I)</option>
-        <option value="Xle-&gt;Cys (L)">Xle-&gt;Cys (L)</option>
-        <option value="Xle-&gt;Gln (I)">Xle-&gt;Gln (I)</option>
-        <option value="Xle-&gt;Gln (L)">Xle-&gt;Gln (L)</option>
-        <option value="Xle-&gt;Glu (I)">Xle-&gt;Glu (I)</option>
-        <option value="Xle-&gt;Glu (L)">Xle-&gt;Glu (L)</option>
-        <option value="Xle-&gt;Gly (I)">Xle-&gt;Gly (I)</option>
-        <option value="Xle-&gt;Gly (L)">Xle-&gt;Gly (L)</option>
-        <option value="Xle-&gt;His (I)">Xle-&gt;His (I)</option>
-        <option value="Xle-&gt;His (L)">Xle-&gt;His (L)</option>
-        <option value="Xle-&gt;Lys (I)">Xle-&gt;Lys (I)</option>
-        <option value="Xle-&gt;Lys (L)">Xle-&gt;Lys (L)</option>
-        <option value="Xle-&gt;Met (I)">Xle-&gt;Met (I)</option>
-        <option value="Xle-&gt;Met (L)">Xle-&gt;Met (L)</option>
-        <option value="Xle-&gt;Phe (I)">Xle-&gt;Phe (I)</option>
-        <option value="Xle-&gt;Phe (L)">Xle-&gt;Phe (L)</option>
-        <option value="Xle-&gt;Pro (I)">Xle-&gt;Pro (I)</option>
-        <option value="Xle-&gt;Pro (L)">Xle-&gt;Pro (L)</option>
-        <option value="Xle-&gt;Ser (I)">Xle-&gt;Ser (I)</option>
-        <option value="Xle-&gt;Ser (L)">Xle-&gt;Ser (L)</option>
-        <option value="Xle-&gt;Thr (I)">Xle-&gt;Thr (I)</option>
-        <option value="Xle-&gt;Thr (L)">Xle-&gt;Thr (L)</option>
-        <option value="Xle-&gt;Trp (I)">Xle-&gt;Trp (I)</option>
-        <option value="Xle-&gt;Trp (L)">Xle-&gt;Trp (L)</option>
-        <option value="Xle-&gt;Tyr (I)">Xle-&gt;Tyr (I)</option>
-        <option value="Xle-&gt;Tyr (L)">Xle-&gt;Tyr (L)</option>
-        <option value="Xle-&gt;Val (I)">Xle-&gt;Val (I)</option>
-        <option value="Xle-&gt;Val (L)">Xle-&gt;Val (L)</option>
-        <option value="Xlink:B10621 (C)">Xlink:B10621 (C)</option>
-        <option value="Xlink:BMOE (C)">Xlink:BMOE (C)</option>
-        <option value="Xlink:BS2G[113] (K)">Xlink:BS2G[113] (K)</option>
-        <option value="Xlink:BS2G[113] (Protein N-term)">Xlink:BS2G[113] (Protein N-term)</option>
-        <option value="Xlink:BS2G[114] (K)">Xlink:BS2G[114] (K)</option>
-        <option value="Xlink:BS2G[114] (Protein N-term)">Xlink:BS2G[114] (Protein N-term)</option>
-        <option value="Xlink:BS2G[217] (K)">Xlink:BS2G[217] (K)</option>
-        <option value="Xlink:BS2G[217] (Protein N-term)">Xlink:BS2G[217] (Protein N-term)</option>
-        <option value="Xlink:BS2G[96] (K)">Xlink:BS2G[96] (K)</option>
-        <option value="Xlink:BS2G[96] (Protein N-term)">Xlink:BS2G[96] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[111] (K)">Xlink:BuUrBu[111] (K)</option>
-        <option value="Xlink:BuUrBu[111] (Protein N-term)">Xlink:BuUrBu[111] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[196] (K)">Xlink:BuUrBu[196] (K)</option>
-        <option value="Xlink:BuUrBu[196] (Protein N-term)">Xlink:BuUrBu[196] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[213] (K)">Xlink:BuUrBu[213] (K)</option>
-        <option value="Xlink:BuUrBu[213] (Protein N-term)">Xlink:BuUrBu[213] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[214] (K)">Xlink:BuUrBu[214] (K)</option>
-        <option value="Xlink:BuUrBu[214] (Protein N-term)">Xlink:BuUrBu[214] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[317] (K)">Xlink:BuUrBu[317] (K)</option>
-        <option value="Xlink:BuUrBu[317] (Protein N-term)">Xlink:BuUrBu[317] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[85] (K)">Xlink:BuUrBu[85] (K)</option>
-        <option value="Xlink:BuUrBu[85] (Protein N-term)">Xlink:BuUrBu[85] (Protein N-term)</option>
-        <option value="Xlink:DFDNB (K)">Xlink:DFDNB (K)</option>
-        <option value="Xlink:DFDNB (N)">Xlink:DFDNB (N)</option>
-        <option value="Xlink:DFDNB (Q)">Xlink:DFDNB (Q)</option>
-        <option value="Xlink:DFDNB (R)">Xlink:DFDNB (R)</option>
-        <option value="Xlink:DMP[122] (K)">Xlink:DMP[122] (K)</option>
-        <option value="Xlink:DMP[122] (Protein N-term)">Xlink:DMP[122] (Protein N-term)</option>
-        <option value="Xlink:DMP[139] (K)">Xlink:DMP[139] (K)</option>
-        <option value="Xlink:DMP[139] (Protein N-term)">Xlink:DMP[139] (Protein N-term)</option>
-        <option value="Xlink:DMP[140] (K)">Xlink:DMP[140] (K)</option>
-        <option value="Xlink:DMP[140] (Protein N-term)">Xlink:DMP[140] (Protein N-term)</option>
-        <option value="Xlink:DMP[154] (K)">Xlink:DMP[154] (K)</option>
-        <option value="Xlink:DMP[154] (Protein N-term)">Xlink:DMP[154] (Protein N-term)</option>
-        <option value="Xlink:DSS[138] (K)">Xlink:DSS[138] (K)</option>
-        <option value="Xlink:DSS[138] (Protein N-term)">Xlink:DSS[138] (Protein N-term)</option>
-        <option value="Xlink:DSS[155] (K)">Xlink:DSS[155] (K)</option>
-        <option value="Xlink:DSS[155] (Protein N-term)">Xlink:DSS[155] (Protein N-term)</option>
-        <option value="Xlink:DSS[156] (K)">Xlink:DSS[156] (K)</option>
-        <option value="Xlink:DSS[156] (Protein N-term)">Xlink:DSS[156] (Protein N-term)</option>
-        <option value="Xlink:DSS[259] (K)">Xlink:DSS[259] (K)</option>
-        <option value="Xlink:DSS[259] (Protein N-term)">Xlink:DSS[259] (Protein N-term)</option>
-        <option value="Xlink:DSSO[104] (K)">Xlink:DSSO[104] (K)</option>
-        <option value="Xlink:DSSO[104] (Protein N-term)">Xlink:DSSO[104] (Protein N-term)</option>
-        <option value="Xlink:DSSO[158] (K)">Xlink:DSSO[158] (K)</option>
-        <option value="Xlink:DSSO[158] (Protein N-term)">Xlink:DSSO[158] (Protein N-term)</option>
-        <option value="Xlink:DSSO[175] (K)">Xlink:DSSO[175] (K)</option>
-        <option value="Xlink:DSSO[175] (Protein N-term)">Xlink:DSSO[175] (Protein N-term)</option>
-        <option value="Xlink:DSSO[176] (K)">Xlink:DSSO[176] (K)</option>
-        <option value="Xlink:DSSO[176] (Protein N-term)">Xlink:DSSO[176] (Protein N-term)</option>
-        <option value="Xlink:DSSO[279] (K)">Xlink:DSSO[279] (K)</option>
-        <option value="Xlink:DSSO[279] (Protein N-term)">Xlink:DSSO[279] (Protein N-term)</option>
-        <option value="Xlink:DSSO[54] (K)">Xlink:DSSO[54] (K)</option>
-        <option value="Xlink:DSSO[54] (Protein N-term)">Xlink:DSSO[54] (Protein N-term)</option>
-        <option value="Xlink:DSSO[86] (K)">Xlink:DSSO[86] (K)</option>
-        <option value="Xlink:DSSO[86] (Protein N-term)">Xlink:DSSO[86] (Protein N-term)</option>
-        <option value="Xlink:DST[114] (K)">Xlink:DST[114] (K)</option>
-        <option value="Xlink:DST[114] (Protein N-term)">Xlink:DST[114] (Protein N-term)</option>
-        <option value="Xlink:DST[132] (K)">Xlink:DST[132] (K)</option>
-        <option value="Xlink:DST[132] (Protein N-term)">Xlink:DST[132] (Protein N-term)</option>
-        <option value="Xlink:DST[56] (K)">Xlink:DST[56] (K)</option>
-        <option value="Xlink:DST[56] (Protein N-term)">Xlink:DST[56] (Protein N-term)</option>
-        <option value="Xlink:DTBP[172] (K)">Xlink:DTBP[172] (K)</option>
-        <option value="Xlink:DTBP[172] (Protein N-term)">Xlink:DTBP[172] (Protein N-term)</option>
-        <option value="Xlink:DTBP[87] (K)">Xlink:DTBP[87] (K)</option>
-        <option value="Xlink:DTBP[87] (Protein N-term)">Xlink:DTBP[87] (Protein N-term)</option>
-        <option value="Xlink:DTSSP[174] (K)">Xlink:DTSSP[174] (K)</option>
-        <option value="Xlink:DTSSP[174] (Protein N-term)">Xlink:DTSSP[174] (Protein N-term)</option>
-        <option value="Xlink:DTSSP[192] (K)">Xlink:DTSSP[192] (K)</option>
-        <option value="Xlink:DTSSP[192] (Protein N-term)">Xlink:DTSSP[192] (Protein N-term)</option>
-        <option value="Xlink:DTSSP[88] (K)">Xlink:DTSSP[88] (K)</option>
-        <option value="Xlink:DTSSP[88] (Protein N-term)">Xlink:DTSSP[88] (Protein N-term)</option>
-        <option value="Xlink:EGS[115] (K)">Xlink:EGS[115] (K)</option>
-        <option value="Xlink:EGS[115] (Protein N-term)">Xlink:EGS[115] (Protein N-term)</option>
-        <option value="Xlink:EGS[226] (K)">Xlink:EGS[226] (K)</option>
-        <option value="Xlink:EGS[226] (Protein N-term)">Xlink:EGS[226] (Protein N-term)</option>
-        <option value="Xlink:EGS[244] (K)">Xlink:EGS[244] (K)</option>
-        <option value="Xlink:EGS[244] (Protein N-term)">Xlink:EGS[244] (Protein N-term)</option>
-        <option value="Xlink:SMCC[219] (C)">Xlink:SMCC[219] (C)</option>
-        <option value="Xlink:SMCC[219] (K)">Xlink:SMCC[219] (K)</option>
-        <option value="Xlink:SMCC[219] (Protein N-term)">Xlink:SMCC[219] (Protein N-term)</option>
-        <option value="Xlink:SMCC[237] (C)">Xlink:SMCC[237] (C)</option>
-        <option value="Xlink:SMCC[237] (K)">Xlink:SMCC[237] (K)</option>
-        <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
-        <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
-        <option value="ZGB (K)">ZGB (K)</option>
-        <option value="ZGB (N-term)">ZGB (N-term)</option>
-        <option value="ZQG (K)">ZQG (K)</option>
-        <expand macro="list_string_san" name="fixed_modifications"/>
-      </param>
-      <param name="variable_modifications" argument="-algorithm:variable_modifications" multiple="true" type="select" optional="true" label="variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
-        <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
-        <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
-        <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
-        <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
-        <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
-        <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
-        <option value="2-succinyl (C)">2-succinyl (C)</option>
-        <option value="2HPG (R)">2HPG (R)</option>
-        <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
-        <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
-        <option value="3sulfo (N-term)">3sulfo (N-term)</option>
-        <option value="4-ONE (C)">4-ONE (C)</option>
-        <option value="4-ONE (H)">4-ONE (H)</option>
-        <option value="4-ONE (K)">4-ONE (K)</option>
-        <option value="4-ONE+Delta:H(-2)O(-1) (C)">4-ONE+Delta:H(-2)O(-1) (C)</option>
-        <option value="4-ONE+Delta:H(-2)O(-1) (H)">4-ONE+Delta:H(-2)O(-1) (H)</option>
-        <option value="4-ONE+Delta:H(-2)O(-1) (K)">4-ONE+Delta:H(-2)O(-1) (K)</option>
-        <option value="4AcAllylGal (C)">4AcAllylGal (C)</option>
-        <option value="a-type-ion (C-term)">a-type-ion (C-term)</option>
-        <option value="AccQTag (K)">AccQTag (K)</option>
-        <option value="AccQTag (N-term)">AccQTag (N-term)</option>
-        <option value="Acetyl (C)">Acetyl (C)</option>
-        <option value="Acetyl (H)">Acetyl (H)</option>
-        <option value="Acetyl (K)">Acetyl (K)</option>
-        <option value="Acetyl (N-term)">Acetyl (N-term)</option>
-        <option value="Acetyl (Protein N-term)">Acetyl (Protein N-term)</option>
-        <option value="Acetyl (R)">Acetyl (R)</option>
-        <option value="Acetyl (S)">Acetyl (S)</option>
-        <option value="Acetyl (T)">Acetyl (T)</option>
-        <option value="Acetyl (Y)">Acetyl (Y)</option>
-        <option value="Acetyl:13C(2) (K)">Acetyl:13C(2) (K)</option>
-        <option value="Acetyl:13C(2) (Protein N-term)">Acetyl:13C(2) (Protein N-term)</option>
-        <option value="Acetyl:2H(3) (H)">Acetyl:2H(3) (H)</option>
-        <option value="Acetyl:2H(3) (K)">Acetyl:2H(3) (K)</option>
-        <option value="Acetyl:2H(3) (N-term)">Acetyl:2H(3) (N-term)</option>
-        <option value="Acetyl:2H(3) (Protein N-term)">Acetyl:2H(3) (Protein N-term)</option>
-        <option value="Acetyl:2H(3) (S)">Acetyl:2H(3) (S)</option>
-        <option value="Acetyl:2H(3) (T)">Acetyl:2H(3) (T)</option>
-        <option value="Acetyl:2H(3) (Y)">Acetyl:2H(3) (Y)</option>
-        <option value="Acetyldeoxyhypusine (K)">Acetyldeoxyhypusine (K)</option>
-        <option value="Acetylhypusine (K)">Acetylhypusine (K)</option>
-        <option value="ADP-Ribosyl (C)">ADP-Ribosyl (C)</option>
-        <option value="ADP-Ribosyl (D)">ADP-Ribosyl (D)</option>
-        <option value="ADP-Ribosyl (E)">ADP-Ribosyl (E)</option>
-        <option value="ADP-Ribosyl (K)">ADP-Ribosyl (K)</option>
-        <option value="ADP-Ribosyl (N)">ADP-Ribosyl (N)</option>
-        <option value="ADP-Ribosyl (R)">ADP-Ribosyl (R)</option>
-        <option value="ADP-Ribosyl (S)">ADP-Ribosyl (S)</option>
-        <option value="ADP-Ribosyl (T)">ADP-Ribosyl (T)</option>
-        <option value="AEBS (H)">AEBS (H)</option>
-        <option value="AEBS (K)">AEBS (K)</option>
-        <option value="AEBS (Protein N-term)">AEBS (Protein N-term)</option>
-        <option value="AEBS (S)">AEBS (S)</option>
-        <option value="AEBS (Y)">AEBS (Y)</option>
-        <option value="AEC-MAEC (S)">AEC-MAEC (S)</option>
-        <option value="AEC-MAEC (T)">AEC-MAEC (T)</option>
-        <option value="AEC-MAEC:2H(4) (S)">AEC-MAEC:2H(4) (S)</option>
-        <option value="AEC-MAEC:2H(4) (T)">AEC-MAEC:2H(4) (T)</option>
-        <option value="AFB1_Dialdehyde (K)">AFB1_Dialdehyde (K)</option>
-        <option value="AHA-Alkyne (M)">AHA-Alkyne (M)</option>
-        <option value="AHA-Alkyne-KDDDD (M)">AHA-Alkyne-KDDDD (M)</option>
-        <option value="AHA-SS (M)">AHA-SS (M)</option>
-        <option value="AHA-SS_CAM (M)">AHA-SS_CAM (M)</option>
-        <option value="Ahx2+Hsl (C-term)">Ahx2+Hsl (C-term)</option>
-        <option value="Ala-&gt;Arg (A)">Ala-&gt;Arg (A)</option>
-        <option value="Ala-&gt;Asn (A)">Ala-&gt;Asn (A)</option>
-        <option value="Ala-&gt;Asp (A)">Ala-&gt;Asp (A)</option>
-        <option value="Ala-&gt;Cys (A)">Ala-&gt;Cys (A)</option>
-        <option value="Ala-&gt;Gln (A)">Ala-&gt;Gln (A)</option>
-        <option value="Ala-&gt;Glu (A)">Ala-&gt;Glu (A)</option>
-        <option value="Ala-&gt;Gly (A)">Ala-&gt;Gly (A)</option>
-        <option value="Ala-&gt;His (A)">Ala-&gt;His (A)</option>
-        <option value="Ala-&gt;Lys (A)">Ala-&gt;Lys (A)</option>
-        <option value="Ala-&gt;Met (A)">Ala-&gt;Met (A)</option>
-        <option value="Ala-&gt;Phe (A)">Ala-&gt;Phe (A)</option>
-        <option value="Ala-&gt;Pro (A)">Ala-&gt;Pro (A)</option>
-        <option value="Ala-&gt;Ser (A)">Ala-&gt;Ser (A)</option>
-        <option value="Ala-&gt;Thr (A)">Ala-&gt;Thr (A)</option>
-        <option value="Ala-&gt;Trp (A)">Ala-&gt;Trp (A)</option>
-        <option value="Ala-&gt;Tyr (A)">Ala-&gt;Tyr (A)</option>
-        <option value="Ala-&gt;Val (A)">Ala-&gt;Val (A)</option>
-        <option value="Ala-&gt;Xle (A)">Ala-&gt;Xle (A)</option>
-        <option value="Amidated (C-term)">Amidated (C-term)</option>
-        <option value="Amidated (Protein C-term)">Amidated (Protein C-term)</option>
-        <option value="Amidine (K)">Amidine (K)</option>
-        <option value="Amidine (N-term)">Amidine (N-term)</option>
-        <option value="Amidino (C)">Amidino (C)</option>
-        <option value="Amino (Y)">Amino (Y)</option>
-        <option value="Ammonia-loss (N)">Ammonia-loss (N)</option>
-        <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
-        <option value="Ammonia-loss (Protein N-term S)">Ammonia-loss (Protein N-term S)</option>
-        <option value="Ammonia-loss (Protein N-term T)">Ammonia-loss (Protein N-term T)</option>
-        <option value="Ammonium (C-term)">Ammonium (C-term)</option>
-        <option value="Ammonium (D)">Ammonium (D)</option>
-        <option value="Ammonium (E)">Ammonium (E)</option>
-        <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
-        <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
-        <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
-        <option value="Archaeol (C)">Archaeol (C)</option>
-        <option value="Arg (N-term)">Arg (N-term)</option>
-        <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
-        <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
-        <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
-        <option value="Arg-&gt;Cys (R)">Arg-&gt;Cys (R)</option>
-        <option value="Arg-&gt;Gln (R)">Arg-&gt;Gln (R)</option>
-        <option value="Arg-&gt;Glu (R)">Arg-&gt;Glu (R)</option>
-        <option value="Arg-&gt;GluSA (R)">Arg-&gt;GluSA (R)</option>
-        <option value="Arg-&gt;Gly (R)">Arg-&gt;Gly (R)</option>
-        <option value="Arg-&gt;His (R)">Arg-&gt;His (R)</option>
-        <option value="Arg-&gt;Lys (R)">Arg-&gt;Lys (R)</option>
-        <option value="Arg-&gt;Met (R)">Arg-&gt;Met (R)</option>
-        <option value="Arg-&gt;Npo (R)">Arg-&gt;Npo (R)</option>
-        <option value="Arg-&gt;Orn (R)">Arg-&gt;Orn (R)</option>
-        <option value="Arg-&gt;Phe (R)">Arg-&gt;Phe (R)</option>
-        <option value="Arg-&gt;Pro (R)">Arg-&gt;Pro (R)</option>
-        <option value="Arg-&gt;Ser (R)">Arg-&gt;Ser (R)</option>
-        <option value="Arg-&gt;Thr (R)">Arg-&gt;Thr (R)</option>
-        <option value="Arg-&gt;Trp (R)">Arg-&gt;Trp (R)</option>
-        <option value="Arg-&gt;Tyr (R)">Arg-&gt;Tyr (R)</option>
-        <option value="Arg-&gt;Val (R)">Arg-&gt;Val (R)</option>
-        <option value="Arg-&gt;Xle (R)">Arg-&gt;Xle (R)</option>
-        <option value="Arg-loss (C-term R)">Arg-loss (C-term R)</option>
-        <option value="Arg2PG (R)">Arg2PG (R)</option>
-        <option value="Argbiotinhydrazide (R)">Argbiotinhydrazide (R)</option>
-        <option value="AROD (C)">AROD (C)</option>
-        <option value="Asn-&gt;Ala (N)">Asn-&gt;Ala (N)</option>
-        <option value="Asn-&gt;Arg (N)">Asn-&gt;Arg (N)</option>
-        <option value="Asn-&gt;Asp (N)">Asn-&gt;Asp (N)</option>
-        <option value="Asn-&gt;Cys (N)">Asn-&gt;Cys (N)</option>
-        <option value="Asn-&gt;Gln (N)">Asn-&gt;Gln (N)</option>
-        <option value="Asn-&gt;Glu (N)">Asn-&gt;Glu (N)</option>
-        <option value="Asn-&gt;Gly (N)">Asn-&gt;Gly (N)</option>
-        <option value="Asn-&gt;His (N)">Asn-&gt;His (N)</option>
-        <option value="Asn-&gt;Lys (N)">Asn-&gt;Lys (N)</option>
-        <option value="Asn-&gt;Met (N)">Asn-&gt;Met (N)</option>
-        <option value="Asn-&gt;Phe (N)">Asn-&gt;Phe (N)</option>
-        <option value="Asn-&gt;Pro (N)">Asn-&gt;Pro (N)</option>
-        <option value="Asn-&gt;Ser (N)">Asn-&gt;Ser (N)</option>
-        <option value="Asn-&gt;Thr (N)">Asn-&gt;Thr (N)</option>
-        <option value="Asn-&gt;Trp (N)">Asn-&gt;Trp (N)</option>
-        <option value="Asn-&gt;Tyr (N)">Asn-&gt;Tyr (N)</option>
-        <option value="Asn-&gt;Val (N)">Asn-&gt;Val (N)</option>
-        <option value="Asn-&gt;Xle (N)">Asn-&gt;Xle (N)</option>
-        <option value="Asp-&gt;Ala (D)">Asp-&gt;Ala (D)</option>
-        <option value="Asp-&gt;Arg (D)">Asp-&gt;Arg (D)</option>
-        <option value="Asp-&gt;Asn (D)">Asp-&gt;Asn (D)</option>
-        <option value="Asp-&gt;Cys (D)">Asp-&gt;Cys (D)</option>
-        <option value="Asp-&gt;Gln (D)">Asp-&gt;Gln (D)</option>
-        <option value="Asp-&gt;Glu (D)">Asp-&gt;Glu (D)</option>
-        <option value="Asp-&gt;Gly (D)">Asp-&gt;Gly (D)</option>
-        <option value="Asp-&gt;His (D)">Asp-&gt;His (D)</option>
-        <option value="Asp-&gt;Lys (D)">Asp-&gt;Lys (D)</option>
-        <option value="Asp-&gt;Met (D)">Asp-&gt;Met (D)</option>
-        <option value="Asp-&gt;Phe (D)">Asp-&gt;Phe (D)</option>
-        <option value="Asp-&gt;Pro (D)">Asp-&gt;Pro (D)</option>
-        <option value="Asp-&gt;Ser (D)">Asp-&gt;Ser (D)</option>
-        <option value="Asp-&gt;Thr (D)">Asp-&gt;Thr (D)</option>
-        <option value="Asp-&gt;Trp (D)">Asp-&gt;Trp (D)</option>
-        <option value="Asp-&gt;Tyr (D)">Asp-&gt;Tyr (D)</option>
-        <option value="Asp-&gt;Val (D)">Asp-&gt;Val (D)</option>
-        <option value="Asp-&gt;Xle (D)">Asp-&gt;Xle (D)</option>
-        <option value="Aspartylurea (H)">Aspartylurea (H)</option>
-        <option value="Atto495Maleimide (C)">Atto495Maleimide (C)</option>
-        <option value="AzidoF (F)">AzidoF (F)</option>
-        <option value="azole (C)">azole (C)</option>
-        <option value="azole (S)">azole (S)</option>
-        <option value="Bacillosamine (N)">Bacillosamine (N)</option>
-        <option value="BADGE (C)">BADGE (C)</option>
-        <option value="BDMAPP (H)">BDMAPP (H)</option>
-        <option value="BDMAPP (K)">BDMAPP (K)</option>
-        <option value="BDMAPP (Protein N-term)">BDMAPP (Protein N-term)</option>
-        <option value="BDMAPP (W)">BDMAPP (W)</option>
-        <option value="BDMAPP (Y)">BDMAPP (Y)</option>
-        <option value="BEMAD_C (C)">BEMAD_C (C)</option>
-        <option value="BEMAD_C:2H(6) (C)">BEMAD_C:2H(6) (C)</option>
-        <option value="BEMAD_ST (S)">BEMAD_ST (S)</option>
-        <option value="BEMAD_ST (T)">BEMAD_ST (T)</option>
-        <option value="BEMAD_ST:2H(6) (S)">BEMAD_ST:2H(6) (S)</option>
-        <option value="BEMAD_ST:2H(6) (T)">BEMAD_ST:2H(6) (T)</option>
-        <option value="Benzoyl (K)">Benzoyl (K)</option>
-        <option value="Benzoyl (N-term)">Benzoyl (N-term)</option>
-        <option value="benzylguanidine (K)">benzylguanidine (K)</option>
-        <option value="betaFNA (C)">betaFNA (C)</option>
-        <option value="betaFNA (K)">betaFNA (K)</option>
-        <option value="BHT (C)">BHT (C)</option>
-        <option value="BHT (H)">BHT (H)</option>
-        <option value="BHT (K)">BHT (K)</option>
-        <option value="BHTOH (C)">BHTOH (C)</option>
-        <option value="BHTOH (H)">BHTOH (H)</option>
-        <option value="BHTOH (K)">BHTOH (K)</option>
-        <option value="Biotin (K)">Biotin (K)</option>
-        <option value="Biotin (N-term)">Biotin (N-term)</option>
-        <option value="Biotin-HPDP (C)">Biotin-HPDP (C)</option>
-        <option value="Biotin-PEG-PRA (M)">Biotin-PEG-PRA (M)</option>
-        <option value="Biotin-PEO-Amine (D)">Biotin-PEO-Amine (D)</option>
-        <option value="Biotin-PEO-Amine (E)">Biotin-PEO-Amine (E)</option>
-        <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
-        <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
-        <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
-        <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
-        <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
-        <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
-        <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
-        <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
-        <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
-        <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
-        <option value="Biotin:Thermo-21328 (K)">Biotin:Thermo-21328 (K)</option>
-        <option value="Biotin:Thermo-21328 (N-term)">Biotin:Thermo-21328 (N-term)</option>
-        <option value="Biotin:Thermo-21330 (K)">Biotin:Thermo-21330 (K)</option>
-        <option value="Biotin:Thermo-21330 (N-term)">Biotin:Thermo-21330 (N-term)</option>
-        <option value="Biotin:Thermo-21345 (Q)">Biotin:Thermo-21345 (Q)</option>
-        <option value="Biotin:Thermo-21360 (X)">Biotin:Thermo-21360 (X)</option>
-        <option value="Biotin:Thermo-21901+2H2O (C)">Biotin:Thermo-21901+2H2O (C)</option>
-        <option value="Biotin:Thermo-21901+H2O (C)">Biotin:Thermo-21901+H2O (C)</option>
-        <option value="Biotin:Thermo-21911 (C)">Biotin:Thermo-21911 (C)</option>
-        <option value="Biotin:Thermo-33033 (X)">Biotin:Thermo-33033 (X)</option>
-        <option value="Biotin:Thermo-33033-H (X)">Biotin:Thermo-33033-H (X)</option>
-        <option value="Biotin:Thermo-88310 (K)">Biotin:Thermo-88310 (K)</option>
-        <option value="Biotin:Thermo-88317 (S)">Biotin:Thermo-88317 (S)</option>
-        <option value="Biotin:Thermo-88317 (Y)">Biotin:Thermo-88317 (Y)</option>
-        <option value="biotinAcrolein298 (C)">biotinAcrolein298 (C)</option>
-        <option value="biotinAcrolein298 (H)">biotinAcrolein298 (H)</option>
-        <option value="biotinAcrolein298 (K)">biotinAcrolein298 (K)</option>
-        <option value="biotinAcrolein298 (Protein N-term)">biotinAcrolein298 (Protein N-term)</option>
-        <option value="BisANS (K)">BisANS (K)</option>
-        <option value="bisANS-sulfonates (K)">bisANS-sulfonates (K)</option>
-        <option value="bisANS-sulfonates (S)">bisANS-sulfonates (S)</option>
-        <option value="bisANS-sulfonates (T)">bisANS-sulfonates (T)</option>
-        <option value="BITC (C)">BITC (C)</option>
-        <option value="BITC (K)">BITC (K)</option>
-        <option value="BITC (N-term)">BITC (N-term)</option>
-        <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
-        <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-        <option value="Bodipy (C)">Bodipy (C)</option>
-        <option value="Brij35 (N-term)">Brij35 (N-term)</option>
-        <option value="Brij58 (N-term)">Brij58 (N-term)</option>
-        <option value="Bromo (F)">Bromo (F)</option>
-        <option value="Bromo (H)">Bromo (H)</option>
-        <option value="Bromo (W)">Bromo (W)</option>
-        <option value="Bromo (Y)">Bromo (Y)</option>
-        <option value="Bromobimane (C)">Bromobimane (C)</option>
-        <option value="Butyryl (K)">Butyryl (K)</option>
-        <option value="C8-QAT (K)">C8-QAT (K)</option>
-        <option value="C8-QAT (N-term)">C8-QAT (N-term)</option>
-        <option value="CAF (N-term)">CAF (N-term)</option>
-        <option value="CAMthiopropanoyl (K)">CAMthiopropanoyl (K)</option>
-        <option value="CAMthiopropanoyl (Protein N-term)">CAMthiopropanoyl (Protein N-term)</option>
-        <option value="Can-FP-biotin (S)">Can-FP-biotin (S)</option>
-        <option value="Can-FP-biotin (T)">Can-FP-biotin (T)</option>
-        <option value="Can-FP-biotin (Y)">Can-FP-biotin (Y)</option>
-        <option value="Carbamidomethyl (C)">Carbamidomethyl (C)</option>
-        <option value="Carbamidomethyl (D)">Carbamidomethyl (D)</option>
-        <option value="Carbamidomethyl (E)">Carbamidomethyl (E)</option>
-        <option value="Carbamidomethyl (H)">Carbamidomethyl (H)</option>
-        <option value="Carbamidomethyl (K)">Carbamidomethyl (K)</option>
-        <option value="Carbamidomethyl (M)">Carbamidomethyl (M)</option>
-        <option value="Carbamidomethyl (N-term)">Carbamidomethyl (N-term)</option>
-        <option value="Carbamidomethyl (S)">Carbamidomethyl (S)</option>
-        <option value="Carbamidomethyl (T)">Carbamidomethyl (T)</option>
-        <option value="Carbamidomethyl (U)">Carbamidomethyl (U)</option>
-        <option value="Carbamidomethyl (Y)">Carbamidomethyl (Y)</option>
-        <option value="CarbamidomethylDTT (C)">CarbamidomethylDTT (C)</option>
-        <option value="Carbamyl (C)">Carbamyl (C)</option>
-        <option value="Carbamyl (K)">Carbamyl (K)</option>
-        <option value="Carbamyl (M)">Carbamyl (M)</option>
-        <option value="Carbamyl (N-term)">Carbamyl (N-term)</option>
-        <option value="Carbamyl (Protein N-term)">Carbamyl (Protein N-term)</option>
-        <option value="Carbamyl (R)">Carbamyl (R)</option>
-        <option value="Carbamyl (S)">Carbamyl (S)</option>
-        <option value="Carbamyl (T)">Carbamyl (T)</option>
-        <option value="Carbamyl (Y)">Carbamyl (Y)</option>
-        <option value="Carbofuran (S)">Carbofuran (S)</option>
-        <option value="Carbonyl (A)">Carbonyl (A)</option>
-        <option value="Carbonyl (E)">Carbonyl (E)</option>
-        <option value="Carbonyl (I)">Carbonyl (I)</option>
-        <option value="Carbonyl (L)">Carbonyl (L)</option>
-        <option value="Carbonyl (Q)">Carbonyl (Q)</option>
-        <option value="Carbonyl (R)">Carbonyl (R)</option>
-        <option value="Carbonyl (S)">Carbonyl (S)</option>
-        <option value="Carbonyl (V)">Carbonyl (V)</option>
-        <option value="Carboxy (D)">Carboxy (D)</option>
-        <option value="Carboxy (E)">Carboxy (E)</option>
-        <option value="Carboxy (K)">Carboxy (K)</option>
-        <option value="Carboxy (Protein N-term M)">Carboxy (Protein N-term M)</option>
-        <option value="Carboxy (W)">Carboxy (W)</option>
-        <option value="Carboxy-&gt;Thiocarboxy (Protein C-term G)">Carboxy-&gt;Thiocarboxy (Protein C-term G)</option>
-        <option value="Carboxyethyl (H)">Carboxyethyl (H)</option>
-        <option value="Carboxyethyl (K)">Carboxyethyl (K)</option>
-        <option value="Carboxyethylpyrrole (K)">Carboxyethylpyrrole (K)</option>
-        <option value="Carboxymethyl (C)">Carboxymethyl (C)</option>
-        <option value="Carboxymethyl (K)">Carboxymethyl (K)</option>
-        <option value="Carboxymethyl (N-term)">Carboxymethyl (N-term)</option>
-        <option value="Carboxymethyl (U)">Carboxymethyl (U)</option>
-        <option value="Carboxymethyl (W)">Carboxymethyl (W)</option>
-        <option value="Carboxymethyl:13C(2) (C)">Carboxymethyl:13C(2) (C)</option>
-        <option value="CarboxymethylDMAP (N-term)">CarboxymethylDMAP (N-term)</option>
-        <option value="CarboxymethylDTT (C)">CarboxymethylDTT (C)</option>
-        <option value="Cation:Ag (C-term)">Cation:Ag (C-term)</option>
-        <option value="Cation:Ag (D)">Cation:Ag (D)</option>
-        <option value="Cation:Ag (E)">Cation:Ag (E)</option>
-        <option value="Cation:Al[III] (C-term)">Cation:Al[III] (C-term)</option>
-        <option value="Cation:Al[III] (D)">Cation:Al[III] (D)</option>
-        <option value="Cation:Al[III] (E)">Cation:Al[III] (E)</option>
-        <option value="Cation:Ca[II] (C-term)">Cation:Ca[II] (C-term)</option>
-        <option value="Cation:Ca[II] (D)">Cation:Ca[II] (D)</option>
-        <option value="Cation:Ca[II] (E)">Cation:Ca[II] (E)</option>
-        <option value="Cation:Cu[I] (C-term)">Cation:Cu[I] (C-term)</option>
-        <option value="Cation:Cu[I] (D)">Cation:Cu[I] (D)</option>
-        <option value="Cation:Cu[I] (E)">Cation:Cu[I] (E)</option>
-        <option value="Cation:Cu[I] (H)">Cation:Cu[I] (H)</option>
-        <option value="Cation:Fe[II] (C-term)">Cation:Fe[II] (C-term)</option>
-        <option value="Cation:Fe[II] (D)">Cation:Fe[II] (D)</option>
-        <option value="Cation:Fe[II] (E)">Cation:Fe[II] (E)</option>
-        <option value="Cation:Fe[III] (C-term)">Cation:Fe[III] (C-term)</option>
-        <option value="Cation:Fe[III] (D)">Cation:Fe[III] (D)</option>
-        <option value="Cation:Fe[III] (E)">Cation:Fe[III] (E)</option>
-        <option value="Cation:K (C-term)">Cation:K (C-term)</option>
-        <option value="Cation:K (D)">Cation:K (D)</option>
-        <option value="Cation:K (E)">Cation:K (E)</option>
-        <option value="Cation:Li (C-term)">Cation:Li (C-term)</option>
-        <option value="Cation:Li (D)">Cation:Li (D)</option>
-        <option value="Cation:Li (E)">Cation:Li (E)</option>
-        <option value="Cation:Mg[II] (C-term)">Cation:Mg[II] (C-term)</option>
-        <option value="Cation:Mg[II] (D)">Cation:Mg[II] (D)</option>
-        <option value="Cation:Mg[II] (E)">Cation:Mg[II] (E)</option>
-        <option value="Cation:Na (C-term)">Cation:Na (C-term)</option>
-        <option value="Cation:Na (D)">Cation:Na (D)</option>
-        <option value="Cation:Na (E)">Cation:Na (E)</option>
-        <option value="Cation:Ni[II] (C-term)">Cation:Ni[II] (C-term)</option>
-        <option value="Cation:Ni[II] (D)">Cation:Ni[II] (D)</option>
-        <option value="Cation:Ni[II] (E)">Cation:Ni[II] (E)</option>
-        <option value="Cation:Zn[II] (C-term)">Cation:Zn[II] (C-term)</option>
-        <option value="Cation:Zn[II] (D)">Cation:Zn[II] (D)</option>
-        <option value="Cation:Zn[II] (E)">Cation:Zn[II] (E)</option>
-        <option value="Cation:Zn[II] (H)">Cation:Zn[II] (H)</option>
-        <option value="cGMP (C)">cGMP (C)</option>
-        <option value="cGMP (S)">cGMP (S)</option>
-        <option value="cGMP+RMP-loss (C)">cGMP+RMP-loss (C)</option>
-        <option value="cGMP+RMP-loss (S)">cGMP+RMP-loss (S)</option>
-        <option value="CHDH (D)">CHDH (D)</option>
-        <option value="Chlorination (W)">Chlorination (W)</option>
-        <option value="Chlorination (Y)">Chlorination (Y)</option>
-        <option value="Cholesterol (Protein C-term)">Cholesterol (Protein C-term)</option>
-        <option value="CIGG (K)">CIGG (K)</option>
-        <option value="CLIP_TRAQ_2 (K)">CLIP_TRAQ_2 (K)</option>
-        <option value="CLIP_TRAQ_2 (N-term)">CLIP_TRAQ_2 (N-term)</option>
-        <option value="CLIP_TRAQ_2 (Y)">CLIP_TRAQ_2 (Y)</option>
-        <option value="CLIP_TRAQ_3 (K)">CLIP_TRAQ_3 (K)</option>
-        <option value="CLIP_TRAQ_3 (N-term)">CLIP_TRAQ_3 (N-term)</option>
-        <option value="CLIP_TRAQ_3 (Y)">CLIP_TRAQ_3 (Y)</option>
-        <option value="CLIP_TRAQ_4 (K)">CLIP_TRAQ_4 (K)</option>
-        <option value="CLIP_TRAQ_4 (N-term)">CLIP_TRAQ_4 (N-term)</option>
-        <option value="CLIP_TRAQ_4 (Y)">CLIP_TRAQ_4 (Y)</option>
-        <option value="CoenzymeA (C)">CoenzymeA (C)</option>
-        <option value="Cresylphosphate (H)">Cresylphosphate (H)</option>
-        <option value="Cresylphosphate (K)">Cresylphosphate (K)</option>
-        <option value="Cresylphosphate (R)">Cresylphosphate (R)</option>
-        <option value="Cresylphosphate (S)">Cresylphosphate (S)</option>
-        <option value="Cresylphosphate (T)">Cresylphosphate (T)</option>
-        <option value="Cresylphosphate (Y)">Cresylphosphate (Y)</option>
-        <option value="CresylSaligeninPhosphate (H)">CresylSaligeninPhosphate (H)</option>
-        <option value="CresylSaligeninPhosphate (K)">CresylSaligeninPhosphate (K)</option>
-        <option value="CresylSaligeninPhosphate (R)">CresylSaligeninPhosphate (R)</option>
-        <option value="CresylSaligeninPhosphate (S)">CresylSaligeninPhosphate (S)</option>
-        <option value="CresylSaligeninPhosphate (T)">CresylSaligeninPhosphate (T)</option>
-        <option value="CresylSaligeninPhosphate (Y)">CresylSaligeninPhosphate (Y)</option>
-        <option value="Crotonaldehyde (C)">Crotonaldehyde (C)</option>
-        <option value="Crotonaldehyde (H)">Crotonaldehyde (H)</option>
-        <option value="Crotonaldehyde (K)">Crotonaldehyde (K)</option>
-        <option value="Crotonyl (K)">Crotonyl (K)</option>
-        <option value="CuSMo (C)">CuSMo (C)</option>
-        <option value="CUSTOM0 (A)">CUSTOM0 (A)</option>
-        <option value="CUSTOM0 (C)">CUSTOM0 (C)</option>
-        <option value="CUSTOM0 (C-term)">CUSTOM0 (C-term)</option>
-        <option value="CUSTOM0 (D)">CUSTOM0 (D)</option>
-        <option value="CUSTOM0 (E)">CUSTOM0 (E)</option>
-        <option value="CUSTOM0 (F)">CUSTOM0 (F)</option>
-        <option value="CUSTOM0 (G)">CUSTOM0 (G)</option>
-        <option value="CUSTOM0 (H)">CUSTOM0 (H)</option>
-        <option value="CUSTOM0 (I)">CUSTOM0 (I)</option>
-        <option value="CUSTOM0 (K)">CUSTOM0 (K)</option>
-        <option value="CUSTOM0 (L)">CUSTOM0 (L)</option>
-        <option value="CUSTOM0 (M)">CUSTOM0 (M)</option>
-        <option value="CUSTOM0 (N)">CUSTOM0 (N)</option>
-        <option value="CUSTOM0 (N-term)">CUSTOM0 (N-term)</option>
-        <option value="CUSTOM0 (P)">CUSTOM0 (P)</option>
-        <option value="CUSTOM0 (Q)">CUSTOM0 (Q)</option>
-        <option value="CUSTOM0 (R)">CUSTOM0 (R)</option>
-        <option value="CUSTOM0 (S)">CUSTOM0 (S)</option>
-        <option value="CUSTOM0 (T)">CUSTOM0 (T)</option>
-        <option value="CUSTOM0 (V)">CUSTOM0 (V)</option>
-        <option value="CUSTOM0 (W)">CUSTOM0 (W)</option>
-        <option value="CUSTOM0 (Y)">CUSTOM0 (Y)</option>
-        <option value="CUSTOM1 (A)">CUSTOM1 (A)</option>
-        <option value="CUSTOM1 (C)">CUSTOM1 (C)</option>
-        <option value="CUSTOM1 (C-term)">CUSTOM1 (C-term)</option>
-        <option value="CUSTOM1 (D)">CUSTOM1 (D)</option>
-        <option value="CUSTOM1 (E)">CUSTOM1 (E)</option>
-        <option value="CUSTOM1 (F)">CUSTOM1 (F)</option>
-        <option value="CUSTOM1 (G)">CUSTOM1 (G)</option>
-        <option value="CUSTOM1 (H)">CUSTOM1 (H)</option>
-        <option value="CUSTOM1 (I)">CUSTOM1 (I)</option>
-        <option value="CUSTOM1 (K)">CUSTOM1 (K)</option>
-        <option value="CUSTOM1 (L)">CUSTOM1 (L)</option>
-        <option value="CUSTOM1 (M)">CUSTOM1 (M)</option>
-        <option value="CUSTOM1 (N)">CUSTOM1 (N)</option>
-        <option value="CUSTOM1 (N-term)">CUSTOM1 (N-term)</option>
-        <option value="CUSTOM1 (P)">CUSTOM1 (P)</option>
-        <option value="CUSTOM1 (Q)">CUSTOM1 (Q)</option>
-        <option value="CUSTOM1 (R)">CUSTOM1 (R)</option>
-        <option value="CUSTOM1 (S)">CUSTOM1 (S)</option>
-        <option value="CUSTOM1 (T)">CUSTOM1 (T)</option>
-        <option value="CUSTOM1 (V)">CUSTOM1 (V)</option>
-        <option value="CUSTOM1 (W)">CUSTOM1 (W)</option>
-        <option value="CUSTOM1 (Y)">CUSTOM1 (Y)</option>
-        <option value="CUSTOM2 (A)">CUSTOM2 (A)</option>
-        <option value="CUSTOM2 (C)">CUSTOM2 (C)</option>
-        <option value="CUSTOM2 (C-term)">CUSTOM2 (C-term)</option>
-        <option value="CUSTOM2 (D)">CUSTOM2 (D)</option>
-        <option value="CUSTOM2 (E)">CUSTOM2 (E)</option>
-        <option value="CUSTOM2 (F)">CUSTOM2 (F)</option>
-        <option value="CUSTOM2 (G)">CUSTOM2 (G)</option>
-        <option value="CUSTOM2 (H)">CUSTOM2 (H)</option>
-        <option value="CUSTOM2 (I)">CUSTOM2 (I)</option>
-        <option value="CUSTOM2 (K)">CUSTOM2 (K)</option>
-        <option value="CUSTOM2 (L)">CUSTOM2 (L)</option>
-        <option value="CUSTOM2 (M)">CUSTOM2 (M)</option>
-        <option value="CUSTOM2 (N)">CUSTOM2 (N)</option>
-        <option value="CUSTOM2 (N-term)">CUSTOM2 (N-term)</option>
-        <option value="CUSTOM2 (P)">CUSTOM2 (P)</option>
-        <option value="CUSTOM2 (Q)">CUSTOM2 (Q)</option>
-        <option value="CUSTOM2 (R)">CUSTOM2 (R)</option>
-        <option value="CUSTOM2 (S)">CUSTOM2 (S)</option>
-        <option value="CUSTOM2 (T)">CUSTOM2 (T)</option>
-        <option value="CUSTOM2 (V)">CUSTOM2 (V)</option>
-        <option value="CUSTOM2 (W)">CUSTOM2 (W)</option>
-        <option value="CUSTOM2 (Y)">CUSTOM2 (Y)</option>
-        <option value="CUSTOM3 (A)">CUSTOM3 (A)</option>
-        <option value="CUSTOM3 (C)">CUSTOM3 (C)</option>
-        <option value="CUSTOM3 (C-term)">CUSTOM3 (C-term)</option>
-        <option value="CUSTOM3 (D)">CUSTOM3 (D)</option>
-        <option value="CUSTOM3 (E)">CUSTOM3 (E)</option>
-        <option value="CUSTOM3 (F)">CUSTOM3 (F)</option>
-        <option value="CUSTOM3 (G)">CUSTOM3 (G)</option>
-        <option value="CUSTOM3 (H)">CUSTOM3 (H)</option>
-        <option value="CUSTOM3 (I)">CUSTOM3 (I)</option>
-        <option value="CUSTOM3 (K)">CUSTOM3 (K)</option>
-        <option value="CUSTOM3 (L)">CUSTOM3 (L)</option>
-        <option value="CUSTOM3 (M)">CUSTOM3 (M)</option>
-        <option value="CUSTOM3 (N)">CUSTOM3 (N)</option>
-        <option value="CUSTOM3 (N-term)">CUSTOM3 (N-term)</option>
-        <option value="CUSTOM3 (P)">CUSTOM3 (P)</option>
-        <option value="CUSTOM3 (Q)">CUSTOM3 (Q)</option>
-        <option value="CUSTOM3 (R)">CUSTOM3 (R)</option>
-        <option value="CUSTOM3 (S)">CUSTOM3 (S)</option>
-        <option value="CUSTOM3 (T)">CUSTOM3 (T)</option>
-        <option value="CUSTOM3 (V)">CUSTOM3 (V)</option>
-        <option value="CUSTOM3 (W)">CUSTOM3 (W)</option>
-        <option value="CUSTOM3 (Y)">CUSTOM3 (Y)</option>
-        <option value="CUSTOM4 (A)">CUSTOM4 (A)</option>
-        <option value="CUSTOM4 (C)">CUSTOM4 (C)</option>
-        <option value="CUSTOM4 (C-term)">CUSTOM4 (C-term)</option>
-        <option value="CUSTOM4 (D)">CUSTOM4 (D)</option>
-        <option value="CUSTOM4 (E)">CUSTOM4 (E)</option>
-        <option value="CUSTOM4 (F)">CUSTOM4 (F)</option>
-        <option value="CUSTOM4 (G)">CUSTOM4 (G)</option>
-        <option value="CUSTOM4 (H)">CUSTOM4 (H)</option>
-        <option value="CUSTOM4 (I)">CUSTOM4 (I)</option>
-        <option value="CUSTOM4 (K)">CUSTOM4 (K)</option>
-        <option value="CUSTOM4 (L)">CUSTOM4 (L)</option>
-        <option value="CUSTOM4 (M)">CUSTOM4 (M)</option>
-        <option value="CUSTOM4 (N)">CUSTOM4 (N)</option>
-        <option value="CUSTOM4 (N-term)">CUSTOM4 (N-term)</option>
-        <option value="CUSTOM4 (P)">CUSTOM4 (P)</option>
-        <option value="CUSTOM4 (Q)">CUSTOM4 (Q)</option>
-        <option value="CUSTOM4 (R)">CUSTOM4 (R)</option>
-        <option value="CUSTOM4 (S)">CUSTOM4 (S)</option>
-        <option value="CUSTOM4 (T)">CUSTOM4 (T)</option>
-        <option value="CUSTOM4 (V)">CUSTOM4 (V)</option>
-        <option value="CUSTOM4 (W)">CUSTOM4 (W)</option>
-        <option value="CUSTOM4 (Y)">CUSTOM4 (Y)</option>
-        <option value="CUSTOM5 (A)">CUSTOM5 (A)</option>
-        <option value="CUSTOM5 (C)">CUSTOM5 (C)</option>
-        <option value="CUSTOM5 (C-term)">CUSTOM5 (C-term)</option>
-        <option value="CUSTOM5 (D)">CUSTOM5 (D)</option>
-        <option value="CUSTOM5 (E)">CUSTOM5 (E)</option>
-        <option value="CUSTOM5 (F)">CUSTOM5 (F)</option>
-        <option value="CUSTOM5 (G)">CUSTOM5 (G)</option>
-        <option value="CUSTOM5 (H)">CUSTOM5 (H)</option>
-        <option value="CUSTOM5 (I)">CUSTOM5 (I)</option>
-        <option value="CUSTOM5 (K)">CUSTOM5 (K)</option>
-        <option value="CUSTOM5 (L)">CUSTOM5 (L)</option>
-        <option value="CUSTOM5 (M)">CUSTOM5 (M)</option>
-        <option value="CUSTOM5 (N)">CUSTOM5 (N)</option>
-        <option value="CUSTOM5 (N-term)">CUSTOM5 (N-term)</option>
-        <option value="CUSTOM5 (P)">CUSTOM5 (P)</option>
-        <option value="CUSTOM5 (Q)">CUSTOM5 (Q)</option>
-        <option value="CUSTOM5 (R)">CUSTOM5 (R)</option>
-        <option value="CUSTOM5 (S)">CUSTOM5 (S)</option>
-        <option value="CUSTOM5 (T)">CUSTOM5 (T)</option>
-        <option value="CUSTOM5 (V)">CUSTOM5 (V)</option>
-        <option value="CUSTOM5 (W)">CUSTOM5 (W)</option>
-        <option value="CUSTOM5 (Y)">CUSTOM5 (Y)</option>
-        <option value="CUSTOM6 (A)">CUSTOM6 (A)</option>
-        <option value="CUSTOM6 (C)">CUSTOM6 (C)</option>
-        <option value="CUSTOM6 (C-term)">CUSTOM6 (C-term)</option>
-        <option value="CUSTOM6 (D)">CUSTOM6 (D)</option>
-        <option value="CUSTOM6 (E)">CUSTOM6 (E)</option>
-        <option value="CUSTOM6 (F)">CUSTOM6 (F)</option>
-        <option value="CUSTOM6 (G)">CUSTOM6 (G)</option>
-        <option value="CUSTOM6 (H)">CUSTOM6 (H)</option>
-        <option value="CUSTOM6 (I)">CUSTOM6 (I)</option>
-        <option value="CUSTOM6 (K)">CUSTOM6 (K)</option>
-        <option value="CUSTOM6 (L)">CUSTOM6 (L)</option>
-        <option value="CUSTOM6 (M)">CUSTOM6 (M)</option>
-        <option value="CUSTOM6 (N)">CUSTOM6 (N)</option>
-        <option value="CUSTOM6 (N-term)">CUSTOM6 (N-term)</option>
-        <option value="CUSTOM6 (P)">CUSTOM6 (P)</option>
-        <option value="CUSTOM6 (Q)">CUSTOM6 (Q)</option>
-        <option value="CUSTOM6 (R)">CUSTOM6 (R)</option>
-        <option value="CUSTOM6 (S)">CUSTOM6 (S)</option>
-        <option value="CUSTOM6 (T)">CUSTOM6 (T)</option>
-        <option value="CUSTOM6 (V)">CUSTOM6 (V)</option>
-        <option value="CUSTOM6 (W)">CUSTOM6 (W)</option>
-        <option value="CUSTOM6 (Y)">CUSTOM6 (Y)</option>
-        <option value="CUSTOM7 (A)">CUSTOM7 (A)</option>
-        <option value="CUSTOM7 (C)">CUSTOM7 (C)</option>
-        <option value="CUSTOM7 (C-term)">CUSTOM7 (C-term)</option>
-        <option value="CUSTOM7 (D)">CUSTOM7 (D)</option>
-        <option value="CUSTOM7 (E)">CUSTOM7 (E)</option>
-        <option value="CUSTOM7 (F)">CUSTOM7 (F)</option>
-        <option value="CUSTOM7 (G)">CUSTOM7 (G)</option>
-        <option value="CUSTOM7 (H)">CUSTOM7 (H)</option>
-        <option value="CUSTOM7 (I)">CUSTOM7 (I)</option>
-        <option value="CUSTOM7 (K)">CUSTOM7 (K)</option>
-        <option value="CUSTOM7 (L)">CUSTOM7 (L)</option>
-        <option value="CUSTOM7 (M)">CUSTOM7 (M)</option>
-        <option value="CUSTOM7 (N)">CUSTOM7 (N)</option>
-        <option value="CUSTOM7 (N-term)">CUSTOM7 (N-term)</option>
-        <option value="CUSTOM7 (P)">CUSTOM7 (P)</option>
-        <option value="CUSTOM7 (Q)">CUSTOM7 (Q)</option>
-        <option value="CUSTOM7 (R)">CUSTOM7 (R)</option>
-        <option value="CUSTOM7 (S)">CUSTOM7 (S)</option>
-        <option value="CUSTOM7 (T)">CUSTOM7 (T)</option>
-        <option value="CUSTOM7 (V)">CUSTOM7 (V)</option>
-        <option value="CUSTOM7 (W)">CUSTOM7 (W)</option>
-        <option value="CUSTOM7 (Y)">CUSTOM7 (Y)</option>
-        <option value="CUSTOM8 (A)">CUSTOM8 (A)</option>
-        <option value="CUSTOM8 (C)">CUSTOM8 (C)</option>
-        <option value="CUSTOM8 (C-term)">CUSTOM8 (C-term)</option>
-        <option value="CUSTOM8 (D)">CUSTOM8 (D)</option>
-        <option value="CUSTOM8 (E)">CUSTOM8 (E)</option>
-        <option value="CUSTOM8 (F)">CUSTOM8 (F)</option>
-        <option value="CUSTOM8 (G)">CUSTOM8 (G)</option>
-        <option value="CUSTOM8 (H)">CUSTOM8 (H)</option>
-        <option value="CUSTOM8 (I)">CUSTOM8 (I)</option>
-        <option value="CUSTOM8 (K)">CUSTOM8 (K)</option>
-        <option value="CUSTOM8 (L)">CUSTOM8 (L)</option>
-        <option value="CUSTOM8 (M)">CUSTOM8 (M)</option>
-        <option value="CUSTOM8 (N)">CUSTOM8 (N)</option>
-        <option value="CUSTOM8 (N-term)">CUSTOM8 (N-term)</option>
-        <option value="CUSTOM8 (P)">CUSTOM8 (P)</option>
-        <option value="CUSTOM8 (Q)">CUSTOM8 (Q)</option>
-        <option value="CUSTOM8 (R)">CUSTOM8 (R)</option>
-        <option value="CUSTOM8 (S)">CUSTOM8 (S)</option>
-        <option value="CUSTOM8 (T)">CUSTOM8 (T)</option>
-        <option value="CUSTOM8 (V)">CUSTOM8 (V)</option>
-        <option value="CUSTOM8 (W)">CUSTOM8 (W)</option>
-        <option value="CUSTOM8 (Y)">CUSTOM8 (Y)</option>
-        <option value="CUSTOM9 (A)">CUSTOM9 (A)</option>
-        <option value="CUSTOM9 (C)">CUSTOM9 (C)</option>
-        <option value="CUSTOM9 (C-term)">CUSTOM9 (C-term)</option>
-        <option value="CUSTOM9 (D)">CUSTOM9 (D)</option>
-        <option value="CUSTOM9 (E)">CUSTOM9 (E)</option>
-        <option value="CUSTOM9 (F)">CUSTOM9 (F)</option>
-        <option value="CUSTOM9 (G)">CUSTOM9 (G)</option>
-        <option value="CUSTOM9 (H)">CUSTOM9 (H)</option>
-        <option value="CUSTOM9 (I)">CUSTOM9 (I)</option>
-        <option value="CUSTOM9 (K)">CUSTOM9 (K)</option>
-        <option value="CUSTOM9 (L)">CUSTOM9 (L)</option>
-        <option value="CUSTOM9 (M)">CUSTOM9 (M)</option>
-        <option value="CUSTOM9 (N)">CUSTOM9 (N)</option>
-        <option value="CUSTOM9 (N-term)">CUSTOM9 (N-term)</option>
-        <option value="CUSTOM9 (P)">CUSTOM9 (P)</option>
-        <option value="CUSTOM9 (Q)">CUSTOM9 (Q)</option>
-        <option value="CUSTOM9 (R)">CUSTOM9 (R)</option>
-        <option value="CUSTOM9 (S)">CUSTOM9 (S)</option>
-        <option value="CUSTOM9 (T)">CUSTOM9 (T)</option>
-        <option value="CUSTOM9 (V)">CUSTOM9 (V)</option>
-        <option value="CUSTOM9 (W)">CUSTOM9 (W)</option>
-        <option value="CUSTOM9 (Y)">CUSTOM9 (Y)</option>
-        <option value="Cy3-maleimide (C)">Cy3-maleimide (C)</option>
-        <option value="Cy3b-maleimide (C)">Cy3b-maleimide (C)</option>
-        <option value="Cyano (C)">Cyano (C)</option>
-        <option value="CyDye-Cy3 (C)">CyDye-Cy3 (C)</option>
-        <option value="CyDye-Cy5 (C)">CyDye-Cy5 (C)</option>
-        <option value="Cys-&gt;Ala (C)">Cys-&gt;Ala (C)</option>
-        <option value="Cys-&gt;Arg (C)">Cys-&gt;Arg (C)</option>
-        <option value="Cys-&gt;Asn (C)">Cys-&gt;Asn (C)</option>
-        <option value="Cys-&gt;Asp (C)">Cys-&gt;Asp (C)</option>
-        <option value="Cys-&gt;CamSec (C)">Cys-&gt;CamSec (C)</option>
-        <option value="Cys-&gt;Dha (C)">Cys-&gt;Dha (C)</option>
-        <option value="Cys-&gt;ethylaminoAla (C)">Cys-&gt;ethylaminoAla (C)</option>
-        <option value="Cys-&gt;Gln (C)">Cys-&gt;Gln (C)</option>
-        <option value="Cys-&gt;Glu (C)">Cys-&gt;Glu (C)</option>
-        <option value="Cys-&gt;Gly (C)">Cys-&gt;Gly (C)</option>
-        <option value="Cys-&gt;His (C)">Cys-&gt;His (C)</option>
-        <option value="Cys-&gt;Lys (C)">Cys-&gt;Lys (C)</option>
-        <option value="Cys-&gt;Met (C)">Cys-&gt;Met (C)</option>
-        <option value="Cys-&gt;methylaminoAla (C)">Cys-&gt;methylaminoAla (C)</option>
-        <option value="Cys-&gt;Oxoalanine (C)">Cys-&gt;Oxoalanine (C)</option>
-        <option value="Cys-&gt;Phe (C)">Cys-&gt;Phe (C)</option>
-        <option value="Cys-&gt;Pro (C)">Cys-&gt;Pro (C)</option>
-        <option value="Cys-&gt;PyruvicAcid (Protein N-term C)">Cys-&gt;PyruvicAcid (Protein N-term C)</option>
-        <option value="Cys-&gt;SecNEM (C)">Cys-&gt;SecNEM (C)</option>
-        <option value="Cys-&gt;SecNEM:2H(5) (C)">Cys-&gt;SecNEM:2H(5) (C)</option>
-        <option value="Cys-&gt;Ser (C)">Cys-&gt;Ser (C)</option>
-        <option value="Cys-&gt;Thr (C)">Cys-&gt;Thr (C)</option>
-        <option value="Cys-&gt;Trp (C)">Cys-&gt;Trp (C)</option>
-        <option value="Cys-&gt;Tyr (C)">Cys-&gt;Tyr (C)</option>
-        <option value="Cys-&gt;Val (C)">Cys-&gt;Val (C)</option>
-        <option value="Cys-&gt;Xle (C)">Cys-&gt;Xle (C)</option>
-        <option value="Cysteinyl (C)">Cysteinyl (C)</option>
-        <option value="cysTMT (C)">cysTMT (C)</option>
-        <option value="cysTMT6plex (C)">cysTMT6plex (C)</option>
-        <option value="Cytopiloyne (C)">Cytopiloyne (C)</option>
-        <option value="Cytopiloyne (K)">Cytopiloyne (K)</option>
-        <option value="Cytopiloyne (N-term)">Cytopiloyne (N-term)</option>
-        <option value="Cytopiloyne (P)">Cytopiloyne (P)</option>
-        <option value="Cytopiloyne (R)">Cytopiloyne (R)</option>
-        <option value="Cytopiloyne (S)">Cytopiloyne (S)</option>
-        <option value="Cytopiloyne (Y)">Cytopiloyne (Y)</option>
-        <option value="Cytopiloyne+water (C)">Cytopiloyne+water (C)</option>
-        <option value="Cytopiloyne+water (K)">Cytopiloyne+water (K)</option>
-        <option value="Cytopiloyne+water (N-term)">Cytopiloyne+water (N-term)</option>
-        <option value="Cytopiloyne+water (R)">Cytopiloyne+water (R)</option>
-        <option value="Cytopiloyne+water (S)">Cytopiloyne+water (S)</option>
-        <option value="Cytopiloyne+water (T)">Cytopiloyne+water (T)</option>
-        <option value="Cytopiloyne+water (Y)">Cytopiloyne+water (Y)</option>
-        <option value="DAET (S)">DAET (S)</option>
-        <option value="DAET (T)">DAET (T)</option>
-        <option value="Dansyl (K)">Dansyl (K)</option>
-        <option value="Dansyl (N-term)">Dansyl (N-term)</option>
-        <option value="Dap-DSP (A)">Dap-DSP (A)</option>
-        <option value="Dap-DSP (E)">Dap-DSP (E)</option>
-        <option value="Dap-DSP (K)">Dap-DSP (K)</option>
-        <option value="Deamidated (N)">Deamidated (N)</option>
-        <option value="Deamidated (Protein N-term F)">Deamidated (Protein N-term F)</option>
-        <option value="Deamidated (Q)">Deamidated (Q)</option>
-        <option value="Deamidated (R)">Deamidated (R)</option>
-        <option value="Deamidated:18O(1) (N)">Deamidated:18O(1) (N)</option>
-        <option value="Deamidated:18O(1) (Q)">Deamidated:18O(1) (Q)</option>
-        <option value="Decanoyl (S)">Decanoyl (S)</option>
-        <option value="Decanoyl (T)">Decanoyl (T)</option>
-        <option value="Decarboxylation (D)">Decarboxylation (D)</option>
-        <option value="Decarboxylation (E)">Decarboxylation (E)</option>
-        <option value="DEDGFLYMVYASQETFG (K)">DEDGFLYMVYASQETFG (K)</option>
-        <option value="Dehydrated (D)">Dehydrated (D)</option>
-        <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
-        <option value="Dehydrated (Protein C-term N)">Dehydrated (Protein C-term N)</option>
-        <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
-        <option value="Dehydrated (S)">Dehydrated (S)</option>
-        <option value="Dehydrated (T)">Dehydrated (T)</option>
-        <option value="Dehydrated (Y)">Dehydrated (Y)</option>
-        <option value="Dehydro (C)">Dehydro (C)</option>
-        <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
-        <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-        <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
-        <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
-        <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
-        <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
-        <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
-        <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
-        <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
-        <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
-        <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
-        <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-        <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
-        <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
-        <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
-        <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
-        <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
-        <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
-        <option value="Delta:H(4)C(3) (K)">Delta:H(4)C(3) (K)</option>
-        <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
-        <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
-        <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
-        <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
-        <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
-        <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
-        <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
-        <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
-        <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
-        <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
-        <option value="Delta:H(6)C(3)O(1) (K)">Delta:H(6)C(3)O(1) (K)</option>
-        <option value="Delta:H(6)C(3)O(1) (Protein N-term)">Delta:H(6)C(3)O(1) (Protein N-term)</option>
-        <option value="Delta:H(6)C(6)O(1) (K)">Delta:H(6)C(6)O(1) (K)</option>
-        <option value="Delta:H(6)C(7)O(4) (R)">Delta:H(6)C(7)O(4) (R)</option>
-        <option value="Delta:H(8)C(6)O(1) (K)">Delta:H(8)C(6)O(1) (K)</option>
-        <option value="Delta:H(8)C(6)O(1) (Protein N-term)">Delta:H(8)C(6)O(1) (Protein N-term)</option>
-        <option value="Delta:H(8)C(6)O(2) (K)">Delta:H(8)C(6)O(2) (K)</option>
-        <option value="Delta:Hg(1) (C)">Delta:Hg(1) (C)</option>
-        <option value="Delta:O(4) (W)">Delta:O(4) (W)</option>
-        <option value="Delta:S(-1)Se(1) (C)">Delta:S(-1)Se(1) (C)</option>
-        <option value="Delta:S(-1)Se(1) (M)">Delta:S(-1)Se(1) (M)</option>
-        <option value="Delta:Se(1) (C)">Delta:Se(1) (C)</option>
-        <option value="Deoxy (D)">Deoxy (D)</option>
-        <option value="Deoxy (S)">Deoxy (S)</option>
-        <option value="Deoxy (T)">Deoxy (T)</option>
-        <option value="Deoxyhypusine (K)">Deoxyhypusine (K)</option>
-        <option value="Deoxyhypusine (Q)">Deoxyhypusine (Q)</option>
-        <option value="DeStreak (C)">DeStreak (C)</option>
-        <option value="Dethiomethyl (M)">Dethiomethyl (M)</option>
-        <option value="dHex (N)">dHex (N)</option>
-        <option value="dHex (S)">dHex (S)</option>
-        <option value="dHex (T)">dHex (T)</option>
-        <option value="dHex(1)Hex(1) (S)">dHex(1)Hex(1) (S)</option>
-        <option value="dHex(1)Hex(1) (T)">dHex(1)Hex(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexA(1)HexNAc(3) (S)">dHex(1)Hex(1)HexA(1)HexNAc(3) (S)</option>
-        <option value="dHex(1)Hex(1)HexA(1)HexNAc(3) (T)">dHex(1)Hex(1)HexA(1)HexNAc(3) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)Kdn(1) (S)">dHex(1)Hex(1)HexNAc(1)Kdn(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)Kdn(1) (T)">dHex(1)Hex(1)HexNAc(1)Kdn(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(1)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(1)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3) (S)">dHex(1)Hex(1)HexNAc(3) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3) (T)">dHex(1)Hex(1)HexNAc(3) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(4) (S)">dHex(1)Hex(1)HexNAc(4) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(4) (T)">dHex(1)Hex(1)HexNAc(4) (T)</option>
-        <option value="dHex(1)Hex(2) (S)">dHex(1)Hex(2) (S)</option>
-        <option value="dHex(1)Hex(2) (T)">dHex(1)Hex(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexA(1) (S)">dHex(1)Hex(2)HexA(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexA(1) (T)">dHex(1)Hex(2)HexA(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(1) (S)">dHex(1)Hex(2)HexA(1)HexNAc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(1) (T)">dHex(1)Hex(2)HexA(1)HexNAc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (S)">dHex(1)Hex(2)HexA(1)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (T)">dHex(1)Hex(2)HexA(1)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1) (S)">dHex(1)Hex(2)HexNAc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1) (T)">dHex(1)Hex(2)HexNAc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)Pent(1) (N)">dHex(1)Hex(2)HexNAc(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3) (N)">dHex(1)Hex(2)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3) (S)">dHex(1)Hex(2)HexNAc(3) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3) (T)">dHex(1)Hex(2)HexNAc(3) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4) (N)">dHex(1)Hex(2)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4) (S)">dHex(1)Hex(2)HexNAc(4) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4) (T)">dHex(1)Hex(2)HexNAc(4) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-        <option value="dHex(1)Hex(3) (S)">dHex(1)Hex(3) (S)</option>
-        <option value="dHex(1)Hex(3) (T)">dHex(1)Hex(3) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(2) (S)">dHex(1)Hex(3)HexA(1)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(2) (T)">dHex(1)Hex(3)HexA(1)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(2)HexNAc(2) (S)">dHex(1)Hex(3)HexA(2)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(2)HexNAc(2) (T)">dHex(1)Hex(3)HexA(2)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(1) (S)">dHex(1)Hex(3)HexNAc(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(1) (T)">dHex(1)Hex(3)HexNAc(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2) (N)">dHex(1)Hex(3)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2) (S)">dHex(1)Hex(3)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2) (T)">dHex(1)Hex(3)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)Pent(1) (N)">dHex(1)Hex(3)HexNAc(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3) (N)">dHex(1)Hex(3)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3) (S)">dHex(1)Hex(3)HexNAc(3) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3) (T)">dHex(1)Hex(3)HexNAc(3) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Pent(1) (N)">dHex(1)Hex(3)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Pent(2) (N)">dHex(1)Hex(3)HexNAc(3)Pent(2) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Pent(3) (N)">dHex(1)Hex(3)HexNAc(3)Pent(3) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4) (N)">dHex(1)Hex(3)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4) (S)">dHex(1)Hex(3)HexNAc(4) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4) (T)">dHex(1)Hex(3)HexNAc(4) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)Pent(1) (N)">dHex(1)Hex(3)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)Pent(2) (N)">dHex(1)Hex(3)HexNAc(4)Pent(2) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)Pent(3) (N)">dHex(1)Hex(3)HexNAc(4)Pent(3) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5) (N)">dHex(1)Hex(3)HexNAc(5) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5) (S)">dHex(1)Hex(3)HexNAc(5) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5) (T)">dHex(1)Hex(3)HexNAc(5) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(5)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(6) (N)">dHex(1)Hex(3)HexNAc(6) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(6) (S)">dHex(1)Hex(3)HexNAc(6) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(6) (T)">dHex(1)Hex(3)HexNAc(6) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4) (S)">dHex(1)Hex(4) (S)</option>
-        <option value="dHex(1)Hex(4) (T)">dHex(1)Hex(4) (T)</option>
-        <option value="dHex(1)Hex(4)HexA(1) (S)">dHex(1)Hex(4)HexA(1) (S)</option>
-        <option value="dHex(1)Hex(4)HexA(1) (T)">dHex(1)Hex(4)HexA(1) (T)</option>
-        <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (S)">dHex(1)Hex(4)HexA(1)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (T)">dHex(1)Hex(4)HexA(1)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(1)Pent(1) (N)">dHex(1)Hex(4)HexNAc(1)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(2) (N)">dHex(1)Hex(4)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(2) (S)">dHex(1)Hex(4)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(4)HexNAc(2) (T)">dHex(1)Hex(4)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(2)Pent(1) (N)">dHex(1)Hex(4)HexNAc(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3) (N)">dHex(1)Hex(4)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)Pent(1) (N)">dHex(1)Hex(4)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4) (N)">dHex(1)Hex(4)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4) (S)">dHex(1)Hex(4)HexNAc(4) (S)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4) (T)">dHex(1)Hex(4)HexNAc(4) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)Pent(1) (N)">dHex(1)Hex(4)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(5) (N)">dHex(1)Hex(4)HexNAc(5) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(5)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(5)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5) (S)">dHex(1)Hex(5) (S)</option>
-        <option value="dHex(1)Hex(5) (T)">dHex(1)Hex(5) (T)</option>
-        <option value="dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N)">dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(2) (N)">dHex(1)Hex(5)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(2)Pent(1) (N)">dHex(1)Hex(5)HexNAc(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3) (N)">dHex(1)Hex(5)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4) (N)">dHex(1)Hex(5)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N)">dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N)">dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)Pent(1) (N)">dHex(1)Hex(5)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)Sulf(2) (N)">dHex(1)Hex(5)HexNAc(4)Sulf(2) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(5) (N)">dHex(1)Hex(5)HexNAc(5) (N)</option>
-        <option value="dHex(1)Hex(6) (S)">dHex(1)Hex(6) (S)</option>
-        <option value="dHex(1)Hex(6) (T)">dHex(1)Hex(6) (T)</option>
-        <option value="dHex(1)Hex(6)HexNAc(2) (N)">dHex(1)Hex(6)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(6)HexNAc(3) (N)">dHex(1)Hex(6)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(6)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(6)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(6)HexNAc(4) (N)">dHex(1)Hex(6)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(2) (N)">dHex(1)Hex(7)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(3) (N)">dHex(1)Hex(7)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(3)Phos(1) (N)">dHex(1)Hex(7)HexNAc(3)Phos(1) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(4) (N)">dHex(1)Hex(7)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(8)HexNAc(2) (N)">dHex(1)Hex(8)HexNAc(2) (N)</option>
-        <option value="dHex(1)HexNAc(3) (S)">dHex(1)HexNAc(3) (S)</option>
-        <option value="dHex(1)HexNAc(3) (T)">dHex(1)HexNAc(3) (T)</option>
-        <option value="dHex(1)HexNAc(4) (S)">dHex(1)HexNAc(4) (S)</option>
-        <option value="dHex(1)HexNAc(4) (T)">dHex(1)HexNAc(4) (T)</option>
-        <option value="dHex(1)HexNAc(5) (S)">dHex(1)HexNAc(5) (S)</option>
-        <option value="dHex(1)HexNAc(5) (T)">dHex(1)HexNAc(5) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(1)Kdn(1) (S)">dHex(2)Hex(1)HexNAc(1)Kdn(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(1)Kdn(1) (T)">dHex(2)Hex(1)HexNAc(1)Kdn(1) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(2)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(2)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)NeuAc(1) (S)">dHex(2)Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)NeuAc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(3) (S)">dHex(2)Hex(1)HexNAc(3) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(3) (T)">dHex(2)Hex(1)HexNAc(3) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2) (S)">dHex(2)Hex(2) (S)</option>
-        <option value="dHex(2)Hex(2) (T)">dHex(2)Hex(2) (T)</option>
-        <option value="dHex(2)Hex(2)HexA(1) (S)">dHex(2)Hex(2)HexA(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexA(1) (T)">dHex(2)Hex(2)HexA(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexA(1)HexNAc(1) (S)">dHex(2)Hex(2)HexA(1)HexNAc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexA(1)HexNAc(1) (T)">dHex(2)Hex(2)HexA(1)HexNAc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(1) (S)">dHex(2)Hex(2)HexNAc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(1) (T)">dHex(2)Hex(2)HexNAc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2) (N)">dHex(2)Hex(2)HexNAc(2) (N)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2) (S)">dHex(2)Hex(2)HexNAc(2) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2) (T)">dHex(2)Hex(2)HexNAc(2) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(2)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(2)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(2)Sulf(2) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(2)Sulf(2) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3) (N)">dHex(2)Hex(2)HexNAc(3) (N)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3) (S)">dHex(2)Hex(2)HexNAc(3) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3) (T)">dHex(2)Hex(2)HexNAc(3) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)NeuAc(1) (S)">dHex(2)Hex(2)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(2)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)NeuGc(1) (S)">dHex(2)Hex(2)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)NeuGc(1) (T)">dHex(2)Hex(2)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(4) (S)">dHex(2)Hex(2)HexNAc(4) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(4) (T)">dHex(2)Hex(2)HexNAc(4) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(5) (S)">dHex(2)Hex(2)HexNAc(5) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(5) (T)">dHex(2)Hex(2)HexNAc(5) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3) (S)">dHex(2)Hex(3) (S)</option>
-        <option value="dHex(2)Hex(3) (T)">dHex(2)Hex(3) (T)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(1)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2) (N)">dHex(2)Hex(3)HexNAc(2) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2) (S)">dHex(2)Hex(3)HexNAc(2) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2) (T)">dHex(2)Hex(3)HexNAc(2) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(3)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(3)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3) (N)">dHex(2)Hex(3)HexNAc(3) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3) (S)">dHex(2)Hex(3)HexNAc(3) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3) (T)">dHex(2)Hex(3)HexNAc(3) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)Pent(1) (N)">dHex(2)Hex(3)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)Pent(2) (N)">dHex(2)Hex(3)HexNAc(3)Pent(2) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4) (N)">dHex(2)Hex(3)HexNAc(4) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4) (S)">dHex(2)Hex(3)HexNAc(4) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4) (T)">dHex(2)Hex(3)HexNAc(4) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4)Pent(1) (N)">dHex(2)Hex(3)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4)Pent(2) (N)">dHex(2)Hex(3)HexNAc(4)Pent(2) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(5) (N)">dHex(2)Hex(3)HexNAc(5) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(5) (S)">dHex(2)Hex(3)HexNAc(5) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(5) (T)">dHex(2)Hex(3)HexNAc(5) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(6) (N)">dHex(2)Hex(3)HexNAc(6) (N)</option>
-        <option value="dHex(2)Hex(4) (S)">dHex(2)Hex(4) (S)</option>
-        <option value="dHex(2)Hex(4) (T)">dHex(2)Hex(4) (T)</option>
-        <option value="dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(4)HexNAc(1) (S)">dHex(2)Hex(4)HexNAc(1) (S)</option>
-        <option value="dHex(2)Hex(4)HexNAc(1) (T)">dHex(2)Hex(4)HexNAc(1) (T)</option>
-        <option value="dHex(2)Hex(4)HexNAc(2) (N)">dHex(2)Hex(4)HexNAc(2) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(2) (S)">dHex(2)Hex(4)HexNAc(2) (S)</option>
-        <option value="dHex(2)Hex(4)HexNAc(2) (T)">dHex(2)Hex(4)HexNAc(2) (T)</option>
-        <option value="dHex(2)Hex(4)HexNAc(3) (N)">dHex(2)Hex(4)HexNAc(3) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(3)Pent(1) (N)">dHex(2)Hex(4)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4) (N)">dHex(2)Hex(4)HexNAc(4) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4) (S)">dHex(2)Hex(4)HexNAc(4) (S)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4) (T)">dHex(2)Hex(4)HexNAc(4) (T)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4)Pent(1) (N)">dHex(2)Hex(4)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(2)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(5) (N)">dHex(2)Hex(4)HexNAc(5) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(5) (S)">dHex(2)Hex(4)HexNAc(5) (S)</option>
-        <option value="dHex(2)Hex(4)HexNAc(5) (T)">dHex(2)Hex(4)HexNAc(5) (T)</option>
-        <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (S)">dHex(2)Hex(5)HexNAc(2)Me(1) (S)</option>
-        <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (T)">dHex(2)Hex(5)HexNAc(2)Me(1) (T)</option>
-        <option value="dHex(2)Hex(5)HexNAc(3)Pent(1) (N)">dHex(2)Hex(5)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(5)HexNAc(4) (N)">dHex(2)Hex(5)HexNAc(4) (N)</option>
-        <option value="dHex(2)HexNAc(2)Kdn(1) (S)">dHex(2)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(2)HexNAc(2)Kdn(1) (T)">dHex(2)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(2)HexNAc(5) (S)">dHex(2)HexNAc(5) (S)</option>
-        <option value="dHex(2)HexNAc(5) (T)">dHex(2)HexNAc(5) (T)</option>
-        <option value="dHex(2)HexNAc(7) (S)">dHex(2)HexNAc(7) (S)</option>
-        <option value="dHex(2)HexNAc(7) (T)">dHex(2)HexNAc(7) (T)</option>
-        <option value="dHex(3)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(3)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(3)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(3)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(3)Hex(1)HexNAc(3)Kdn(1) (S)">dHex(3)Hex(1)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(3)Hex(1)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(1)HexNAc(3)Kdn(1) (T)</option>
-        <option value="dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(2) (S)">dHex(3)Hex(2)HexNAc(2) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(2) (T)">dHex(3)Hex(2)HexNAc(2) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(3)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(3) (S)">dHex(3)Hex(2)HexNAc(3) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(3) (T)">dHex(3)Hex(2)HexNAc(3) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (S)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(4) (S)">dHex(3)Hex(2)HexNAc(4) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(4) (T)">dHex(3)Hex(2)HexNAc(4) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(1) (S)">dHex(3)Hex(3)HexNAc(1) (S)</option>
-        <option value="dHex(3)Hex(3)HexNAc(1) (T)">dHex(3)Hex(3)HexNAc(1) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(2) (S)">dHex(3)Hex(3)HexNAc(2) (S)</option>
-        <option value="dHex(3)Hex(3)HexNAc(2) (T)">dHex(3)Hex(3)HexNAc(2) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3) (S)">dHex(3)Hex(3)HexNAc(3) (S)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3) (T)">dHex(3)Hex(3)HexNAc(3) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3)Pent(1) (N)">dHex(3)Hex(3)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(3)Hex(3)HexNAc(4) (N)">dHex(3)Hex(3)HexNAc(4) (N)</option>
-        <option value="dHex(3)Hex(3)HexNAc(4)Pent(1) (N)">dHex(3)Hex(3)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(3)Hex(4)HexNAc(4) (N)">dHex(3)Hex(4)HexNAc(4) (N)</option>
-        <option value="dHex(3)Hex(4)HexNAc(4) (S)">dHex(3)Hex(4)HexNAc(4) (S)</option>
-        <option value="dHex(3)Hex(4)HexNAc(4) (T)">dHex(3)Hex(4)HexNAc(4) (T)</option>
-        <option value="dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(3)HexNAc(3)Kdn(1) (S)">dHex(3)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(3)HexNAc(3)Kdn(1) (T)">dHex(3)HexNAc(3)Kdn(1) (T)</option>
-        <option value="dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)">dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)</option>
-        <option value="dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)">dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)</option>
-        <option value="dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)">dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)">dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)</option>
-        <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(4)Hex(2)HexNAc(3) (S)">dHex(4)Hex(2)HexNAc(3) (S)</option>
-        <option value="dHex(4)Hex(2)HexNAc(3) (T)">dHex(4)Hex(2)HexNAc(3) (T)</option>
-        <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="dHex(4)Hex(3)HexNAc(3) (S)">dHex(4)Hex(3)HexNAc(3) (S)</option>
-        <option value="dHex(4)Hex(3)HexNAc(3) (T)">dHex(4)Hex(3)HexNAc(3) (T)</option>
-        <option value="dHex(4)HexNAc(3)Kdn(1) (S)">dHex(4)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(4)HexNAc(3)Kdn(1) (T)">dHex(4)HexNAc(3)Kdn(1) (T)</option>
-        <option value="DHP (C)">DHP (C)</option>
-        <option value="Diacylglycerol (C)">Diacylglycerol (C)</option>
-        <option value="DiART6plex (K)">DiART6plex (K)</option>
-        <option value="DiART6plex (N-term)">DiART6plex (N-term)</option>
-        <option value="DiART6plex (Protein N-term)">DiART6plex (Protein N-term)</option>
-        <option value="DiART6plex (Y)">DiART6plex (Y)</option>
-        <option value="DiART6plex115 (K)">DiART6plex115 (K)</option>
-        <option value="DiART6plex115 (N-term)">DiART6plex115 (N-term)</option>
-        <option value="DiART6plex115 (Protein N-term)">DiART6plex115 (Protein N-term)</option>
-        <option value="DiART6plex115 (Y)">DiART6plex115 (Y)</option>
-        <option value="DiART6plex116/119 (K)">DiART6plex116/119 (K)</option>
-        <option value="DiART6plex116/119 (N-term)">DiART6plex116/119 (N-term)</option>
-        <option value="DiART6plex116/119 (Protein N-term)">DiART6plex116/119 (Protein N-term)</option>
-        <option value="DiART6plex116/119 (Y)">DiART6plex116/119 (Y)</option>
-        <option value="DiART6plex117 (K)">DiART6plex117 (K)</option>
-        <option value="DiART6plex117 (N-term)">DiART6plex117 (N-term)</option>
-        <option value="DiART6plex117 (Protein N-term)">DiART6plex117 (Protein N-term)</option>
-        <option value="DiART6plex117 (Y)">DiART6plex117 (Y)</option>
-        <option value="DiART6plex118 (K)">DiART6plex118 (K)</option>
-        <option value="DiART6plex118 (N-term)">DiART6plex118 (N-term)</option>
-        <option value="DiART6plex118 (Protein N-term)">DiART6plex118 (Protein N-term)</option>
-        <option value="DiART6plex118 (Y)">DiART6plex118 (Y)</option>
-        <option value="Dibromo (Y)">Dibromo (Y)</option>
-        <option value="Dicarbamidomethyl (C)">Dicarbamidomethyl (C)</option>
-        <option value="Dicarbamidomethyl (H)">Dicarbamidomethyl (H)</option>
-        <option value="Dicarbamidomethyl (K)">Dicarbamidomethyl (K)</option>
-        <option value="Dicarbamidomethyl (N-term)">Dicarbamidomethyl (N-term)</option>
-        <option value="Dicarbamidomethyl (R)">Dicarbamidomethyl (R)</option>
-        <option value="dichlorination (C)">dichlorination (C)</option>
-        <option value="dichlorination (Y)">dichlorination (Y)</option>
-        <option value="Didehydro (C-term K)">Didehydro (C-term K)</option>
-        <option value="Didehydro (S)">Didehydro (S)</option>
-        <option value="Didehydro (T)">Didehydro (T)</option>
-        <option value="Didehydro (Y)">Didehydro (Y)</option>
-        <option value="Didehydroretinylidene (K)">Didehydroretinylidene (K)</option>
-        <option value="Diethyl (K)">Diethyl (K)</option>
-        <option value="Diethyl (N-term)">Diethyl (N-term)</option>
-        <option value="Diethylphosphate (C)">Diethylphosphate (C)</option>
-        <option value="Diethylphosphate (H)">Diethylphosphate (H)</option>
-        <option value="Diethylphosphate (K)">Diethylphosphate (K)</option>
-        <option value="Diethylphosphate (N-term)">Diethylphosphate (N-term)</option>
-        <option value="Diethylphosphate (S)">Diethylphosphate (S)</option>
-        <option value="Diethylphosphate (T)">Diethylphosphate (T)</option>
-        <option value="Diethylphosphate (Y)">Diethylphosphate (Y)</option>
-        <option value="Diethylphosphothione (C)">Diethylphosphothione (C)</option>
-        <option value="Diethylphosphothione (H)">Diethylphosphothione (H)</option>
-        <option value="Diethylphosphothione (K)">Diethylphosphothione (K)</option>
-        <option value="Diethylphosphothione (S)">Diethylphosphothione (S)</option>
-        <option value="Diethylphosphothione (T)">Diethylphosphothione (T)</option>
-        <option value="Diethylphosphothione (Y)">Diethylphosphothione (Y)</option>
-        <option value="Difuran (Y)">Difuran (Y)</option>
-        <option value="Dihydroxyimidazolidine (R)">Dihydroxyimidazolidine (R)</option>
-        <option value="Diiodo (H)">Diiodo (H)</option>
-        <option value="Diiodo (Y)">Diiodo (Y)</option>
-        <option value="Diironsubcluster (C)">Diironsubcluster (C)</option>
-        <option value="Diisopropylphosphate (K)">Diisopropylphosphate (K)</option>
-        <option value="Diisopropylphosphate (N-term)">Diisopropylphosphate (N-term)</option>
-        <option value="Diisopropylphosphate (S)">Diisopropylphosphate (S)</option>
-        <option value="Diisopropylphosphate (T)">Diisopropylphosphate (T)</option>
-        <option value="Diisopropylphosphate (Y)">Diisopropylphosphate (Y)</option>
-        <option value="DiLeu4plex (K)">DiLeu4plex (K)</option>
-        <option value="DiLeu4plex (N-term)">DiLeu4plex (N-term)</option>
-        <option value="DiLeu4plex (Y)">DiLeu4plex (Y)</option>
-        <option value="DiLeu4plex115 (K)">DiLeu4plex115 (K)</option>
-        <option value="DiLeu4plex115 (N-term)">DiLeu4plex115 (N-term)</option>
-        <option value="DiLeu4plex115 (Y)">DiLeu4plex115 (Y)</option>
-        <option value="DiLeu4plex117 (K)">DiLeu4plex117 (K)</option>
-        <option value="DiLeu4plex117 (N-term)">DiLeu4plex117 (N-term)</option>
-        <option value="DiLeu4plex117 (Y)">DiLeu4plex117 (Y)</option>
-        <option value="DiLeu4plex118 (K)">DiLeu4plex118 (K)</option>
-        <option value="DiLeu4plex118 (N-term)">DiLeu4plex118 (N-term)</option>
-        <option value="DiLeu4plex118 (Y)">DiLeu4plex118 (Y)</option>
-        <option value="Dimethyl (K)">Dimethyl (K)</option>
-        <option value="Dimethyl (N)">Dimethyl (N)</option>
-        <option value="Dimethyl (N-term)">Dimethyl (N-term)</option>
-        <option value="Dimethyl (Protein N-term P)">Dimethyl (Protein N-term P)</option>
-        <option value="Dimethyl (Protein N-term)">Dimethyl (Protein N-term)</option>
-        <option value="Dimethyl (R)">Dimethyl (R)</option>
-        <option value="Dimethyl:2H(2)13C (K)">Dimethyl:2H(2)13C (K)</option>
-        <option value="Dimethyl:2H(2)13C (N)">Dimethyl:2H(2)13C (N)</option>
-        <option value="Dimethyl:2H(2)13C (N-term)">Dimethyl:2H(2)13C (N-term)</option>
-        <option value="Dimethyl:2H(2)13C (Protein N-term P)">Dimethyl:2H(2)13C (Protein N-term P)</option>
-        <option value="Dimethyl:2H(2)13C (R)">Dimethyl:2H(2)13C (R)</option>
-        <option value="Dimethyl:2H(4) (K)">Dimethyl:2H(4) (K)</option>
-        <option value="Dimethyl:2H(4) (N-term)">Dimethyl:2H(4) (N-term)</option>
-        <option value="Dimethyl:2H(4) (Protein N-term)">Dimethyl:2H(4) (Protein N-term)</option>
-        <option value="Dimethyl:2H(4) (R)">Dimethyl:2H(4) (R)</option>
-        <option value="Dimethyl:2H(4)13C(2) (K)">Dimethyl:2H(4)13C(2) (K)</option>
-        <option value="Dimethyl:2H(4)13C(2) (N-term)">Dimethyl:2H(4)13C(2) (N-term)</option>
-        <option value="Dimethyl:2H(4)13C(2) (Protein N-term)">Dimethyl:2H(4)13C(2) (Protein N-term)</option>
-        <option value="Dimethyl:2H(4)13C(2) (R)">Dimethyl:2H(4)13C(2) (R)</option>
-        <option value="Dimethyl:2H(6) (K)">Dimethyl:2H(6) (K)</option>
-        <option value="Dimethyl:2H(6) (N-term)">Dimethyl:2H(6) (N-term)</option>
-        <option value="Dimethyl:2H(6) (R)">Dimethyl:2H(6) (R)</option>
-        <option value="Dimethyl:2H(6)13C(2) (K)">Dimethyl:2H(6)13C(2) (K)</option>
-        <option value="Dimethyl:2H(6)13C(2) (N-term)">Dimethyl:2H(6)13C(2) (N-term)</option>
-        <option value="Dimethyl:2H(6)13C(2) (Protein N-term)">Dimethyl:2H(6)13C(2) (Protein N-term)</option>
-        <option value="Dimethyl:2H(6)13C(2) (R)">Dimethyl:2H(6)13C(2) (R)</option>
-        <option value="DimethylamineGMBS (C)">DimethylamineGMBS (C)</option>
-        <option value="Dimethylaminoethyl (C)">Dimethylaminoethyl (C)</option>
-        <option value="DimethylArsino (C)">DimethylArsino (C)</option>
-        <option value="Dimethylphosphothione (C)">Dimethylphosphothione (C)</option>
-        <option value="Dimethylphosphothione (H)">Dimethylphosphothione (H)</option>
-        <option value="Dimethylphosphothione (K)">Dimethylphosphothione (K)</option>
-        <option value="Dimethylphosphothione (S)">Dimethylphosphothione (S)</option>
-        <option value="Dimethylphosphothione (T)">Dimethylphosphothione (T)</option>
-        <option value="Dimethylphosphothione (Y)">Dimethylphosphothione (Y)</option>
-        <option value="DimethylpyrroleAdduct (K)">DimethylpyrroleAdduct (K)</option>
-        <option value="Dioxidation (C)">Dioxidation (C)</option>
-        <option value="Dioxidation (E)">Dioxidation (E)</option>
-        <option value="Dioxidation (F)">Dioxidation (F)</option>
-        <option value="Dioxidation (I)">Dioxidation (I)</option>
-        <option value="Dioxidation (K)">Dioxidation (K)</option>
-        <option value="Dioxidation (L)">Dioxidation (L)</option>
-        <option value="Dioxidation (M)">Dioxidation (M)</option>
-        <option value="Dioxidation (P)">Dioxidation (P)</option>
-        <option value="Dioxidation (R)">Dioxidation (R)</option>
-        <option value="Dioxidation (U)">Dioxidation (U)</option>
-        <option value="Dioxidation (V)">Dioxidation (V)</option>
-        <option value="Dioxidation (W)">Dioxidation (W)</option>
-        <option value="Dioxidation (Y)">Dioxidation (Y)</option>
-        <option value="Diphthamide (H)">Diphthamide (H)</option>
-        <option value="Dipyridyl (C)">Dipyridyl (C)</option>
-        <option value="Dipyrrolylmethanemethyl (C)">Dipyrrolylmethanemethyl (C)</option>
-        <option value="DMPO (C)">DMPO (C)</option>
-        <option value="DMPO (H)">DMPO (H)</option>
-        <option value="DMPO (Y)">DMPO (Y)</option>
-        <option value="DNCB_hapten (C)">DNCB_hapten (C)</option>
-        <option value="DNCB_hapten (H)">DNCB_hapten (H)</option>
-        <option value="DNCB_hapten (K)">DNCB_hapten (K)</option>
-        <option value="DNCB_hapten (Y)">DNCB_hapten (Y)</option>
-        <option value="dNIC (K)">dNIC (K)</option>
-        <option value="dNIC (N-term)">dNIC (N-term)</option>
-        <option value="DNPS (C)">DNPS (C)</option>
-        <option value="DNPS (W)">DNPS (W)</option>
-        <option value="DTT (C)">DTT (C)</option>
-        <option value="DyLight-maleimide (C)">DyLight-maleimide (C)</option>
-        <option value="DYn-2 (C)">DYn-2 (C)</option>
-        <option value="EDEDTIDVFQQQTGG (K)">EDEDTIDVFQQQTGG (K)</option>
-        <option value="EDT-iodoacetyl-PEO-biotin (S)">EDT-iodoacetyl-PEO-biotin (S)</option>
-        <option value="EDT-iodoacetyl-PEO-biotin (T)">EDT-iodoacetyl-PEO-biotin (T)</option>
-        <option value="EDT-maleimide-PEO-biotin (S)">EDT-maleimide-PEO-biotin (S)</option>
-        <option value="EDT-maleimide-PEO-biotin (T)">EDT-maleimide-PEO-biotin (T)</option>
-        <option value="EEEDVIEVYQEQTGG (K)">EEEDVIEVYQEQTGG (K)</option>
-        <option value="EGCG1 (C)">EGCG1 (C)</option>
-        <option value="EGCG2 (C)">EGCG2 (C)</option>
-        <option value="EHD-diphenylpentanone (C)">EHD-diphenylpentanone (C)</option>
-        <option value="EHD-diphenylpentanone (M)">EHD-diphenylpentanone (M)</option>
-        <option value="EQAT (C)">EQAT (C)</option>
-        <option value="EQAT:2H(5) (C)">EQAT:2H(5) (C)</option>
-        <option value="EQIGG (K)">EQIGG (K)</option>
-        <option value="ESP (K)">ESP (K)</option>
-        <option value="ESP (N-term)">ESP (N-term)</option>
-        <option value="ESP:2H(10) (K)">ESP:2H(10) (K)</option>
-        <option value="ESP:2H(10) (N-term)">ESP:2H(10) (N-term)</option>
-        <option value="Ethanedithiol (S)">Ethanedithiol (S)</option>
-        <option value="Ethanedithiol (T)">Ethanedithiol (T)</option>
-        <option value="Ethanolamine (C)">Ethanolamine (C)</option>
-        <option value="Ethanolamine (C-term)">Ethanolamine (C-term)</option>
-        <option value="Ethanolamine (D)">Ethanolamine (D)</option>
-        <option value="Ethanolamine (E)">Ethanolamine (E)</option>
-        <option value="Ethanolyl (C)">Ethanolyl (C)</option>
-        <option value="Ethanolyl (K)">Ethanolyl (K)</option>
-        <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-        <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
-        <option value="Ethyl (C-term)">Ethyl (C-term)</option>
-        <option value="Ethyl (D)">Ethyl (D)</option>
-        <option value="Ethyl (E)">Ethyl (E)</option>
-        <option value="Ethyl (K)">Ethyl (K)</option>
-        <option value="Ethyl (N-term)">Ethyl (N-term)</option>
-        <option value="Ethyl (Protein N-term)">Ethyl (Protein N-term)</option>
-        <option value="Ethyl+Deamidated (N)">Ethyl+Deamidated (N)</option>
-        <option value="Ethyl+Deamidated (Q)">Ethyl+Deamidated (Q)</option>
-        <option value="ethylamino (S)">ethylamino (S)</option>
-        <option value="ethylamino (T)">ethylamino (T)</option>
-        <option value="Ethylphosphate (K)">Ethylphosphate (K)</option>
-        <option value="Ethylphosphate (N-term)">Ethylphosphate (N-term)</option>
-        <option value="Ethylphosphate (S)">Ethylphosphate (S)</option>
-        <option value="Ethylphosphate (T)">Ethylphosphate (T)</option>
-        <option value="Ethylphosphate (Y)">Ethylphosphate (Y)</option>
-        <option value="ethylsulfonylethyl (C)">ethylsulfonylethyl (C)</option>
-        <option value="ethylsulfonylethyl (H)">ethylsulfonylethyl (H)</option>
-        <option value="ethylsulfonylethyl (K)">ethylsulfonylethyl (K)</option>
-        <option value="ExacTagAmine (K)">ExacTagAmine (K)</option>
-        <option value="ExacTagThiol (C)">ExacTagThiol (C)</option>
-        <option value="FAD (C)">FAD (C)</option>
-        <option value="FAD (H)">FAD (H)</option>
-        <option value="FAD (Y)">FAD (Y)</option>
-        <option value="Farnesyl (C)">Farnesyl (C)</option>
-        <option value="Fluorescein (C)">Fluorescein (C)</option>
-        <option value="Fluorescein-tyramine (Y)">Fluorescein-tyramine (Y)</option>
-        <option value="Fluoro (A)">Fluoro (A)</option>
-        <option value="Fluoro (F)">Fluoro (F)</option>
-        <option value="Fluoro (W)">Fluoro (W)</option>
-        <option value="Fluoro (Y)">Fluoro (Y)</option>
-        <option value="FMN (S)">FMN (S)</option>
-        <option value="FMN (T)">FMN (T)</option>
-        <option value="FMNC (C)">FMNC (C)</option>
-        <option value="FMNH (C)">FMNH (C)</option>
-        <option value="FMNH (H)">FMNH (H)</option>
-        <option value="FNEM (C)">FNEM (C)</option>
-        <option value="Formyl (K)">Formyl (K)</option>
-        <option value="Formyl (N-term)">Formyl (N-term)</option>
-        <option value="Formyl (Protein N-term)">Formyl (Protein N-term)</option>
-        <option value="Formyl (S)">Formyl (S)</option>
-        <option value="Formyl (T)">Formyl (T)</option>
-        <option value="Formylasparagine (H)">Formylasparagine (H)</option>
-        <option value="FormylMet (Protein N-term)">FormylMet (Protein N-term)</option>
-        <option value="FP-Biotin (K)">FP-Biotin (K)</option>
-        <option value="FP-Biotin (S)">FP-Biotin (S)</option>
-        <option value="FP-Biotin (T)">FP-Biotin (T)</option>
-        <option value="FP-Biotin (Y)">FP-Biotin (Y)</option>
-        <option value="FTC (C)">FTC (C)</option>
-        <option value="FTC (K)">FTC (K)</option>
-        <option value="FTC (P)">FTC (P)</option>
-        <option value="FTC (R)">FTC (R)</option>
-        <option value="FTC (S)">FTC (S)</option>
-        <option value="Furan (Y)">Furan (Y)</option>
-        <option value="G-H1 (R)">G-H1 (R)</option>
-        <option value="Galactosyl (K)">Galactosyl (K)</option>
-        <option value="Galactosyl (N-term)">Galactosyl (N-term)</option>
-        <option value="GEE (Q)">GEE (Q)</option>
-        <option value="GeranylGeranyl (C)">GeranylGeranyl (C)</option>
-        <option value="GG (C)">GG (C)</option>
-        <option value="GG (K)">GG (K)</option>
-        <option value="GG (Protein N-term)">GG (Protein N-term)</option>
-        <option value="GG (S)">GG (S)</option>
-        <option value="GG (T)">GG (T)</option>
-        <option value="GGQ (K)">GGQ (K)</option>
-        <option value="GIST-Quat (K)">GIST-Quat (K)</option>
-        <option value="GIST-Quat (N-term)">GIST-Quat (N-term)</option>
-        <option value="GIST-Quat:2H(3) (K)">GIST-Quat:2H(3) (K)</option>
-        <option value="GIST-Quat:2H(3) (N-term)">GIST-Quat:2H(3) (N-term)</option>
-        <option value="GIST-Quat:2H(6) (K)">GIST-Quat:2H(6) (K)</option>
-        <option value="GIST-Quat:2H(6) (N-term)">GIST-Quat:2H(6) (N-term)</option>
-        <option value="GIST-Quat:2H(9) (K)">GIST-Quat:2H(9) (K)</option>
-        <option value="GIST-Quat:2H(9) (N-term)">GIST-Quat:2H(9) (N-term)</option>
-        <option value="Gln-&gt;Ala (Q)">Gln-&gt;Ala (Q)</option>
-        <option value="Gln-&gt;Arg (Q)">Gln-&gt;Arg (Q)</option>
-        <option value="Gln-&gt;Asn (Q)">Gln-&gt;Asn (Q)</option>
-        <option value="Gln-&gt;Asp (Q)">Gln-&gt;Asp (Q)</option>
-        <option value="Gln-&gt;Cys (Q)">Gln-&gt;Cys (Q)</option>
-        <option value="Gln-&gt;Glu (Q)">Gln-&gt;Glu (Q)</option>
-        <option value="Gln-&gt;Gly (Q)">Gln-&gt;Gly (Q)</option>
-        <option value="Gln-&gt;His (Q)">Gln-&gt;His (Q)</option>
-        <option value="Gln-&gt;Lys (Q)">Gln-&gt;Lys (Q)</option>
-        <option value="Gln-&gt;Met (Q)">Gln-&gt;Met (Q)</option>
-        <option value="Gln-&gt;Phe (Q)">Gln-&gt;Phe (Q)</option>
-        <option value="Gln-&gt;Pro (Q)">Gln-&gt;Pro (Q)</option>
-        <option value="Gln-&gt;pyro-Glu (N-term Q)">Gln-&gt;pyro-Glu (N-term Q)</option>
-        <option value="Gln-&gt;Ser (Q)">Gln-&gt;Ser (Q)</option>
-        <option value="Gln-&gt;Thr (Q)">Gln-&gt;Thr (Q)</option>
-        <option value="Gln-&gt;Trp (Q)">Gln-&gt;Trp (Q)</option>
-        <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
-        <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
-        <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
-        <option value="Glu (E)">Glu (E)</option>
-        <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
-        <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
-        <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
-        <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
-        <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
-        <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
-        <option value="Glu-&gt;Gln (E)">Glu-&gt;Gln (E)</option>
-        <option value="Glu-&gt;Gly (E)">Glu-&gt;Gly (E)</option>
-        <option value="Glu-&gt;His (E)">Glu-&gt;His (E)</option>
-        <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
-        <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
-        <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
-        <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
-        <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
-        <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
-        <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
-        <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
-        <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
-        <option value="Glu-&gt;Val (E)">Glu-&gt;Val (E)</option>
-        <option value="Glu-&gt;Xle (E)">Glu-&gt;Xle (E)</option>
-        <option value="glucosone (R)">glucosone (R)</option>
-        <option value="Glucosylgalactosyl (K)">Glucosylgalactosyl (K)</option>
-        <option value="Glucuronyl (Protein N-term)">Glucuronyl (Protein N-term)</option>
-        <option value="Glucuronyl (S)">Glucuronyl (S)</option>
-        <option value="Glucuronyl (T)">Glucuronyl (T)</option>
-        <option value="GluGlu (E)">GluGlu (E)</option>
-        <option value="GluGlu (Protein C-term)">GluGlu (Protein C-term)</option>
-        <option value="GluGluGlu (E)">GluGluGlu (E)</option>
-        <option value="GluGluGlu (Protein C-term)">GluGluGlu (Protein C-term)</option>
-        <option value="GluGluGluGlu (E)">GluGluGluGlu (E)</option>
-        <option value="GluGluGluGlu (Protein C-term)">GluGluGluGlu (Protein C-term)</option>
-        <option value="Gluratylation (K)">Gluratylation (K)</option>
-        <option value="Glutathione (C)">Glutathione (C)</option>
-        <option value="Gly (K)">Gly (K)</option>
-        <option value="Gly (S)">Gly (S)</option>
-        <option value="Gly (T)">Gly (T)</option>
-        <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
-        <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
-        <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
-        <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
-        <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
-        <option value="Gly-&gt;Gln (G)">Gly-&gt;Gln (G)</option>
-        <option value="Gly-&gt;Glu (G)">Gly-&gt;Glu (G)</option>
-        <option value="Gly-&gt;His (G)">Gly-&gt;His (G)</option>
-        <option value="Gly-&gt;Lys (G)">Gly-&gt;Lys (G)</option>
-        <option value="Gly-&gt;Met (G)">Gly-&gt;Met (G)</option>
-        <option value="Gly-&gt;Phe (G)">Gly-&gt;Phe (G)</option>
-        <option value="Gly-&gt;Pro (G)">Gly-&gt;Pro (G)</option>
-        <option value="Gly-&gt;Ser (G)">Gly-&gt;Ser (G)</option>
-        <option value="Gly-&gt;Thr (G)">Gly-&gt;Thr (G)</option>
-        <option value="Gly-&gt;Trp (G)">Gly-&gt;Trp (G)</option>
-        <option value="Gly-&gt;Tyr (G)">Gly-&gt;Tyr (G)</option>
-        <option value="Gly-&gt;Val (G)">Gly-&gt;Val (G)</option>
-        <option value="Gly-&gt;Xle (G)">Gly-&gt;Xle (G)</option>
-        <option value="Gly-loss+Amide (C-term G)">Gly-loss+Amide (C-term G)</option>
-        <option value="Glycerophospho (S)">Glycerophospho (S)</option>
-        <option value="GlycerylPE (E)">GlycerylPE (E)</option>
-        <option value="glycidamide (K)">glycidamide (K)</option>
-        <option value="glycidamide (N-term)">glycidamide (N-term)</option>
-        <option value="Glycosyl (P)">Glycosyl (P)</option>
-        <option value="glyoxalAGE (R)">glyoxalAGE (R)</option>
-        <option value="GNLLFLACYCIGG (K)">GNLLFLACYCIGG (K)</option>
-        <option value="GPIanchor (Protein C-term)">GPIanchor (Protein C-term)</option>
-        <option value="Guanidinyl (K)">Guanidinyl (K)</option>
-        <option value="Guanidinyl (N-term)">Guanidinyl (N-term)</option>
-        <option value="Haloxon (C)">Haloxon (C)</option>
-        <option value="Haloxon (H)">Haloxon (H)</option>
-        <option value="Haloxon (K)">Haloxon (K)</option>
-        <option value="Haloxon (S)">Haloxon (S)</option>
-        <option value="Haloxon (T)">Haloxon (T)</option>
-        <option value="Haloxon (Y)">Haloxon (Y)</option>
-        <option value="HCysteinyl (C)">HCysteinyl (C)</option>
-        <option value="HCysThiolactone (K)">HCysThiolactone (K)</option>
-        <option value="Heme (C)">Heme (C)</option>
-        <option value="Heme (H)">Heme (H)</option>
-        <option value="Hep (K)">Hep (K)</option>
-        <option value="Hep (N)">Hep (N)</option>
-        <option value="Hep (Q)">Hep (Q)</option>
-        <option value="Hep (R)">Hep (R)</option>
-        <option value="Hep (S)">Hep (S)</option>
-        <option value="Hep (T)">Hep (T)</option>
-        <option value="Hex (C)">Hex (C)</option>
-        <option value="Hex (K)">Hex (K)</option>
-        <option value="Hex (N)">Hex (N)</option>
-        <option value="Hex (N-term)">Hex (N-term)</option>
-        <option value="Hex (R)">Hex (R)</option>
-        <option value="Hex (S)">Hex (S)</option>
-        <option value="Hex (T)">Hex (T)</option>
-        <option value="Hex (W)">Hex (W)</option>
-        <option value="Hex (Y)">Hex (Y)</option>
-        <option value="Hex(1)HexA(1) (S)">Hex(1)HexA(1) (S)</option>
-        <option value="Hex(1)HexA(1) (T)">Hex(1)HexA(1) (T)</option>
-        <option value="Hex(1)HexA(1)HexNAc(1) (S)">Hex(1)HexA(1)HexNAc(1) (S)</option>
-        <option value="Hex(1)HexA(1)HexNAc(1) (T)">Hex(1)HexA(1)HexNAc(1) (T)</option>
-        <option value="Hex(1)HexA(1)HexNAc(2) (S)">Hex(1)HexA(1)HexNAc(2) (S)</option>
-        <option value="Hex(1)HexA(1)HexNAc(2) (T)">Hex(1)HexA(1)HexNAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(1) (N)">Hex(1)HexNAc(1) (N)</option>
-        <option value="Hex(1)HexNAc(1) (S)">Hex(1)HexNAc(1) (S)</option>
-        <option value="Hex(1)HexNAc(1) (T)">Hex(1)HexNAc(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1) (N)">Hex(1)HexNAc(1)dHex(1) (N)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1) (S)">Hex(1)HexNAc(1)dHex(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1) (T)">Hex(1)HexNAc(1)dHex(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1)Me(1) (S)">Hex(1)HexNAc(1)dHex(1)Me(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1)Me(1) (T)">Hex(1)HexNAc(1)dHex(1)Me(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1)Me(2) (S)">Hex(1)HexNAc(1)dHex(1)Me(2) (S)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1)Me(2) (T)">Hex(1)HexNAc(1)dHex(1)Me(2) (T)</option>
-        <option value="Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S)">Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T)">Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1) (N)">Hex(1)HexNAc(1)NeuAc(1) (N)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1) (S)">Hex(1)HexNAc(1)NeuAc(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1) (T)">Hex(1)HexNAc(1)NeuAc(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S)">Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T)">Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S)">Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T)">Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T)">Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2) (N)">Hex(1)HexNAc(1)NeuAc(2) (N)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2) (S)">Hex(1)HexNAc(1)NeuAc(2) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2) (T)">Hex(1)HexNAc(1)NeuAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S)">Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T)">Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S)">Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T)">Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(3) (S)">Hex(1)HexNAc(1)NeuAc(3) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(3) (T)">Hex(1)HexNAc(1)NeuAc(3) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(1) (S)">Hex(1)HexNAc(1)NeuGc(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(1) (T)">Hex(1)HexNAc(1)NeuGc(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(2) (S)">Hex(1)HexNAc(1)NeuGc(2) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(2) (T)">Hex(1)HexNAc(1)NeuGc(2) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(3) (S)">Hex(1)HexNAc(1)NeuGc(3) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(3) (T)">Hex(1)HexNAc(1)NeuGc(3) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(4) (S)">Hex(1)HexNAc(1)NeuGc(4) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(4) (T)">Hex(1)HexNAc(1)NeuGc(4) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(5) (S)">Hex(1)HexNAc(1)NeuGc(5) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(5) (T)">Hex(1)HexNAc(1)NeuGc(5) (T)</option>
-        <option value="Hex(1)HexNAc(1)Phos(1) (S)">Hex(1)HexNAc(1)Phos(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)Phos(1) (T)">Hex(1)HexNAc(1)Phos(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)Sulf(1) (S)">Hex(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)Sulf(1) (T)">Hex(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(2) (N)">Hex(1)HexNAc(2) (N)</option>
-        <option value="Hex(1)HexNAc(2) (S)">Hex(1)HexNAc(2) (S)</option>
-        <option value="Hex(1)HexNAc(2) (T)">Hex(1)HexNAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(2)dHex(1) (N)">Hex(1)HexNAc(2)dHex(1) (N)</option>
-        <option value="Hex(1)HexNAc(2)dHex(1) (S)">Hex(1)HexNAc(2)dHex(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)dHex(1) (T)">Hex(1)HexNAc(2)dHex(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)dHex(1)Pent(1) (N)">Hex(1)HexNAc(2)dHex(1)Pent(1) (N)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2) (N)">Hex(1)HexNAc(2)dHex(2) (N)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2) (S)">Hex(1)HexNAc(2)dHex(2) (S)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2) (T)">Hex(1)HexNAc(2)dHex(2) (T)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(1) (S)">Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(1) (T)">Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(2) (S)">Hex(1)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(2) (T)">Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T)">Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuGc(1) (S)">Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuGc(1) (T)">Hex(1)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)Pent(1) (N)">Hex(1)HexNAc(2)Pent(1) (N)</option>
-        <option value="Hex(1)HexNAc(2)Sulf(1) (S)">Hex(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)Sulf(1) (T)">Hex(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(3) (S)">Hex(1)HexNAc(3) (S)</option>
-        <option value="Hex(1)HexNAc(3) (T)">Hex(1)HexNAc(3) (T)</option>
-        <option value="Hex(1)HexNAc(3)NeuAc(1) (S)">Hex(1)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="Hex(1)HexNAc(3)NeuAc(1) (T)">Hex(1)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="Hex(1)HexNAc(3)NeuAc(2) (S)">Hex(1)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="Hex(1)HexNAc(3)NeuAc(2) (T)">Hex(1)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(3)NeuGc(1) (S)">Hex(1)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="Hex(1)HexNAc(3)NeuGc(1) (T)">Hex(1)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="Hex(1)HexNAc(3)Sulf(1) (S)">Hex(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(3)Sulf(1) (T)">Hex(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)</option>
-        <option value="Hex(1)NeuAc(1) (S)">Hex(1)NeuAc(1) (S)</option>
-        <option value="Hex(1)NeuAc(1) (T)">Hex(1)NeuAc(1) (T)</option>
-        <option value="Hex(1)NeuAc(1)Pent(1) (S)">Hex(1)NeuAc(1)Pent(1) (S)</option>
-        <option value="Hex(1)NeuAc(1)Pent(1) (T)">Hex(1)NeuAc(1)Pent(1) (T)</option>
-        <option value="Hex(1)NeuGc(1) (S)">Hex(1)NeuGc(1) (S)</option>
-        <option value="Hex(1)NeuGc(1) (T)">Hex(1)NeuGc(1) (T)</option>
-        <option value="Hex(1)Pent(1) (S)">Hex(1)Pent(1) (S)</option>
-        <option value="Hex(1)Pent(1) (T)">Hex(1)Pent(1) (T)</option>
-        <option value="Hex(1)Pent(2) (S)">Hex(1)Pent(2) (S)</option>
-        <option value="Hex(1)Pent(2) (T)">Hex(1)Pent(2) (T)</option>
-        <option value="Hex(1)Pent(2)Me(1) (S)">Hex(1)Pent(2)Me(1) (S)</option>
-        <option value="Hex(1)Pent(2)Me(1) (T)">Hex(1)Pent(2)Me(1) (T)</option>
-        <option value="Hex(1)Pent(3) (S)">Hex(1)Pent(3) (S)</option>
-        <option value="Hex(1)Pent(3) (T)">Hex(1)Pent(3) (T)</option>
-        <option value="Hex(1)Pent(3)Me(1) (S)">Hex(1)Pent(3)Me(1) (S)</option>
-        <option value="Hex(1)Pent(3)Me(1) (T)">Hex(1)Pent(3)Me(1) (T)</option>
-        <option value="Hex(10)HexNAc(1) (N)">Hex(10)HexNAc(1) (N)</option>
-        <option value="Hex(10)Phos(3) (S)">Hex(10)Phos(3) (S)</option>
-        <option value="Hex(10)Phos(3) (T)">Hex(10)Phos(3) (T)</option>
-        <option value="Hex(2) (K)">Hex(2) (K)</option>
-        <option value="Hex(2) (R)">Hex(2) (R)</option>
-        <option value="Hex(2) (S)">Hex(2) (S)</option>
-        <option value="Hex(2) (T)">Hex(2) (T)</option>
-        <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)Pent(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)Pent(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(1) (N)">Hex(2)HexNAc(1) (N)</option>
-        <option value="Hex(2)HexNAc(1) (S)">Hex(2)HexNAc(1) (S)</option>
-        <option value="Hex(2)HexNAc(1) (T)">Hex(2)HexNAc(1) (T)</option>
-        <option value="Hex(2)HexNAc(1)Me(1) (S)">Hex(2)HexNAc(1)Me(1) (S)</option>
-        <option value="Hex(2)HexNAc(1)Me(1) (T)">Hex(2)HexNAc(1)Me(1) (T)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(1) (S)">Hex(2)HexNAc(1)NeuGc(1) (S)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(1) (T)">Hex(2)HexNAc(1)NeuGc(1) (T)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(2) (S)">Hex(2)HexNAc(1)NeuGc(2) (S)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(2) (T)">Hex(2)HexNAc(1)NeuGc(2) (T)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(3) (S)">Hex(2)HexNAc(1)NeuGc(3) (S)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(3) (T)">Hex(2)HexNAc(1)NeuGc(3) (T)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(4) (S)">Hex(2)HexNAc(1)NeuGc(4) (S)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(4) (T)">Hex(2)HexNAc(1)NeuGc(4) (T)</option>
-        <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (S)">Hex(2)HexNAc(1)Pent(1)HexA(1) (S)</option>
-        <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (T)">Hex(2)HexNAc(1)Pent(1)HexA(1) (T)</option>
-        <option value="Hex(2)HexNAc(1)Sulf(1) (S)">Hex(2)HexNAc(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(1)Sulf(1) (T)">Hex(2)HexNAc(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(2) (N)">Hex(2)HexNAc(2) (N)</option>
-        <option value="Hex(2)HexNAc(2) (S)">Hex(2)HexNAc(2) (S)</option>
-        <option value="Hex(2)HexNAc(2) (T)">Hex(2)HexNAc(2) (T)</option>
-        <option value="Hex(2)HexNAc(2)dHex(1) (N)">Hex(2)HexNAc(2)dHex(1) (N)</option>
-        <option value="Hex(2)HexNAc(2)dHex(1) (S)">Hex(2)HexNAc(2)dHex(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)dHex(1) (T)">Hex(2)HexNAc(2)dHex(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1) (N)">Hex(2)HexNAc(2)NeuAc(1) (N)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1) (S)">Hex(2)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1) (T)">Hex(2)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(2) (S)">Hex(2)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(2) (T)">Hex(2)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuGc(1) (S)">Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuGc(1) (T)">Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)Pent(1) (N)">Hex(2)HexNAc(2)Pent(1) (N)</option>
-        <option value="Hex(2)HexNAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(3) (N)">Hex(2)HexNAc(3) (N)</option>
-        <option value="Hex(2)HexNAc(3) (S)">Hex(2)HexNAc(3) (S)</option>
-        <option value="Hex(2)HexNAc(3) (T)">Hex(2)HexNAc(3) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(2) (S)">Hex(2)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(2) (T)">Hex(2)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(3) (S)">Hex(2)HexNAc(3)NeuAc(3) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(3) (T)">Hex(2)HexNAc(3)NeuAc(3) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(1) (T)">Hex(2)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(2) (S)">Hex(2)HexNAc(3)NeuGc(2) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(2) (T)">Hex(2)HexNAc(3)NeuGc(2) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(3) (S)">Hex(2)HexNAc(3)NeuGc(3) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(3) (T)">Hex(2)HexNAc(3)NeuGc(3) (T)</option>
-        <option value="Hex(2)HexNAc(3)Sulf(1) (S)">Hex(2)HexNAc(3)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(3)Sulf(1) (T)">Hex(2)HexNAc(3)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(4) (N)">Hex(2)HexNAc(4) (N)</option>
-        <option value="Hex(2)HexNAc(4) (S)">Hex(2)HexNAc(4) (S)</option>
-        <option value="Hex(2)HexNAc(4) (T)">Hex(2)HexNAc(4) (T)</option>
-        <option value="Hex(2)HexNAc(4)NeuAc(1) (S)">Hex(2)HexNAc(4)NeuAc(1) (S)</option>
-        <option value="Hex(2)HexNAc(4)NeuAc(1) (T)">Hex(2)HexNAc(4)NeuAc(1) (T)</option>
-        <option value="Hex(2)HexNAc(5) (S)">Hex(2)HexNAc(5) (S)</option>
-        <option value="Hex(2)HexNAc(5) (T)">Hex(2)HexNAc(5) (T)</option>
-        <option value="Hex(2)NeuAc(1) (S)">Hex(2)NeuAc(1) (S)</option>
-        <option value="Hex(2)NeuAc(1) (T)">Hex(2)NeuAc(1) (T)</option>
-        <option value="Hex(2)Pent(2) (S)">Hex(2)Pent(2) (S)</option>
-        <option value="Hex(2)Pent(2) (T)">Hex(2)Pent(2) (T)</option>
-        <option value="Hex(2)Pent(2)Me(1) (S)">Hex(2)Pent(2)Me(1) (S)</option>
-        <option value="Hex(2)Pent(2)Me(1) (T)">Hex(2)Pent(2)Me(1) (T)</option>
-        <option value="Hex(2)Sulf(1) (S)">Hex(2)Sulf(1) (S)</option>
-        <option value="Hex(2)Sulf(1) (T)">Hex(2)Sulf(1) (T)</option>
-        <option value="Hex(3) (N)">Hex(3) (N)</option>
-        <option value="Hex(3) (S)">Hex(3) (S)</option>
-        <option value="Hex(3) (T)">Hex(3) (T)</option>
-        <option value="Hex(3)HexNAc(1) (N)">Hex(3)HexNAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(1) (S)">Hex(3)HexNAc(1) (S)</option>
-        <option value="Hex(3)HexNAc(1) (T)">Hex(3)HexNAc(1) (T)</option>
-        <option value="Hex(3)HexNAc(1)HexA(1) (S)">Hex(3)HexNAc(1)HexA(1) (S)</option>
-        <option value="Hex(3)HexNAc(1)HexA(1) (T)">Hex(3)HexNAc(1)HexA(1) (T)</option>
-        <option value="Hex(3)HexNAc(1)Me(1) (S)">Hex(3)HexNAc(1)Me(1) (S)</option>
-        <option value="Hex(3)HexNAc(1)Me(1) (T)">Hex(3)HexNAc(1)Me(1) (T)</option>
-        <option value="Hex(3)HexNAc(1)Pent(1) (N)">Hex(3)HexNAc(1)Pent(1) (N)</option>
-        <option value="Hex(3)HexNAc(2) (N)">Hex(3)HexNAc(2) (N)</option>
-        <option value="Hex(3)HexNAc(2) (S)">Hex(3)HexNAc(2) (S)</option>
-        <option value="Hex(3)HexNAc(2) (T)">Hex(3)HexNAc(2) (T)</option>
-        <option value="Hex(3)HexNAc(2)NeuAc(1) (N)">Hex(3)HexNAc(2)NeuAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(2)NeuAc(2) (S)">Hex(3)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="Hex(3)HexNAc(2)NeuAc(2) (T)">Hex(3)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="Hex(3)HexNAc(2)Pent(1) (N)">Hex(3)HexNAc(2)Pent(1) (N)</option>
-        <option value="Hex(3)HexNAc(2)Phos(1) (N)">Hex(3)HexNAc(2)Phos(1) (N)</option>
-        <option value="Hex(3)HexNAc(3) (N)">Hex(3)HexNAc(3) (N)</option>
-        <option value="Hex(3)HexNAc(3) (S)">Hex(3)HexNAc(3) (S)</option>
-        <option value="Hex(3)HexNAc(3) (T)">Hex(3)HexNAc(3) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(1) (S)">Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(1) (T)">Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(2) (S)">Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(2) (T)">Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(3) (S)">Hex(3)HexNAc(3)NeuAc(3) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(3) (T)">Hex(3)HexNAc(3)NeuAc(3) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuGc(1) (S)">Hex(3)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuGc(1) (T)">Hex(3)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)Pent(1) (N)">Hex(3)HexNAc(3)Pent(1) (N)</option>
-        <option value="Hex(3)HexNAc(3)Sulf(1) (N)">Hex(3)HexNAc(3)Sulf(1) (N)</option>
-        <option value="Hex(3)HexNAc(3)Sulf(1) (S)">Hex(3)HexNAc(3)Sulf(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)Sulf(1) (T)">Hex(3)HexNAc(3)Sulf(1) (T)</option>
-        <option value="Hex(3)HexNAc(4) (N)">Hex(3)HexNAc(4) (N)</option>
-        <option value="Hex(3)HexNAc(4) (S)">Hex(3)HexNAc(4) (S)</option>
-        <option value="Hex(3)HexNAc(4) (T)">Hex(3)HexNAc(4) (T)</option>
-        <option value="Hex(3)HexNAc(4)NeuAc(1) (N)">Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(4)NeuAc(2) (N)">Hex(3)HexNAc(4)NeuAc(2) (N)</option>
-        <option value="Hex(3)HexNAc(4)Pent(1) (N)">Hex(3)HexNAc(4)Pent(1) (N)</option>
-        <option value="Hex(3)HexNAc(4)Sulf(1) (N)">Hex(3)HexNAc(4)Sulf(1) (N)</option>
-        <option value="Hex(3)HexNAc(5) (N)">Hex(3)HexNAc(5) (N)</option>
-        <option value="Hex(3)HexNAc(5) (S)">Hex(3)HexNAc(5) (S)</option>
-        <option value="Hex(3)HexNAc(5) (T)">Hex(3)HexNAc(5) (T)</option>
-        <option value="Hex(3)HexNAc(5)NeuAc(1) (N)">Hex(3)HexNAc(5)NeuAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(5)Sulf(1) (N)">Hex(3)HexNAc(5)Sulf(1) (N)</option>
-        <option value="Hex(3)HexNAc(6) (N)">Hex(3)HexNAc(6) (N)</option>
-        <option value="Hex(3)HexNAc(6) (S)">Hex(3)HexNAc(6) (S)</option>
-        <option value="Hex(3)HexNAc(6) (T)">Hex(3)HexNAc(6) (T)</option>
-        <option value="Hex(3)HexNAc(6)NeuAc(1) (N)">Hex(3)HexNAc(6)NeuAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(6)Sulf(1) (N)">Hex(3)HexNAc(6)Sulf(1) (N)</option>
-        <option value="Hex(3)HexNAc(6)Sulf(2) (N)">Hex(3)HexNAc(6)Sulf(2) (N)</option>
-        <option value="Hex(3)HexNAc(7) (N)">Hex(3)HexNAc(7) (N)</option>
-        <option value="Hex(3)HexNAc(7)Sulf(1) (N)">Hex(3)HexNAc(7)Sulf(1) (N)</option>
-        <option value="Hex(4) (S)">Hex(4) (S)</option>
-        <option value="Hex(4) (T)">Hex(4) (T)</option>
-        <option value="Hex(4)HexA(1) (S)">Hex(4)HexA(1) (S)</option>
-        <option value="Hex(4)HexA(1) (T)">Hex(4)HexA(1) (T)</option>
-        <option value="Hex(4)HexA(1)HexNAc(1) (S)">Hex(4)HexA(1)HexNAc(1) (S)</option>
-        <option value="Hex(4)HexA(1)HexNAc(1) (T)">Hex(4)HexA(1)HexNAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(1) (N)">Hex(4)HexNAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(1) (S)">Hex(4)HexNAc(1) (S)</option>
-        <option value="Hex(4)HexNAc(1) (T)">Hex(4)HexNAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(2) (N)">Hex(4)HexNAc(2) (N)</option>
-        <option value="Hex(4)HexNAc(2)NeuAc(1) (N)">Hex(4)HexNAc(2)NeuAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(2)NeuAc(1) (S)">Hex(4)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="Hex(4)HexNAc(2)NeuAc(1) (T)">Hex(4)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(2)Pent(1) (N)">Hex(4)HexNAc(2)Pent(1) (N)</option>
-        <option value="Hex(4)HexNAc(3) (N)">Hex(4)HexNAc(3) (N)</option>
-        <option value="Hex(4)HexNAc(3) (S)">Hex(4)HexNAc(3) (S)</option>
-        <option value="Hex(4)HexNAc(3) (T)">Hex(4)HexNAc(3) (T)</option>
-        <option value="Hex(4)HexNAc(3)NeuAc(1) (N)">Hex(4)HexNAc(3)NeuAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(3)NeuAc(1) (S)">Hex(4)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="Hex(4)HexNAc(3)NeuAc(1) (T)">Hex(4)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(3)NeuAc(2) (N)">Hex(4)HexNAc(3)NeuAc(2) (N)</option>
-        <option value="Hex(4)HexNAc(3)NeuGc(1) (N)">Hex(4)HexNAc(3)NeuGc(1) (N)</option>
-        <option value="Hex(4)HexNAc(3)Pent(1) (N)">Hex(4)HexNAc(3)Pent(1) (N)</option>
-        <option value="Hex(4)HexNAc(4) (N)">Hex(4)HexNAc(4) (N)</option>
-        <option value="Hex(4)HexNAc(4) (S)">Hex(4)HexNAc(4) (S)</option>
-        <option value="Hex(4)HexNAc(4) (T)">Hex(4)HexNAc(4) (T)</option>
-        <option value="Hex(4)HexNAc(4)Me(2)Pent(1) (N)">Hex(4)HexNAc(4)Me(2)Pent(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1) (N)">Hex(4)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1) (S)">Hex(4)HexNAc(4)NeuAc(1) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1) (T)">Hex(4)HexNAc(4)NeuAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1) (N)">Hex(4)HexNAc(4)NeuGc(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1) (S)">Hex(4)HexNAc(4)NeuGc(1) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1) (T)">Hex(4)HexNAc(4)NeuGc(1) (T)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)</option>
-        <option value="Hex(4)HexNAc(4)Pent(1) (N)">Hex(4)HexNAc(4)Pent(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)Sulf(1) (N)">Hex(4)HexNAc(4)Sulf(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)Sulf(2) (S)">Hex(4)HexNAc(4)Sulf(2) (S)</option>
-        <option value="Hex(4)HexNAc(4)Sulf(2) (T)">Hex(4)HexNAc(4)Sulf(2) (T)</option>
-        <option value="Hex(4)HexNAc(5) (N)">Hex(4)HexNAc(5) (N)</option>
-        <option value="Hex(4)HexNAc(5)NeuAc(1) (N)">Hex(4)HexNAc(5)NeuAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(5)Sulf(1) (N)">Hex(4)HexNAc(5)Sulf(1) (N)</option>
-        <option value="Hex(4)HexNAc(6) (N)">Hex(4)HexNAc(6) (N)</option>
-        <option value="Hex(4)Phos(1) (S)">Hex(4)Phos(1) (S)</option>
-        <option value="Hex(4)Phos(1) (T)">Hex(4)Phos(1) (T)</option>
-        <option value="Hex(5) (S)">Hex(5) (S)</option>
-        <option value="Hex(5) (T)">Hex(5) (T)</option>
-        <option value="Hex(5)HexA(1) (S)">Hex(5)HexA(1) (S)</option>
-        <option value="Hex(5)HexA(1) (T)">Hex(5)HexA(1) (T)</option>
-        <option value="Hex(5)HexNAc(1) (N)">Hex(5)HexNAc(1) (N)</option>
-        <option value="Hex(5)HexNAc(1) (S)">Hex(5)HexNAc(1) (S)</option>
-        <option value="Hex(5)HexNAc(1) (T)">Hex(5)HexNAc(1) (T)</option>
-        <option value="Hex(5)HexNAc(2) (N)">Hex(5)HexNAc(2) (N)</option>
-        <option value="Hex(5)HexNAc(2)Phos(1) (N)">Hex(5)HexNAc(2)Phos(1) (N)</option>
-        <option value="Hex(5)HexNAc(3) (N)">Hex(5)HexNAc(3) (N)</option>
-        <option value="Hex(5)HexNAc(3)Pent(1) (N)">Hex(5)HexNAc(3)Pent(1) (N)</option>
-        <option value="Hex(5)HexNAc(4) (N)">Hex(5)HexNAc(4) (N)</option>
-        <option value="Hex(5)HexNAc(4) (S)">Hex(5)HexNAc(4) (S)</option>
-        <option value="Hex(5)HexNAc(4) (T)">Hex(5)HexNAc(4) (T)</option>
-        <option value="Hex(5)HexNAc(4)Me(2)Pent(1) (N)">Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(1) (N)">Hex(5)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(2) (N)">Hex(5)HexNAc(4)NeuAc(2) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuGc(1) (N)">Hex(5)HexNAc(4)NeuGc(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)Sulf(1) (N)">Hex(5)HexNAc(4)Sulf(1) (N)</option>
-        <option value="Hex(5)HexNAc(5) (N)">Hex(5)HexNAc(5) (N)</option>
-        <option value="Hex(5)HexNAc(5) (S)">Hex(5)HexNAc(5) (S)</option>
-        <option value="Hex(5)HexNAc(5) (T)">Hex(5)HexNAc(5) (T)</option>
-        <option value="Hex(5)Phos(1) (S)">Hex(5)Phos(1) (S)</option>
-        <option value="Hex(5)Phos(1) (T)">Hex(5)Phos(1) (T)</option>
-        <option value="Hex(5)Phos(3) (S)">Hex(5)Phos(3) (S)</option>
-        <option value="Hex(5)Phos(3) (T)">Hex(5)Phos(3) (T)</option>
-        <option value="Hex(6)HexNAc(1) (N)">Hex(6)HexNAc(1) (N)</option>
-        <option value="Hex(6)HexNAc(2) (N)">Hex(6)HexNAc(2) (N)</option>
-        <option value="Hex(6)HexNAc(2)Phos(1) (N)">Hex(6)HexNAc(2)Phos(1) (N)</option>
-        <option value="Hex(6)HexNAc(3) (N)">Hex(6)HexNAc(3) (N)</option>
-        <option value="Hex(6)HexNAc(3)Phos(1) (N)">Hex(6)HexNAc(3)Phos(1) (N)</option>
-        <option value="Hex(6)HexNAc(4) (N)">Hex(6)HexNAc(4) (N)</option>
-        <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
-        <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
-        <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
-        <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
-        <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
-        <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
-        <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
-        <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
-        <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
-        <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
-        <option value="Hex(7)HexNAc(2) (N)">Hex(7)HexNAc(2) (N)</option>
-        <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
-        <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
-        <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
-        <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
-        <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
-        <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
-        <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
-        <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
-        <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
-        <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
-        <option value="Hex(8)Phos(3) (T)">Hex(8)Phos(3) (T)</option>
-        <option value="Hex(9) (N)">Hex(9) (N)</option>
-        <option value="Hex(9)HexNAc(1) (N)">Hex(9)HexNAc(1) (N)</option>
-        <option value="Hex(9)HexNAc(2) (N)">Hex(9)HexNAc(2) (N)</option>
-        <option value="Hex(9)Phos(3) (S)">Hex(9)Phos(3) (S)</option>
-        <option value="Hex(9)Phos(3) (T)">Hex(9)Phos(3) (T)</option>
-        <option value="HexA(2)HexNAc(3) (S)">HexA(2)HexNAc(3) (S)</option>
-        <option value="HexA(2)HexNAc(3) (T)">HexA(2)HexNAc(3) (T)</option>
-        <option value="HexN (K)">HexN (K)</option>
-        <option value="HexN (N)">HexN (N)</option>
-        <option value="HexN (S)">HexN (S)</option>
-        <option value="HexN (T)">HexN (T)</option>
-        <option value="HexN (W)">HexN (W)</option>
-        <option value="HexNAc (C)">HexNAc (C)</option>
-        <option value="HexNAc (N)">HexNAc (N)</option>
-        <option value="HexNAc (S)">HexNAc (S)</option>
-        <option value="HexNAc (T)">HexNAc (T)</option>
-        <option value="HexNAc(1)dHex(1) (N)">HexNAc(1)dHex(1) (N)</option>
-        <option value="HexNAc(1)dHex(1) (S)">HexNAc(1)dHex(1) (S)</option>
-        <option value="HexNAc(1)dHex(1) (T)">HexNAc(1)dHex(1) (T)</option>
-        <option value="HexNAc(1)dHex(2) (N)">HexNAc(1)dHex(2) (N)</option>
-        <option value="HexNAc(1)Kdn(2) (S)">HexNAc(1)Kdn(2) (S)</option>
-        <option value="HexNAc(1)Kdn(2) (T)">HexNAc(1)Kdn(2) (T)</option>
-        <option value="HexNAc(1)NeuAc(1) (S)">HexNAc(1)NeuAc(1) (S)</option>
-        <option value="HexNAc(1)NeuAc(1) (T)">HexNAc(1)NeuAc(1) (T)</option>
-        <option value="HexNAc(1)NeuGc(1) (S)">HexNAc(1)NeuGc(1) (S)</option>
-        <option value="HexNAc(1)NeuGc(1) (T)">HexNAc(1)NeuGc(1) (T)</option>
-        <option value="HexNAc(1)NeuGc(2) (S)">HexNAc(1)NeuGc(2) (S)</option>
-        <option value="HexNAc(1)NeuGc(2) (T)">HexNAc(1)NeuGc(2) (T)</option>
-        <option value="HexNAc(2) (N)">HexNAc(2) (N)</option>
-        <option value="HexNAc(2) (S)">HexNAc(2) (S)</option>
-        <option value="HexNAc(2) (T)">HexNAc(2) (T)</option>
-        <option value="HexNAc(2)dHex(1) (N)">HexNAc(2)dHex(1) (N)</option>
-        <option value="HexNAc(2)dHex(2) (N)">HexNAc(2)dHex(2) (N)</option>
-        <option value="HexNAc(2)NeuAc(1) (S)">HexNAc(2)NeuAc(1) (S)</option>
-        <option value="HexNAc(2)NeuAc(1) (T)">HexNAc(2)NeuAc(1) (T)</option>
-        <option value="HexNAc(2)NeuAc(1)Sulf(1) (S)">HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="HexNAc(2)NeuAc(1)Sulf(1) (T)">HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="HexNAc(2)NeuGc(1) (S)">HexNAc(2)NeuGc(1) (S)</option>
-        <option value="HexNAc(2)NeuGc(1) (T)">HexNAc(2)NeuGc(1) (T)</option>
-        <option value="HexNAc(2)Sulf(1) (S)">HexNAc(2)Sulf(1) (S)</option>
-        <option value="HexNAc(2)Sulf(1) (T)">HexNAc(2)Sulf(1) (T)</option>
-        <option value="HexNAc(3) (S)">HexNAc(3) (S)</option>
-        <option value="HexNAc(3) (T)">HexNAc(3) (T)</option>
-        <option value="HexNAc(3)Sulf(1) (S)">HexNAc(3)Sulf(1) (S)</option>
-        <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
-        <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
-        <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
-        <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
-        <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
-        <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
-        <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
-        <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
-        <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
-        <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
-        <option value="His-&gt;Gln (H)">His-&gt;Gln (H)</option>
-        <option value="His-&gt;Glu (H)">His-&gt;Glu (H)</option>
-        <option value="His-&gt;Gly (H)">His-&gt;Gly (H)</option>
-        <option value="His-&gt;Lys (H)">His-&gt;Lys (H)</option>
-        <option value="His-&gt;Met (H)">His-&gt;Met (H)</option>
-        <option value="His-&gt;Phe (H)">His-&gt;Phe (H)</option>
-        <option value="His-&gt;Pro (H)">His-&gt;Pro (H)</option>
-        <option value="His-&gt;Ser (H)">His-&gt;Ser (H)</option>
-        <option value="His-&gt;Thr (H)">His-&gt;Thr (H)</option>
-        <option value="His-&gt;Trp (H)">His-&gt;Trp (H)</option>
-        <option value="His-&gt;Tyr (H)">His-&gt;Tyr (H)</option>
-        <option value="His-&gt;Val (H)">His-&gt;Val (H)</option>
-        <option value="His-&gt;Xle (H)">His-&gt;Xle (H)</option>
-        <option value="HMVK (C)">HMVK (C)</option>
-        <option value="HN2_mustard (C)">HN2_mustard (C)</option>
-        <option value="HN2_mustard (H)">HN2_mustard (H)</option>
-        <option value="HN2_mustard (K)">HN2_mustard (K)</option>
-        <option value="HN3_mustard (C)">HN3_mustard (C)</option>
-        <option value="HN3_mustard (H)">HN3_mustard (H)</option>
-        <option value="HN3_mustard (K)">HN3_mustard (K)</option>
-        <option value="HNE (A)">HNE (A)</option>
-        <option value="HNE (C)">HNE (C)</option>
-        <option value="HNE (H)">HNE (H)</option>
-        <option value="HNE (K)">HNE (K)</option>
-        <option value="HNE (L)">HNE (L)</option>
-        <option value="HNE+Delta:H(2) (C)">HNE+Delta:H(2) (C)</option>
-        <option value="HNE+Delta:H(2) (H)">HNE+Delta:H(2) (H)</option>
-        <option value="HNE+Delta:H(2) (K)">HNE+Delta:H(2) (K)</option>
-        <option value="HNE-BAHAH (C)">HNE-BAHAH (C)</option>
-        <option value="HNE-BAHAH (H)">HNE-BAHAH (H)</option>
-        <option value="HNE-BAHAH (K)">HNE-BAHAH (K)</option>
-        <option value="HNE-Delta:H(2)O (C)">HNE-Delta:H(2)O (C)</option>
-        <option value="HNE-Delta:H(2)O (H)">HNE-Delta:H(2)O (H)</option>
-        <option value="HNE-Delta:H(2)O (K)">HNE-Delta:H(2)O (K)</option>
-        <option value="Homocysteic_acid (M)">Homocysteic_acid (M)</option>
-        <option value="HPG (R)">HPG (R)</option>
-        <option value="Hydroxamic_acid (D)">Hydroxamic_acid (D)</option>
-        <option value="Hydroxamic_acid (E)">Hydroxamic_acid (E)</option>
-        <option value="Hydroxycinnamyl (C)">Hydroxycinnamyl (C)</option>
-        <option value="Hydroxyfarnesyl (C)">Hydroxyfarnesyl (C)</option>
-        <option value="Hydroxyheme (E)">Hydroxyheme (E)</option>
-        <option value="hydroxyisobutyryl (K)">hydroxyisobutyryl (K)</option>
-        <option value="Hydroxymethyl (N)">Hydroxymethyl (N)</option>
-        <option value="HydroxymethylOP (K)">HydroxymethylOP (K)</option>
-        <option value="Hydroxytrimethyl (K)">Hydroxytrimethyl (K)</option>
-        <option value="Hypusine (K)">Hypusine (K)</option>
-        <option value="IASD (C)">IASD (C)</option>
-        <option value="IBTP (C)">IBTP (C)</option>
-        <option value="ICAT-C (C)">ICAT-C (C)</option>
-        <option value="ICAT-C:13C(9) (C)">ICAT-C:13C(9) (C)</option>
-        <option value="ICAT-D (C)">ICAT-D (C)</option>
-        <option value="ICAT-D:2H(8) (C)">ICAT-D:2H(8) (C)</option>
-        <option value="ICAT-G (C)">ICAT-G (C)</option>
-        <option value="ICAT-G:2H(8) (C)">ICAT-G:2H(8) (C)</option>
-        <option value="ICAT-H (C)">ICAT-H (C)</option>
-        <option value="ICAT-H:13C(6) (C)">ICAT-H:13C(6) (C)</option>
-        <option value="ICDID (C)">ICDID (C)</option>
-        <option value="ICDID:2H(6) (C)">ICDID:2H(6) (C)</option>
-        <option value="ICPL (K)">ICPL (K)</option>
-        <option value="ICPL (N-term)">ICPL (N-term)</option>
-        <option value="ICPL (Protein N-term)">ICPL (Protein N-term)</option>
-        <option value="ICPL:13C(6) (K)">ICPL:13C(6) (K)</option>
-        <option value="ICPL:13C(6) (N-term)">ICPL:13C(6) (N-term)</option>
-        <option value="ICPL:13C(6) (Protein N-term)">ICPL:13C(6) (Protein N-term)</option>
-        <option value="ICPL:13C(6)2H(4) (K)">ICPL:13C(6)2H(4) (K)</option>
-        <option value="ICPL:13C(6)2H(4) (N-term)">ICPL:13C(6)2H(4) (N-term)</option>
-        <option value="ICPL:13C(6)2H(4) (Protein N-term)">ICPL:13C(6)2H(4) (Protein N-term)</option>
-        <option value="ICPL:2H(4) (K)">ICPL:2H(4) (K)</option>
-        <option value="ICPL:2H(4) (N-term)">ICPL:2H(4) (N-term)</option>
-        <option value="ICPL:2H(4) (Protein N-term)">ICPL:2H(4) (Protein N-term)</option>
-        <option value="IDEnT (C)">IDEnT (C)</option>
-        <option value="IED-Biotin (C)">IED-Biotin (C)</option>
-        <option value="IGBP (C)">IGBP (C)</option>
-        <option value="IGBP:13C(2) (C)">IGBP:13C(2) (C)</option>
-        <option value="IMEHex(2)NeuAc(1) (K)">IMEHex(2)NeuAc(1) (K)</option>
-        <option value="IMID (K)">IMID (K)</option>
-        <option value="IMID:2H(4) (K)">IMID:2H(4) (K)</option>
-        <option value="Iminobiotin (K)">Iminobiotin (K)</option>
-        <option value="Iminobiotin (N-term)">Iminobiotin (N-term)</option>
-        <option value="Iodo (H)">Iodo (H)</option>
-        <option value="Iodo (Y)">Iodo (Y)</option>
-        <option value="Iodoacetanilide (C)">Iodoacetanilide (C)</option>
-        <option value="Iodoacetanilide (K)">Iodoacetanilide (K)</option>
-        <option value="Iodoacetanilide (N-term)">Iodoacetanilide (N-term)</option>
-        <option value="Iodoacetanilide:13C(6) (C)">Iodoacetanilide:13C(6) (C)</option>
-        <option value="Iodoacetanilide:13C(6) (K)">Iodoacetanilide:13C(6) (K)</option>
-        <option value="Iodoacetanilide:13C(6) (N-term)">Iodoacetanilide:13C(6) (N-term)</option>
-        <option value="iodoTMT (C)">iodoTMT (C)</option>
-        <option value="iodoTMT (D)">iodoTMT (D)</option>
-        <option value="iodoTMT (E)">iodoTMT (E)</option>
-        <option value="iodoTMT (H)">iodoTMT (H)</option>
-        <option value="iodoTMT (K)">iodoTMT (K)</option>
-        <option value="iodoTMT6plex (C)">iodoTMT6plex (C)</option>
-        <option value="iodoTMT6plex (D)">iodoTMT6plex (D)</option>
-        <option value="iodoTMT6plex (E)">iodoTMT6plex (E)</option>
-        <option value="iodoTMT6plex (H)">iodoTMT6plex (H)</option>
-        <option value="iodoTMT6plex (K)">iodoTMT6plex (K)</option>
-        <option value="IodoU-AMP (F)">IodoU-AMP (F)</option>
-        <option value="IodoU-AMP (W)">IodoU-AMP (W)</option>
-        <option value="IodoU-AMP (Y)">IodoU-AMP (Y)</option>
-        <option value="ISD_z+2_ion (N-term)">ISD_z+2_ion (N-term)</option>
-        <option value="Isopropylphospho (S)">Isopropylphospho (S)</option>
-        <option value="Isopropylphospho (T)">Isopropylphospho (T)</option>
-        <option value="Isopropylphospho (Y)">Isopropylphospho (Y)</option>
-        <option value="iTRAQ4plex (C)">iTRAQ4plex (C)</option>
-        <option value="iTRAQ4plex (H)">iTRAQ4plex (H)</option>
-        <option value="iTRAQ4plex (K)">iTRAQ4plex (K)</option>
-        <option value="iTRAQ4plex (N-term)">iTRAQ4plex (N-term)</option>
-        <option value="iTRAQ4plex (Protein N-term)">iTRAQ4plex (Protein N-term)</option>
-        <option value="iTRAQ4plex (S)">iTRAQ4plex (S)</option>
-        <option value="iTRAQ4plex (T)">iTRAQ4plex (T)</option>
-        <option value="iTRAQ4plex (Y)">iTRAQ4plex (Y)</option>
-        <option value="iTRAQ4plex114 (C)">iTRAQ4plex114 (C)</option>
-        <option value="iTRAQ4plex114 (K)">iTRAQ4plex114 (K)</option>
-        <option value="iTRAQ4plex114 (N-term)">iTRAQ4plex114 (N-term)</option>
-        <option value="iTRAQ4plex114 (Y)">iTRAQ4plex114 (Y)</option>
-        <option value="iTRAQ4plex115 (C)">iTRAQ4plex115 (C)</option>
-        <option value="iTRAQ4plex115 (K)">iTRAQ4plex115 (K)</option>
-        <option value="iTRAQ4plex115 (N-term)">iTRAQ4plex115 (N-term)</option>
-        <option value="iTRAQ4plex115 (Y)">iTRAQ4plex115 (Y)</option>
-        <option value="iTRAQ8plex (C)">iTRAQ8plex (C)</option>
-        <option value="iTRAQ8plex (H)">iTRAQ8plex (H)</option>
-        <option value="iTRAQ8plex (K)">iTRAQ8plex (K)</option>
-        <option value="iTRAQ8plex (N-term)">iTRAQ8plex (N-term)</option>
-        <option value="iTRAQ8plex (Protein N-term)">iTRAQ8plex (Protein N-term)</option>
-        <option value="iTRAQ8plex (S)">iTRAQ8plex (S)</option>
-        <option value="iTRAQ8plex (T)">iTRAQ8plex (T)</option>
-        <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
-        <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
-        <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
-        <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
-        <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
-        <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
-        <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
-        <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
-        <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
-        <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
-        <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
-        <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
-        <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
-        <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
-        <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
-        <option value="Label:13C(5)15N(1) (E)">Label:13C(5)15N(1) (E)</option>
-        <option value="Label:13C(5)15N(1) (M)">Label:13C(5)15N(1) (M)</option>
-        <option value="Label:13C(5)15N(1) (P)">Label:13C(5)15N(1) (P)</option>
-        <option value="Label:13C(5)15N(1) (V)">Label:13C(5)15N(1) (V)</option>
-        <option value="Label:13C(6) (I)">Label:13C(6) (I)</option>
-        <option value="Label:13C(6) (K)">Label:13C(6) (K)</option>
-        <option value="Label:13C(6) (L)">Label:13C(6) (L)</option>
-        <option value="Label:13C(6) (R)">Label:13C(6) (R)</option>
-        <option value="Label:13C(6)+Acetyl (K)">Label:13C(6)+Acetyl (K)</option>
-        <option value="Label:13C(6)+Dimethyl (K)">Label:13C(6)+Dimethyl (K)</option>
-        <option value="Label:13C(6)+GG (K)">Label:13C(6)+GG (K)</option>
-        <option value="Label:13C(6)15N(1) (I)">Label:13C(6)15N(1) (I)</option>
-        <option value="Label:13C(6)15N(1) (L)">Label:13C(6)15N(1) (L)</option>
-        <option value="Label:13C(6)15N(2) (K)">Label:13C(6)15N(2) (K)</option>
-        <option value="Label:13C(6)15N(2)+Acetyl (K)">Label:13C(6)15N(2)+Acetyl (K)</option>
-        <option value="Label:13C(6)15N(2)+Dimethyl (K)">Label:13C(6)15N(2)+Dimethyl (K)</option>
-        <option value="Label:13C(6)15N(2)+GG (K)">Label:13C(6)15N(2)+GG (K)</option>
-        <option value="Label:13C(6)15N(4) (R)">Label:13C(6)15N(4) (R)</option>
-        <option value="Label:13C(6)15N(4)+Dimethyl (R)">Label:13C(6)15N(4)+Dimethyl (R)</option>
-        <option value="Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R)">Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R)</option>
-        <option value="Label:13C(6)15N(4)+Methyl (R)">Label:13C(6)15N(4)+Methyl (R)</option>
-        <option value="Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R)">Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R)</option>
-        <option value="Label:13C(9) (F)">Label:13C(9) (F)</option>
-        <option value="Label:13C(9) (Y)">Label:13C(9) (Y)</option>
-        <option value="Label:13C(9)+Phospho (Y)">Label:13C(9)+Phospho (Y)</option>
-        <option value="Label:13C(9)15N(1) (F)">Label:13C(9)15N(1) (F)</option>
-        <option value="Label:15N(1) (A)">Label:15N(1) (A)</option>
-        <option value="Label:15N(1) (C)">Label:15N(1) (C)</option>
-        <option value="Label:15N(1) (D)">Label:15N(1) (D)</option>
-        <option value="Label:15N(1) (E)">Label:15N(1) (E)</option>
-        <option value="Label:15N(1) (F)">Label:15N(1) (F)</option>
-        <option value="Label:15N(1) (G)">Label:15N(1) (G)</option>
-        <option value="Label:15N(1) (I)">Label:15N(1) (I)</option>
-        <option value="Label:15N(1) (L)">Label:15N(1) (L)</option>
-        <option value="Label:15N(1) (M)">Label:15N(1) (M)</option>
-        <option value="Label:15N(1) (P)">Label:15N(1) (P)</option>
-        <option value="Label:15N(1) (S)">Label:15N(1) (S)</option>
-        <option value="Label:15N(1) (T)">Label:15N(1) (T)</option>
-        <option value="Label:15N(1) (V)">Label:15N(1) (V)</option>
-        <option value="Label:15N(1) (Y)">Label:15N(1) (Y)</option>
-        <option value="Label:15N(2) (K)">Label:15N(2) (K)</option>
-        <option value="Label:15N(2) (N)">Label:15N(2) (N)</option>
-        <option value="Label:15N(2) (Q)">Label:15N(2) (Q)</option>
-        <option value="Label:15N(2) (W)">Label:15N(2) (W)</option>
-        <option value="Label:15N(2)2H(9) (K)">Label:15N(2)2H(9) (K)</option>
-        <option value="Label:15N(3) (H)">Label:15N(3) (H)</option>
-        <option value="Label:15N(4) (R)">Label:15N(4) (R)</option>
-        <option value="Label:18O(1) (C-term)">Label:18O(1) (C-term)</option>
-        <option value="Label:18O(1) (S)">Label:18O(1) (S)</option>
-        <option value="Label:18O(1) (T)">Label:18O(1) (T)</option>
-        <option value="Label:18O(1) (Y)">Label:18O(1) (Y)</option>
-        <option value="Label:18O(2) (C-term)">Label:18O(2) (C-term)</option>
-        <option value="Label:2H(10) (L)">Label:2H(10) (L)</option>
-        <option value="Label:2H(3) (L)">Label:2H(3) (L)</option>
-        <option value="Label:2H(3) (M)">Label:2H(3) (M)</option>
-        <option value="Label:2H(3)+Oxidation (M)">Label:2H(3)+Oxidation (M)</option>
-        <option value="Label:2H(4) (A)">Label:2H(4) (A)</option>
-        <option value="Label:2H(4) (F)">Label:2H(4) (F)</option>
-        <option value="Label:2H(4) (K)">Label:2H(4) (K)</option>
-        <option value="Label:2H(4) (U)">Label:2H(4) (U)</option>
-        <option value="Label:2H(4) (Y)">Label:2H(4) (Y)</option>
-        <option value="Label:2H(4)+Acetyl (K)">Label:2H(4)+Acetyl (K)</option>
-        <option value="Label:2H(4)+GG (K)">Label:2H(4)+GG (K)</option>
-        <option value="Label:2H(4)13C(1) (R)">Label:2H(4)13C(1) (R)</option>
-        <option value="Label:2H(6)15N(1) (P)">Label:2H(6)15N(1) (P)</option>
-        <option value="Label:2H(7)15N(4) (R)">Label:2H(7)15N(4) (R)</option>
-        <option value="Label:2H(9)13C(6)15N(2) (K)">Label:2H(9)13C(6)15N(2) (K)</option>
-        <option value="lapachenole (C)">lapachenole (C)</option>
-        <option value="Leu-&gt;MetOx (L)">Leu-&gt;MetOx (L)</option>
-        <option value="LG-anhydrolactam (K)">LG-anhydrolactam (K)</option>
-        <option value="LG-anhydrolactam (N-term)">LG-anhydrolactam (N-term)</option>
-        <option value="LG-anhyropyrrole (K)">LG-anhyropyrrole (K)</option>
-        <option value="LG-anhyropyrrole (N-term)">LG-anhyropyrrole (N-term)</option>
-        <option value="LG-Hlactam-K (K)">LG-Hlactam-K (K)</option>
-        <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
-        <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
-        <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
-        <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
-        <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
-        <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
-        <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
-        <option value="Lipoyl (K)">Lipoyl (K)</option>
-        <option value="LRGG (K)">LRGG (K)</option>
-        <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
-        <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
-        <option value="Lys (N-term)">Lys (N-term)</option>
-        <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
-        <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
-        <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
-        <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
-        <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
-        <option value="Lys-&gt;Asp (K)">Lys-&gt;Asp (K)</option>
-        <option value="Lys-&gt;CamCys (K)">Lys-&gt;CamCys (K)</option>
-        <option value="Lys-&gt;Cys (K)">Lys-&gt;Cys (K)</option>
-        <option value="Lys-&gt;Gln (K)">Lys-&gt;Gln (K)</option>
-        <option value="Lys-&gt;Glu (K)">Lys-&gt;Glu (K)</option>
-        <option value="Lys-&gt;Gly (K)">Lys-&gt;Gly (K)</option>
-        <option value="Lys-&gt;His (K)">Lys-&gt;His (K)</option>
-        <option value="Lys-&gt;Met (K)">Lys-&gt;Met (K)</option>
-        <option value="Lys-&gt;MetOx (K)">Lys-&gt;MetOx (K)</option>
-        <option value="Lys-&gt;Phe (K)">Lys-&gt;Phe (K)</option>
-        <option value="Lys-&gt;Pro (K)">Lys-&gt;Pro (K)</option>
-        <option value="Lys-&gt;Ser (K)">Lys-&gt;Ser (K)</option>
-        <option value="Lys-&gt;Thr (K)">Lys-&gt;Thr (K)</option>
-        <option value="Lys-&gt;Trp (K)">Lys-&gt;Trp (K)</option>
-        <option value="Lys-&gt;Tyr (K)">Lys-&gt;Tyr (K)</option>
-        <option value="Lys-&gt;Val (K)">Lys-&gt;Val (K)</option>
-        <option value="Lys-&gt;Xle (K)">Lys-&gt;Xle (K)</option>
-        <option value="Lys-loss (Protein C-term K)">Lys-loss (Protein C-term K)</option>
-        <option value="Lysbiotinhydrazide (K)">Lysbiotinhydrazide (K)</option>
-        <option value="maleimide (C)">maleimide (C)</option>
-        <option value="maleimide (K)">maleimide (K)</option>
-        <option value="Maleimide-PEO2-Biotin (C)">Maleimide-PEO2-Biotin (C)</option>
-        <option value="maleimide3 (C)">maleimide3 (C)</option>
-        <option value="maleimide3 (K)">maleimide3 (K)</option>
-        <option value="maleimide5 (C)">maleimide5 (C)</option>
-        <option value="maleimide5 (K)">maleimide5 (K)</option>
-        <option value="Malonyl (C)">Malonyl (C)</option>
-        <option value="Malonyl (K)">Malonyl (K)</option>
-        <option value="Malonyl (S)">Malonyl (S)</option>
-        <option value="MDCC (C)">MDCC (C)</option>
-        <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
-        <option value="Menadione (C)">Menadione (C)</option>
-        <option value="Menadione (K)">Menadione (K)</option>
-        <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
-        <option value="Menadione-HQ (K)">Menadione-HQ (K)</option>
-        <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
-        <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
-        <option value="MesitylOxide (H)">MesitylOxide (H)</option>
-        <option value="MesitylOxide (K)">MesitylOxide (K)</option>
-        <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
-        <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
-        <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
-        <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
-        <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
-        <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
-        <option value="Met-&gt;AspSA (M)">Met-&gt;AspSA (M)</option>
-        <option value="Met-&gt;Cys (M)">Met-&gt;Cys (M)</option>
-        <option value="Met-&gt;Gln (M)">Met-&gt;Gln (M)</option>
-        <option value="Met-&gt;Glu (M)">Met-&gt;Glu (M)</option>
-        <option value="Met-&gt;Gly (M)">Met-&gt;Gly (M)</option>
-        <option value="Met-&gt;His (M)">Met-&gt;His (M)</option>
-        <option value="Met-&gt;Hpg (M)">Met-&gt;Hpg (M)</option>
-        <option value="Met-&gt;Hse (C-term M)">Met-&gt;Hse (C-term M)</option>
-        <option value="Met-&gt;Hsl (C-term M)">Met-&gt;Hsl (C-term M)</option>
-        <option value="Met-&gt;Lys (M)">Met-&gt;Lys (M)</option>
-        <option value="Met-&gt;Phe (M)">Met-&gt;Phe (M)</option>
-        <option value="Met-&gt;Pro (M)">Met-&gt;Pro (M)</option>
-        <option value="Met-&gt;Ser (M)">Met-&gt;Ser (M)</option>
-        <option value="Met-&gt;Thr (M)">Met-&gt;Thr (M)</option>
-        <option value="Met-&gt;Trp (M)">Met-&gt;Trp (M)</option>
-        <option value="Met-&gt;Tyr (M)">Met-&gt;Tyr (M)</option>
-        <option value="Met-&gt;Val (M)">Met-&gt;Val (M)</option>
-        <option value="Met-&gt;Xle (M)">Met-&gt;Xle (M)</option>
-        <option value="Met-loss (Protein N-term M)">Met-loss (Protein N-term M)</option>
-        <option value="Met-loss+Acetyl (Protein N-term M)">Met-loss+Acetyl (Protein N-term M)</option>
-        <option value="Methamidophos-O (C)">Methamidophos-O (C)</option>
-        <option value="Methamidophos-O (H)">Methamidophos-O (H)</option>
-        <option value="Methamidophos-O (K)">Methamidophos-O (K)</option>
-        <option value="Methamidophos-O (S)">Methamidophos-O (S)</option>
-        <option value="Methamidophos-O (T)">Methamidophos-O (T)</option>
-        <option value="Methamidophos-O (Y)">Methamidophos-O (Y)</option>
-        <option value="Methamidophos-S (C)">Methamidophos-S (C)</option>
-        <option value="Methamidophos-S (H)">Methamidophos-S (H)</option>
-        <option value="Methamidophos-S (K)">Methamidophos-S (K)</option>
-        <option value="Methamidophos-S (S)">Methamidophos-S (S)</option>
-        <option value="Methamidophos-S (T)">Methamidophos-S (T)</option>
-        <option value="Methamidophos-S (Y)">Methamidophos-S (Y)</option>
-        <option value="Methyl (C)">Methyl (C)</option>
-        <option value="Methyl (C-term)">Methyl (C-term)</option>
-        <option value="Methyl (D)">Methyl (D)</option>
-        <option value="Methyl (E)">Methyl (E)</option>
-        <option value="Methyl (H)">Methyl (H)</option>
-        <option value="Methyl (I)">Methyl (I)</option>
-        <option value="Methyl (K)">Methyl (K)</option>
-        <option value="Methyl (L)">Methyl (L)</option>
-        <option value="Methyl (N)">Methyl (N)</option>
-        <option value="Methyl (N-term)">Methyl (N-term)</option>
-        <option value="Methyl (Protein N-term)">Methyl (Protein N-term)</option>
-        <option value="Methyl (Q)">Methyl (Q)</option>
-        <option value="Methyl (R)">Methyl (R)</option>
-        <option value="Methyl (S)">Methyl (S)</option>
-        <option value="Methyl (T)">Methyl (T)</option>
-        <option value="Methyl+Acetyl:2H(3) (K)">Methyl+Acetyl:2H(3) (K)</option>
-        <option value="Methyl+Deamidated (N)">Methyl+Deamidated (N)</option>
-        <option value="Methyl+Deamidated (Q)">Methyl+Deamidated (Q)</option>
-        <option value="Methyl-PEO12-Maleimide (C)">Methyl-PEO12-Maleimide (C)</option>
-        <option value="Methyl:2H(2) (K)">Methyl:2H(2) (K)</option>
-        <option value="Methyl:2H(2) (N-term)">Methyl:2H(2) (N-term)</option>
-        <option value="Methyl:2H(2)13C (C)">Methyl:2H(2)13C (C)</option>
-        <option value="Methyl:2H(2)13C (C-term)">Methyl:2H(2)13C (C-term)</option>
-        <option value="Methyl:2H(2)13C (D)">Methyl:2H(2)13C (D)</option>
-        <option value="Methyl:2H(2)13C (E)">Methyl:2H(2)13C (E)</option>
-        <option value="Methyl:2H(2)13C (H)">Methyl:2H(2)13C (H)</option>
-        <option value="Methyl:2H(2)13C (I)">Methyl:2H(2)13C (I)</option>
-        <option value="Methyl:2H(2)13C (K)">Methyl:2H(2)13C (K)</option>
-        <option value="Methyl:2H(2)13C (L)">Methyl:2H(2)13C (L)</option>
-        <option value="Methyl:2H(2)13C (N)">Methyl:2H(2)13C (N)</option>
-        <option value="Methyl:2H(2)13C (N-term)">Methyl:2H(2)13C (N-term)</option>
-        <option value="Methyl:2H(2)13C (Protein N-term)">Methyl:2H(2)13C (Protein N-term)</option>
-        <option value="Methyl:2H(2)13C (Q)">Methyl:2H(2)13C (Q)</option>
-        <option value="Methyl:2H(2)13C (R)">Methyl:2H(2)13C (R)</option>
-        <option value="Methyl:2H(2)13C (S)">Methyl:2H(2)13C (S)</option>
-        <option value="Methyl:2H(2)13C (T)">Methyl:2H(2)13C (T)</option>
-        <option value="Methyl:2H(3) (D)">Methyl:2H(3) (D)</option>
-        <option value="Methyl:2H(3) (E)">Methyl:2H(3) (E)</option>
-        <option value="Methyl:2H(3) (K)">Methyl:2H(3) (K)</option>
-        <option value="Methyl:2H(3) (R)">Methyl:2H(3) (R)</option>
-        <option value="Methyl:2H(3) (X)">Methyl:2H(3) (X)</option>
-        <option value="Methyl:2H(3)+Acetyl:2H(3) (K)">Methyl:2H(3)+Acetyl:2H(3) (K)</option>
-        <option value="Methyl:2H(3)13C(1) (K)">Methyl:2H(3)13C(1) (K)</option>
-        <option value="Methyl:2H(3)13C(1) (N-term)">Methyl:2H(3)13C(1) (N-term)</option>
-        <option value="Methyl:2H(3)13C(1) (R)">Methyl:2H(3)13C(1) (R)</option>
-        <option value="Methylamine (S)">Methylamine (S)</option>
-        <option value="Methylamine (T)">Methylamine (T)</option>
-        <option value="Methylmalonylation (S)">Methylmalonylation (S)</option>
-        <option value="methylol (K)">methylol (K)</option>
-        <option value="methylol (W)">methylol (W)</option>
-        <option value="methylol (Y)">methylol (Y)</option>
-        <option value="Methylphosphonate (S)">Methylphosphonate (S)</option>
-        <option value="Methylphosphonate (T)">Methylphosphonate (T)</option>
-        <option value="Methylphosphonate (Y)">Methylphosphonate (Y)</option>
-        <option value="Methylpyrroline (K)">Methylpyrroline (K)</option>
-        <option value="methylsulfonylethyl (C)">methylsulfonylethyl (C)</option>
-        <option value="methylsulfonylethyl (H)">methylsulfonylethyl (H)</option>
-        <option value="methylsulfonylethyl (K)">methylsulfonylethyl (K)</option>
-        <option value="Methylthio (C)">Methylthio (C)</option>
-        <option value="Methylthio (D)">Methylthio (D)</option>
-        <option value="Methylthio (K)">Methylthio (K)</option>
-        <option value="Methylthio (N)">Methylthio (N)</option>
-        <option value="Methylthio (N-term)">Methylthio (N-term)</option>
-        <option value="MG-H1 (R)">MG-H1 (R)</option>
-        <option value="Microcin (Protein C-term)">Microcin (Protein C-term)</option>
-        <option value="MicrocinC7 (Protein C-term)">MicrocinC7 (Protein C-term)</option>
-        <option value="MM-diphenylpentanone (C)">MM-diphenylpentanone (C)</option>
-        <option value="Molybdopterin (C)">Molybdopterin (C)</option>
-        <option value="MolybdopterinGD (C)">MolybdopterinGD (C)</option>
-        <option value="MolybdopterinGD (D)">MolybdopterinGD (D)</option>
-        <option value="MolybdopterinGD (U)">MolybdopterinGD (U)</option>
-        <option value="MolybdopterinGD+Delta:S(-1)Se(1) (C)">MolybdopterinGD+Delta:S(-1)Se(1) (C)</option>
-        <option value="monomethylphosphothione (C)">monomethylphosphothione (C)</option>
-        <option value="monomethylphosphothione (H)">monomethylphosphothione (H)</option>
-        <option value="monomethylphosphothione (K)">monomethylphosphothione (K)</option>
-        <option value="monomethylphosphothione (S)">monomethylphosphothione (S)</option>
-        <option value="monomethylphosphothione (T)">monomethylphosphothione (T)</option>
-        <option value="monomethylphosphothione (Y)">monomethylphosphothione (Y)</option>
-        <option value="mTRAQ (H)">mTRAQ (H)</option>
-        <option value="mTRAQ (K)">mTRAQ (K)</option>
-        <option value="mTRAQ (N-term)">mTRAQ (N-term)</option>
-        <option value="mTRAQ (S)">mTRAQ (S)</option>
-        <option value="mTRAQ (T)">mTRAQ (T)</option>
-        <option value="mTRAQ (Y)">mTRAQ (Y)</option>
-        <option value="mTRAQ:13C(3)15N(1) (H)">mTRAQ:13C(3)15N(1) (H)</option>
-        <option value="mTRAQ:13C(3)15N(1) (K)">mTRAQ:13C(3)15N(1) (K)</option>
-        <option value="mTRAQ:13C(3)15N(1) (N-term)">mTRAQ:13C(3)15N(1) (N-term)</option>
-        <option value="mTRAQ:13C(3)15N(1) (S)">mTRAQ:13C(3)15N(1) (S)</option>
-        <option value="mTRAQ:13C(3)15N(1) (T)">mTRAQ:13C(3)15N(1) (T)</option>
-        <option value="mTRAQ:13C(3)15N(1) (Y)">mTRAQ:13C(3)15N(1) (Y)</option>
-        <option value="mTRAQ:13C(6)15N(2) (H)">mTRAQ:13C(6)15N(2) (H)</option>
-        <option value="mTRAQ:13C(6)15N(2) (K)">mTRAQ:13C(6)15N(2) (K)</option>
-        <option value="mTRAQ:13C(6)15N(2) (N-term)">mTRAQ:13C(6)15N(2) (N-term)</option>
-        <option value="mTRAQ:13C(6)15N(2) (S)">mTRAQ:13C(6)15N(2) (S)</option>
-        <option value="mTRAQ:13C(6)15N(2) (T)">mTRAQ:13C(6)15N(2) (T)</option>
-        <option value="mTRAQ:13C(6)15N(2) (Y)">mTRAQ:13C(6)15N(2) (Y)</option>
-        <option value="MTSL (C)">MTSL (C)</option>
-        <option value="MurNAc (A)">MurNAc (A)</option>
-        <option value="Myristoleyl (Protein N-term G)">Myristoleyl (Protein N-term G)</option>
-        <option value="Myristoyl (C)">Myristoyl (C)</option>
-        <option value="Myristoyl (K)">Myristoyl (K)</option>
-        <option value="Myristoyl (N-term G)">Myristoyl (N-term G)</option>
-        <option value="Myristoyl+Delta:H(-4) (Protein N-term G)">Myristoyl+Delta:H(-4) (Protein N-term G)</option>
-        <option value="N-dimethylphosphate (S)">N-dimethylphosphate (S)</option>
-        <option value="NA-LNO2 (C)">NA-LNO2 (C)</option>
-        <option value="NA-LNO2 (H)">NA-LNO2 (H)</option>
-        <option value="NA-OA-NO2 (C)">NA-OA-NO2 (C)</option>
-        <option value="NA-OA-NO2 (H)">NA-OA-NO2 (H)</option>
-        <option value="NBS (W)">NBS (W)</option>
-        <option value="NBS:13C(6) (W)">NBS:13C(6) (W)</option>
-        <option value="NDA (K)">NDA (K)</option>
-        <option value="NDA (N-term)">NDA (N-term)</option>
-        <option value="NEIAA (C)">NEIAA (C)</option>
-        <option value="NEIAA (Y)">NEIAA (Y)</option>
-        <option value="NEIAA:2H(5) (C)">NEIAA:2H(5) (C)</option>
-        <option value="NEIAA:2H(5) (Y)">NEIAA:2H(5) (Y)</option>
-        <option value="NEM:2H(5) (C)">NEM:2H(5) (C)</option>
-        <option value="NEM:2H(5)+H2O (C)">NEM:2H(5)+H2O (C)</option>
-        <option value="NEMsulfur (C)">NEMsulfur (C)</option>
-        <option value="NEMsulfurWater (C)">NEMsulfurWater (C)</option>
-        <option value="Nethylmaleimide (C)">Nethylmaleimide (C)</option>
-        <option value="Nethylmaleimide+water (C)">Nethylmaleimide+water (C)</option>
-        <option value="Nethylmaleimide+water (K)">Nethylmaleimide+water (K)</option>
-        <option value="NeuAc (N)">NeuAc (N)</option>
-        <option value="NeuAc (S)">NeuAc (S)</option>
-        <option value="NeuAc (T)">NeuAc (T)</option>
-        <option value="NeuGc (N)">NeuGc (N)</option>
-        <option value="NeuGc (S)">NeuGc (S)</option>
-        <option value="NeuGc (T)">NeuGc (T)</option>
-        <option value="NHS-fluorescein (K)">NHS-fluorescein (K)</option>
-        <option value="NHS-LC-Biotin (K)">NHS-LC-Biotin (K)</option>
-        <option value="NHS-LC-Biotin (N-term)">NHS-LC-Biotin (N-term)</option>
-        <option value="NIC (K)">NIC (K)</option>
-        <option value="NIC (N-term)">NIC (N-term)</option>
-        <option value="NIPCAM (C)">NIPCAM (C)</option>
-        <option value="Nitrene (Y)">Nitrene (Y)</option>
-        <option value="Nitro (F)">Nitro (F)</option>
-        <option value="Nitro (W)">Nitro (W)</option>
-        <option value="Nitro (Y)">Nitro (Y)</option>
-        <option value="Nitrosyl (C)">Nitrosyl (C)</option>
-        <option value="Nitrosyl (Y)">Nitrosyl (Y)</option>
-        <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
-        <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
-        <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
-        <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
-        <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-        <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
-        <option value="NP40 (N-term)">NP40 (N-term)</option>
-        <option value="NQIGG (K)">NQIGG (K)</option>
-        <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
-        <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
-        <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
-        <option value="O-Et-N-diMePhospho (S)">O-Et-N-diMePhospho (S)</option>
-        <option value="O-Isopropylmethylphosphonate (S)">O-Isopropylmethylphosphonate (S)</option>
-        <option value="O-Isopropylmethylphosphonate (T)">O-Isopropylmethylphosphonate (T)</option>
-        <option value="O-Isopropylmethylphosphonate (Y)">O-Isopropylmethylphosphonate (Y)</option>
-        <option value="O-Methylphosphate (S)">O-Methylphosphate (S)</option>
-        <option value="O-Methylphosphate (T)">O-Methylphosphate (T)</option>
-        <option value="O-Methylphosphate (Y)">O-Methylphosphate (Y)</option>
-        <option value="O-pinacolylmethylphosphonate (H)">O-pinacolylmethylphosphonate (H)</option>
-        <option value="O-pinacolylmethylphosphonate (K)">O-pinacolylmethylphosphonate (K)</option>
-        <option value="O-pinacolylmethylphosphonate (S)">O-pinacolylmethylphosphonate (S)</option>
-        <option value="O-pinacolylmethylphosphonate (T)">O-pinacolylmethylphosphonate (T)</option>
-        <option value="O-pinacolylmethylphosphonate (Y)">O-pinacolylmethylphosphonate (Y)</option>
-        <option value="Octanoyl (C)">Octanoyl (C)</option>
-        <option value="Octanoyl (S)">Octanoyl (S)</option>
-        <option value="Octanoyl (T)">Octanoyl (T)</option>
-        <option value="OxArgBiotin (R)">OxArgBiotin (R)</option>
-        <option value="OxArgBiotinRed (R)">OxArgBiotinRed (R)</option>
-        <option value="Oxidation (C)">Oxidation (C)</option>
-        <option value="Oxidation (C-term G)">Oxidation (C-term G)</option>
-        <option value="Oxidation (D)">Oxidation (D)</option>
-        <option value="Oxidation (E)">Oxidation (E)</option>
-        <option value="Oxidation (F)">Oxidation (F)</option>
-        <option value="Oxidation (H)">Oxidation (H)</option>
-        <option value="Oxidation (I)">Oxidation (I)</option>
-        <option value="Oxidation (K)">Oxidation (K)</option>
-        <option value="Oxidation (L)">Oxidation (L)</option>
-        <option value="Oxidation (M)">Oxidation (M)</option>
-        <option value="Oxidation (N)">Oxidation (N)</option>
-        <option value="Oxidation (P)">Oxidation (P)</option>
-        <option value="Oxidation (Q)">Oxidation (Q)</option>
-        <option value="Oxidation (R)">Oxidation (R)</option>
-        <option value="Oxidation (S)">Oxidation (S)</option>
-        <option value="Oxidation (T)">Oxidation (T)</option>
-        <option value="Oxidation (U)">Oxidation (U)</option>
-        <option value="Oxidation (V)">Oxidation (V)</option>
-        <option value="Oxidation (W)">Oxidation (W)</option>
-        <option value="Oxidation (Y)">Oxidation (Y)</option>
-        <option value="Oxidation+NEM (C)">Oxidation+NEM (C)</option>
-        <option value="OxLysBiotin (K)">OxLysBiotin (K)</option>
-        <option value="OxLysBiotinRed (K)">OxLysBiotinRed (K)</option>
-        <option value="OxProBiotin (P)">OxProBiotin (P)</option>
-        <option value="OxProBiotinRed (P)">OxProBiotinRed (P)</option>
-        <option value="Palmitoleyl (C)">Palmitoleyl (C)</option>
-        <option value="Palmitoleyl (S)">Palmitoleyl (S)</option>
-        <option value="Palmitoleyl (T)">Palmitoleyl (T)</option>
-        <option value="Palmitoyl (C)">Palmitoyl (C)</option>
-        <option value="Palmitoyl (K)">Palmitoyl (K)</option>
-        <option value="Palmitoyl (Protein N-term)">Palmitoyl (Protein N-term)</option>
-        <option value="Palmitoyl (S)">Palmitoyl (S)</option>
-        <option value="Palmitoyl (T)">Palmitoyl (T)</option>
-        <option value="PEITC (C)">PEITC (C)</option>
-        <option value="PEITC (K)">PEITC (K)</option>
-        <option value="PEITC (N-term)">PEITC (N-term)</option>
-        <option value="Pent(1)HexNAc(1) (S)">Pent(1)HexNAc(1) (S)</option>
-        <option value="Pent(1)HexNAc(1) (T)">Pent(1)HexNAc(1) (T)</option>
-        <option value="Pent(2) (S)">Pent(2) (S)</option>
-        <option value="Pent(2) (T)">Pent(2) (T)</option>
-        <option value="Pentose (S)">Pentose (S)</option>
-        <option value="Pentose (T)">Pentose (T)</option>
-        <option value="Pentylamine (Q)">Pentylamine (Q)</option>
-        <option value="PEO-Iodoacetyl-LC-Biotin (C)">PEO-Iodoacetyl-LC-Biotin (C)</option>
-        <option value="PET (S)">PET (S)</option>
-        <option value="PET (T)">PET (T)</option>
-        <option value="Phe-&gt;Ala (F)">Phe-&gt;Ala (F)</option>
-        <option value="Phe-&gt;Arg (F)">Phe-&gt;Arg (F)</option>
-        <option value="Phe-&gt;Asn (F)">Phe-&gt;Asn (F)</option>
-        <option value="Phe-&gt;Asp (F)">Phe-&gt;Asp (F)</option>
-        <option value="Phe-&gt;CamCys (F)">Phe-&gt;CamCys (F)</option>
-        <option value="Phe-&gt;Cys (F)">Phe-&gt;Cys (F)</option>
-        <option value="Phe-&gt;Gln (F)">Phe-&gt;Gln (F)</option>
-        <option value="Phe-&gt;Glu (F)">Phe-&gt;Glu (F)</option>
-        <option value="Phe-&gt;Gly (F)">Phe-&gt;Gly (F)</option>
-        <option value="Phe-&gt;His (F)">Phe-&gt;His (F)</option>
-        <option value="Phe-&gt;Lys (F)">Phe-&gt;Lys (F)</option>
-        <option value="Phe-&gt;Met (F)">Phe-&gt;Met (F)</option>
-        <option value="Phe-&gt;Pro (F)">Phe-&gt;Pro (F)</option>
-        <option value="Phe-&gt;Ser (F)">Phe-&gt;Ser (F)</option>
-        <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
-        <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
-        <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
-        <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
-        <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
-        <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
-        <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
-        <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
-        <option value="Phospho (C)">Phospho (C)</option>
-        <option value="Phospho (D)">Phospho (D)</option>
-        <option value="Phospho (E)">Phospho (E)</option>
-        <option value="Phospho (H)">Phospho (H)</option>
-        <option value="Phospho (K)">Phospho (K)</option>
-        <option value="Phospho (R)">Phospho (R)</option>
-        <option value="Phospho (S)">Phospho (S)</option>
-        <option value="Phospho (T)">Phospho (T)</option>
-        <option value="Phospho (Y)">Phospho (Y)</option>
-        <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
-        <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
-        <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
-        <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
-        <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
-        <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
-        <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
-        <option value="Phosphogluconoylation (K)">Phosphogluconoylation (K)</option>
-        <option value="Phosphogluconoylation (N-term)">Phosphogluconoylation (N-term)</option>
-        <option value="Phosphoguanosine (H)">Phosphoguanosine (H)</option>
-        <option value="Phosphoguanosine (K)">Phosphoguanosine (K)</option>
-        <option value="PhosphoHex (S)">PhosphoHex (S)</option>
-        <option value="PhosphoHex (T)">PhosphoHex (T)</option>
-        <option value="PhosphoHex(2) (N)">PhosphoHex(2) (N)</option>
-        <option value="PhosphoHex(2) (S)">PhosphoHex(2) (S)</option>
-        <option value="PhosphoHex(2) (T)">PhosphoHex(2) (T)</option>
-        <option value="PhosphoHexNAc (S)">PhosphoHexNAc (S)</option>
-        <option value="PhosphoHexNAc (T)">PhosphoHexNAc (T)</option>
-        <option value="Phosphopantetheine (S)">Phosphopantetheine (S)</option>
-        <option value="Phosphopropargyl (S)">Phosphopropargyl (S)</option>
-        <option value="Phosphopropargyl (T)">Phosphopropargyl (T)</option>
-        <option value="Phosphopropargyl (Y)">Phosphopropargyl (Y)</option>
-        <option value="phosphoRibosyl (D)">phosphoRibosyl (D)</option>
-        <option value="phosphoRibosyl (E)">phosphoRibosyl (E)</option>
-        <option value="phosphoRibosyl (R)">phosphoRibosyl (R)</option>
-        <option value="PhosphoribosyldephosphoCoA (S)">PhosphoribosyldephosphoCoA (S)</option>
-        <option value="PhosphoUridine (H)">PhosphoUridine (H)</option>
-        <option value="PhosphoUridine (Y)">PhosphoUridine (Y)</option>
-        <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
-        <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
-        <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
-        <option value="Piperidine (K)">Piperidine (K)</option>
-        <option value="Piperidine (N-term)">Piperidine (N-term)</option>
-        <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
-        <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
-        <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
-        <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
-        <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
-        <option value="Pro-&gt;Gln (P)">Pro-&gt;Gln (P)</option>
-        <option value="Pro-&gt;Glu (P)">Pro-&gt;Glu (P)</option>
-        <option value="Pro-&gt;Gly (P)">Pro-&gt;Gly (P)</option>
-        <option value="Pro-&gt;HAVA (P)">Pro-&gt;HAVA (P)</option>
-        <option value="Pro-&gt;His (P)">Pro-&gt;His (P)</option>
-        <option value="Pro-&gt;Lys (P)">Pro-&gt;Lys (P)</option>
-        <option value="Pro-&gt;Met (P)">Pro-&gt;Met (P)</option>
-        <option value="Pro-&gt;Phe (P)">Pro-&gt;Phe (P)</option>
-        <option value="Pro-&gt;pyro-Glu (P)">Pro-&gt;pyro-Glu (P)</option>
-        <option value="Pro-&gt;Pyrrolidinone (P)">Pro-&gt;Pyrrolidinone (P)</option>
-        <option value="Pro-&gt;Pyrrolidone (P)">Pro-&gt;Pyrrolidone (P)</option>
-        <option value="Pro-&gt;Ser (P)">Pro-&gt;Ser (P)</option>
-        <option value="Pro-&gt;Thr (P)">Pro-&gt;Thr (P)</option>
-        <option value="Pro-&gt;Trp (P)">Pro-&gt;Trp (P)</option>
-        <option value="Pro-&gt;Tyr (P)">Pro-&gt;Tyr (P)</option>
-        <option value="Pro-&gt;Val (P)">Pro-&gt;Val (P)</option>
-        <option value="Pro-&gt;Xle (P)">Pro-&gt;Xle (P)</option>
-        <option value="probiotinhydrazide (P)">probiotinhydrazide (P)</option>
-        <option value="Propargylamine (C-term)">Propargylamine (C-term)</option>
-        <option value="Propargylamine (D)">Propargylamine (D)</option>
-        <option value="Propargylamine (E)">Propargylamine (E)</option>
-        <option value="Propionamide (C)">Propionamide (C)</option>
-        <option value="Propionamide (K)">Propionamide (K)</option>
-        <option value="Propionamide (N-term)">Propionamide (N-term)</option>
-        <option value="Propionamide:2H(3) (C)">Propionamide:2H(3) (C)</option>
-        <option value="Propionyl (K)">Propionyl (K)</option>
-        <option value="Propionyl (N-term)">Propionyl (N-term)</option>
-        <option value="Propionyl (Protein N-term)">Propionyl (Protein N-term)</option>
-        <option value="Propionyl (S)">Propionyl (S)</option>
-        <option value="Propionyl (T)">Propionyl (T)</option>
-        <option value="Propionyl:13C(3) (K)">Propionyl:13C(3) (K)</option>
-        <option value="Propionyl:13C(3) (N-term)">Propionyl:13C(3) (N-term)</option>
-        <option value="Propiophenone (C)">Propiophenone (C)</option>
-        <option value="Propiophenone (H)">Propiophenone (H)</option>
-        <option value="Propiophenone (K)">Propiophenone (K)</option>
-        <option value="Propiophenone (R)">Propiophenone (R)</option>
-        <option value="Propiophenone (S)">Propiophenone (S)</option>
-        <option value="Propiophenone (T)">Propiophenone (T)</option>
-        <option value="Propiophenone (W)">Propiophenone (W)</option>
-        <option value="Propyl (C-term)">Propyl (C-term)</option>
-        <option value="Propyl (D)">Propyl (D)</option>
-        <option value="Propyl (E)">Propyl (E)</option>
-        <option value="Propyl (K)">Propyl (K)</option>
-        <option value="Propyl (N-term)">Propyl (N-term)</option>
-        <option value="Propyl (Protein C-term)">Propyl (Protein C-term)</option>
-        <option value="Propyl:2H(6) (K)">Propyl:2H(6) (K)</option>
-        <option value="Propyl:2H(6) (N-term)">Propyl:2H(6) (N-term)</option>
-        <option value="PropylNAGthiazoline (C)">PropylNAGthiazoline (C)</option>
-        <option value="PS_Hapten (C)">PS_Hapten (C)</option>
-        <option value="PS_Hapten (H)">PS_Hapten (H)</option>
-        <option value="PS_Hapten (K)">PS_Hapten (K)</option>
-        <option value="pupylation (K)">pupylation (K)</option>
-        <option value="Puromycin (C-term)">Puromycin (C-term)</option>
-        <option value="PyMIC (N-term)">PyMIC (N-term)</option>
-        <option value="PyridoxalPhosphate (K)">PyridoxalPhosphate (K)</option>
-        <option value="PyridoxalPhosphateH2 (K)">PyridoxalPhosphateH2 (K)</option>
-        <option value="Pyridylacetyl (K)">Pyridylacetyl (K)</option>
-        <option value="Pyridylacetyl (N-term)">Pyridylacetyl (N-term)</option>
-        <option value="Pyridylethyl (C)">Pyridylethyl (C)</option>
-        <option value="Pyro-carbamidomethyl (N-term C)">Pyro-carbamidomethyl (N-term C)</option>
-        <option value="pyrophospho (S)">pyrophospho (S)</option>
-        <option value="pyrophospho (T)">pyrophospho (T)</option>
-        <option value="PyruvicAcidIminyl (K)">PyruvicAcidIminyl (K)</option>
-        <option value="PyruvicAcidIminyl (Protein N-term C)">PyruvicAcidIminyl (Protein N-term C)</option>
-        <option value="PyruvicAcidIminyl (Protein N-term V)">PyruvicAcidIminyl (Protein N-term V)</option>
-        <option value="QAT (C)">QAT (C)</option>
-        <option value="QAT:2H(3) (C)">QAT:2H(3) (C)</option>
-        <option value="QEQTGG (K)">QEQTGG (K)</option>
-        <option value="QQQTGG (K)">QQQTGG (K)</option>
-        <option value="QTGG (K)">QTGG (K)</option>
-        <option value="Quinone (W)">Quinone (W)</option>
-        <option value="Quinone (Y)">Quinone (Y)</option>
-        <option value="Retinylidene (K)">Retinylidene (K)</option>
-        <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
-        <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
-        <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-        <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-        <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-        <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-        <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-        <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-        <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-        <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-        <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
-        <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
-        <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
-        <option value="Saligenin (H)">Saligenin (H)</option>
-        <option value="Saligenin (K)">Saligenin (K)</option>
-        <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
-        <option value="Ser-&gt;Arg (S)">Ser-&gt;Arg (S)</option>
-        <option value="Ser-&gt;Asn (S)">Ser-&gt;Asn (S)</option>
-        <option value="Ser-&gt;Asp (S)">Ser-&gt;Asp (S)</option>
-        <option value="Ser-&gt;Cys (S)">Ser-&gt;Cys (S)</option>
-        <option value="Ser-&gt;Gln (S)">Ser-&gt;Gln (S)</option>
-        <option value="Ser-&gt;Glu (S)">Ser-&gt;Glu (S)</option>
-        <option value="Ser-&gt;Gly (S)">Ser-&gt;Gly (S)</option>
-        <option value="Ser-&gt;His (S)">Ser-&gt;His (S)</option>
-        <option value="Ser-&gt;LacticAcid (Protein N-term S)">Ser-&gt;LacticAcid (Protein N-term S)</option>
-        <option value="Ser-&gt;Lys (S)">Ser-&gt;Lys (S)</option>
-        <option value="Ser-&gt;Met (S)">Ser-&gt;Met (S)</option>
-        <option value="Ser-&gt;Phe (S)">Ser-&gt;Phe (S)</option>
-        <option value="Ser-&gt;Pro (S)">Ser-&gt;Pro (S)</option>
-        <option value="Ser-&gt;Thr (S)">Ser-&gt;Thr (S)</option>
-        <option value="Ser-&gt;Trp (S)">Ser-&gt;Trp (S)</option>
-        <option value="Ser-&gt;Tyr (S)">Ser-&gt;Tyr (S)</option>
-        <option value="Ser-&gt;Val (S)">Ser-&gt;Val (S)</option>
-        <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
-        <option value="serotonylation (Q)">serotonylation (Q)</option>
-        <option value="shTMT (K)">shTMT (K)</option>
-        <option value="shTMT (N-term)">shTMT (N-term)</option>
-        <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
-        <option value="SMA (K)">SMA (K)</option>
-        <option value="SMA (N-term)">SMA (N-term)</option>
-        <option value="spermidine (Q)">spermidine (Q)</option>
-        <option value="spermine (Q)">spermine (Q)</option>
-        <option value="SPITC (K)">SPITC (K)</option>
-        <option value="SPITC (N-term)">SPITC (N-term)</option>
-        <option value="SPITC:13C(6) (K)">SPITC:13C(6) (K)</option>
-        <option value="SPITC:13C(6) (N-term)">SPITC:13C(6) (N-term)</option>
-        <option value="Succinyl (K)">Succinyl (K)</option>
-        <option value="Succinyl (N-term)">Succinyl (N-term)</option>
-        <option value="Succinyl (Protein N-term)">Succinyl (Protein N-term)</option>
-        <option value="Succinyl:13C(4) (K)">Succinyl:13C(4) (K)</option>
-        <option value="Succinyl:13C(4) (N-term)">Succinyl:13C(4) (N-term)</option>
-        <option value="Succinyl:2H(4) (K)">Succinyl:2H(4) (K)</option>
-        <option value="Succinyl:2H(4) (N-term)">Succinyl:2H(4) (N-term)</option>
-        <option value="SulfanilicAcid (C-term)">SulfanilicAcid (C-term)</option>
-        <option value="SulfanilicAcid (D)">SulfanilicAcid (D)</option>
-        <option value="SulfanilicAcid (E)">SulfanilicAcid (E)</option>
-        <option value="SulfanilicAcid:13C(6) (C-term)">SulfanilicAcid:13C(6) (C-term)</option>
-        <option value="SulfanilicAcid:13C(6) (D)">SulfanilicAcid:13C(6) (D)</option>
-        <option value="SulfanilicAcid:13C(6) (E)">SulfanilicAcid:13C(6) (E)</option>
-        <option value="Sulfide (C)">Sulfide (C)</option>
-        <option value="Sulfide (D)">Sulfide (D)</option>
-        <option value="Sulfide (W)">Sulfide (W)</option>
-        <option value="Sulfo (C)">Sulfo (C)</option>
-        <option value="Sulfo (S)">Sulfo (S)</option>
-        <option value="Sulfo (T)">Sulfo (T)</option>
-        <option value="Sulfo (Y)">Sulfo (Y)</option>
-        <option value="sulfo+amino (Y)">sulfo+amino (Y)</option>
-        <option value="Sulfo-NHS-LC-LC-Biotin (K)">Sulfo-NHS-LC-LC-Biotin (K)</option>
-        <option value="Sulfo-NHS-LC-LC-Biotin (N-term)">Sulfo-NHS-LC-LC-Biotin (N-term)</option>
-        <option value="SulfoGMBS (C)">SulfoGMBS (C)</option>
-        <option value="SulfurDioxide (C)">SulfurDioxide (C)</option>
-        <option value="SUMO2135 (K)">SUMO2135 (K)</option>
-        <option value="SUMO3549 (K)">SUMO3549 (K)</option>
-        <option value="TAMRA-FP (S)">TAMRA-FP (S)</option>
-        <option value="TAMRA-FP (Y)">TAMRA-FP (Y)</option>
-        <option value="Thiadiazole (C)">Thiadiazole (C)</option>
-        <option value="Thiazolidine (C)">Thiazolidine (C)</option>
-        <option value="Thiazolidine (F)">Thiazolidine (F)</option>
-        <option value="Thiazolidine (H)">Thiazolidine (H)</option>
-        <option value="Thiazolidine (K)">Thiazolidine (K)</option>
-        <option value="Thiazolidine (Protein N-term)">Thiazolidine (Protein N-term)</option>
-        <option value="Thiazolidine (R)">Thiazolidine (R)</option>
-        <option value="Thiazolidine (W)">Thiazolidine (W)</option>
-        <option value="Thiazolidine (Y)">Thiazolidine (Y)</option>
-        <option value="thioacylPA (K)">thioacylPA (K)</option>
-        <option value="Thiophos-S-S-biotin (S)">Thiophos-S-S-biotin (S)</option>
-        <option value="Thiophos-S-S-biotin (T)">Thiophos-S-S-biotin (T)</option>
-        <option value="Thiophos-S-S-biotin (Y)">Thiophos-S-S-biotin (Y)</option>
-        <option value="Thiophospho (S)">Thiophospho (S)</option>
-        <option value="Thiophospho (T)">Thiophospho (T)</option>
-        <option value="Thiophospho (Y)">Thiophospho (Y)</option>
-        <option value="Thr-&gt;Ala (T)">Thr-&gt;Ala (T)</option>
-        <option value="Thr-&gt;Arg (T)">Thr-&gt;Arg (T)</option>
-        <option value="Thr-&gt;Asn (T)">Thr-&gt;Asn (T)</option>
-        <option value="Thr-&gt;Asp (T)">Thr-&gt;Asp (T)</option>
-        <option value="Thr-&gt;Cys (T)">Thr-&gt;Cys (T)</option>
-        <option value="Thr-&gt;Gln (T)">Thr-&gt;Gln (T)</option>
-        <option value="Thr-&gt;Glu (T)">Thr-&gt;Glu (T)</option>
-        <option value="Thr-&gt;Gly (T)">Thr-&gt;Gly (T)</option>
-        <option value="Thr-&gt;His (T)">Thr-&gt;His (T)</option>
-        <option value="Thr-&gt;Lys (T)">Thr-&gt;Lys (T)</option>
-        <option value="Thr-&gt;Met (T)">Thr-&gt;Met (T)</option>
-        <option value="Thr-&gt;Phe (T)">Thr-&gt;Phe (T)</option>
-        <option value="Thr-&gt;Pro (T)">Thr-&gt;Pro (T)</option>
-        <option value="Thr-&gt;Ser (T)">Thr-&gt;Ser (T)</option>
-        <option value="Thr-&gt;Trp (T)">Thr-&gt;Trp (T)</option>
-        <option value="Thr-&gt;Tyr (T)">Thr-&gt;Tyr (T)</option>
-        <option value="Thr-&gt;Val (T)">Thr-&gt;Val (T)</option>
-        <option value="Thr-&gt;Xle (T)">Thr-&gt;Xle (T)</option>
-        <option value="Thrbiotinhydrazide (T)">Thrbiotinhydrazide (T)</option>
-        <option value="Thyroxine (Y)">Thyroxine (Y)</option>
-        <option value="TMAB (K)">TMAB (K)</option>
-        <option value="TMAB (N-term)">TMAB (N-term)</option>
-        <option value="TMAB:2H(9) (K)">TMAB:2H(9) (K)</option>
-        <option value="TMAB:2H(9) (N-term)">TMAB:2H(9) (N-term)</option>
-        <option value="TMPP-Ac (K)">TMPP-Ac (K)</option>
-        <option value="TMPP-Ac (N-term)">TMPP-Ac (N-term)</option>
-        <option value="TMPP-Ac (Y)">TMPP-Ac (Y)</option>
-        <option value="TMPP-Ac:13C(9) (K)">TMPP-Ac:13C(9) (K)</option>
-        <option value="TMPP-Ac:13C(9) (N-term)">TMPP-Ac:13C(9) (N-term)</option>
-        <option value="TMPP-Ac:13C(9) (Y)">TMPP-Ac:13C(9) (Y)</option>
-        <option value="TMT (H)">TMT (H)</option>
-        <option value="TMT (K)">TMT (K)</option>
-        <option value="TMT (N-term)">TMT (N-term)</option>
-        <option value="TMT (Protein N-term)">TMT (Protein N-term)</option>
-        <option value="TMT (S)">TMT (S)</option>
-        <option value="TMT (T)">TMT (T)</option>
-        <option value="TMT2plex (H)">TMT2plex (H)</option>
-        <option value="TMT2plex (K)">TMT2plex (K)</option>
-        <option value="TMT2plex (N-term)">TMT2plex (N-term)</option>
-        <option value="TMT2plex (Protein N-term)">TMT2plex (Protein N-term)</option>
-        <option value="TMT2plex (S)">TMT2plex (S)</option>
-        <option value="TMT2plex (T)">TMT2plex (T)</option>
-        <option value="TMT6plex (H)">TMT6plex (H)</option>
-        <option value="TMT6plex (K)">TMT6plex (K)</option>
-        <option value="TMT6plex (N-term)">TMT6plex (N-term)</option>
-        <option value="TMT6plex (Protein N-term)">TMT6plex (Protein N-term)</option>
-        <option value="TMT6plex (S)">TMT6plex (S)</option>
-        <option value="TMT6plex (T)">TMT6plex (T)</option>
-        <option value="TMTpro (H)">TMTpro (H)</option>
-        <option value="TMTpro (K)">TMTpro (K)</option>
-        <option value="TMTpro (N-term)">TMTpro (N-term)</option>
-        <option value="TMTpro (Protein N-term)">TMTpro (Protein N-term)</option>
-        <option value="TMTpro (S)">TMTpro (S)</option>
-        <option value="TMTpro (T)">TMTpro (T)</option>
-        <option value="TMTpro_zero (H)">TMTpro_zero (H)</option>
-        <option value="TMTpro_zero (K)">TMTpro_zero (K)</option>
-        <option value="TMTpro_zero (N-term)">TMTpro_zero (N-term)</option>
-        <option value="TMTpro_zero (Protein N-term)">TMTpro_zero (Protein N-term)</option>
-        <option value="TMTpro_zero (S)">TMTpro_zero (S)</option>
-        <option value="TMTpro_zero (T)">TMTpro_zero (T)</option>
-        <option value="TNBS (K)">TNBS (K)</option>
-        <option value="TNBS (N-term)">TNBS (N-term)</option>
-        <option value="trifluoro (L)">trifluoro (L)</option>
-        <option value="Triiodo (Y)">Triiodo (Y)</option>
-        <option value="Triiodothyronine (Y)">Triiodothyronine (Y)</option>
-        <option value="Trimethyl (K)">Trimethyl (K)</option>
-        <option value="Trimethyl (Protein N-term A)">Trimethyl (Protein N-term A)</option>
-        <option value="Trimethyl (R)">Trimethyl (R)</option>
-        <option value="Trimethyl:13C(3)2H(9) (K)">Trimethyl:13C(3)2H(9) (K)</option>
-        <option value="Trimethyl:13C(3)2H(9) (R)">Trimethyl:13C(3)2H(9) (R)</option>
-        <option value="Trimethyl:2H(9) (K)">Trimethyl:2H(9) (K)</option>
-        <option value="Trimethyl:2H(9) (R)">Trimethyl:2H(9) (R)</option>
-        <option value="Trioxidation (C)">Trioxidation (C)</option>
-        <option value="Trioxidation (F)">Trioxidation (F)</option>
-        <option value="Trioxidation (W)">Trioxidation (W)</option>
-        <option value="Trioxidation (Y)">Trioxidation (Y)</option>
-        <option value="Tripalmitate (Protein N-term C)">Tripalmitate (Protein N-term C)</option>
-        <option value="Tris (N)">Tris (N)</option>
-        <option value="Triton (C-term)">Triton (C-term)</option>
-        <option value="Triton (N-term)">Triton (N-term)</option>
-        <option value="Trp-&gt;Ala (W)">Trp-&gt;Ala (W)</option>
-        <option value="Trp-&gt;Arg (W)">Trp-&gt;Arg (W)</option>
-        <option value="Trp-&gt;Asn (W)">Trp-&gt;Asn (W)</option>
-        <option value="Trp-&gt;Asp (W)">Trp-&gt;Asp (W)</option>
-        <option value="Trp-&gt;Cys (W)">Trp-&gt;Cys (W)</option>
-        <option value="Trp-&gt;Gln (W)">Trp-&gt;Gln (W)</option>
-        <option value="Trp-&gt;Glu (W)">Trp-&gt;Glu (W)</option>
-        <option value="Trp-&gt;Gly (W)">Trp-&gt;Gly (W)</option>
-        <option value="Trp-&gt;His (W)">Trp-&gt;His (W)</option>
-        <option value="Trp-&gt;Hydroxykynurenin (W)">Trp-&gt;Hydroxykynurenin (W)</option>
-        <option value="Trp-&gt;Kynurenin (W)">Trp-&gt;Kynurenin (W)</option>
-        <option value="Trp-&gt;Lys (W)">Trp-&gt;Lys (W)</option>
-        <option value="Trp-&gt;Met (W)">Trp-&gt;Met (W)</option>
-        <option value="Trp-&gt;Oxolactone (W)">Trp-&gt;Oxolactone (W)</option>
-        <option value="Trp-&gt;Phe (W)">Trp-&gt;Phe (W)</option>
-        <option value="Trp-&gt;Pro (W)">Trp-&gt;Pro (W)</option>
-        <option value="Trp-&gt;Ser (W)">Trp-&gt;Ser (W)</option>
-        <option value="Trp-&gt;Thr (W)">Trp-&gt;Thr (W)</option>
-        <option value="Trp-&gt;Tyr (W)">Trp-&gt;Tyr (W)</option>
-        <option value="Trp-&gt;Val (W)">Trp-&gt;Val (W)</option>
-        <option value="Trp-&gt;Xle (W)">Trp-&gt;Xle (W)</option>
-        <option value="Tween20 (N-term)">Tween20 (N-term)</option>
-        <option value="Tween80 (C-term)">Tween80 (C-term)</option>
-        <option value="Tyr-&gt;Ala (Y)">Tyr-&gt;Ala (Y)</option>
-        <option value="Tyr-&gt;Arg (Y)">Tyr-&gt;Arg (Y)</option>
-        <option value="Tyr-&gt;Asn (Y)">Tyr-&gt;Asn (Y)</option>
-        <option value="Tyr-&gt;Asp (Y)">Tyr-&gt;Asp (Y)</option>
-        <option value="Tyr-&gt;Cys (Y)">Tyr-&gt;Cys (Y)</option>
-        <option value="Tyr-&gt;Dha (Y)">Tyr-&gt;Dha (Y)</option>
-        <option value="Tyr-&gt;Gln (Y)">Tyr-&gt;Gln (Y)</option>
-        <option value="Tyr-&gt;Glu (Y)">Tyr-&gt;Glu (Y)</option>
-        <option value="Tyr-&gt;Gly (Y)">Tyr-&gt;Gly (Y)</option>
-        <option value="Tyr-&gt;His (Y)">Tyr-&gt;His (Y)</option>
-        <option value="Tyr-&gt;Lys (Y)">Tyr-&gt;Lys (Y)</option>
-        <option value="Tyr-&gt;Met (Y)">Tyr-&gt;Met (Y)</option>
-        <option value="Tyr-&gt;Phe (Y)">Tyr-&gt;Phe (Y)</option>
-        <option value="Tyr-&gt;Pro (Y)">Tyr-&gt;Pro (Y)</option>
-        <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
-        <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
-        <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
-        <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
-        <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-        <option value="Ub-amide (C)">Ub-amide (C)</option>
-        <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
-        <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
-        <option value="Ub-VME (C)">Ub-VME (C)</option>
-        <option value="UgiJoullie (D)">UgiJoullie (D)</option>
-        <option value="UgiJoullie (E)">UgiJoullie (E)</option>
-        <option value="UgiJoullieProGly (D)">UgiJoullieProGly (D)</option>
-        <option value="UgiJoullieProGly (E)">UgiJoullieProGly (E)</option>
-        <option value="UgiJoullieProGlyProGly (D)">UgiJoullieProGlyProGly (D)</option>
-        <option value="UgiJoullieProGlyProGly (E)">UgiJoullieProGlyProGly (E)</option>
-        <option value="Unknown:162 (C-term)">Unknown:162 (C-term)</option>
-        <option value="Unknown:162 (D)">Unknown:162 (D)</option>
-        <option value="Unknown:162 (E)">Unknown:162 (E)</option>
-        <option value="Unknown:162 (N-term)">Unknown:162 (N-term)</option>
-        <option value="Unknown:177 (C-term)">Unknown:177 (C-term)</option>
-        <option value="Unknown:177 (D)">Unknown:177 (D)</option>
-        <option value="Unknown:177 (E)">Unknown:177 (E)</option>
-        <option value="Unknown:177 (N-term)">Unknown:177 (N-term)</option>
-        <option value="Unknown:210 (C-term)">Unknown:210 (C-term)</option>
-        <option value="Unknown:210 (D)">Unknown:210 (D)</option>
-        <option value="Unknown:210 (E)">Unknown:210 (E)</option>
-        <option value="Unknown:210 (N-term)">Unknown:210 (N-term)</option>
-        <option value="Unknown:216 (C-term)">Unknown:216 (C-term)</option>
-        <option value="Unknown:216 (D)">Unknown:216 (D)</option>
-        <option value="Unknown:216 (E)">Unknown:216 (E)</option>
-        <option value="Unknown:216 (N-term)">Unknown:216 (N-term)</option>
-        <option value="Unknown:234 (C-term)">Unknown:234 (C-term)</option>
-        <option value="Unknown:234 (D)">Unknown:234 (D)</option>
-        <option value="Unknown:234 (E)">Unknown:234 (E)</option>
-        <option value="Unknown:234 (N-term)">Unknown:234 (N-term)</option>
-        <option value="Unknown:248 (C-term)">Unknown:248 (C-term)</option>
-        <option value="Unknown:248 (D)">Unknown:248 (D)</option>
-        <option value="Unknown:248 (E)">Unknown:248 (E)</option>
-        <option value="Unknown:248 (N-term)">Unknown:248 (N-term)</option>
-        <option value="Unknown:250 (C-term)">Unknown:250 (C-term)</option>
-        <option value="Unknown:250 (D)">Unknown:250 (D)</option>
-        <option value="Unknown:250 (E)">Unknown:250 (E)</option>
-        <option value="Unknown:250 (N-term)">Unknown:250 (N-term)</option>
-        <option value="Unknown:302 (C-term)">Unknown:302 (C-term)</option>
-        <option value="Unknown:302 (D)">Unknown:302 (D)</option>
-        <option value="Unknown:302 (E)">Unknown:302 (E)</option>
-        <option value="Unknown:302 (N-term)">Unknown:302 (N-term)</option>
-        <option value="Unknown:306 (C-term)">Unknown:306 (C-term)</option>
-        <option value="Unknown:306 (D)">Unknown:306 (D)</option>
-        <option value="Unknown:306 (E)">Unknown:306 (E)</option>
-        <option value="Unknown:306 (N-term)">Unknown:306 (N-term)</option>
-        <option value="Unknown:420 (C-term)">Unknown:420 (C-term)</option>
-        <option value="Unknown:420 (N-term)">Unknown:420 (N-term)</option>
-        <option value="Val-&gt;Ala (V)">Val-&gt;Ala (V)</option>
-        <option value="Val-&gt;Arg (V)">Val-&gt;Arg (V)</option>
-        <option value="Val-&gt;Asn (V)">Val-&gt;Asn (V)</option>
-        <option value="Val-&gt;Asp (V)">Val-&gt;Asp (V)</option>
-        <option value="Val-&gt;Cys (V)">Val-&gt;Cys (V)</option>
-        <option value="Val-&gt;Gln (V)">Val-&gt;Gln (V)</option>
-        <option value="Val-&gt;Glu (V)">Val-&gt;Glu (V)</option>
-        <option value="Val-&gt;Gly (V)">Val-&gt;Gly (V)</option>
-        <option value="Val-&gt;His (V)">Val-&gt;His (V)</option>
-        <option value="Val-&gt;Lys (V)">Val-&gt;Lys (V)</option>
-        <option value="Val-&gt;Met (V)">Val-&gt;Met (V)</option>
-        <option value="Val-&gt;Phe (V)">Val-&gt;Phe (V)</option>
-        <option value="Val-&gt;Pro (V)">Val-&gt;Pro (V)</option>
-        <option value="Val-&gt;Ser (V)">Val-&gt;Ser (V)</option>
-        <option value="Val-&gt;Thr (V)">Val-&gt;Thr (V)</option>
-        <option value="Val-&gt;Trp (V)">Val-&gt;Trp (V)</option>
-        <option value="Val-&gt;Tyr (V)">Val-&gt;Tyr (V)</option>
-        <option value="Val-&gt;Xle (V)">Val-&gt;Xle (V)</option>
-        <option value="VFQQQTGG (K)">VFQQQTGG (K)</option>
-        <option value="VIEVYQEQTGG (K)">VIEVYQEQTGG (K)</option>
-        <option value="Withaferin (C)">Withaferin (C)</option>
-        <option value="Xle-&gt;Ala (I)">Xle-&gt;Ala (I)</option>
-        <option value="Xle-&gt;Ala (L)">Xle-&gt;Ala (L)</option>
-        <option value="Xle-&gt;Arg (I)">Xle-&gt;Arg (I)</option>
-        <option value="Xle-&gt;Arg (L)">Xle-&gt;Arg (L)</option>
-        <option value="Xle-&gt;Asn (I)">Xle-&gt;Asn (I)</option>
-        <option value="Xle-&gt;Asn (L)">Xle-&gt;Asn (L)</option>
-        <option value="Xle-&gt;Asp (I)">Xle-&gt;Asp (I)</option>
-        <option value="Xle-&gt;Asp (L)">Xle-&gt;Asp (L)</option>
-        <option value="Xle-&gt;Cys (I)">Xle-&gt;Cys (I)</option>
-        <option value="Xle-&gt;Cys (L)">Xle-&gt;Cys (L)</option>
-        <option value="Xle-&gt;Gln (I)">Xle-&gt;Gln (I)</option>
-        <option value="Xle-&gt;Gln (L)">Xle-&gt;Gln (L)</option>
-        <option value="Xle-&gt;Glu (I)">Xle-&gt;Glu (I)</option>
-        <option value="Xle-&gt;Glu (L)">Xle-&gt;Glu (L)</option>
-        <option value="Xle-&gt;Gly (I)">Xle-&gt;Gly (I)</option>
-        <option value="Xle-&gt;Gly (L)">Xle-&gt;Gly (L)</option>
-        <option value="Xle-&gt;His (I)">Xle-&gt;His (I)</option>
-        <option value="Xle-&gt;His (L)">Xle-&gt;His (L)</option>
-        <option value="Xle-&gt;Lys (I)">Xle-&gt;Lys (I)</option>
-        <option value="Xle-&gt;Lys (L)">Xle-&gt;Lys (L)</option>
-        <option value="Xle-&gt;Met (I)">Xle-&gt;Met (I)</option>
-        <option value="Xle-&gt;Met (L)">Xle-&gt;Met (L)</option>
-        <option value="Xle-&gt;Phe (I)">Xle-&gt;Phe (I)</option>
-        <option value="Xle-&gt;Phe (L)">Xle-&gt;Phe (L)</option>
-        <option value="Xle-&gt;Pro (I)">Xle-&gt;Pro (I)</option>
-        <option value="Xle-&gt;Pro (L)">Xle-&gt;Pro (L)</option>
-        <option value="Xle-&gt;Ser (I)">Xle-&gt;Ser (I)</option>
-        <option value="Xle-&gt;Ser (L)">Xle-&gt;Ser (L)</option>
-        <option value="Xle-&gt;Thr (I)">Xle-&gt;Thr (I)</option>
-        <option value="Xle-&gt;Thr (L)">Xle-&gt;Thr (L)</option>
-        <option value="Xle-&gt;Trp (I)">Xle-&gt;Trp (I)</option>
-        <option value="Xle-&gt;Trp (L)">Xle-&gt;Trp (L)</option>
-        <option value="Xle-&gt;Tyr (I)">Xle-&gt;Tyr (I)</option>
-        <option value="Xle-&gt;Tyr (L)">Xle-&gt;Tyr (L)</option>
-        <option value="Xle-&gt;Val (I)">Xle-&gt;Val (I)</option>
-        <option value="Xle-&gt;Val (L)">Xle-&gt;Val (L)</option>
-        <option value="Xlink:B10621 (C)">Xlink:B10621 (C)</option>
-        <option value="Xlink:BMOE (C)">Xlink:BMOE (C)</option>
-        <option value="Xlink:BS2G[113] (K)">Xlink:BS2G[113] (K)</option>
-        <option value="Xlink:BS2G[113] (Protein N-term)">Xlink:BS2G[113] (Protein N-term)</option>
-        <option value="Xlink:BS2G[114] (K)">Xlink:BS2G[114] (K)</option>
-        <option value="Xlink:BS2G[114] (Protein N-term)">Xlink:BS2G[114] (Protein N-term)</option>
-        <option value="Xlink:BS2G[217] (K)">Xlink:BS2G[217] (K)</option>
-        <option value="Xlink:BS2G[217] (Protein N-term)">Xlink:BS2G[217] (Protein N-term)</option>
-        <option value="Xlink:BS2G[96] (K)">Xlink:BS2G[96] (K)</option>
-        <option value="Xlink:BS2G[96] (Protein N-term)">Xlink:BS2G[96] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[111] (K)">Xlink:BuUrBu[111] (K)</option>
-        <option value="Xlink:BuUrBu[111] (Protein N-term)">Xlink:BuUrBu[111] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[196] (K)">Xlink:BuUrBu[196] (K)</option>
-        <option value="Xlink:BuUrBu[196] (Protein N-term)">Xlink:BuUrBu[196] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[213] (K)">Xlink:BuUrBu[213] (K)</option>
-        <option value="Xlink:BuUrBu[213] (Protein N-term)">Xlink:BuUrBu[213] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[214] (K)">Xlink:BuUrBu[214] (K)</option>
-        <option value="Xlink:BuUrBu[214] (Protein N-term)">Xlink:BuUrBu[214] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[317] (K)">Xlink:BuUrBu[317] (K)</option>
-        <option value="Xlink:BuUrBu[317] (Protein N-term)">Xlink:BuUrBu[317] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[85] (K)">Xlink:BuUrBu[85] (K)</option>
-        <option value="Xlink:BuUrBu[85] (Protein N-term)">Xlink:BuUrBu[85] (Protein N-term)</option>
-        <option value="Xlink:DFDNB (K)">Xlink:DFDNB (K)</option>
-        <option value="Xlink:DFDNB (N)">Xlink:DFDNB (N)</option>
-        <option value="Xlink:DFDNB (Q)">Xlink:DFDNB (Q)</option>
-        <option value="Xlink:DFDNB (R)">Xlink:DFDNB (R)</option>
-        <option value="Xlink:DMP[122] (K)">Xlink:DMP[122] (K)</option>
-        <option value="Xlink:DMP[122] (Protein N-term)">Xlink:DMP[122] (Protein N-term)</option>
-        <option value="Xlink:DMP[139] (K)">Xlink:DMP[139] (K)</option>
-        <option value="Xlink:DMP[139] (Protein N-term)">Xlink:DMP[139] (Protein N-term)</option>
-        <option value="Xlink:DMP[140] (K)">Xlink:DMP[140] (K)</option>
-        <option value="Xlink:DMP[140] (Protein N-term)">Xlink:DMP[140] (Protein N-term)</option>
-        <option value="Xlink:DMP[154] (K)">Xlink:DMP[154] (K)</option>
-        <option value="Xlink:DMP[154] (Protein N-term)">Xlink:DMP[154] (Protein N-term)</option>
-        <option value="Xlink:DSS[138] (K)">Xlink:DSS[138] (K)</option>
-        <option value="Xlink:DSS[138] (Protein N-term)">Xlink:DSS[138] (Protein N-term)</option>
-        <option value="Xlink:DSS[155] (K)">Xlink:DSS[155] (K)</option>
-        <option value="Xlink:DSS[155] (Protein N-term)">Xlink:DSS[155] (Protein N-term)</option>
-        <option value="Xlink:DSS[156] (K)">Xlink:DSS[156] (K)</option>
-        <option value="Xlink:DSS[156] (Protein N-term)">Xlink:DSS[156] (Protein N-term)</option>
-        <option value="Xlink:DSS[259] (K)">Xlink:DSS[259] (K)</option>
-        <option value="Xlink:DSS[259] (Protein N-term)">Xlink:DSS[259] (Protein N-term)</option>
-        <option value="Xlink:DSSO[104] (K)">Xlink:DSSO[104] (K)</option>
-        <option value="Xlink:DSSO[104] (Protein N-term)">Xlink:DSSO[104] (Protein N-term)</option>
-        <option value="Xlink:DSSO[158] (K)">Xlink:DSSO[158] (K)</option>
-        <option value="Xlink:DSSO[158] (Protein N-term)">Xlink:DSSO[158] (Protein N-term)</option>
-        <option value="Xlink:DSSO[175] (K)">Xlink:DSSO[175] (K)</option>
-        <option value="Xlink:DSSO[175] (Protein N-term)">Xlink:DSSO[175] (Protein N-term)</option>
-        <option value="Xlink:DSSO[176] (K)">Xlink:DSSO[176] (K)</option>
-        <option value="Xlink:DSSO[176] (Protein N-term)">Xlink:DSSO[176] (Protein N-term)</option>
-        <option value="Xlink:DSSO[279] (K)">Xlink:DSSO[279] (K)</option>
-        <option value="Xlink:DSSO[279] (Protein N-term)">Xlink:DSSO[279] (Protein N-term)</option>
-        <option value="Xlink:DSSO[54] (K)">Xlink:DSSO[54] (K)</option>
-        <option value="Xlink:DSSO[54] (Protein N-term)">Xlink:DSSO[54] (Protein N-term)</option>
-        <option value="Xlink:DSSO[86] (K)">Xlink:DSSO[86] (K)</option>
-        <option value="Xlink:DSSO[86] (Protein N-term)">Xlink:DSSO[86] (Protein N-term)</option>
-        <option value="Xlink:DST[114] (K)">Xlink:DST[114] (K)</option>
-        <option value="Xlink:DST[114] (Protein N-term)">Xlink:DST[114] (Protein N-term)</option>
-        <option value="Xlink:DST[132] (K)">Xlink:DST[132] (K)</option>
-        <option value="Xlink:DST[132] (Protein N-term)">Xlink:DST[132] (Protein N-term)</option>
-        <option value="Xlink:DST[56] (K)">Xlink:DST[56] (K)</option>
-        <option value="Xlink:DST[56] (Protein N-term)">Xlink:DST[56] (Protein N-term)</option>
-        <option value="Xlink:DTBP[172] (K)">Xlink:DTBP[172] (K)</option>
-        <option value="Xlink:DTBP[172] (Protein N-term)">Xlink:DTBP[172] (Protein N-term)</option>
-        <option value="Xlink:DTBP[87] (K)">Xlink:DTBP[87] (K)</option>
-        <option value="Xlink:DTBP[87] (Protein N-term)">Xlink:DTBP[87] (Protein N-term)</option>
-        <option value="Xlink:DTSSP[174] (K)">Xlink:DTSSP[174] (K)</option>
-        <option value="Xlink:DTSSP[174] (Protein N-term)">Xlink:DTSSP[174] (Protein N-term)</option>
-        <option value="Xlink:DTSSP[192] (K)">Xlink:DTSSP[192] (K)</option>
-        <option value="Xlink:DTSSP[192] (Protein N-term)">Xlink:DTSSP[192] (Protein N-term)</option>
-        <option value="Xlink:DTSSP[88] (K)">Xlink:DTSSP[88] (K)</option>
-        <option value="Xlink:DTSSP[88] (Protein N-term)">Xlink:DTSSP[88] (Protein N-term)</option>
-        <option value="Xlink:EGS[115] (K)">Xlink:EGS[115] (K)</option>
-        <option value="Xlink:EGS[115] (Protein N-term)">Xlink:EGS[115] (Protein N-term)</option>
-        <option value="Xlink:EGS[226] (K)">Xlink:EGS[226] (K)</option>
-        <option value="Xlink:EGS[226] (Protein N-term)">Xlink:EGS[226] (Protein N-term)</option>
-        <option value="Xlink:EGS[244] (K)">Xlink:EGS[244] (K)</option>
-        <option value="Xlink:EGS[244] (Protein N-term)">Xlink:EGS[244] (Protein N-term)</option>
-        <option value="Xlink:SMCC[219] (C)">Xlink:SMCC[219] (C)</option>
-        <option value="Xlink:SMCC[219] (K)">Xlink:SMCC[219] (K)</option>
-        <option value="Xlink:SMCC[219] (Protein N-term)">Xlink:SMCC[219] (Protein N-term)</option>
-        <option value="Xlink:SMCC[237] (C)">Xlink:SMCC[237] (C)</option>
-        <option value="Xlink:SMCC[237] (K)">Xlink:SMCC[237] (K)</option>
-        <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
-        <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
-        <option value="ZGB (K)">ZGB (K)</option>
-        <option value="ZGB (N-term)">ZGB (N-term)</option>
-        <option value="ZQG (K)">ZQG (K)</option>
-        <expand macro="list_string_san" name="variable_modifications"/>
-      </param>
-      <param name="residue_set" argument="-algorithm:residue_set" type="text" optional="true" value="Natural19WithoutI" label="The predefined amino acid set that should be used, see doc of ResidueDB for possible residue sets" help="">
-        <expand macro="list_string_san" name="residue_set"/>
-      </param>
-    </section>
-    <expand macro="adv_opts_macro">
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><!-- TOPP_CompNovo_1 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="CompNovo_1_input.mzML"/>
-      <output name="out" file="CompNovo_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <section name="algorithm">
-        <param name="max_number_aa_per_decomp" value="4"/>
-        <param name="tryptic_only" value="true"/>
-        <param name="precursor_mass_tolerance" value="0.3"/>
-        <param name="fragment_mass_tolerance" value="0.3"/>
-        <param name="max_number_pivot" value="9"/>
-        <param name="max_subscore_number" value="40"/>
-        <param name="decomp_weights_precision" value="0.01"/>
-        <param name="double_charged_iso_threshold" value="0.6"/>
-        <param name="max_mz" value="2000.0"/>
-        <param name="min_mz" value="200.0"/>
-        <param name="max_isotope_to_score" value="3"/>
-        <param name="max_decomp_weight" value="450.0"/>
-        <param name="max_isotope" value="3"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="estimate_precursor_mz" value="true"/>
-        <param name="number_of_prescoring_hits" value="250"/>
-        <param name="fixed_modifications"/>
-        <param name="variable_modifications"/>
-        <param name="residue_set" value="Natural19WithoutI"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
-  <help><![CDATA[Performs a de novo peptide identification using the CompNovo engine.
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_CompNovo.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/CompNovoCID.xml b/tools/openms/CompNovoCID.xml
deleted file mode 100644
index d8a3e2ada..000000000
--- a/tools/openms/CompNovoCID.xml
+++ /dev/null
@@ -1,5984 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
-<tool id="CompNovoCID" name="CompNovoCID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Performs a de novo peptide identification using the CompNovo engine.</description>
-  <macros>
-    <token name="@EXECUTABLE@">CompNovoCID</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-mkdir out &&
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in
-'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
--out
-'out/output.${gxy2omsext("idxml")}'
-
-## Postprocessing
-&& mv 'out/output.${gxy2omsext("idxml")}' '$out'
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
-  </configfiles>
-  <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file in mzML format" help=" select mzml data sets(s)"/>
-    <section name="algorithm" title="Algorithm section" help="" expanded="false">
-      <param name="max_number_aa_per_decomp" argument="-algorithm:max_number_aa_per_decomp" type="integer" optional="true" value="4" label="maximal amino acid frequency per decomposition" help=""/>
-      <param name="tryptic_only" argument="-algorithm:tryptic_only" type="boolean" truevalue="true" falsevalue="false" checked="true" label="if set to true only tryptic peptides are reported" help=""/>
-      <param name="precursor_mass_tolerance" argument="-algorithm:precursor_mass_tolerance" type="float" optional="true" value="1.5" label="precursor mass tolerance" help=""/>
-      <param name="fragment_mass_tolerance" argument="-algorithm:fragment_mass_tolerance" type="float" optional="true" value="0.3" label="fragment mass tolerance" help=""/>
-      <param name="max_number_pivot" argument="-algorithm:max_number_pivot" type="integer" optional="true" value="9" label="maximal number of pivot ions to be used" help=""/>
-      <param name="max_subscore_number" argument="-algorithm:max_subscore_number" type="integer" optional="true" value="40" label="maximal number of solutions of a subsegment that are kept" help=""/>
-      <param name="decomp_weights_precision" argument="-algorithm:decomp_weights_precision" type="float" optional="true" value="0.01" label="precision used to calculate the decompositions, this only affects cache usage!" help=""/>
-      <param name="double_charged_iso_threshold" argument="-algorithm:double_charged_iso_threshold" type="float" optional="true" value="0.6" label="minimal isotope intensity correlation of doubly charged ions to be used to score the single scored ions" help=""/>
-      <param name="max_mz" argument="-algorithm:max_mz" type="float" optional="true" value="2000.0" label="maximal m/z value used to calculate isotope distributions" help=""/>
-      <param name="min_mz" argument="-algorithm:min_mz" type="float" optional="true" value="200.0" label="minimal m/z value used to calculate the isotope distributions" help=""/>
-      <param name="max_isotope_to_score" argument="-algorithm:max_isotope_to_score" type="integer" optional="true" value="3" label="max isotope peak to be considered in the scoring" help=""/>
-      <param name="max_decomp_weight" argument="-algorithm:max_decomp_weight" type="float" optional="true" value="450.0" label="maximal m/z difference used to calculate the decompositions" help=""/>
-      <param name="max_isotope" argument="-algorithm:max_isotope" type="integer" optional="true" value="3" label="max isotope used in the theoretical spectra to score" help=""/>
-      <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" value="1" label="maximal number of missed cleavages allowed per peptide" help=""/>
-      <param name="number_of_hits" argument="-algorithm:number_of_hits" type="integer" optional="true" value="100" label="maximal number of hits which are reported per spectrum" help=""/>
-      <param name="estimate_precursor_mz" argument="-algorithm:estimate_precursor_mz" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If set to true, the precursor charge will be estimated" help="e.g. from the precursor peaks of the ETD spectrum.. The input is believed otherwise"/>
-      <param name="number_of_prescoring_hits" argument="-algorithm:number_of_prescoring_hits" type="integer" optional="true" value="250" label="how many sequences are kept after first rough scoring for better scoring" help=""/>
-      <param name="fixed_modifications" argument="-algorithm:fixed_modifications" multiple="true" type="select" optional="true" label="fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
-        <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
-        <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
-        <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
-        <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
-        <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
-        <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
-        <option value="2-succinyl (C)">2-succinyl (C)</option>
-        <option value="2HPG (R)">2HPG (R)</option>
-        <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
-        <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
-        <option value="3sulfo (N-term)">3sulfo (N-term)</option>
-        <option value="4-ONE (C)">4-ONE (C)</option>
-        <option value="4-ONE (H)">4-ONE (H)</option>
-        <option value="4-ONE (K)">4-ONE (K)</option>
-        <option value="4-ONE+Delta:H(-2)O(-1) (C)">4-ONE+Delta:H(-2)O(-1) (C)</option>
-        <option value="4-ONE+Delta:H(-2)O(-1) (H)">4-ONE+Delta:H(-2)O(-1) (H)</option>
-        <option value="4-ONE+Delta:H(-2)O(-1) (K)">4-ONE+Delta:H(-2)O(-1) (K)</option>
-        <option value="4AcAllylGal (C)">4AcAllylGal (C)</option>
-        <option value="a-type-ion (C-term)">a-type-ion (C-term)</option>
-        <option value="AccQTag (K)">AccQTag (K)</option>
-        <option value="AccQTag (N-term)">AccQTag (N-term)</option>
-        <option value="Acetyl (C)">Acetyl (C)</option>
-        <option value="Acetyl (H)">Acetyl (H)</option>
-        <option value="Acetyl (K)">Acetyl (K)</option>
-        <option value="Acetyl (N-term)">Acetyl (N-term)</option>
-        <option value="Acetyl (Protein N-term)">Acetyl (Protein N-term)</option>
-        <option value="Acetyl (R)">Acetyl (R)</option>
-        <option value="Acetyl (S)">Acetyl (S)</option>
-        <option value="Acetyl (T)">Acetyl (T)</option>
-        <option value="Acetyl (Y)">Acetyl (Y)</option>
-        <option value="Acetyl:13C(2) (K)">Acetyl:13C(2) (K)</option>
-        <option value="Acetyl:13C(2) (Protein N-term)">Acetyl:13C(2) (Protein N-term)</option>
-        <option value="Acetyl:2H(3) (H)">Acetyl:2H(3) (H)</option>
-        <option value="Acetyl:2H(3) (K)">Acetyl:2H(3) (K)</option>
-        <option value="Acetyl:2H(3) (N-term)">Acetyl:2H(3) (N-term)</option>
-        <option value="Acetyl:2H(3) (Protein N-term)">Acetyl:2H(3) (Protein N-term)</option>
-        <option value="Acetyl:2H(3) (S)">Acetyl:2H(3) (S)</option>
-        <option value="Acetyl:2H(3) (T)">Acetyl:2H(3) (T)</option>
-        <option value="Acetyl:2H(3) (Y)">Acetyl:2H(3) (Y)</option>
-        <option value="Acetyldeoxyhypusine (K)">Acetyldeoxyhypusine (K)</option>
-        <option value="Acetylhypusine (K)">Acetylhypusine (K)</option>
-        <option value="ADP-Ribosyl (C)">ADP-Ribosyl (C)</option>
-        <option value="ADP-Ribosyl (D)">ADP-Ribosyl (D)</option>
-        <option value="ADP-Ribosyl (E)">ADP-Ribosyl (E)</option>
-        <option value="ADP-Ribosyl (K)">ADP-Ribosyl (K)</option>
-        <option value="ADP-Ribosyl (N)">ADP-Ribosyl (N)</option>
-        <option value="ADP-Ribosyl (R)">ADP-Ribosyl (R)</option>
-        <option value="ADP-Ribosyl (S)">ADP-Ribosyl (S)</option>
-        <option value="ADP-Ribosyl (T)">ADP-Ribosyl (T)</option>
-        <option value="AEBS (H)">AEBS (H)</option>
-        <option value="AEBS (K)">AEBS (K)</option>
-        <option value="AEBS (Protein N-term)">AEBS (Protein N-term)</option>
-        <option value="AEBS (S)">AEBS (S)</option>
-        <option value="AEBS (Y)">AEBS (Y)</option>
-        <option value="AEC-MAEC (S)">AEC-MAEC (S)</option>
-        <option value="AEC-MAEC (T)">AEC-MAEC (T)</option>
-        <option value="AEC-MAEC:2H(4) (S)">AEC-MAEC:2H(4) (S)</option>
-        <option value="AEC-MAEC:2H(4) (T)">AEC-MAEC:2H(4) (T)</option>
-        <option value="AFB1_Dialdehyde (K)">AFB1_Dialdehyde (K)</option>
-        <option value="AHA-Alkyne (M)">AHA-Alkyne (M)</option>
-        <option value="AHA-Alkyne-KDDDD (M)">AHA-Alkyne-KDDDD (M)</option>
-        <option value="AHA-SS (M)">AHA-SS (M)</option>
-        <option value="AHA-SS_CAM (M)">AHA-SS_CAM (M)</option>
-        <option value="Ahx2+Hsl (C-term)">Ahx2+Hsl (C-term)</option>
-        <option value="Ala-&gt;Arg (A)">Ala-&gt;Arg (A)</option>
-        <option value="Ala-&gt;Asn (A)">Ala-&gt;Asn (A)</option>
-        <option value="Ala-&gt;Asp (A)">Ala-&gt;Asp (A)</option>
-        <option value="Ala-&gt;Cys (A)">Ala-&gt;Cys (A)</option>
-        <option value="Ala-&gt;Gln (A)">Ala-&gt;Gln (A)</option>
-        <option value="Ala-&gt;Glu (A)">Ala-&gt;Glu (A)</option>
-        <option value="Ala-&gt;Gly (A)">Ala-&gt;Gly (A)</option>
-        <option value="Ala-&gt;His (A)">Ala-&gt;His (A)</option>
-        <option value="Ala-&gt;Lys (A)">Ala-&gt;Lys (A)</option>
-        <option value="Ala-&gt;Met (A)">Ala-&gt;Met (A)</option>
-        <option value="Ala-&gt;Phe (A)">Ala-&gt;Phe (A)</option>
-        <option value="Ala-&gt;Pro (A)">Ala-&gt;Pro (A)</option>
-        <option value="Ala-&gt;Ser (A)">Ala-&gt;Ser (A)</option>
-        <option value="Ala-&gt;Thr (A)">Ala-&gt;Thr (A)</option>
-        <option value="Ala-&gt;Trp (A)">Ala-&gt;Trp (A)</option>
-        <option value="Ala-&gt;Tyr (A)">Ala-&gt;Tyr (A)</option>
-        <option value="Ala-&gt;Val (A)">Ala-&gt;Val (A)</option>
-        <option value="Ala-&gt;Xle (A)">Ala-&gt;Xle (A)</option>
-        <option value="Amidated (C-term)">Amidated (C-term)</option>
-        <option value="Amidated (Protein C-term)">Amidated (Protein C-term)</option>
-        <option value="Amidine (K)">Amidine (K)</option>
-        <option value="Amidine (N-term)">Amidine (N-term)</option>
-        <option value="Amidino (C)">Amidino (C)</option>
-        <option value="Amino (Y)">Amino (Y)</option>
-        <option value="Ammonia-loss (N)">Ammonia-loss (N)</option>
-        <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
-        <option value="Ammonia-loss (Protein N-term S)">Ammonia-loss (Protein N-term S)</option>
-        <option value="Ammonia-loss (Protein N-term T)">Ammonia-loss (Protein N-term T)</option>
-        <option value="Ammonium (C-term)">Ammonium (C-term)</option>
-        <option value="Ammonium (D)">Ammonium (D)</option>
-        <option value="Ammonium (E)">Ammonium (E)</option>
-        <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
-        <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
-        <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
-        <option value="Archaeol (C)">Archaeol (C)</option>
-        <option value="Arg (N-term)">Arg (N-term)</option>
-        <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
-        <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
-        <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
-        <option value="Arg-&gt;Cys (R)">Arg-&gt;Cys (R)</option>
-        <option value="Arg-&gt;Gln (R)">Arg-&gt;Gln (R)</option>
-        <option value="Arg-&gt;Glu (R)">Arg-&gt;Glu (R)</option>
-        <option value="Arg-&gt;GluSA (R)">Arg-&gt;GluSA (R)</option>
-        <option value="Arg-&gt;Gly (R)">Arg-&gt;Gly (R)</option>
-        <option value="Arg-&gt;His (R)">Arg-&gt;His (R)</option>
-        <option value="Arg-&gt;Lys (R)">Arg-&gt;Lys (R)</option>
-        <option value="Arg-&gt;Met (R)">Arg-&gt;Met (R)</option>
-        <option value="Arg-&gt;Npo (R)">Arg-&gt;Npo (R)</option>
-        <option value="Arg-&gt;Orn (R)">Arg-&gt;Orn (R)</option>
-        <option value="Arg-&gt;Phe (R)">Arg-&gt;Phe (R)</option>
-        <option value="Arg-&gt;Pro (R)">Arg-&gt;Pro (R)</option>
-        <option value="Arg-&gt;Ser (R)">Arg-&gt;Ser (R)</option>
-        <option value="Arg-&gt;Thr (R)">Arg-&gt;Thr (R)</option>
-        <option value="Arg-&gt;Trp (R)">Arg-&gt;Trp (R)</option>
-        <option value="Arg-&gt;Tyr (R)">Arg-&gt;Tyr (R)</option>
-        <option value="Arg-&gt;Val (R)">Arg-&gt;Val (R)</option>
-        <option value="Arg-&gt;Xle (R)">Arg-&gt;Xle (R)</option>
-        <option value="Arg-loss (C-term R)">Arg-loss (C-term R)</option>
-        <option value="Arg2PG (R)">Arg2PG (R)</option>
-        <option value="Argbiotinhydrazide (R)">Argbiotinhydrazide (R)</option>
-        <option value="AROD (C)">AROD (C)</option>
-        <option value="Asn-&gt;Ala (N)">Asn-&gt;Ala (N)</option>
-        <option value="Asn-&gt;Arg (N)">Asn-&gt;Arg (N)</option>
-        <option value="Asn-&gt;Asp (N)">Asn-&gt;Asp (N)</option>
-        <option value="Asn-&gt;Cys (N)">Asn-&gt;Cys (N)</option>
-        <option value="Asn-&gt;Gln (N)">Asn-&gt;Gln (N)</option>
-        <option value="Asn-&gt;Glu (N)">Asn-&gt;Glu (N)</option>
-        <option value="Asn-&gt;Gly (N)">Asn-&gt;Gly (N)</option>
-        <option value="Asn-&gt;His (N)">Asn-&gt;His (N)</option>
-        <option value="Asn-&gt;Lys (N)">Asn-&gt;Lys (N)</option>
-        <option value="Asn-&gt;Met (N)">Asn-&gt;Met (N)</option>
-        <option value="Asn-&gt;Phe (N)">Asn-&gt;Phe (N)</option>
-        <option value="Asn-&gt;Pro (N)">Asn-&gt;Pro (N)</option>
-        <option value="Asn-&gt;Ser (N)">Asn-&gt;Ser (N)</option>
-        <option value="Asn-&gt;Thr (N)">Asn-&gt;Thr (N)</option>
-        <option value="Asn-&gt;Trp (N)">Asn-&gt;Trp (N)</option>
-        <option value="Asn-&gt;Tyr (N)">Asn-&gt;Tyr (N)</option>
-        <option value="Asn-&gt;Val (N)">Asn-&gt;Val (N)</option>
-        <option value="Asn-&gt;Xle (N)">Asn-&gt;Xle (N)</option>
-        <option value="Asp-&gt;Ala (D)">Asp-&gt;Ala (D)</option>
-        <option value="Asp-&gt;Arg (D)">Asp-&gt;Arg (D)</option>
-        <option value="Asp-&gt;Asn (D)">Asp-&gt;Asn (D)</option>
-        <option value="Asp-&gt;Cys (D)">Asp-&gt;Cys (D)</option>
-        <option value="Asp-&gt;Gln (D)">Asp-&gt;Gln (D)</option>
-        <option value="Asp-&gt;Glu (D)">Asp-&gt;Glu (D)</option>
-        <option value="Asp-&gt;Gly (D)">Asp-&gt;Gly (D)</option>
-        <option value="Asp-&gt;His (D)">Asp-&gt;His (D)</option>
-        <option value="Asp-&gt;Lys (D)">Asp-&gt;Lys (D)</option>
-        <option value="Asp-&gt;Met (D)">Asp-&gt;Met (D)</option>
-        <option value="Asp-&gt;Phe (D)">Asp-&gt;Phe (D)</option>
-        <option value="Asp-&gt;Pro (D)">Asp-&gt;Pro (D)</option>
-        <option value="Asp-&gt;Ser (D)">Asp-&gt;Ser (D)</option>
-        <option value="Asp-&gt;Thr (D)">Asp-&gt;Thr (D)</option>
-        <option value="Asp-&gt;Trp (D)">Asp-&gt;Trp (D)</option>
-        <option value="Asp-&gt;Tyr (D)">Asp-&gt;Tyr (D)</option>
-        <option value="Asp-&gt;Val (D)">Asp-&gt;Val (D)</option>
-        <option value="Asp-&gt;Xle (D)">Asp-&gt;Xle (D)</option>
-        <option value="Aspartylurea (H)">Aspartylurea (H)</option>
-        <option value="Atto495Maleimide (C)">Atto495Maleimide (C)</option>
-        <option value="AzidoF (F)">AzidoF (F)</option>
-        <option value="azole (C)">azole (C)</option>
-        <option value="azole (S)">azole (S)</option>
-        <option value="Bacillosamine (N)">Bacillosamine (N)</option>
-        <option value="BADGE (C)">BADGE (C)</option>
-        <option value="BDMAPP (H)">BDMAPP (H)</option>
-        <option value="BDMAPP (K)">BDMAPP (K)</option>
-        <option value="BDMAPP (Protein N-term)">BDMAPP (Protein N-term)</option>
-        <option value="BDMAPP (W)">BDMAPP (W)</option>
-        <option value="BDMAPP (Y)">BDMAPP (Y)</option>
-        <option value="BEMAD_C (C)">BEMAD_C (C)</option>
-        <option value="BEMAD_C:2H(6) (C)">BEMAD_C:2H(6) (C)</option>
-        <option value="BEMAD_ST (S)">BEMAD_ST (S)</option>
-        <option value="BEMAD_ST (T)">BEMAD_ST (T)</option>
-        <option value="BEMAD_ST:2H(6) (S)">BEMAD_ST:2H(6) (S)</option>
-        <option value="BEMAD_ST:2H(6) (T)">BEMAD_ST:2H(6) (T)</option>
-        <option value="Benzoyl (K)">Benzoyl (K)</option>
-        <option value="Benzoyl (N-term)">Benzoyl (N-term)</option>
-        <option value="benzylguanidine (K)">benzylguanidine (K)</option>
-        <option value="betaFNA (C)">betaFNA (C)</option>
-        <option value="betaFNA (K)">betaFNA (K)</option>
-        <option value="BHT (C)">BHT (C)</option>
-        <option value="BHT (H)">BHT (H)</option>
-        <option value="BHT (K)">BHT (K)</option>
-        <option value="BHTOH (C)">BHTOH (C)</option>
-        <option value="BHTOH (H)">BHTOH (H)</option>
-        <option value="BHTOH (K)">BHTOH (K)</option>
-        <option value="Biotin (K)">Biotin (K)</option>
-        <option value="Biotin (N-term)">Biotin (N-term)</option>
-        <option value="Biotin-HPDP (C)">Biotin-HPDP (C)</option>
-        <option value="Biotin-PEG-PRA (M)">Biotin-PEG-PRA (M)</option>
-        <option value="Biotin-PEO-Amine (D)">Biotin-PEO-Amine (D)</option>
-        <option value="Biotin-PEO-Amine (E)">Biotin-PEO-Amine (E)</option>
-        <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
-        <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
-        <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
-        <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
-        <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
-        <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
-        <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
-        <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
-        <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
-        <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
-        <option value="Biotin:Thermo-21328 (K)">Biotin:Thermo-21328 (K)</option>
-        <option value="Biotin:Thermo-21328 (N-term)">Biotin:Thermo-21328 (N-term)</option>
-        <option value="Biotin:Thermo-21330 (K)">Biotin:Thermo-21330 (K)</option>
-        <option value="Biotin:Thermo-21330 (N-term)">Biotin:Thermo-21330 (N-term)</option>
-        <option value="Biotin:Thermo-21345 (Q)">Biotin:Thermo-21345 (Q)</option>
-        <option value="Biotin:Thermo-21360 (X)">Biotin:Thermo-21360 (X)</option>
-        <option value="Biotin:Thermo-21901+2H2O (C)">Biotin:Thermo-21901+2H2O (C)</option>
-        <option value="Biotin:Thermo-21901+H2O (C)">Biotin:Thermo-21901+H2O (C)</option>
-        <option value="Biotin:Thermo-21911 (C)">Biotin:Thermo-21911 (C)</option>
-        <option value="Biotin:Thermo-33033 (X)">Biotin:Thermo-33033 (X)</option>
-        <option value="Biotin:Thermo-33033-H (X)">Biotin:Thermo-33033-H (X)</option>
-        <option value="Biotin:Thermo-88310 (K)">Biotin:Thermo-88310 (K)</option>
-        <option value="Biotin:Thermo-88317 (S)">Biotin:Thermo-88317 (S)</option>
-        <option value="Biotin:Thermo-88317 (Y)">Biotin:Thermo-88317 (Y)</option>
-        <option value="biotinAcrolein298 (C)">biotinAcrolein298 (C)</option>
-        <option value="biotinAcrolein298 (H)">biotinAcrolein298 (H)</option>
-        <option value="biotinAcrolein298 (K)">biotinAcrolein298 (K)</option>
-        <option value="biotinAcrolein298 (Protein N-term)">biotinAcrolein298 (Protein N-term)</option>
-        <option value="BisANS (K)">BisANS (K)</option>
-        <option value="bisANS-sulfonates (K)">bisANS-sulfonates (K)</option>
-        <option value="bisANS-sulfonates (S)">bisANS-sulfonates (S)</option>
-        <option value="bisANS-sulfonates (T)">bisANS-sulfonates (T)</option>
-        <option value="BITC (C)">BITC (C)</option>
-        <option value="BITC (K)">BITC (K)</option>
-        <option value="BITC (N-term)">BITC (N-term)</option>
-        <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
-        <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-        <option value="Bodipy (C)">Bodipy (C)</option>
-        <option value="Brij35 (N-term)">Brij35 (N-term)</option>
-        <option value="Brij58 (N-term)">Brij58 (N-term)</option>
-        <option value="Bromo (F)">Bromo (F)</option>
-        <option value="Bromo (H)">Bromo (H)</option>
-        <option value="Bromo (W)">Bromo (W)</option>
-        <option value="Bromo (Y)">Bromo (Y)</option>
-        <option value="Bromobimane (C)">Bromobimane (C)</option>
-        <option value="Butyryl (K)">Butyryl (K)</option>
-        <option value="C8-QAT (K)">C8-QAT (K)</option>
-        <option value="C8-QAT (N-term)">C8-QAT (N-term)</option>
-        <option value="CAF (N-term)">CAF (N-term)</option>
-        <option value="CAMthiopropanoyl (K)">CAMthiopropanoyl (K)</option>
-        <option value="CAMthiopropanoyl (Protein N-term)">CAMthiopropanoyl (Protein N-term)</option>
-        <option value="Can-FP-biotin (S)">Can-FP-biotin (S)</option>
-        <option value="Can-FP-biotin (T)">Can-FP-biotin (T)</option>
-        <option value="Can-FP-biotin (Y)">Can-FP-biotin (Y)</option>
-        <option value="Carbamidomethyl (C)">Carbamidomethyl (C)</option>
-        <option value="Carbamidomethyl (D)">Carbamidomethyl (D)</option>
-        <option value="Carbamidomethyl (E)">Carbamidomethyl (E)</option>
-        <option value="Carbamidomethyl (H)">Carbamidomethyl (H)</option>
-        <option value="Carbamidomethyl (K)">Carbamidomethyl (K)</option>
-        <option value="Carbamidomethyl (M)">Carbamidomethyl (M)</option>
-        <option value="Carbamidomethyl (N-term)">Carbamidomethyl (N-term)</option>
-        <option value="Carbamidomethyl (S)">Carbamidomethyl (S)</option>
-        <option value="Carbamidomethyl (T)">Carbamidomethyl (T)</option>
-        <option value="Carbamidomethyl (U)">Carbamidomethyl (U)</option>
-        <option value="Carbamidomethyl (Y)">Carbamidomethyl (Y)</option>
-        <option value="CarbamidomethylDTT (C)">CarbamidomethylDTT (C)</option>
-        <option value="Carbamyl (C)">Carbamyl (C)</option>
-        <option value="Carbamyl (K)">Carbamyl (K)</option>
-        <option value="Carbamyl (M)">Carbamyl (M)</option>
-        <option value="Carbamyl (N-term)">Carbamyl (N-term)</option>
-        <option value="Carbamyl (Protein N-term)">Carbamyl (Protein N-term)</option>
-        <option value="Carbamyl (R)">Carbamyl (R)</option>
-        <option value="Carbamyl (S)">Carbamyl (S)</option>
-        <option value="Carbamyl (T)">Carbamyl (T)</option>
-        <option value="Carbamyl (Y)">Carbamyl (Y)</option>
-        <option value="Carbofuran (S)">Carbofuran (S)</option>
-        <option value="Carbonyl (A)">Carbonyl (A)</option>
-        <option value="Carbonyl (E)">Carbonyl (E)</option>
-        <option value="Carbonyl (I)">Carbonyl (I)</option>
-        <option value="Carbonyl (L)">Carbonyl (L)</option>
-        <option value="Carbonyl (Q)">Carbonyl (Q)</option>
-        <option value="Carbonyl (R)">Carbonyl (R)</option>
-        <option value="Carbonyl (S)">Carbonyl (S)</option>
-        <option value="Carbonyl (V)">Carbonyl (V)</option>
-        <option value="Carboxy (D)">Carboxy (D)</option>
-        <option value="Carboxy (E)">Carboxy (E)</option>
-        <option value="Carboxy (K)">Carboxy (K)</option>
-        <option value="Carboxy (Protein N-term M)">Carboxy (Protein N-term M)</option>
-        <option value="Carboxy (W)">Carboxy (W)</option>
-        <option value="Carboxy-&gt;Thiocarboxy (Protein C-term G)">Carboxy-&gt;Thiocarboxy (Protein C-term G)</option>
-        <option value="Carboxyethyl (H)">Carboxyethyl (H)</option>
-        <option value="Carboxyethyl (K)">Carboxyethyl (K)</option>
-        <option value="Carboxyethylpyrrole (K)">Carboxyethylpyrrole (K)</option>
-        <option value="Carboxymethyl (C)">Carboxymethyl (C)</option>
-        <option value="Carboxymethyl (K)">Carboxymethyl (K)</option>
-        <option value="Carboxymethyl (N-term)">Carboxymethyl (N-term)</option>
-        <option value="Carboxymethyl (U)">Carboxymethyl (U)</option>
-        <option value="Carboxymethyl (W)">Carboxymethyl (W)</option>
-        <option value="Carboxymethyl:13C(2) (C)">Carboxymethyl:13C(2) (C)</option>
-        <option value="CarboxymethylDMAP (N-term)">CarboxymethylDMAP (N-term)</option>
-        <option value="CarboxymethylDTT (C)">CarboxymethylDTT (C)</option>
-        <option value="Cation:Ag (C-term)">Cation:Ag (C-term)</option>
-        <option value="Cation:Ag (D)">Cation:Ag (D)</option>
-        <option value="Cation:Ag (E)">Cation:Ag (E)</option>
-        <option value="Cation:Al[III] (C-term)">Cation:Al[III] (C-term)</option>
-        <option value="Cation:Al[III] (D)">Cation:Al[III] (D)</option>
-        <option value="Cation:Al[III] (E)">Cation:Al[III] (E)</option>
-        <option value="Cation:Ca[II] (C-term)">Cation:Ca[II] (C-term)</option>
-        <option value="Cation:Ca[II] (D)">Cation:Ca[II] (D)</option>
-        <option value="Cation:Ca[II] (E)">Cation:Ca[II] (E)</option>
-        <option value="Cation:Cu[I] (C-term)">Cation:Cu[I] (C-term)</option>
-        <option value="Cation:Cu[I] (D)">Cation:Cu[I] (D)</option>
-        <option value="Cation:Cu[I] (E)">Cation:Cu[I] (E)</option>
-        <option value="Cation:Cu[I] (H)">Cation:Cu[I] (H)</option>
-        <option value="Cation:Fe[II] (C-term)">Cation:Fe[II] (C-term)</option>
-        <option value="Cation:Fe[II] (D)">Cation:Fe[II] (D)</option>
-        <option value="Cation:Fe[II] (E)">Cation:Fe[II] (E)</option>
-        <option value="Cation:Fe[III] (C-term)">Cation:Fe[III] (C-term)</option>
-        <option value="Cation:Fe[III] (D)">Cation:Fe[III] (D)</option>
-        <option value="Cation:Fe[III] (E)">Cation:Fe[III] (E)</option>
-        <option value="Cation:K (C-term)">Cation:K (C-term)</option>
-        <option value="Cation:K (D)">Cation:K (D)</option>
-        <option value="Cation:K (E)">Cation:K (E)</option>
-        <option value="Cation:Li (C-term)">Cation:Li (C-term)</option>
-        <option value="Cation:Li (D)">Cation:Li (D)</option>
-        <option value="Cation:Li (E)">Cation:Li (E)</option>
-        <option value="Cation:Mg[II] (C-term)">Cation:Mg[II] (C-term)</option>
-        <option value="Cation:Mg[II] (D)">Cation:Mg[II] (D)</option>
-        <option value="Cation:Mg[II] (E)">Cation:Mg[II] (E)</option>
-        <option value="Cation:Na (C-term)">Cation:Na (C-term)</option>
-        <option value="Cation:Na (D)">Cation:Na (D)</option>
-        <option value="Cation:Na (E)">Cation:Na (E)</option>
-        <option value="Cation:Ni[II] (C-term)">Cation:Ni[II] (C-term)</option>
-        <option value="Cation:Ni[II] (D)">Cation:Ni[II] (D)</option>
-        <option value="Cation:Ni[II] (E)">Cation:Ni[II] (E)</option>
-        <option value="Cation:Zn[II] (C-term)">Cation:Zn[II] (C-term)</option>
-        <option value="Cation:Zn[II] (D)">Cation:Zn[II] (D)</option>
-        <option value="Cation:Zn[II] (E)">Cation:Zn[II] (E)</option>
-        <option value="Cation:Zn[II] (H)">Cation:Zn[II] (H)</option>
-        <option value="cGMP (C)">cGMP (C)</option>
-        <option value="cGMP (S)">cGMP (S)</option>
-        <option value="cGMP+RMP-loss (C)">cGMP+RMP-loss (C)</option>
-        <option value="cGMP+RMP-loss (S)">cGMP+RMP-loss (S)</option>
-        <option value="CHDH (D)">CHDH (D)</option>
-        <option value="Chlorination (W)">Chlorination (W)</option>
-        <option value="Chlorination (Y)">Chlorination (Y)</option>
-        <option value="Cholesterol (Protein C-term)">Cholesterol (Protein C-term)</option>
-        <option value="CIGG (K)">CIGG (K)</option>
-        <option value="CLIP_TRAQ_2 (K)">CLIP_TRAQ_2 (K)</option>
-        <option value="CLIP_TRAQ_2 (N-term)">CLIP_TRAQ_2 (N-term)</option>
-        <option value="CLIP_TRAQ_2 (Y)">CLIP_TRAQ_2 (Y)</option>
-        <option value="CLIP_TRAQ_3 (K)">CLIP_TRAQ_3 (K)</option>
-        <option value="CLIP_TRAQ_3 (N-term)">CLIP_TRAQ_3 (N-term)</option>
-        <option value="CLIP_TRAQ_3 (Y)">CLIP_TRAQ_3 (Y)</option>
-        <option value="CLIP_TRAQ_4 (K)">CLIP_TRAQ_4 (K)</option>
-        <option value="CLIP_TRAQ_4 (N-term)">CLIP_TRAQ_4 (N-term)</option>
-        <option value="CLIP_TRAQ_4 (Y)">CLIP_TRAQ_4 (Y)</option>
-        <option value="CoenzymeA (C)">CoenzymeA (C)</option>
-        <option value="Cresylphosphate (H)">Cresylphosphate (H)</option>
-        <option value="Cresylphosphate (K)">Cresylphosphate (K)</option>
-        <option value="Cresylphosphate (R)">Cresylphosphate (R)</option>
-        <option value="Cresylphosphate (S)">Cresylphosphate (S)</option>
-        <option value="Cresylphosphate (T)">Cresylphosphate (T)</option>
-        <option value="Cresylphosphate (Y)">Cresylphosphate (Y)</option>
-        <option value="CresylSaligeninPhosphate (H)">CresylSaligeninPhosphate (H)</option>
-        <option value="CresylSaligeninPhosphate (K)">CresylSaligeninPhosphate (K)</option>
-        <option value="CresylSaligeninPhosphate (R)">CresylSaligeninPhosphate (R)</option>
-        <option value="CresylSaligeninPhosphate (S)">CresylSaligeninPhosphate (S)</option>
-        <option value="CresylSaligeninPhosphate (T)">CresylSaligeninPhosphate (T)</option>
-        <option value="CresylSaligeninPhosphate (Y)">CresylSaligeninPhosphate (Y)</option>
-        <option value="Crotonaldehyde (C)">Crotonaldehyde (C)</option>
-        <option value="Crotonaldehyde (H)">Crotonaldehyde (H)</option>
-        <option value="Crotonaldehyde (K)">Crotonaldehyde (K)</option>
-        <option value="Crotonyl (K)">Crotonyl (K)</option>
-        <option value="CuSMo (C)">CuSMo (C)</option>
-        <option value="CUSTOM0 (A)">CUSTOM0 (A)</option>
-        <option value="CUSTOM0 (C)">CUSTOM0 (C)</option>
-        <option value="CUSTOM0 (C-term)">CUSTOM0 (C-term)</option>
-        <option value="CUSTOM0 (D)">CUSTOM0 (D)</option>
-        <option value="CUSTOM0 (E)">CUSTOM0 (E)</option>
-        <option value="CUSTOM0 (F)">CUSTOM0 (F)</option>
-        <option value="CUSTOM0 (G)">CUSTOM0 (G)</option>
-        <option value="CUSTOM0 (H)">CUSTOM0 (H)</option>
-        <option value="CUSTOM0 (I)">CUSTOM0 (I)</option>
-        <option value="CUSTOM0 (K)">CUSTOM0 (K)</option>
-        <option value="CUSTOM0 (L)">CUSTOM0 (L)</option>
-        <option value="CUSTOM0 (M)">CUSTOM0 (M)</option>
-        <option value="CUSTOM0 (N)">CUSTOM0 (N)</option>
-        <option value="CUSTOM0 (N-term)">CUSTOM0 (N-term)</option>
-        <option value="CUSTOM0 (P)">CUSTOM0 (P)</option>
-        <option value="CUSTOM0 (Q)">CUSTOM0 (Q)</option>
-        <option value="CUSTOM0 (R)">CUSTOM0 (R)</option>
-        <option value="CUSTOM0 (S)">CUSTOM0 (S)</option>
-        <option value="CUSTOM0 (T)">CUSTOM0 (T)</option>
-        <option value="CUSTOM0 (V)">CUSTOM0 (V)</option>
-        <option value="CUSTOM0 (W)">CUSTOM0 (W)</option>
-        <option value="CUSTOM0 (Y)">CUSTOM0 (Y)</option>
-        <option value="CUSTOM1 (A)">CUSTOM1 (A)</option>
-        <option value="CUSTOM1 (C)">CUSTOM1 (C)</option>
-        <option value="CUSTOM1 (C-term)">CUSTOM1 (C-term)</option>
-        <option value="CUSTOM1 (D)">CUSTOM1 (D)</option>
-        <option value="CUSTOM1 (E)">CUSTOM1 (E)</option>
-        <option value="CUSTOM1 (F)">CUSTOM1 (F)</option>
-        <option value="CUSTOM1 (G)">CUSTOM1 (G)</option>
-        <option value="CUSTOM1 (H)">CUSTOM1 (H)</option>
-        <option value="CUSTOM1 (I)">CUSTOM1 (I)</option>
-        <option value="CUSTOM1 (K)">CUSTOM1 (K)</option>
-        <option value="CUSTOM1 (L)">CUSTOM1 (L)</option>
-        <option value="CUSTOM1 (M)">CUSTOM1 (M)</option>
-        <option value="CUSTOM1 (N)">CUSTOM1 (N)</option>
-        <option value="CUSTOM1 (N-term)">CUSTOM1 (N-term)</option>
-        <option value="CUSTOM1 (P)">CUSTOM1 (P)</option>
-        <option value="CUSTOM1 (Q)">CUSTOM1 (Q)</option>
-        <option value="CUSTOM1 (R)">CUSTOM1 (R)</option>
-        <option value="CUSTOM1 (S)">CUSTOM1 (S)</option>
-        <option value="CUSTOM1 (T)">CUSTOM1 (T)</option>
-        <option value="CUSTOM1 (V)">CUSTOM1 (V)</option>
-        <option value="CUSTOM1 (W)">CUSTOM1 (W)</option>
-        <option value="CUSTOM1 (Y)">CUSTOM1 (Y)</option>
-        <option value="CUSTOM2 (A)">CUSTOM2 (A)</option>
-        <option value="CUSTOM2 (C)">CUSTOM2 (C)</option>
-        <option value="CUSTOM2 (C-term)">CUSTOM2 (C-term)</option>
-        <option value="CUSTOM2 (D)">CUSTOM2 (D)</option>
-        <option value="CUSTOM2 (E)">CUSTOM2 (E)</option>
-        <option value="CUSTOM2 (F)">CUSTOM2 (F)</option>
-        <option value="CUSTOM2 (G)">CUSTOM2 (G)</option>
-        <option value="CUSTOM2 (H)">CUSTOM2 (H)</option>
-        <option value="CUSTOM2 (I)">CUSTOM2 (I)</option>
-        <option value="CUSTOM2 (K)">CUSTOM2 (K)</option>
-        <option value="CUSTOM2 (L)">CUSTOM2 (L)</option>
-        <option value="CUSTOM2 (M)">CUSTOM2 (M)</option>
-        <option value="CUSTOM2 (N)">CUSTOM2 (N)</option>
-        <option value="CUSTOM2 (N-term)">CUSTOM2 (N-term)</option>
-        <option value="CUSTOM2 (P)">CUSTOM2 (P)</option>
-        <option value="CUSTOM2 (Q)">CUSTOM2 (Q)</option>
-        <option value="CUSTOM2 (R)">CUSTOM2 (R)</option>
-        <option value="CUSTOM2 (S)">CUSTOM2 (S)</option>
-        <option value="CUSTOM2 (T)">CUSTOM2 (T)</option>
-        <option value="CUSTOM2 (V)">CUSTOM2 (V)</option>
-        <option value="CUSTOM2 (W)">CUSTOM2 (W)</option>
-        <option value="CUSTOM2 (Y)">CUSTOM2 (Y)</option>
-        <option value="CUSTOM3 (A)">CUSTOM3 (A)</option>
-        <option value="CUSTOM3 (C)">CUSTOM3 (C)</option>
-        <option value="CUSTOM3 (C-term)">CUSTOM3 (C-term)</option>
-        <option value="CUSTOM3 (D)">CUSTOM3 (D)</option>
-        <option value="CUSTOM3 (E)">CUSTOM3 (E)</option>
-        <option value="CUSTOM3 (F)">CUSTOM3 (F)</option>
-        <option value="CUSTOM3 (G)">CUSTOM3 (G)</option>
-        <option value="CUSTOM3 (H)">CUSTOM3 (H)</option>
-        <option value="CUSTOM3 (I)">CUSTOM3 (I)</option>
-        <option value="CUSTOM3 (K)">CUSTOM3 (K)</option>
-        <option value="CUSTOM3 (L)">CUSTOM3 (L)</option>
-        <option value="CUSTOM3 (M)">CUSTOM3 (M)</option>
-        <option value="CUSTOM3 (N)">CUSTOM3 (N)</option>
-        <option value="CUSTOM3 (N-term)">CUSTOM3 (N-term)</option>
-        <option value="CUSTOM3 (P)">CUSTOM3 (P)</option>
-        <option value="CUSTOM3 (Q)">CUSTOM3 (Q)</option>
-        <option value="CUSTOM3 (R)">CUSTOM3 (R)</option>
-        <option value="CUSTOM3 (S)">CUSTOM3 (S)</option>
-        <option value="CUSTOM3 (T)">CUSTOM3 (T)</option>
-        <option value="CUSTOM3 (V)">CUSTOM3 (V)</option>
-        <option value="CUSTOM3 (W)">CUSTOM3 (W)</option>
-        <option value="CUSTOM3 (Y)">CUSTOM3 (Y)</option>
-        <option value="CUSTOM4 (A)">CUSTOM4 (A)</option>
-        <option value="CUSTOM4 (C)">CUSTOM4 (C)</option>
-        <option value="CUSTOM4 (C-term)">CUSTOM4 (C-term)</option>
-        <option value="CUSTOM4 (D)">CUSTOM4 (D)</option>
-        <option value="CUSTOM4 (E)">CUSTOM4 (E)</option>
-        <option value="CUSTOM4 (F)">CUSTOM4 (F)</option>
-        <option value="CUSTOM4 (G)">CUSTOM4 (G)</option>
-        <option value="CUSTOM4 (H)">CUSTOM4 (H)</option>
-        <option value="CUSTOM4 (I)">CUSTOM4 (I)</option>
-        <option value="CUSTOM4 (K)">CUSTOM4 (K)</option>
-        <option value="CUSTOM4 (L)">CUSTOM4 (L)</option>
-        <option value="CUSTOM4 (M)">CUSTOM4 (M)</option>
-        <option value="CUSTOM4 (N)">CUSTOM4 (N)</option>
-        <option value="CUSTOM4 (N-term)">CUSTOM4 (N-term)</option>
-        <option value="CUSTOM4 (P)">CUSTOM4 (P)</option>
-        <option value="CUSTOM4 (Q)">CUSTOM4 (Q)</option>
-        <option value="CUSTOM4 (R)">CUSTOM4 (R)</option>
-        <option value="CUSTOM4 (S)">CUSTOM4 (S)</option>
-        <option value="CUSTOM4 (T)">CUSTOM4 (T)</option>
-        <option value="CUSTOM4 (V)">CUSTOM4 (V)</option>
-        <option value="CUSTOM4 (W)">CUSTOM4 (W)</option>
-        <option value="CUSTOM4 (Y)">CUSTOM4 (Y)</option>
-        <option value="CUSTOM5 (A)">CUSTOM5 (A)</option>
-        <option value="CUSTOM5 (C)">CUSTOM5 (C)</option>
-        <option value="CUSTOM5 (C-term)">CUSTOM5 (C-term)</option>
-        <option value="CUSTOM5 (D)">CUSTOM5 (D)</option>
-        <option value="CUSTOM5 (E)">CUSTOM5 (E)</option>
-        <option value="CUSTOM5 (F)">CUSTOM5 (F)</option>
-        <option value="CUSTOM5 (G)">CUSTOM5 (G)</option>
-        <option value="CUSTOM5 (H)">CUSTOM5 (H)</option>
-        <option value="CUSTOM5 (I)">CUSTOM5 (I)</option>
-        <option value="CUSTOM5 (K)">CUSTOM5 (K)</option>
-        <option value="CUSTOM5 (L)">CUSTOM5 (L)</option>
-        <option value="CUSTOM5 (M)">CUSTOM5 (M)</option>
-        <option value="CUSTOM5 (N)">CUSTOM5 (N)</option>
-        <option value="CUSTOM5 (N-term)">CUSTOM5 (N-term)</option>
-        <option value="CUSTOM5 (P)">CUSTOM5 (P)</option>
-        <option value="CUSTOM5 (Q)">CUSTOM5 (Q)</option>
-        <option value="CUSTOM5 (R)">CUSTOM5 (R)</option>
-        <option value="CUSTOM5 (S)">CUSTOM5 (S)</option>
-        <option value="CUSTOM5 (T)">CUSTOM5 (T)</option>
-        <option value="CUSTOM5 (V)">CUSTOM5 (V)</option>
-        <option value="CUSTOM5 (W)">CUSTOM5 (W)</option>
-        <option value="CUSTOM5 (Y)">CUSTOM5 (Y)</option>
-        <option value="CUSTOM6 (A)">CUSTOM6 (A)</option>
-        <option value="CUSTOM6 (C)">CUSTOM6 (C)</option>
-        <option value="CUSTOM6 (C-term)">CUSTOM6 (C-term)</option>
-        <option value="CUSTOM6 (D)">CUSTOM6 (D)</option>
-        <option value="CUSTOM6 (E)">CUSTOM6 (E)</option>
-        <option value="CUSTOM6 (F)">CUSTOM6 (F)</option>
-        <option value="CUSTOM6 (G)">CUSTOM6 (G)</option>
-        <option value="CUSTOM6 (H)">CUSTOM6 (H)</option>
-        <option value="CUSTOM6 (I)">CUSTOM6 (I)</option>
-        <option value="CUSTOM6 (K)">CUSTOM6 (K)</option>
-        <option value="CUSTOM6 (L)">CUSTOM6 (L)</option>
-        <option value="CUSTOM6 (M)">CUSTOM6 (M)</option>
-        <option value="CUSTOM6 (N)">CUSTOM6 (N)</option>
-        <option value="CUSTOM6 (N-term)">CUSTOM6 (N-term)</option>
-        <option value="CUSTOM6 (P)">CUSTOM6 (P)</option>
-        <option value="CUSTOM6 (Q)">CUSTOM6 (Q)</option>
-        <option value="CUSTOM6 (R)">CUSTOM6 (R)</option>
-        <option value="CUSTOM6 (S)">CUSTOM6 (S)</option>
-        <option value="CUSTOM6 (T)">CUSTOM6 (T)</option>
-        <option value="CUSTOM6 (V)">CUSTOM6 (V)</option>
-        <option value="CUSTOM6 (W)">CUSTOM6 (W)</option>
-        <option value="CUSTOM6 (Y)">CUSTOM6 (Y)</option>
-        <option value="CUSTOM7 (A)">CUSTOM7 (A)</option>
-        <option value="CUSTOM7 (C)">CUSTOM7 (C)</option>
-        <option value="CUSTOM7 (C-term)">CUSTOM7 (C-term)</option>
-        <option value="CUSTOM7 (D)">CUSTOM7 (D)</option>
-        <option value="CUSTOM7 (E)">CUSTOM7 (E)</option>
-        <option value="CUSTOM7 (F)">CUSTOM7 (F)</option>
-        <option value="CUSTOM7 (G)">CUSTOM7 (G)</option>
-        <option value="CUSTOM7 (H)">CUSTOM7 (H)</option>
-        <option value="CUSTOM7 (I)">CUSTOM7 (I)</option>
-        <option value="CUSTOM7 (K)">CUSTOM7 (K)</option>
-        <option value="CUSTOM7 (L)">CUSTOM7 (L)</option>
-        <option value="CUSTOM7 (M)">CUSTOM7 (M)</option>
-        <option value="CUSTOM7 (N)">CUSTOM7 (N)</option>
-        <option value="CUSTOM7 (N-term)">CUSTOM7 (N-term)</option>
-        <option value="CUSTOM7 (P)">CUSTOM7 (P)</option>
-        <option value="CUSTOM7 (Q)">CUSTOM7 (Q)</option>
-        <option value="CUSTOM7 (R)">CUSTOM7 (R)</option>
-        <option value="CUSTOM7 (S)">CUSTOM7 (S)</option>
-        <option value="CUSTOM7 (T)">CUSTOM7 (T)</option>
-        <option value="CUSTOM7 (V)">CUSTOM7 (V)</option>
-        <option value="CUSTOM7 (W)">CUSTOM7 (W)</option>
-        <option value="CUSTOM7 (Y)">CUSTOM7 (Y)</option>
-        <option value="CUSTOM8 (A)">CUSTOM8 (A)</option>
-        <option value="CUSTOM8 (C)">CUSTOM8 (C)</option>
-        <option value="CUSTOM8 (C-term)">CUSTOM8 (C-term)</option>
-        <option value="CUSTOM8 (D)">CUSTOM8 (D)</option>
-        <option value="CUSTOM8 (E)">CUSTOM8 (E)</option>
-        <option value="CUSTOM8 (F)">CUSTOM8 (F)</option>
-        <option value="CUSTOM8 (G)">CUSTOM8 (G)</option>
-        <option value="CUSTOM8 (H)">CUSTOM8 (H)</option>
-        <option value="CUSTOM8 (I)">CUSTOM8 (I)</option>
-        <option value="CUSTOM8 (K)">CUSTOM8 (K)</option>
-        <option value="CUSTOM8 (L)">CUSTOM8 (L)</option>
-        <option value="CUSTOM8 (M)">CUSTOM8 (M)</option>
-        <option value="CUSTOM8 (N)">CUSTOM8 (N)</option>
-        <option value="CUSTOM8 (N-term)">CUSTOM8 (N-term)</option>
-        <option value="CUSTOM8 (P)">CUSTOM8 (P)</option>
-        <option value="CUSTOM8 (Q)">CUSTOM8 (Q)</option>
-        <option value="CUSTOM8 (R)">CUSTOM8 (R)</option>
-        <option value="CUSTOM8 (S)">CUSTOM8 (S)</option>
-        <option value="CUSTOM8 (T)">CUSTOM8 (T)</option>
-        <option value="CUSTOM8 (V)">CUSTOM8 (V)</option>
-        <option value="CUSTOM8 (W)">CUSTOM8 (W)</option>
-        <option value="CUSTOM8 (Y)">CUSTOM8 (Y)</option>
-        <option value="CUSTOM9 (A)">CUSTOM9 (A)</option>
-        <option value="CUSTOM9 (C)">CUSTOM9 (C)</option>
-        <option value="CUSTOM9 (C-term)">CUSTOM9 (C-term)</option>
-        <option value="CUSTOM9 (D)">CUSTOM9 (D)</option>
-        <option value="CUSTOM9 (E)">CUSTOM9 (E)</option>
-        <option value="CUSTOM9 (F)">CUSTOM9 (F)</option>
-        <option value="CUSTOM9 (G)">CUSTOM9 (G)</option>
-        <option value="CUSTOM9 (H)">CUSTOM9 (H)</option>
-        <option value="CUSTOM9 (I)">CUSTOM9 (I)</option>
-        <option value="CUSTOM9 (K)">CUSTOM9 (K)</option>
-        <option value="CUSTOM9 (L)">CUSTOM9 (L)</option>
-        <option value="CUSTOM9 (M)">CUSTOM9 (M)</option>
-        <option value="CUSTOM9 (N)">CUSTOM9 (N)</option>
-        <option value="CUSTOM9 (N-term)">CUSTOM9 (N-term)</option>
-        <option value="CUSTOM9 (P)">CUSTOM9 (P)</option>
-        <option value="CUSTOM9 (Q)">CUSTOM9 (Q)</option>
-        <option value="CUSTOM9 (R)">CUSTOM9 (R)</option>
-        <option value="CUSTOM9 (S)">CUSTOM9 (S)</option>
-        <option value="CUSTOM9 (T)">CUSTOM9 (T)</option>
-        <option value="CUSTOM9 (V)">CUSTOM9 (V)</option>
-        <option value="CUSTOM9 (W)">CUSTOM9 (W)</option>
-        <option value="CUSTOM9 (Y)">CUSTOM9 (Y)</option>
-        <option value="Cy3-maleimide (C)">Cy3-maleimide (C)</option>
-        <option value="Cy3b-maleimide (C)">Cy3b-maleimide (C)</option>
-        <option value="Cyano (C)">Cyano (C)</option>
-        <option value="CyDye-Cy3 (C)">CyDye-Cy3 (C)</option>
-        <option value="CyDye-Cy5 (C)">CyDye-Cy5 (C)</option>
-        <option value="Cys-&gt;Ala (C)">Cys-&gt;Ala (C)</option>
-        <option value="Cys-&gt;Arg (C)">Cys-&gt;Arg (C)</option>
-        <option value="Cys-&gt;Asn (C)">Cys-&gt;Asn (C)</option>
-        <option value="Cys-&gt;Asp (C)">Cys-&gt;Asp (C)</option>
-        <option value="Cys-&gt;CamSec (C)">Cys-&gt;CamSec (C)</option>
-        <option value="Cys-&gt;Dha (C)">Cys-&gt;Dha (C)</option>
-        <option value="Cys-&gt;ethylaminoAla (C)">Cys-&gt;ethylaminoAla (C)</option>
-        <option value="Cys-&gt;Gln (C)">Cys-&gt;Gln (C)</option>
-        <option value="Cys-&gt;Glu (C)">Cys-&gt;Glu (C)</option>
-        <option value="Cys-&gt;Gly (C)">Cys-&gt;Gly (C)</option>
-        <option value="Cys-&gt;His (C)">Cys-&gt;His (C)</option>
-        <option value="Cys-&gt;Lys (C)">Cys-&gt;Lys (C)</option>
-        <option value="Cys-&gt;Met (C)">Cys-&gt;Met (C)</option>
-        <option value="Cys-&gt;methylaminoAla (C)">Cys-&gt;methylaminoAla (C)</option>
-        <option value="Cys-&gt;Oxoalanine (C)">Cys-&gt;Oxoalanine (C)</option>
-        <option value="Cys-&gt;Phe (C)">Cys-&gt;Phe (C)</option>
-        <option value="Cys-&gt;Pro (C)">Cys-&gt;Pro (C)</option>
-        <option value="Cys-&gt;PyruvicAcid (Protein N-term C)">Cys-&gt;PyruvicAcid (Protein N-term C)</option>
-        <option value="Cys-&gt;SecNEM (C)">Cys-&gt;SecNEM (C)</option>
-        <option value="Cys-&gt;SecNEM:2H(5) (C)">Cys-&gt;SecNEM:2H(5) (C)</option>
-        <option value="Cys-&gt;Ser (C)">Cys-&gt;Ser (C)</option>
-        <option value="Cys-&gt;Thr (C)">Cys-&gt;Thr (C)</option>
-        <option value="Cys-&gt;Trp (C)">Cys-&gt;Trp (C)</option>
-        <option value="Cys-&gt;Tyr (C)">Cys-&gt;Tyr (C)</option>
-        <option value="Cys-&gt;Val (C)">Cys-&gt;Val (C)</option>
-        <option value="Cys-&gt;Xle (C)">Cys-&gt;Xle (C)</option>
-        <option value="Cysteinyl (C)">Cysteinyl (C)</option>
-        <option value="cysTMT (C)">cysTMT (C)</option>
-        <option value="cysTMT6plex (C)">cysTMT6plex (C)</option>
-        <option value="Cytopiloyne (C)">Cytopiloyne (C)</option>
-        <option value="Cytopiloyne (K)">Cytopiloyne (K)</option>
-        <option value="Cytopiloyne (N-term)">Cytopiloyne (N-term)</option>
-        <option value="Cytopiloyne (P)">Cytopiloyne (P)</option>
-        <option value="Cytopiloyne (R)">Cytopiloyne (R)</option>
-        <option value="Cytopiloyne (S)">Cytopiloyne (S)</option>
-        <option value="Cytopiloyne (Y)">Cytopiloyne (Y)</option>
-        <option value="Cytopiloyne+water (C)">Cytopiloyne+water (C)</option>
-        <option value="Cytopiloyne+water (K)">Cytopiloyne+water (K)</option>
-        <option value="Cytopiloyne+water (N-term)">Cytopiloyne+water (N-term)</option>
-        <option value="Cytopiloyne+water (R)">Cytopiloyne+water (R)</option>
-        <option value="Cytopiloyne+water (S)">Cytopiloyne+water (S)</option>
-        <option value="Cytopiloyne+water (T)">Cytopiloyne+water (T)</option>
-        <option value="Cytopiloyne+water (Y)">Cytopiloyne+water (Y)</option>
-        <option value="DAET (S)">DAET (S)</option>
-        <option value="DAET (T)">DAET (T)</option>
-        <option value="Dansyl (K)">Dansyl (K)</option>
-        <option value="Dansyl (N-term)">Dansyl (N-term)</option>
-        <option value="Dap-DSP (A)">Dap-DSP (A)</option>
-        <option value="Dap-DSP (E)">Dap-DSP (E)</option>
-        <option value="Dap-DSP (K)">Dap-DSP (K)</option>
-        <option value="Deamidated (N)">Deamidated (N)</option>
-        <option value="Deamidated (Protein N-term F)">Deamidated (Protein N-term F)</option>
-        <option value="Deamidated (Q)">Deamidated (Q)</option>
-        <option value="Deamidated (R)">Deamidated (R)</option>
-        <option value="Deamidated:18O(1) (N)">Deamidated:18O(1) (N)</option>
-        <option value="Deamidated:18O(1) (Q)">Deamidated:18O(1) (Q)</option>
-        <option value="Decanoyl (S)">Decanoyl (S)</option>
-        <option value="Decanoyl (T)">Decanoyl (T)</option>
-        <option value="Decarboxylation (D)">Decarboxylation (D)</option>
-        <option value="Decarboxylation (E)">Decarboxylation (E)</option>
-        <option value="DEDGFLYMVYASQETFG (K)">DEDGFLYMVYASQETFG (K)</option>
-        <option value="Dehydrated (D)">Dehydrated (D)</option>
-        <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
-        <option value="Dehydrated (Protein C-term N)">Dehydrated (Protein C-term N)</option>
-        <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
-        <option value="Dehydrated (S)">Dehydrated (S)</option>
-        <option value="Dehydrated (T)">Dehydrated (T)</option>
-        <option value="Dehydrated (Y)">Dehydrated (Y)</option>
-        <option value="Dehydro (C)">Dehydro (C)</option>
-        <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
-        <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-        <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
-        <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
-        <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
-        <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
-        <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
-        <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
-        <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
-        <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
-        <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
-        <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-        <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
-        <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
-        <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
-        <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
-        <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
-        <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
-        <option value="Delta:H(4)C(3) (K)">Delta:H(4)C(3) (K)</option>
-        <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
-        <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
-        <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
-        <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
-        <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
-        <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
-        <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
-        <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
-        <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
-        <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
-        <option value="Delta:H(6)C(3)O(1) (K)">Delta:H(6)C(3)O(1) (K)</option>
-        <option value="Delta:H(6)C(3)O(1) (Protein N-term)">Delta:H(6)C(3)O(1) (Protein N-term)</option>
-        <option value="Delta:H(6)C(6)O(1) (K)">Delta:H(6)C(6)O(1) (K)</option>
-        <option value="Delta:H(6)C(7)O(4) (R)">Delta:H(6)C(7)O(4) (R)</option>
-        <option value="Delta:H(8)C(6)O(1) (K)">Delta:H(8)C(6)O(1) (K)</option>
-        <option value="Delta:H(8)C(6)O(1) (Protein N-term)">Delta:H(8)C(6)O(1) (Protein N-term)</option>
-        <option value="Delta:H(8)C(6)O(2) (K)">Delta:H(8)C(6)O(2) (K)</option>
-        <option value="Delta:Hg(1) (C)">Delta:Hg(1) (C)</option>
-        <option value="Delta:O(4) (W)">Delta:O(4) (W)</option>
-        <option value="Delta:S(-1)Se(1) (C)">Delta:S(-1)Se(1) (C)</option>
-        <option value="Delta:S(-1)Se(1) (M)">Delta:S(-1)Se(1) (M)</option>
-        <option value="Delta:Se(1) (C)">Delta:Se(1) (C)</option>
-        <option value="Deoxy (D)">Deoxy (D)</option>
-        <option value="Deoxy (S)">Deoxy (S)</option>
-        <option value="Deoxy (T)">Deoxy (T)</option>
-        <option value="Deoxyhypusine (K)">Deoxyhypusine (K)</option>
-        <option value="Deoxyhypusine (Q)">Deoxyhypusine (Q)</option>
-        <option value="DeStreak (C)">DeStreak (C)</option>
-        <option value="Dethiomethyl (M)">Dethiomethyl (M)</option>
-        <option value="dHex (N)">dHex (N)</option>
-        <option value="dHex (S)">dHex (S)</option>
-        <option value="dHex (T)">dHex (T)</option>
-        <option value="dHex(1)Hex(1) (S)">dHex(1)Hex(1) (S)</option>
-        <option value="dHex(1)Hex(1) (T)">dHex(1)Hex(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexA(1)HexNAc(3) (S)">dHex(1)Hex(1)HexA(1)HexNAc(3) (S)</option>
-        <option value="dHex(1)Hex(1)HexA(1)HexNAc(3) (T)">dHex(1)Hex(1)HexA(1)HexNAc(3) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)Kdn(1) (S)">dHex(1)Hex(1)HexNAc(1)Kdn(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)Kdn(1) (T)">dHex(1)Hex(1)HexNAc(1)Kdn(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(1)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(1)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3) (S)">dHex(1)Hex(1)HexNAc(3) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3) (T)">dHex(1)Hex(1)HexNAc(3) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(4) (S)">dHex(1)Hex(1)HexNAc(4) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(4) (T)">dHex(1)Hex(1)HexNAc(4) (T)</option>
-        <option value="dHex(1)Hex(2) (S)">dHex(1)Hex(2) (S)</option>
-        <option value="dHex(1)Hex(2) (T)">dHex(1)Hex(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexA(1) (S)">dHex(1)Hex(2)HexA(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexA(1) (T)">dHex(1)Hex(2)HexA(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(1) (S)">dHex(1)Hex(2)HexA(1)HexNAc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(1) (T)">dHex(1)Hex(2)HexA(1)HexNAc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (S)">dHex(1)Hex(2)HexA(1)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (T)">dHex(1)Hex(2)HexA(1)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1) (S)">dHex(1)Hex(2)HexNAc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1) (T)">dHex(1)Hex(2)HexNAc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)Pent(1) (N)">dHex(1)Hex(2)HexNAc(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3) (N)">dHex(1)Hex(2)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3) (S)">dHex(1)Hex(2)HexNAc(3) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3) (T)">dHex(1)Hex(2)HexNAc(3) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4) (N)">dHex(1)Hex(2)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4) (S)">dHex(1)Hex(2)HexNAc(4) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4) (T)">dHex(1)Hex(2)HexNAc(4) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-        <option value="dHex(1)Hex(3) (S)">dHex(1)Hex(3) (S)</option>
-        <option value="dHex(1)Hex(3) (T)">dHex(1)Hex(3) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(2) (S)">dHex(1)Hex(3)HexA(1)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(2) (T)">dHex(1)Hex(3)HexA(1)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(2)HexNAc(2) (S)">dHex(1)Hex(3)HexA(2)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(2)HexNAc(2) (T)">dHex(1)Hex(3)HexA(2)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(1) (S)">dHex(1)Hex(3)HexNAc(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(1) (T)">dHex(1)Hex(3)HexNAc(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2) (N)">dHex(1)Hex(3)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2) (S)">dHex(1)Hex(3)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2) (T)">dHex(1)Hex(3)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)Pent(1) (N)">dHex(1)Hex(3)HexNAc(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3) (N)">dHex(1)Hex(3)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3) (S)">dHex(1)Hex(3)HexNAc(3) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3) (T)">dHex(1)Hex(3)HexNAc(3) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Pent(1) (N)">dHex(1)Hex(3)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Pent(2) (N)">dHex(1)Hex(3)HexNAc(3)Pent(2) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Pent(3) (N)">dHex(1)Hex(3)HexNAc(3)Pent(3) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4) (N)">dHex(1)Hex(3)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4) (S)">dHex(1)Hex(3)HexNAc(4) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4) (T)">dHex(1)Hex(3)HexNAc(4) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)Pent(1) (N)">dHex(1)Hex(3)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)Pent(2) (N)">dHex(1)Hex(3)HexNAc(4)Pent(2) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)Pent(3) (N)">dHex(1)Hex(3)HexNAc(4)Pent(3) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5) (N)">dHex(1)Hex(3)HexNAc(5) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5) (S)">dHex(1)Hex(3)HexNAc(5) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5) (T)">dHex(1)Hex(3)HexNAc(5) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(5)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(6) (N)">dHex(1)Hex(3)HexNAc(6) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(6) (S)">dHex(1)Hex(3)HexNAc(6) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(6) (T)">dHex(1)Hex(3)HexNAc(6) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4) (S)">dHex(1)Hex(4) (S)</option>
-        <option value="dHex(1)Hex(4) (T)">dHex(1)Hex(4) (T)</option>
-        <option value="dHex(1)Hex(4)HexA(1) (S)">dHex(1)Hex(4)HexA(1) (S)</option>
-        <option value="dHex(1)Hex(4)HexA(1) (T)">dHex(1)Hex(4)HexA(1) (T)</option>
-        <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (S)">dHex(1)Hex(4)HexA(1)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (T)">dHex(1)Hex(4)HexA(1)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(1)Pent(1) (N)">dHex(1)Hex(4)HexNAc(1)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(2) (N)">dHex(1)Hex(4)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(2) (S)">dHex(1)Hex(4)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(4)HexNAc(2) (T)">dHex(1)Hex(4)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(2)Pent(1) (N)">dHex(1)Hex(4)HexNAc(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3) (N)">dHex(1)Hex(4)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)Pent(1) (N)">dHex(1)Hex(4)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4) (N)">dHex(1)Hex(4)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4) (S)">dHex(1)Hex(4)HexNAc(4) (S)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4) (T)">dHex(1)Hex(4)HexNAc(4) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)Pent(1) (N)">dHex(1)Hex(4)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(5) (N)">dHex(1)Hex(4)HexNAc(5) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(5)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(5)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5) (S)">dHex(1)Hex(5) (S)</option>
-        <option value="dHex(1)Hex(5) (T)">dHex(1)Hex(5) (T)</option>
-        <option value="dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N)">dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(2) (N)">dHex(1)Hex(5)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(2)Pent(1) (N)">dHex(1)Hex(5)HexNAc(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3) (N)">dHex(1)Hex(5)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4) (N)">dHex(1)Hex(5)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N)">dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N)">dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)Pent(1) (N)">dHex(1)Hex(5)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)Sulf(2) (N)">dHex(1)Hex(5)HexNAc(4)Sulf(2) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(5) (N)">dHex(1)Hex(5)HexNAc(5) (N)</option>
-        <option value="dHex(1)Hex(6) (S)">dHex(1)Hex(6) (S)</option>
-        <option value="dHex(1)Hex(6) (T)">dHex(1)Hex(6) (T)</option>
-        <option value="dHex(1)Hex(6)HexNAc(2) (N)">dHex(1)Hex(6)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(6)HexNAc(3) (N)">dHex(1)Hex(6)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(6)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(6)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(6)HexNAc(4) (N)">dHex(1)Hex(6)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(2) (N)">dHex(1)Hex(7)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(3) (N)">dHex(1)Hex(7)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(3)Phos(1) (N)">dHex(1)Hex(7)HexNAc(3)Phos(1) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(4) (N)">dHex(1)Hex(7)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(8)HexNAc(2) (N)">dHex(1)Hex(8)HexNAc(2) (N)</option>
-        <option value="dHex(1)HexNAc(3) (S)">dHex(1)HexNAc(3) (S)</option>
-        <option value="dHex(1)HexNAc(3) (T)">dHex(1)HexNAc(3) (T)</option>
-        <option value="dHex(1)HexNAc(4) (S)">dHex(1)HexNAc(4) (S)</option>
-        <option value="dHex(1)HexNAc(4) (T)">dHex(1)HexNAc(4) (T)</option>
-        <option value="dHex(1)HexNAc(5) (S)">dHex(1)HexNAc(5) (S)</option>
-        <option value="dHex(1)HexNAc(5) (T)">dHex(1)HexNAc(5) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(1)Kdn(1) (S)">dHex(2)Hex(1)HexNAc(1)Kdn(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(1)Kdn(1) (T)">dHex(2)Hex(1)HexNAc(1)Kdn(1) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(2)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(2)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)NeuAc(1) (S)">dHex(2)Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)NeuAc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(3) (S)">dHex(2)Hex(1)HexNAc(3) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(3) (T)">dHex(2)Hex(1)HexNAc(3) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2) (S)">dHex(2)Hex(2) (S)</option>
-        <option value="dHex(2)Hex(2) (T)">dHex(2)Hex(2) (T)</option>
-        <option value="dHex(2)Hex(2)HexA(1) (S)">dHex(2)Hex(2)HexA(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexA(1) (T)">dHex(2)Hex(2)HexA(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexA(1)HexNAc(1) (S)">dHex(2)Hex(2)HexA(1)HexNAc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexA(1)HexNAc(1) (T)">dHex(2)Hex(2)HexA(1)HexNAc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(1) (S)">dHex(2)Hex(2)HexNAc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(1) (T)">dHex(2)Hex(2)HexNAc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2) (N)">dHex(2)Hex(2)HexNAc(2) (N)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2) (S)">dHex(2)Hex(2)HexNAc(2) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2) (T)">dHex(2)Hex(2)HexNAc(2) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(2)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(2)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(2)Sulf(2) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(2)Sulf(2) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3) (N)">dHex(2)Hex(2)HexNAc(3) (N)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3) (S)">dHex(2)Hex(2)HexNAc(3) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3) (T)">dHex(2)Hex(2)HexNAc(3) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)NeuAc(1) (S)">dHex(2)Hex(2)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(2)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)NeuGc(1) (S)">dHex(2)Hex(2)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)NeuGc(1) (T)">dHex(2)Hex(2)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(4) (S)">dHex(2)Hex(2)HexNAc(4) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(4) (T)">dHex(2)Hex(2)HexNAc(4) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(5) (S)">dHex(2)Hex(2)HexNAc(5) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(5) (T)">dHex(2)Hex(2)HexNAc(5) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3) (S)">dHex(2)Hex(3) (S)</option>
-        <option value="dHex(2)Hex(3) (T)">dHex(2)Hex(3) (T)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(1)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2) (N)">dHex(2)Hex(3)HexNAc(2) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2) (S)">dHex(2)Hex(3)HexNAc(2) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2) (T)">dHex(2)Hex(3)HexNAc(2) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(3)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(3)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3) (N)">dHex(2)Hex(3)HexNAc(3) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3) (S)">dHex(2)Hex(3)HexNAc(3) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3) (T)">dHex(2)Hex(3)HexNAc(3) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)Pent(1) (N)">dHex(2)Hex(3)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)Pent(2) (N)">dHex(2)Hex(3)HexNAc(3)Pent(2) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4) (N)">dHex(2)Hex(3)HexNAc(4) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4) (S)">dHex(2)Hex(3)HexNAc(4) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4) (T)">dHex(2)Hex(3)HexNAc(4) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4)Pent(1) (N)">dHex(2)Hex(3)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4)Pent(2) (N)">dHex(2)Hex(3)HexNAc(4)Pent(2) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(5) (N)">dHex(2)Hex(3)HexNAc(5) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(5) (S)">dHex(2)Hex(3)HexNAc(5) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(5) (T)">dHex(2)Hex(3)HexNAc(5) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(6) (N)">dHex(2)Hex(3)HexNAc(6) (N)</option>
-        <option value="dHex(2)Hex(4) (S)">dHex(2)Hex(4) (S)</option>
-        <option value="dHex(2)Hex(4) (T)">dHex(2)Hex(4) (T)</option>
-        <option value="dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(4)HexNAc(1) (S)">dHex(2)Hex(4)HexNAc(1) (S)</option>
-        <option value="dHex(2)Hex(4)HexNAc(1) (T)">dHex(2)Hex(4)HexNAc(1) (T)</option>
-        <option value="dHex(2)Hex(4)HexNAc(2) (N)">dHex(2)Hex(4)HexNAc(2) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(2) (S)">dHex(2)Hex(4)HexNAc(2) (S)</option>
-        <option value="dHex(2)Hex(4)HexNAc(2) (T)">dHex(2)Hex(4)HexNAc(2) (T)</option>
-        <option value="dHex(2)Hex(4)HexNAc(3) (N)">dHex(2)Hex(4)HexNAc(3) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(3)Pent(1) (N)">dHex(2)Hex(4)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4) (N)">dHex(2)Hex(4)HexNAc(4) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4) (S)">dHex(2)Hex(4)HexNAc(4) (S)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4) (T)">dHex(2)Hex(4)HexNAc(4) (T)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4)Pent(1) (N)">dHex(2)Hex(4)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(2)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(5) (N)">dHex(2)Hex(4)HexNAc(5) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(5) (S)">dHex(2)Hex(4)HexNAc(5) (S)</option>
-        <option value="dHex(2)Hex(4)HexNAc(5) (T)">dHex(2)Hex(4)HexNAc(5) (T)</option>
-        <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (S)">dHex(2)Hex(5)HexNAc(2)Me(1) (S)</option>
-        <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (T)">dHex(2)Hex(5)HexNAc(2)Me(1) (T)</option>
-        <option value="dHex(2)Hex(5)HexNAc(3)Pent(1) (N)">dHex(2)Hex(5)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(5)HexNAc(4) (N)">dHex(2)Hex(5)HexNAc(4) (N)</option>
-        <option value="dHex(2)HexNAc(2)Kdn(1) (S)">dHex(2)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(2)HexNAc(2)Kdn(1) (T)">dHex(2)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(2)HexNAc(5) (S)">dHex(2)HexNAc(5) (S)</option>
-        <option value="dHex(2)HexNAc(5) (T)">dHex(2)HexNAc(5) (T)</option>
-        <option value="dHex(2)HexNAc(7) (S)">dHex(2)HexNAc(7) (S)</option>
-        <option value="dHex(2)HexNAc(7) (T)">dHex(2)HexNAc(7) (T)</option>
-        <option value="dHex(3)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(3)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(3)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(3)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(3)Hex(1)HexNAc(3)Kdn(1) (S)">dHex(3)Hex(1)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(3)Hex(1)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(1)HexNAc(3)Kdn(1) (T)</option>
-        <option value="dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(2) (S)">dHex(3)Hex(2)HexNAc(2) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(2) (T)">dHex(3)Hex(2)HexNAc(2) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(3)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(3) (S)">dHex(3)Hex(2)HexNAc(3) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(3) (T)">dHex(3)Hex(2)HexNAc(3) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (S)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(4) (S)">dHex(3)Hex(2)HexNAc(4) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(4) (T)">dHex(3)Hex(2)HexNAc(4) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(1) (S)">dHex(3)Hex(3)HexNAc(1) (S)</option>
-        <option value="dHex(3)Hex(3)HexNAc(1) (T)">dHex(3)Hex(3)HexNAc(1) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(2) (S)">dHex(3)Hex(3)HexNAc(2) (S)</option>
-        <option value="dHex(3)Hex(3)HexNAc(2) (T)">dHex(3)Hex(3)HexNAc(2) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3) (S)">dHex(3)Hex(3)HexNAc(3) (S)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3) (T)">dHex(3)Hex(3)HexNAc(3) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3)Pent(1) (N)">dHex(3)Hex(3)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(3)Hex(3)HexNAc(4) (N)">dHex(3)Hex(3)HexNAc(4) (N)</option>
-        <option value="dHex(3)Hex(3)HexNAc(4)Pent(1) (N)">dHex(3)Hex(3)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(3)Hex(4)HexNAc(4) (N)">dHex(3)Hex(4)HexNAc(4) (N)</option>
-        <option value="dHex(3)Hex(4)HexNAc(4) (S)">dHex(3)Hex(4)HexNAc(4) (S)</option>
-        <option value="dHex(3)Hex(4)HexNAc(4) (T)">dHex(3)Hex(4)HexNAc(4) (T)</option>
-        <option value="dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(3)HexNAc(3)Kdn(1) (S)">dHex(3)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(3)HexNAc(3)Kdn(1) (T)">dHex(3)HexNAc(3)Kdn(1) (T)</option>
-        <option value="dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)">dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)</option>
-        <option value="dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)">dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)</option>
-        <option value="dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)">dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)">dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)</option>
-        <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(4)Hex(2)HexNAc(3) (S)">dHex(4)Hex(2)HexNAc(3) (S)</option>
-        <option value="dHex(4)Hex(2)HexNAc(3) (T)">dHex(4)Hex(2)HexNAc(3) (T)</option>
-        <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="dHex(4)Hex(3)HexNAc(3) (S)">dHex(4)Hex(3)HexNAc(3) (S)</option>
-        <option value="dHex(4)Hex(3)HexNAc(3) (T)">dHex(4)Hex(3)HexNAc(3) (T)</option>
-        <option value="dHex(4)HexNAc(3)Kdn(1) (S)">dHex(4)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(4)HexNAc(3)Kdn(1) (T)">dHex(4)HexNAc(3)Kdn(1) (T)</option>
-        <option value="DHP (C)">DHP (C)</option>
-        <option value="Diacylglycerol (C)">Diacylglycerol (C)</option>
-        <option value="DiART6plex (K)">DiART6plex (K)</option>
-        <option value="DiART6plex (N-term)">DiART6plex (N-term)</option>
-        <option value="DiART6plex (Protein N-term)">DiART6plex (Protein N-term)</option>
-        <option value="DiART6plex (Y)">DiART6plex (Y)</option>
-        <option value="DiART6plex115 (K)">DiART6plex115 (K)</option>
-        <option value="DiART6plex115 (N-term)">DiART6plex115 (N-term)</option>
-        <option value="DiART6plex115 (Protein N-term)">DiART6plex115 (Protein N-term)</option>
-        <option value="DiART6plex115 (Y)">DiART6plex115 (Y)</option>
-        <option value="DiART6plex116/119 (K)">DiART6plex116/119 (K)</option>
-        <option value="DiART6plex116/119 (N-term)">DiART6plex116/119 (N-term)</option>
-        <option value="DiART6plex116/119 (Protein N-term)">DiART6plex116/119 (Protein N-term)</option>
-        <option value="DiART6plex116/119 (Y)">DiART6plex116/119 (Y)</option>
-        <option value="DiART6plex117 (K)">DiART6plex117 (K)</option>
-        <option value="DiART6plex117 (N-term)">DiART6plex117 (N-term)</option>
-        <option value="DiART6plex117 (Protein N-term)">DiART6plex117 (Protein N-term)</option>
-        <option value="DiART6plex117 (Y)">DiART6plex117 (Y)</option>
-        <option value="DiART6plex118 (K)">DiART6plex118 (K)</option>
-        <option value="DiART6plex118 (N-term)">DiART6plex118 (N-term)</option>
-        <option value="DiART6plex118 (Protein N-term)">DiART6plex118 (Protein N-term)</option>
-        <option value="DiART6plex118 (Y)">DiART6plex118 (Y)</option>
-        <option value="Dibromo (Y)">Dibromo (Y)</option>
-        <option value="Dicarbamidomethyl (C)">Dicarbamidomethyl (C)</option>
-        <option value="Dicarbamidomethyl (H)">Dicarbamidomethyl (H)</option>
-        <option value="Dicarbamidomethyl (K)">Dicarbamidomethyl (K)</option>
-        <option value="Dicarbamidomethyl (N-term)">Dicarbamidomethyl (N-term)</option>
-        <option value="Dicarbamidomethyl (R)">Dicarbamidomethyl (R)</option>
-        <option value="dichlorination (C)">dichlorination (C)</option>
-        <option value="dichlorination (Y)">dichlorination (Y)</option>
-        <option value="Didehydro (C-term K)">Didehydro (C-term K)</option>
-        <option value="Didehydro (S)">Didehydro (S)</option>
-        <option value="Didehydro (T)">Didehydro (T)</option>
-        <option value="Didehydro (Y)">Didehydro (Y)</option>
-        <option value="Didehydroretinylidene (K)">Didehydroretinylidene (K)</option>
-        <option value="Diethyl (K)">Diethyl (K)</option>
-        <option value="Diethyl (N-term)">Diethyl (N-term)</option>
-        <option value="Diethylphosphate (C)">Diethylphosphate (C)</option>
-        <option value="Diethylphosphate (H)">Diethylphosphate (H)</option>
-        <option value="Diethylphosphate (K)">Diethylphosphate (K)</option>
-        <option value="Diethylphosphate (N-term)">Diethylphosphate (N-term)</option>
-        <option value="Diethylphosphate (S)">Diethylphosphate (S)</option>
-        <option value="Diethylphosphate (T)">Diethylphosphate (T)</option>
-        <option value="Diethylphosphate (Y)">Diethylphosphate (Y)</option>
-        <option value="Diethylphosphothione (C)">Diethylphosphothione (C)</option>
-        <option value="Diethylphosphothione (H)">Diethylphosphothione (H)</option>
-        <option value="Diethylphosphothione (K)">Diethylphosphothione (K)</option>
-        <option value="Diethylphosphothione (S)">Diethylphosphothione (S)</option>
-        <option value="Diethylphosphothione (T)">Diethylphosphothione (T)</option>
-        <option value="Diethylphosphothione (Y)">Diethylphosphothione (Y)</option>
-        <option value="Difuran (Y)">Difuran (Y)</option>
-        <option value="Dihydroxyimidazolidine (R)">Dihydroxyimidazolidine (R)</option>
-        <option value="Diiodo (H)">Diiodo (H)</option>
-        <option value="Diiodo (Y)">Diiodo (Y)</option>
-        <option value="Diironsubcluster (C)">Diironsubcluster (C)</option>
-        <option value="Diisopropylphosphate (K)">Diisopropylphosphate (K)</option>
-        <option value="Diisopropylphosphate (N-term)">Diisopropylphosphate (N-term)</option>
-        <option value="Diisopropylphosphate (S)">Diisopropylphosphate (S)</option>
-        <option value="Diisopropylphosphate (T)">Diisopropylphosphate (T)</option>
-        <option value="Diisopropylphosphate (Y)">Diisopropylphosphate (Y)</option>
-        <option value="DiLeu4plex (K)">DiLeu4plex (K)</option>
-        <option value="DiLeu4plex (N-term)">DiLeu4plex (N-term)</option>
-        <option value="DiLeu4plex (Y)">DiLeu4plex (Y)</option>
-        <option value="DiLeu4plex115 (K)">DiLeu4plex115 (K)</option>
-        <option value="DiLeu4plex115 (N-term)">DiLeu4plex115 (N-term)</option>
-        <option value="DiLeu4plex115 (Y)">DiLeu4plex115 (Y)</option>
-        <option value="DiLeu4plex117 (K)">DiLeu4plex117 (K)</option>
-        <option value="DiLeu4plex117 (N-term)">DiLeu4plex117 (N-term)</option>
-        <option value="DiLeu4plex117 (Y)">DiLeu4plex117 (Y)</option>
-        <option value="DiLeu4plex118 (K)">DiLeu4plex118 (K)</option>
-        <option value="DiLeu4plex118 (N-term)">DiLeu4plex118 (N-term)</option>
-        <option value="DiLeu4plex118 (Y)">DiLeu4plex118 (Y)</option>
-        <option value="Dimethyl (K)">Dimethyl (K)</option>
-        <option value="Dimethyl (N)">Dimethyl (N)</option>
-        <option value="Dimethyl (N-term)">Dimethyl (N-term)</option>
-        <option value="Dimethyl (Protein N-term P)">Dimethyl (Protein N-term P)</option>
-        <option value="Dimethyl (Protein N-term)">Dimethyl (Protein N-term)</option>
-        <option value="Dimethyl (R)">Dimethyl (R)</option>
-        <option value="Dimethyl:2H(2)13C (K)">Dimethyl:2H(2)13C (K)</option>
-        <option value="Dimethyl:2H(2)13C (N)">Dimethyl:2H(2)13C (N)</option>
-        <option value="Dimethyl:2H(2)13C (N-term)">Dimethyl:2H(2)13C (N-term)</option>
-        <option value="Dimethyl:2H(2)13C (Protein N-term P)">Dimethyl:2H(2)13C (Protein N-term P)</option>
-        <option value="Dimethyl:2H(2)13C (R)">Dimethyl:2H(2)13C (R)</option>
-        <option value="Dimethyl:2H(4) (K)">Dimethyl:2H(4) (K)</option>
-        <option value="Dimethyl:2H(4) (N-term)">Dimethyl:2H(4) (N-term)</option>
-        <option value="Dimethyl:2H(4) (Protein N-term)">Dimethyl:2H(4) (Protein N-term)</option>
-        <option value="Dimethyl:2H(4) (R)">Dimethyl:2H(4) (R)</option>
-        <option value="Dimethyl:2H(4)13C(2) (K)">Dimethyl:2H(4)13C(2) (K)</option>
-        <option value="Dimethyl:2H(4)13C(2) (N-term)">Dimethyl:2H(4)13C(2) (N-term)</option>
-        <option value="Dimethyl:2H(4)13C(2) (Protein N-term)">Dimethyl:2H(4)13C(2) (Protein N-term)</option>
-        <option value="Dimethyl:2H(4)13C(2) (R)">Dimethyl:2H(4)13C(2) (R)</option>
-        <option value="Dimethyl:2H(6) (K)">Dimethyl:2H(6) (K)</option>
-        <option value="Dimethyl:2H(6) (N-term)">Dimethyl:2H(6) (N-term)</option>
-        <option value="Dimethyl:2H(6) (R)">Dimethyl:2H(6) (R)</option>
-        <option value="Dimethyl:2H(6)13C(2) (K)">Dimethyl:2H(6)13C(2) (K)</option>
-        <option value="Dimethyl:2H(6)13C(2) (N-term)">Dimethyl:2H(6)13C(2) (N-term)</option>
-        <option value="Dimethyl:2H(6)13C(2) (Protein N-term)">Dimethyl:2H(6)13C(2) (Protein N-term)</option>
-        <option value="Dimethyl:2H(6)13C(2) (R)">Dimethyl:2H(6)13C(2) (R)</option>
-        <option value="DimethylamineGMBS (C)">DimethylamineGMBS (C)</option>
-        <option value="Dimethylaminoethyl (C)">Dimethylaminoethyl (C)</option>
-        <option value="DimethylArsino (C)">DimethylArsino (C)</option>
-        <option value="Dimethylphosphothione (C)">Dimethylphosphothione (C)</option>
-        <option value="Dimethylphosphothione (H)">Dimethylphosphothione (H)</option>
-        <option value="Dimethylphosphothione (K)">Dimethylphosphothione (K)</option>
-        <option value="Dimethylphosphothione (S)">Dimethylphosphothione (S)</option>
-        <option value="Dimethylphosphothione (T)">Dimethylphosphothione (T)</option>
-        <option value="Dimethylphosphothione (Y)">Dimethylphosphothione (Y)</option>
-        <option value="DimethylpyrroleAdduct (K)">DimethylpyrroleAdduct (K)</option>
-        <option value="Dioxidation (C)">Dioxidation (C)</option>
-        <option value="Dioxidation (E)">Dioxidation (E)</option>
-        <option value="Dioxidation (F)">Dioxidation (F)</option>
-        <option value="Dioxidation (I)">Dioxidation (I)</option>
-        <option value="Dioxidation (K)">Dioxidation (K)</option>
-        <option value="Dioxidation (L)">Dioxidation (L)</option>
-        <option value="Dioxidation (M)">Dioxidation (M)</option>
-        <option value="Dioxidation (P)">Dioxidation (P)</option>
-        <option value="Dioxidation (R)">Dioxidation (R)</option>
-        <option value="Dioxidation (U)">Dioxidation (U)</option>
-        <option value="Dioxidation (V)">Dioxidation (V)</option>
-        <option value="Dioxidation (W)">Dioxidation (W)</option>
-        <option value="Dioxidation (Y)">Dioxidation (Y)</option>
-        <option value="Diphthamide (H)">Diphthamide (H)</option>
-        <option value="Dipyridyl (C)">Dipyridyl (C)</option>
-        <option value="Dipyrrolylmethanemethyl (C)">Dipyrrolylmethanemethyl (C)</option>
-        <option value="DMPO (C)">DMPO (C)</option>
-        <option value="DMPO (H)">DMPO (H)</option>
-        <option value="DMPO (Y)">DMPO (Y)</option>
-        <option value="DNCB_hapten (C)">DNCB_hapten (C)</option>
-        <option value="DNCB_hapten (H)">DNCB_hapten (H)</option>
-        <option value="DNCB_hapten (K)">DNCB_hapten (K)</option>
-        <option value="DNCB_hapten (Y)">DNCB_hapten (Y)</option>
-        <option value="dNIC (K)">dNIC (K)</option>
-        <option value="dNIC (N-term)">dNIC (N-term)</option>
-        <option value="DNPS (C)">DNPS (C)</option>
-        <option value="DNPS (W)">DNPS (W)</option>
-        <option value="DTT (C)">DTT (C)</option>
-        <option value="DyLight-maleimide (C)">DyLight-maleimide (C)</option>
-        <option value="DYn-2 (C)">DYn-2 (C)</option>
-        <option value="EDEDTIDVFQQQTGG (K)">EDEDTIDVFQQQTGG (K)</option>
-        <option value="EDT-iodoacetyl-PEO-biotin (S)">EDT-iodoacetyl-PEO-biotin (S)</option>
-        <option value="EDT-iodoacetyl-PEO-biotin (T)">EDT-iodoacetyl-PEO-biotin (T)</option>
-        <option value="EDT-maleimide-PEO-biotin (S)">EDT-maleimide-PEO-biotin (S)</option>
-        <option value="EDT-maleimide-PEO-biotin (T)">EDT-maleimide-PEO-biotin (T)</option>
-        <option value="EEEDVIEVYQEQTGG (K)">EEEDVIEVYQEQTGG (K)</option>
-        <option value="EGCG1 (C)">EGCG1 (C)</option>
-        <option value="EGCG2 (C)">EGCG2 (C)</option>
-        <option value="EHD-diphenylpentanone (C)">EHD-diphenylpentanone (C)</option>
-        <option value="EHD-diphenylpentanone (M)">EHD-diphenylpentanone (M)</option>
-        <option value="EQAT (C)">EQAT (C)</option>
-        <option value="EQAT:2H(5) (C)">EQAT:2H(5) (C)</option>
-        <option value="EQIGG (K)">EQIGG (K)</option>
-        <option value="ESP (K)">ESP (K)</option>
-        <option value="ESP (N-term)">ESP (N-term)</option>
-        <option value="ESP:2H(10) (K)">ESP:2H(10) (K)</option>
-        <option value="ESP:2H(10) (N-term)">ESP:2H(10) (N-term)</option>
-        <option value="Ethanedithiol (S)">Ethanedithiol (S)</option>
-        <option value="Ethanedithiol (T)">Ethanedithiol (T)</option>
-        <option value="Ethanolamine (C)">Ethanolamine (C)</option>
-        <option value="Ethanolamine (C-term)">Ethanolamine (C-term)</option>
-        <option value="Ethanolamine (D)">Ethanolamine (D)</option>
-        <option value="Ethanolamine (E)">Ethanolamine (E)</option>
-        <option value="Ethanolyl (C)">Ethanolyl (C)</option>
-        <option value="Ethanolyl (K)">Ethanolyl (K)</option>
-        <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-        <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
-        <option value="Ethyl (C-term)">Ethyl (C-term)</option>
-        <option value="Ethyl (D)">Ethyl (D)</option>
-        <option value="Ethyl (E)">Ethyl (E)</option>
-        <option value="Ethyl (K)">Ethyl (K)</option>
-        <option value="Ethyl (N-term)">Ethyl (N-term)</option>
-        <option value="Ethyl (Protein N-term)">Ethyl (Protein N-term)</option>
-        <option value="Ethyl+Deamidated (N)">Ethyl+Deamidated (N)</option>
-        <option value="Ethyl+Deamidated (Q)">Ethyl+Deamidated (Q)</option>
-        <option value="ethylamino (S)">ethylamino (S)</option>
-        <option value="ethylamino (T)">ethylamino (T)</option>
-        <option value="Ethylphosphate (K)">Ethylphosphate (K)</option>
-        <option value="Ethylphosphate (N-term)">Ethylphosphate (N-term)</option>
-        <option value="Ethylphosphate (S)">Ethylphosphate (S)</option>
-        <option value="Ethylphosphate (T)">Ethylphosphate (T)</option>
-        <option value="Ethylphosphate (Y)">Ethylphosphate (Y)</option>
-        <option value="ethylsulfonylethyl (C)">ethylsulfonylethyl (C)</option>
-        <option value="ethylsulfonylethyl (H)">ethylsulfonylethyl (H)</option>
-        <option value="ethylsulfonylethyl (K)">ethylsulfonylethyl (K)</option>
-        <option value="ExacTagAmine (K)">ExacTagAmine (K)</option>
-        <option value="ExacTagThiol (C)">ExacTagThiol (C)</option>
-        <option value="FAD (C)">FAD (C)</option>
-        <option value="FAD (H)">FAD (H)</option>
-        <option value="FAD (Y)">FAD (Y)</option>
-        <option value="Farnesyl (C)">Farnesyl (C)</option>
-        <option value="Fluorescein (C)">Fluorescein (C)</option>
-        <option value="Fluorescein-tyramine (Y)">Fluorescein-tyramine (Y)</option>
-        <option value="Fluoro (A)">Fluoro (A)</option>
-        <option value="Fluoro (F)">Fluoro (F)</option>
-        <option value="Fluoro (W)">Fluoro (W)</option>
-        <option value="Fluoro (Y)">Fluoro (Y)</option>
-        <option value="FMN (S)">FMN (S)</option>
-        <option value="FMN (T)">FMN (T)</option>
-        <option value="FMNC (C)">FMNC (C)</option>
-        <option value="FMNH (C)">FMNH (C)</option>
-        <option value="FMNH (H)">FMNH (H)</option>
-        <option value="FNEM (C)">FNEM (C)</option>
-        <option value="Formyl (K)">Formyl (K)</option>
-        <option value="Formyl (N-term)">Formyl (N-term)</option>
-        <option value="Formyl (Protein N-term)">Formyl (Protein N-term)</option>
-        <option value="Formyl (S)">Formyl (S)</option>
-        <option value="Formyl (T)">Formyl (T)</option>
-        <option value="Formylasparagine (H)">Formylasparagine (H)</option>
-        <option value="FormylMet (Protein N-term)">FormylMet (Protein N-term)</option>
-        <option value="FP-Biotin (K)">FP-Biotin (K)</option>
-        <option value="FP-Biotin (S)">FP-Biotin (S)</option>
-        <option value="FP-Biotin (T)">FP-Biotin (T)</option>
-        <option value="FP-Biotin (Y)">FP-Biotin (Y)</option>
-        <option value="FTC (C)">FTC (C)</option>
-        <option value="FTC (K)">FTC (K)</option>
-        <option value="FTC (P)">FTC (P)</option>
-        <option value="FTC (R)">FTC (R)</option>
-        <option value="FTC (S)">FTC (S)</option>
-        <option value="Furan (Y)">Furan (Y)</option>
-        <option value="G-H1 (R)">G-H1 (R)</option>
-        <option value="Galactosyl (K)">Galactosyl (K)</option>
-        <option value="Galactosyl (N-term)">Galactosyl (N-term)</option>
-        <option value="GEE (Q)">GEE (Q)</option>
-        <option value="GeranylGeranyl (C)">GeranylGeranyl (C)</option>
-        <option value="GG (C)">GG (C)</option>
-        <option value="GG (K)">GG (K)</option>
-        <option value="GG (Protein N-term)">GG (Protein N-term)</option>
-        <option value="GG (S)">GG (S)</option>
-        <option value="GG (T)">GG (T)</option>
-        <option value="GGQ (K)">GGQ (K)</option>
-        <option value="GIST-Quat (K)">GIST-Quat (K)</option>
-        <option value="GIST-Quat (N-term)">GIST-Quat (N-term)</option>
-        <option value="GIST-Quat:2H(3) (K)">GIST-Quat:2H(3) (K)</option>
-        <option value="GIST-Quat:2H(3) (N-term)">GIST-Quat:2H(3) (N-term)</option>
-        <option value="GIST-Quat:2H(6) (K)">GIST-Quat:2H(6) (K)</option>
-        <option value="GIST-Quat:2H(6) (N-term)">GIST-Quat:2H(6) (N-term)</option>
-        <option value="GIST-Quat:2H(9) (K)">GIST-Quat:2H(9) (K)</option>
-        <option value="GIST-Quat:2H(9) (N-term)">GIST-Quat:2H(9) (N-term)</option>
-        <option value="Gln-&gt;Ala (Q)">Gln-&gt;Ala (Q)</option>
-        <option value="Gln-&gt;Arg (Q)">Gln-&gt;Arg (Q)</option>
-        <option value="Gln-&gt;Asn (Q)">Gln-&gt;Asn (Q)</option>
-        <option value="Gln-&gt;Asp (Q)">Gln-&gt;Asp (Q)</option>
-        <option value="Gln-&gt;Cys (Q)">Gln-&gt;Cys (Q)</option>
-        <option value="Gln-&gt;Glu (Q)">Gln-&gt;Glu (Q)</option>
-        <option value="Gln-&gt;Gly (Q)">Gln-&gt;Gly (Q)</option>
-        <option value="Gln-&gt;His (Q)">Gln-&gt;His (Q)</option>
-        <option value="Gln-&gt;Lys (Q)">Gln-&gt;Lys (Q)</option>
-        <option value="Gln-&gt;Met (Q)">Gln-&gt;Met (Q)</option>
-        <option value="Gln-&gt;Phe (Q)">Gln-&gt;Phe (Q)</option>
-        <option value="Gln-&gt;Pro (Q)">Gln-&gt;Pro (Q)</option>
-        <option value="Gln-&gt;pyro-Glu (N-term Q)">Gln-&gt;pyro-Glu (N-term Q)</option>
-        <option value="Gln-&gt;Ser (Q)">Gln-&gt;Ser (Q)</option>
-        <option value="Gln-&gt;Thr (Q)">Gln-&gt;Thr (Q)</option>
-        <option value="Gln-&gt;Trp (Q)">Gln-&gt;Trp (Q)</option>
-        <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
-        <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
-        <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
-        <option value="Glu (E)">Glu (E)</option>
-        <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
-        <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
-        <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
-        <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
-        <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
-        <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
-        <option value="Glu-&gt;Gln (E)">Glu-&gt;Gln (E)</option>
-        <option value="Glu-&gt;Gly (E)">Glu-&gt;Gly (E)</option>
-        <option value="Glu-&gt;His (E)">Glu-&gt;His (E)</option>
-        <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
-        <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
-        <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
-        <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
-        <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
-        <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
-        <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
-        <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
-        <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
-        <option value="Glu-&gt;Val (E)">Glu-&gt;Val (E)</option>
-        <option value="Glu-&gt;Xle (E)">Glu-&gt;Xle (E)</option>
-        <option value="glucosone (R)">glucosone (R)</option>
-        <option value="Glucosylgalactosyl (K)">Glucosylgalactosyl (K)</option>
-        <option value="Glucuronyl (Protein N-term)">Glucuronyl (Protein N-term)</option>
-        <option value="Glucuronyl (S)">Glucuronyl (S)</option>
-        <option value="Glucuronyl (T)">Glucuronyl (T)</option>
-        <option value="GluGlu (E)">GluGlu (E)</option>
-        <option value="GluGlu (Protein C-term)">GluGlu (Protein C-term)</option>
-        <option value="GluGluGlu (E)">GluGluGlu (E)</option>
-        <option value="GluGluGlu (Protein C-term)">GluGluGlu (Protein C-term)</option>
-        <option value="GluGluGluGlu (E)">GluGluGluGlu (E)</option>
-        <option value="GluGluGluGlu (Protein C-term)">GluGluGluGlu (Protein C-term)</option>
-        <option value="Gluratylation (K)">Gluratylation (K)</option>
-        <option value="Glutathione (C)">Glutathione (C)</option>
-        <option value="Gly (K)">Gly (K)</option>
-        <option value="Gly (S)">Gly (S)</option>
-        <option value="Gly (T)">Gly (T)</option>
-        <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
-        <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
-        <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
-        <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
-        <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
-        <option value="Gly-&gt;Gln (G)">Gly-&gt;Gln (G)</option>
-        <option value="Gly-&gt;Glu (G)">Gly-&gt;Glu (G)</option>
-        <option value="Gly-&gt;His (G)">Gly-&gt;His (G)</option>
-        <option value="Gly-&gt;Lys (G)">Gly-&gt;Lys (G)</option>
-        <option value="Gly-&gt;Met (G)">Gly-&gt;Met (G)</option>
-        <option value="Gly-&gt;Phe (G)">Gly-&gt;Phe (G)</option>
-        <option value="Gly-&gt;Pro (G)">Gly-&gt;Pro (G)</option>
-        <option value="Gly-&gt;Ser (G)">Gly-&gt;Ser (G)</option>
-        <option value="Gly-&gt;Thr (G)">Gly-&gt;Thr (G)</option>
-        <option value="Gly-&gt;Trp (G)">Gly-&gt;Trp (G)</option>
-        <option value="Gly-&gt;Tyr (G)">Gly-&gt;Tyr (G)</option>
-        <option value="Gly-&gt;Val (G)">Gly-&gt;Val (G)</option>
-        <option value="Gly-&gt;Xle (G)">Gly-&gt;Xle (G)</option>
-        <option value="Gly-loss+Amide (C-term G)">Gly-loss+Amide (C-term G)</option>
-        <option value="Glycerophospho (S)">Glycerophospho (S)</option>
-        <option value="GlycerylPE (E)">GlycerylPE (E)</option>
-        <option value="glycidamide (K)">glycidamide (K)</option>
-        <option value="glycidamide (N-term)">glycidamide (N-term)</option>
-        <option value="Glycosyl (P)">Glycosyl (P)</option>
-        <option value="glyoxalAGE (R)">glyoxalAGE (R)</option>
-        <option value="GNLLFLACYCIGG (K)">GNLLFLACYCIGG (K)</option>
-        <option value="GPIanchor (Protein C-term)">GPIanchor (Protein C-term)</option>
-        <option value="Guanidinyl (K)">Guanidinyl (K)</option>
-        <option value="Guanidinyl (N-term)">Guanidinyl (N-term)</option>
-        <option value="Haloxon (C)">Haloxon (C)</option>
-        <option value="Haloxon (H)">Haloxon (H)</option>
-        <option value="Haloxon (K)">Haloxon (K)</option>
-        <option value="Haloxon (S)">Haloxon (S)</option>
-        <option value="Haloxon (T)">Haloxon (T)</option>
-        <option value="Haloxon (Y)">Haloxon (Y)</option>
-        <option value="HCysteinyl (C)">HCysteinyl (C)</option>
-        <option value="HCysThiolactone (K)">HCysThiolactone (K)</option>
-        <option value="Heme (C)">Heme (C)</option>
-        <option value="Heme (H)">Heme (H)</option>
-        <option value="Hep (K)">Hep (K)</option>
-        <option value="Hep (N)">Hep (N)</option>
-        <option value="Hep (Q)">Hep (Q)</option>
-        <option value="Hep (R)">Hep (R)</option>
-        <option value="Hep (S)">Hep (S)</option>
-        <option value="Hep (T)">Hep (T)</option>
-        <option value="Hex (C)">Hex (C)</option>
-        <option value="Hex (K)">Hex (K)</option>
-        <option value="Hex (N)">Hex (N)</option>
-        <option value="Hex (N-term)">Hex (N-term)</option>
-        <option value="Hex (R)">Hex (R)</option>
-        <option value="Hex (S)">Hex (S)</option>
-        <option value="Hex (T)">Hex (T)</option>
-        <option value="Hex (W)">Hex (W)</option>
-        <option value="Hex (Y)">Hex (Y)</option>
-        <option value="Hex(1)HexA(1) (S)">Hex(1)HexA(1) (S)</option>
-        <option value="Hex(1)HexA(1) (T)">Hex(1)HexA(1) (T)</option>
-        <option value="Hex(1)HexA(1)HexNAc(1) (S)">Hex(1)HexA(1)HexNAc(1) (S)</option>
-        <option value="Hex(1)HexA(1)HexNAc(1) (T)">Hex(1)HexA(1)HexNAc(1) (T)</option>
-        <option value="Hex(1)HexA(1)HexNAc(2) (S)">Hex(1)HexA(1)HexNAc(2) (S)</option>
-        <option value="Hex(1)HexA(1)HexNAc(2) (T)">Hex(1)HexA(1)HexNAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(1) (N)">Hex(1)HexNAc(1) (N)</option>
-        <option value="Hex(1)HexNAc(1) (S)">Hex(1)HexNAc(1) (S)</option>
-        <option value="Hex(1)HexNAc(1) (T)">Hex(1)HexNAc(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1) (N)">Hex(1)HexNAc(1)dHex(1) (N)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1) (S)">Hex(1)HexNAc(1)dHex(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1) (T)">Hex(1)HexNAc(1)dHex(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1)Me(1) (S)">Hex(1)HexNAc(1)dHex(1)Me(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1)Me(1) (T)">Hex(1)HexNAc(1)dHex(1)Me(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1)Me(2) (S)">Hex(1)HexNAc(1)dHex(1)Me(2) (S)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1)Me(2) (T)">Hex(1)HexNAc(1)dHex(1)Me(2) (T)</option>
-        <option value="Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S)">Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T)">Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1) (N)">Hex(1)HexNAc(1)NeuAc(1) (N)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1) (S)">Hex(1)HexNAc(1)NeuAc(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1) (T)">Hex(1)HexNAc(1)NeuAc(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S)">Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T)">Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S)">Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T)">Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T)">Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2) (N)">Hex(1)HexNAc(1)NeuAc(2) (N)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2) (S)">Hex(1)HexNAc(1)NeuAc(2) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2) (T)">Hex(1)HexNAc(1)NeuAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S)">Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T)">Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S)">Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T)">Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(3) (S)">Hex(1)HexNAc(1)NeuAc(3) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(3) (T)">Hex(1)HexNAc(1)NeuAc(3) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(1) (S)">Hex(1)HexNAc(1)NeuGc(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(1) (T)">Hex(1)HexNAc(1)NeuGc(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(2) (S)">Hex(1)HexNAc(1)NeuGc(2) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(2) (T)">Hex(1)HexNAc(1)NeuGc(2) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(3) (S)">Hex(1)HexNAc(1)NeuGc(3) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(3) (T)">Hex(1)HexNAc(1)NeuGc(3) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(4) (S)">Hex(1)HexNAc(1)NeuGc(4) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(4) (T)">Hex(1)HexNAc(1)NeuGc(4) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(5) (S)">Hex(1)HexNAc(1)NeuGc(5) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(5) (T)">Hex(1)HexNAc(1)NeuGc(5) (T)</option>
-        <option value="Hex(1)HexNAc(1)Phos(1) (S)">Hex(1)HexNAc(1)Phos(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)Phos(1) (T)">Hex(1)HexNAc(1)Phos(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)Sulf(1) (S)">Hex(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)Sulf(1) (T)">Hex(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(2) (N)">Hex(1)HexNAc(2) (N)</option>
-        <option value="Hex(1)HexNAc(2) (S)">Hex(1)HexNAc(2) (S)</option>
-        <option value="Hex(1)HexNAc(2) (T)">Hex(1)HexNAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(2)dHex(1) (N)">Hex(1)HexNAc(2)dHex(1) (N)</option>
-        <option value="Hex(1)HexNAc(2)dHex(1) (S)">Hex(1)HexNAc(2)dHex(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)dHex(1) (T)">Hex(1)HexNAc(2)dHex(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)dHex(1)Pent(1) (N)">Hex(1)HexNAc(2)dHex(1)Pent(1) (N)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2) (N)">Hex(1)HexNAc(2)dHex(2) (N)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2) (S)">Hex(1)HexNAc(2)dHex(2) (S)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2) (T)">Hex(1)HexNAc(2)dHex(2) (T)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(1) (S)">Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(1) (T)">Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(2) (S)">Hex(1)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(2) (T)">Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T)">Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuGc(1) (S)">Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuGc(1) (T)">Hex(1)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)Pent(1) (N)">Hex(1)HexNAc(2)Pent(1) (N)</option>
-        <option value="Hex(1)HexNAc(2)Sulf(1) (S)">Hex(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)Sulf(1) (T)">Hex(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(3) (S)">Hex(1)HexNAc(3) (S)</option>
-        <option value="Hex(1)HexNAc(3) (T)">Hex(1)HexNAc(3) (T)</option>
-        <option value="Hex(1)HexNAc(3)NeuAc(1) (S)">Hex(1)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="Hex(1)HexNAc(3)NeuAc(1) (T)">Hex(1)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="Hex(1)HexNAc(3)NeuAc(2) (S)">Hex(1)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="Hex(1)HexNAc(3)NeuAc(2) (T)">Hex(1)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(3)NeuGc(1) (S)">Hex(1)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="Hex(1)HexNAc(3)NeuGc(1) (T)">Hex(1)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="Hex(1)HexNAc(3)Sulf(1) (S)">Hex(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(3)Sulf(1) (T)">Hex(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)</option>
-        <option value="Hex(1)NeuAc(1) (S)">Hex(1)NeuAc(1) (S)</option>
-        <option value="Hex(1)NeuAc(1) (T)">Hex(1)NeuAc(1) (T)</option>
-        <option value="Hex(1)NeuAc(1)Pent(1) (S)">Hex(1)NeuAc(1)Pent(1) (S)</option>
-        <option value="Hex(1)NeuAc(1)Pent(1) (T)">Hex(1)NeuAc(1)Pent(1) (T)</option>
-        <option value="Hex(1)NeuGc(1) (S)">Hex(1)NeuGc(1) (S)</option>
-        <option value="Hex(1)NeuGc(1) (T)">Hex(1)NeuGc(1) (T)</option>
-        <option value="Hex(1)Pent(1) (S)">Hex(1)Pent(1) (S)</option>
-        <option value="Hex(1)Pent(1) (T)">Hex(1)Pent(1) (T)</option>
-        <option value="Hex(1)Pent(2) (S)">Hex(1)Pent(2) (S)</option>
-        <option value="Hex(1)Pent(2) (T)">Hex(1)Pent(2) (T)</option>
-        <option value="Hex(1)Pent(2)Me(1) (S)">Hex(1)Pent(2)Me(1) (S)</option>
-        <option value="Hex(1)Pent(2)Me(1) (T)">Hex(1)Pent(2)Me(1) (T)</option>
-        <option value="Hex(1)Pent(3) (S)">Hex(1)Pent(3) (S)</option>
-        <option value="Hex(1)Pent(3) (T)">Hex(1)Pent(3) (T)</option>
-        <option value="Hex(1)Pent(3)Me(1) (S)">Hex(1)Pent(3)Me(1) (S)</option>
-        <option value="Hex(1)Pent(3)Me(1) (T)">Hex(1)Pent(3)Me(1) (T)</option>
-        <option value="Hex(10)HexNAc(1) (N)">Hex(10)HexNAc(1) (N)</option>
-        <option value="Hex(10)Phos(3) (S)">Hex(10)Phos(3) (S)</option>
-        <option value="Hex(10)Phos(3) (T)">Hex(10)Phos(3) (T)</option>
-        <option value="Hex(2) (K)">Hex(2) (K)</option>
-        <option value="Hex(2) (R)">Hex(2) (R)</option>
-        <option value="Hex(2) (S)">Hex(2) (S)</option>
-        <option value="Hex(2) (T)">Hex(2) (T)</option>
-        <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)Pent(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)Pent(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(1) (N)">Hex(2)HexNAc(1) (N)</option>
-        <option value="Hex(2)HexNAc(1) (S)">Hex(2)HexNAc(1) (S)</option>
-        <option value="Hex(2)HexNAc(1) (T)">Hex(2)HexNAc(1) (T)</option>
-        <option value="Hex(2)HexNAc(1)Me(1) (S)">Hex(2)HexNAc(1)Me(1) (S)</option>
-        <option value="Hex(2)HexNAc(1)Me(1) (T)">Hex(2)HexNAc(1)Me(1) (T)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(1) (S)">Hex(2)HexNAc(1)NeuGc(1) (S)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(1) (T)">Hex(2)HexNAc(1)NeuGc(1) (T)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(2) (S)">Hex(2)HexNAc(1)NeuGc(2) (S)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(2) (T)">Hex(2)HexNAc(1)NeuGc(2) (T)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(3) (S)">Hex(2)HexNAc(1)NeuGc(3) (S)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(3) (T)">Hex(2)HexNAc(1)NeuGc(3) (T)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(4) (S)">Hex(2)HexNAc(1)NeuGc(4) (S)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(4) (T)">Hex(2)HexNAc(1)NeuGc(4) (T)</option>
-        <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (S)">Hex(2)HexNAc(1)Pent(1)HexA(1) (S)</option>
-        <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (T)">Hex(2)HexNAc(1)Pent(1)HexA(1) (T)</option>
-        <option value="Hex(2)HexNAc(1)Sulf(1) (S)">Hex(2)HexNAc(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(1)Sulf(1) (T)">Hex(2)HexNAc(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(2) (N)">Hex(2)HexNAc(2) (N)</option>
-        <option value="Hex(2)HexNAc(2) (S)">Hex(2)HexNAc(2) (S)</option>
-        <option value="Hex(2)HexNAc(2) (T)">Hex(2)HexNAc(2) (T)</option>
-        <option value="Hex(2)HexNAc(2)dHex(1) (N)">Hex(2)HexNAc(2)dHex(1) (N)</option>
-        <option value="Hex(2)HexNAc(2)dHex(1) (S)">Hex(2)HexNAc(2)dHex(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)dHex(1) (T)">Hex(2)HexNAc(2)dHex(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1) (N)">Hex(2)HexNAc(2)NeuAc(1) (N)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1) (S)">Hex(2)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1) (T)">Hex(2)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(2) (S)">Hex(2)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(2) (T)">Hex(2)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuGc(1) (S)">Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuGc(1) (T)">Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)Pent(1) (N)">Hex(2)HexNAc(2)Pent(1) (N)</option>
-        <option value="Hex(2)HexNAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(3) (N)">Hex(2)HexNAc(3) (N)</option>
-        <option value="Hex(2)HexNAc(3) (S)">Hex(2)HexNAc(3) (S)</option>
-        <option value="Hex(2)HexNAc(3) (T)">Hex(2)HexNAc(3) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(2) (S)">Hex(2)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(2) (T)">Hex(2)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(3) (S)">Hex(2)HexNAc(3)NeuAc(3) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(3) (T)">Hex(2)HexNAc(3)NeuAc(3) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(1) (T)">Hex(2)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(2) (S)">Hex(2)HexNAc(3)NeuGc(2) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(2) (T)">Hex(2)HexNAc(3)NeuGc(2) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(3) (S)">Hex(2)HexNAc(3)NeuGc(3) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(3) (T)">Hex(2)HexNAc(3)NeuGc(3) (T)</option>
-        <option value="Hex(2)HexNAc(3)Sulf(1) (S)">Hex(2)HexNAc(3)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(3)Sulf(1) (T)">Hex(2)HexNAc(3)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(4) (N)">Hex(2)HexNAc(4) (N)</option>
-        <option value="Hex(2)HexNAc(4) (S)">Hex(2)HexNAc(4) (S)</option>
-        <option value="Hex(2)HexNAc(4) (T)">Hex(2)HexNAc(4) (T)</option>
-        <option value="Hex(2)HexNAc(4)NeuAc(1) (S)">Hex(2)HexNAc(4)NeuAc(1) (S)</option>
-        <option value="Hex(2)HexNAc(4)NeuAc(1) (T)">Hex(2)HexNAc(4)NeuAc(1) (T)</option>
-        <option value="Hex(2)HexNAc(5) (S)">Hex(2)HexNAc(5) (S)</option>
-        <option value="Hex(2)HexNAc(5) (T)">Hex(2)HexNAc(5) (T)</option>
-        <option value="Hex(2)NeuAc(1) (S)">Hex(2)NeuAc(1) (S)</option>
-        <option value="Hex(2)NeuAc(1) (T)">Hex(2)NeuAc(1) (T)</option>
-        <option value="Hex(2)Pent(2) (S)">Hex(2)Pent(2) (S)</option>
-        <option value="Hex(2)Pent(2) (T)">Hex(2)Pent(2) (T)</option>
-        <option value="Hex(2)Pent(2)Me(1) (S)">Hex(2)Pent(2)Me(1) (S)</option>
-        <option value="Hex(2)Pent(2)Me(1) (T)">Hex(2)Pent(2)Me(1) (T)</option>
-        <option value="Hex(2)Sulf(1) (S)">Hex(2)Sulf(1) (S)</option>
-        <option value="Hex(2)Sulf(1) (T)">Hex(2)Sulf(1) (T)</option>
-        <option value="Hex(3) (N)">Hex(3) (N)</option>
-        <option value="Hex(3) (S)">Hex(3) (S)</option>
-        <option value="Hex(3) (T)">Hex(3) (T)</option>
-        <option value="Hex(3)HexNAc(1) (N)">Hex(3)HexNAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(1) (S)">Hex(3)HexNAc(1) (S)</option>
-        <option value="Hex(3)HexNAc(1) (T)">Hex(3)HexNAc(1) (T)</option>
-        <option value="Hex(3)HexNAc(1)HexA(1) (S)">Hex(3)HexNAc(1)HexA(1) (S)</option>
-        <option value="Hex(3)HexNAc(1)HexA(1) (T)">Hex(3)HexNAc(1)HexA(1) (T)</option>
-        <option value="Hex(3)HexNAc(1)Me(1) (S)">Hex(3)HexNAc(1)Me(1) (S)</option>
-        <option value="Hex(3)HexNAc(1)Me(1) (T)">Hex(3)HexNAc(1)Me(1) (T)</option>
-        <option value="Hex(3)HexNAc(1)Pent(1) (N)">Hex(3)HexNAc(1)Pent(1) (N)</option>
-        <option value="Hex(3)HexNAc(2) (N)">Hex(3)HexNAc(2) (N)</option>
-        <option value="Hex(3)HexNAc(2) (S)">Hex(3)HexNAc(2) (S)</option>
-        <option value="Hex(3)HexNAc(2) (T)">Hex(3)HexNAc(2) (T)</option>
-        <option value="Hex(3)HexNAc(2)NeuAc(1) (N)">Hex(3)HexNAc(2)NeuAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(2)NeuAc(2) (S)">Hex(3)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="Hex(3)HexNAc(2)NeuAc(2) (T)">Hex(3)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="Hex(3)HexNAc(2)Pent(1) (N)">Hex(3)HexNAc(2)Pent(1) (N)</option>
-        <option value="Hex(3)HexNAc(2)Phos(1) (N)">Hex(3)HexNAc(2)Phos(1) (N)</option>
-        <option value="Hex(3)HexNAc(3) (N)">Hex(3)HexNAc(3) (N)</option>
-        <option value="Hex(3)HexNAc(3) (S)">Hex(3)HexNAc(3) (S)</option>
-        <option value="Hex(3)HexNAc(3) (T)">Hex(3)HexNAc(3) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(1) (S)">Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(1) (T)">Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(2) (S)">Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(2) (T)">Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(3) (S)">Hex(3)HexNAc(3)NeuAc(3) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(3) (T)">Hex(3)HexNAc(3)NeuAc(3) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuGc(1) (S)">Hex(3)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuGc(1) (T)">Hex(3)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)Pent(1) (N)">Hex(3)HexNAc(3)Pent(1) (N)</option>
-        <option value="Hex(3)HexNAc(3)Sulf(1) (N)">Hex(3)HexNAc(3)Sulf(1) (N)</option>
-        <option value="Hex(3)HexNAc(3)Sulf(1) (S)">Hex(3)HexNAc(3)Sulf(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)Sulf(1) (T)">Hex(3)HexNAc(3)Sulf(1) (T)</option>
-        <option value="Hex(3)HexNAc(4) (N)">Hex(3)HexNAc(4) (N)</option>
-        <option value="Hex(3)HexNAc(4) (S)">Hex(3)HexNAc(4) (S)</option>
-        <option value="Hex(3)HexNAc(4) (T)">Hex(3)HexNAc(4) (T)</option>
-        <option value="Hex(3)HexNAc(4)NeuAc(1) (N)">Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(4)NeuAc(2) (N)">Hex(3)HexNAc(4)NeuAc(2) (N)</option>
-        <option value="Hex(3)HexNAc(4)Pent(1) (N)">Hex(3)HexNAc(4)Pent(1) (N)</option>
-        <option value="Hex(3)HexNAc(4)Sulf(1) (N)">Hex(3)HexNAc(4)Sulf(1) (N)</option>
-        <option value="Hex(3)HexNAc(5) (N)">Hex(3)HexNAc(5) (N)</option>
-        <option value="Hex(3)HexNAc(5) (S)">Hex(3)HexNAc(5) (S)</option>
-        <option value="Hex(3)HexNAc(5) (T)">Hex(3)HexNAc(5) (T)</option>
-        <option value="Hex(3)HexNAc(5)NeuAc(1) (N)">Hex(3)HexNAc(5)NeuAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(5)Sulf(1) (N)">Hex(3)HexNAc(5)Sulf(1) (N)</option>
-        <option value="Hex(3)HexNAc(6) (N)">Hex(3)HexNAc(6) (N)</option>
-        <option value="Hex(3)HexNAc(6) (S)">Hex(3)HexNAc(6) (S)</option>
-        <option value="Hex(3)HexNAc(6) (T)">Hex(3)HexNAc(6) (T)</option>
-        <option value="Hex(3)HexNAc(6)NeuAc(1) (N)">Hex(3)HexNAc(6)NeuAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(6)Sulf(1) (N)">Hex(3)HexNAc(6)Sulf(1) (N)</option>
-        <option value="Hex(3)HexNAc(6)Sulf(2) (N)">Hex(3)HexNAc(6)Sulf(2) (N)</option>
-        <option value="Hex(3)HexNAc(7) (N)">Hex(3)HexNAc(7) (N)</option>
-        <option value="Hex(3)HexNAc(7)Sulf(1) (N)">Hex(3)HexNAc(7)Sulf(1) (N)</option>
-        <option value="Hex(4) (S)">Hex(4) (S)</option>
-        <option value="Hex(4) (T)">Hex(4) (T)</option>
-        <option value="Hex(4)HexA(1) (S)">Hex(4)HexA(1) (S)</option>
-        <option value="Hex(4)HexA(1) (T)">Hex(4)HexA(1) (T)</option>
-        <option value="Hex(4)HexA(1)HexNAc(1) (S)">Hex(4)HexA(1)HexNAc(1) (S)</option>
-        <option value="Hex(4)HexA(1)HexNAc(1) (T)">Hex(4)HexA(1)HexNAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(1) (N)">Hex(4)HexNAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(1) (S)">Hex(4)HexNAc(1) (S)</option>
-        <option value="Hex(4)HexNAc(1) (T)">Hex(4)HexNAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(2) (N)">Hex(4)HexNAc(2) (N)</option>
-        <option value="Hex(4)HexNAc(2)NeuAc(1) (N)">Hex(4)HexNAc(2)NeuAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(2)NeuAc(1) (S)">Hex(4)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="Hex(4)HexNAc(2)NeuAc(1) (T)">Hex(4)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(2)Pent(1) (N)">Hex(4)HexNAc(2)Pent(1) (N)</option>
-        <option value="Hex(4)HexNAc(3) (N)">Hex(4)HexNAc(3) (N)</option>
-        <option value="Hex(4)HexNAc(3) (S)">Hex(4)HexNAc(3) (S)</option>
-        <option value="Hex(4)HexNAc(3) (T)">Hex(4)HexNAc(3) (T)</option>
-        <option value="Hex(4)HexNAc(3)NeuAc(1) (N)">Hex(4)HexNAc(3)NeuAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(3)NeuAc(1) (S)">Hex(4)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="Hex(4)HexNAc(3)NeuAc(1) (T)">Hex(4)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(3)NeuAc(2) (N)">Hex(4)HexNAc(3)NeuAc(2) (N)</option>
-        <option value="Hex(4)HexNAc(3)NeuGc(1) (N)">Hex(4)HexNAc(3)NeuGc(1) (N)</option>
-        <option value="Hex(4)HexNAc(3)Pent(1) (N)">Hex(4)HexNAc(3)Pent(1) (N)</option>
-        <option value="Hex(4)HexNAc(4) (N)">Hex(4)HexNAc(4) (N)</option>
-        <option value="Hex(4)HexNAc(4) (S)">Hex(4)HexNAc(4) (S)</option>
-        <option value="Hex(4)HexNAc(4) (T)">Hex(4)HexNAc(4) (T)</option>
-        <option value="Hex(4)HexNAc(4)Me(2)Pent(1) (N)">Hex(4)HexNAc(4)Me(2)Pent(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1) (N)">Hex(4)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1) (S)">Hex(4)HexNAc(4)NeuAc(1) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1) (T)">Hex(4)HexNAc(4)NeuAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1) (N)">Hex(4)HexNAc(4)NeuGc(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1) (S)">Hex(4)HexNAc(4)NeuGc(1) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1) (T)">Hex(4)HexNAc(4)NeuGc(1) (T)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)</option>
-        <option value="Hex(4)HexNAc(4)Pent(1) (N)">Hex(4)HexNAc(4)Pent(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)Sulf(1) (N)">Hex(4)HexNAc(4)Sulf(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)Sulf(2) (S)">Hex(4)HexNAc(4)Sulf(2) (S)</option>
-        <option value="Hex(4)HexNAc(4)Sulf(2) (T)">Hex(4)HexNAc(4)Sulf(2) (T)</option>
-        <option value="Hex(4)HexNAc(5) (N)">Hex(4)HexNAc(5) (N)</option>
-        <option value="Hex(4)HexNAc(5)NeuAc(1) (N)">Hex(4)HexNAc(5)NeuAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(5)Sulf(1) (N)">Hex(4)HexNAc(5)Sulf(1) (N)</option>
-        <option value="Hex(4)HexNAc(6) (N)">Hex(4)HexNAc(6) (N)</option>
-        <option value="Hex(4)Phos(1) (S)">Hex(4)Phos(1) (S)</option>
-        <option value="Hex(4)Phos(1) (T)">Hex(4)Phos(1) (T)</option>
-        <option value="Hex(5) (S)">Hex(5) (S)</option>
-        <option value="Hex(5) (T)">Hex(5) (T)</option>
-        <option value="Hex(5)HexA(1) (S)">Hex(5)HexA(1) (S)</option>
-        <option value="Hex(5)HexA(1) (T)">Hex(5)HexA(1) (T)</option>
-        <option value="Hex(5)HexNAc(1) (N)">Hex(5)HexNAc(1) (N)</option>
-        <option value="Hex(5)HexNAc(1) (S)">Hex(5)HexNAc(1) (S)</option>
-        <option value="Hex(5)HexNAc(1) (T)">Hex(5)HexNAc(1) (T)</option>
-        <option value="Hex(5)HexNAc(2) (N)">Hex(5)HexNAc(2) (N)</option>
-        <option value="Hex(5)HexNAc(2)Phos(1) (N)">Hex(5)HexNAc(2)Phos(1) (N)</option>
-        <option value="Hex(5)HexNAc(3) (N)">Hex(5)HexNAc(3) (N)</option>
-        <option value="Hex(5)HexNAc(3)Pent(1) (N)">Hex(5)HexNAc(3)Pent(1) (N)</option>
-        <option value="Hex(5)HexNAc(4) (N)">Hex(5)HexNAc(4) (N)</option>
-        <option value="Hex(5)HexNAc(4) (S)">Hex(5)HexNAc(4) (S)</option>
-        <option value="Hex(5)HexNAc(4) (T)">Hex(5)HexNAc(4) (T)</option>
-        <option value="Hex(5)HexNAc(4)Me(2)Pent(1) (N)">Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(1) (N)">Hex(5)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(2) (N)">Hex(5)HexNAc(4)NeuAc(2) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuGc(1) (N)">Hex(5)HexNAc(4)NeuGc(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)Sulf(1) (N)">Hex(5)HexNAc(4)Sulf(1) (N)</option>
-        <option value="Hex(5)HexNAc(5) (N)">Hex(5)HexNAc(5) (N)</option>
-        <option value="Hex(5)HexNAc(5) (S)">Hex(5)HexNAc(5) (S)</option>
-        <option value="Hex(5)HexNAc(5) (T)">Hex(5)HexNAc(5) (T)</option>
-        <option value="Hex(5)Phos(1) (S)">Hex(5)Phos(1) (S)</option>
-        <option value="Hex(5)Phos(1) (T)">Hex(5)Phos(1) (T)</option>
-        <option value="Hex(5)Phos(3) (S)">Hex(5)Phos(3) (S)</option>
-        <option value="Hex(5)Phos(3) (T)">Hex(5)Phos(3) (T)</option>
-        <option value="Hex(6)HexNAc(1) (N)">Hex(6)HexNAc(1) (N)</option>
-        <option value="Hex(6)HexNAc(2) (N)">Hex(6)HexNAc(2) (N)</option>
-        <option value="Hex(6)HexNAc(2)Phos(1) (N)">Hex(6)HexNAc(2)Phos(1) (N)</option>
-        <option value="Hex(6)HexNAc(3) (N)">Hex(6)HexNAc(3) (N)</option>
-        <option value="Hex(6)HexNAc(3)Phos(1) (N)">Hex(6)HexNAc(3)Phos(1) (N)</option>
-        <option value="Hex(6)HexNAc(4) (N)">Hex(6)HexNAc(4) (N)</option>
-        <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
-        <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
-        <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
-        <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
-        <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
-        <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
-        <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
-        <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
-        <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
-        <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
-        <option value="Hex(7)HexNAc(2) (N)">Hex(7)HexNAc(2) (N)</option>
-        <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
-        <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
-        <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
-        <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
-        <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
-        <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
-        <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
-        <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
-        <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
-        <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
-        <option value="Hex(8)Phos(3) (T)">Hex(8)Phos(3) (T)</option>
-        <option value="Hex(9) (N)">Hex(9) (N)</option>
-        <option value="Hex(9)HexNAc(1) (N)">Hex(9)HexNAc(1) (N)</option>
-        <option value="Hex(9)HexNAc(2) (N)">Hex(9)HexNAc(2) (N)</option>
-        <option value="Hex(9)Phos(3) (S)">Hex(9)Phos(3) (S)</option>
-        <option value="Hex(9)Phos(3) (T)">Hex(9)Phos(3) (T)</option>
-        <option value="HexA(2)HexNAc(3) (S)">HexA(2)HexNAc(3) (S)</option>
-        <option value="HexA(2)HexNAc(3) (T)">HexA(2)HexNAc(3) (T)</option>
-        <option value="HexN (K)">HexN (K)</option>
-        <option value="HexN (N)">HexN (N)</option>
-        <option value="HexN (S)">HexN (S)</option>
-        <option value="HexN (T)">HexN (T)</option>
-        <option value="HexN (W)">HexN (W)</option>
-        <option value="HexNAc (C)">HexNAc (C)</option>
-        <option value="HexNAc (N)">HexNAc (N)</option>
-        <option value="HexNAc (S)">HexNAc (S)</option>
-        <option value="HexNAc (T)">HexNAc (T)</option>
-        <option value="HexNAc(1)dHex(1) (N)">HexNAc(1)dHex(1) (N)</option>
-        <option value="HexNAc(1)dHex(1) (S)">HexNAc(1)dHex(1) (S)</option>
-        <option value="HexNAc(1)dHex(1) (T)">HexNAc(1)dHex(1) (T)</option>
-        <option value="HexNAc(1)dHex(2) (N)">HexNAc(1)dHex(2) (N)</option>
-        <option value="HexNAc(1)Kdn(2) (S)">HexNAc(1)Kdn(2) (S)</option>
-        <option value="HexNAc(1)Kdn(2) (T)">HexNAc(1)Kdn(2) (T)</option>
-        <option value="HexNAc(1)NeuAc(1) (S)">HexNAc(1)NeuAc(1) (S)</option>
-        <option value="HexNAc(1)NeuAc(1) (T)">HexNAc(1)NeuAc(1) (T)</option>
-        <option value="HexNAc(1)NeuGc(1) (S)">HexNAc(1)NeuGc(1) (S)</option>
-        <option value="HexNAc(1)NeuGc(1) (T)">HexNAc(1)NeuGc(1) (T)</option>
-        <option value="HexNAc(1)NeuGc(2) (S)">HexNAc(1)NeuGc(2) (S)</option>
-        <option value="HexNAc(1)NeuGc(2) (T)">HexNAc(1)NeuGc(2) (T)</option>
-        <option value="HexNAc(2) (N)">HexNAc(2) (N)</option>
-        <option value="HexNAc(2) (S)">HexNAc(2) (S)</option>
-        <option value="HexNAc(2) (T)">HexNAc(2) (T)</option>
-        <option value="HexNAc(2)dHex(1) (N)">HexNAc(2)dHex(1) (N)</option>
-        <option value="HexNAc(2)dHex(2) (N)">HexNAc(2)dHex(2) (N)</option>
-        <option value="HexNAc(2)NeuAc(1) (S)">HexNAc(2)NeuAc(1) (S)</option>
-        <option value="HexNAc(2)NeuAc(1) (T)">HexNAc(2)NeuAc(1) (T)</option>
-        <option value="HexNAc(2)NeuAc(1)Sulf(1) (S)">HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="HexNAc(2)NeuAc(1)Sulf(1) (T)">HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="HexNAc(2)NeuGc(1) (S)">HexNAc(2)NeuGc(1) (S)</option>
-        <option value="HexNAc(2)NeuGc(1) (T)">HexNAc(2)NeuGc(1) (T)</option>
-        <option value="HexNAc(2)Sulf(1) (S)">HexNAc(2)Sulf(1) (S)</option>
-        <option value="HexNAc(2)Sulf(1) (T)">HexNAc(2)Sulf(1) (T)</option>
-        <option value="HexNAc(3) (S)">HexNAc(3) (S)</option>
-        <option value="HexNAc(3) (T)">HexNAc(3) (T)</option>
-        <option value="HexNAc(3)Sulf(1) (S)">HexNAc(3)Sulf(1) (S)</option>
-        <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
-        <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
-        <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
-        <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
-        <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
-        <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
-        <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
-        <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
-        <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
-        <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
-        <option value="His-&gt;Gln (H)">His-&gt;Gln (H)</option>
-        <option value="His-&gt;Glu (H)">His-&gt;Glu (H)</option>
-        <option value="His-&gt;Gly (H)">His-&gt;Gly (H)</option>
-        <option value="His-&gt;Lys (H)">His-&gt;Lys (H)</option>
-        <option value="His-&gt;Met (H)">His-&gt;Met (H)</option>
-        <option value="His-&gt;Phe (H)">His-&gt;Phe (H)</option>
-        <option value="His-&gt;Pro (H)">His-&gt;Pro (H)</option>
-        <option value="His-&gt;Ser (H)">His-&gt;Ser (H)</option>
-        <option value="His-&gt;Thr (H)">His-&gt;Thr (H)</option>
-        <option value="His-&gt;Trp (H)">His-&gt;Trp (H)</option>
-        <option value="His-&gt;Tyr (H)">His-&gt;Tyr (H)</option>
-        <option value="His-&gt;Val (H)">His-&gt;Val (H)</option>
-        <option value="His-&gt;Xle (H)">His-&gt;Xle (H)</option>
-        <option value="HMVK (C)">HMVK (C)</option>
-        <option value="HN2_mustard (C)">HN2_mustard (C)</option>
-        <option value="HN2_mustard (H)">HN2_mustard (H)</option>
-        <option value="HN2_mustard (K)">HN2_mustard (K)</option>
-        <option value="HN3_mustard (C)">HN3_mustard (C)</option>
-        <option value="HN3_mustard (H)">HN3_mustard (H)</option>
-        <option value="HN3_mustard (K)">HN3_mustard (K)</option>
-        <option value="HNE (A)">HNE (A)</option>
-        <option value="HNE (C)">HNE (C)</option>
-        <option value="HNE (H)">HNE (H)</option>
-        <option value="HNE (K)">HNE (K)</option>
-        <option value="HNE (L)">HNE (L)</option>
-        <option value="HNE+Delta:H(2) (C)">HNE+Delta:H(2) (C)</option>
-        <option value="HNE+Delta:H(2) (H)">HNE+Delta:H(2) (H)</option>
-        <option value="HNE+Delta:H(2) (K)">HNE+Delta:H(2) (K)</option>
-        <option value="HNE-BAHAH (C)">HNE-BAHAH (C)</option>
-        <option value="HNE-BAHAH (H)">HNE-BAHAH (H)</option>
-        <option value="HNE-BAHAH (K)">HNE-BAHAH (K)</option>
-        <option value="HNE-Delta:H(2)O (C)">HNE-Delta:H(2)O (C)</option>
-        <option value="HNE-Delta:H(2)O (H)">HNE-Delta:H(2)O (H)</option>
-        <option value="HNE-Delta:H(2)O (K)">HNE-Delta:H(2)O (K)</option>
-        <option value="Homocysteic_acid (M)">Homocysteic_acid (M)</option>
-        <option value="HPG (R)">HPG (R)</option>
-        <option value="Hydroxamic_acid (D)">Hydroxamic_acid (D)</option>
-        <option value="Hydroxamic_acid (E)">Hydroxamic_acid (E)</option>
-        <option value="Hydroxycinnamyl (C)">Hydroxycinnamyl (C)</option>
-        <option value="Hydroxyfarnesyl (C)">Hydroxyfarnesyl (C)</option>
-        <option value="Hydroxyheme (E)">Hydroxyheme (E)</option>
-        <option value="hydroxyisobutyryl (K)">hydroxyisobutyryl (K)</option>
-        <option value="Hydroxymethyl (N)">Hydroxymethyl (N)</option>
-        <option value="HydroxymethylOP (K)">HydroxymethylOP (K)</option>
-        <option value="Hydroxytrimethyl (K)">Hydroxytrimethyl (K)</option>
-        <option value="Hypusine (K)">Hypusine (K)</option>
-        <option value="IASD (C)">IASD (C)</option>
-        <option value="IBTP (C)">IBTP (C)</option>
-        <option value="ICAT-C (C)">ICAT-C (C)</option>
-        <option value="ICAT-C:13C(9) (C)">ICAT-C:13C(9) (C)</option>
-        <option value="ICAT-D (C)">ICAT-D (C)</option>
-        <option value="ICAT-D:2H(8) (C)">ICAT-D:2H(8) (C)</option>
-        <option value="ICAT-G (C)">ICAT-G (C)</option>
-        <option value="ICAT-G:2H(8) (C)">ICAT-G:2H(8) (C)</option>
-        <option value="ICAT-H (C)">ICAT-H (C)</option>
-        <option value="ICAT-H:13C(6) (C)">ICAT-H:13C(6) (C)</option>
-        <option value="ICDID (C)">ICDID (C)</option>
-        <option value="ICDID:2H(6) (C)">ICDID:2H(6) (C)</option>
-        <option value="ICPL (K)">ICPL (K)</option>
-        <option value="ICPL (N-term)">ICPL (N-term)</option>
-        <option value="ICPL (Protein N-term)">ICPL (Protein N-term)</option>
-        <option value="ICPL:13C(6) (K)">ICPL:13C(6) (K)</option>
-        <option value="ICPL:13C(6) (N-term)">ICPL:13C(6) (N-term)</option>
-        <option value="ICPL:13C(6) (Protein N-term)">ICPL:13C(6) (Protein N-term)</option>
-        <option value="ICPL:13C(6)2H(4) (K)">ICPL:13C(6)2H(4) (K)</option>
-        <option value="ICPL:13C(6)2H(4) (N-term)">ICPL:13C(6)2H(4) (N-term)</option>
-        <option value="ICPL:13C(6)2H(4) (Protein N-term)">ICPL:13C(6)2H(4) (Protein N-term)</option>
-        <option value="ICPL:2H(4) (K)">ICPL:2H(4) (K)</option>
-        <option value="ICPL:2H(4) (N-term)">ICPL:2H(4) (N-term)</option>
-        <option value="ICPL:2H(4) (Protein N-term)">ICPL:2H(4) (Protein N-term)</option>
-        <option value="IDEnT (C)">IDEnT (C)</option>
-        <option value="IED-Biotin (C)">IED-Biotin (C)</option>
-        <option value="IGBP (C)">IGBP (C)</option>
-        <option value="IGBP:13C(2) (C)">IGBP:13C(2) (C)</option>
-        <option value="IMEHex(2)NeuAc(1) (K)">IMEHex(2)NeuAc(1) (K)</option>
-        <option value="IMID (K)">IMID (K)</option>
-        <option value="IMID:2H(4) (K)">IMID:2H(4) (K)</option>
-        <option value="Iminobiotin (K)">Iminobiotin (K)</option>
-        <option value="Iminobiotin (N-term)">Iminobiotin (N-term)</option>
-        <option value="Iodo (H)">Iodo (H)</option>
-        <option value="Iodo (Y)">Iodo (Y)</option>
-        <option value="Iodoacetanilide (C)">Iodoacetanilide (C)</option>
-        <option value="Iodoacetanilide (K)">Iodoacetanilide (K)</option>
-        <option value="Iodoacetanilide (N-term)">Iodoacetanilide (N-term)</option>
-        <option value="Iodoacetanilide:13C(6) (C)">Iodoacetanilide:13C(6) (C)</option>
-        <option value="Iodoacetanilide:13C(6) (K)">Iodoacetanilide:13C(6) (K)</option>
-        <option value="Iodoacetanilide:13C(6) (N-term)">Iodoacetanilide:13C(6) (N-term)</option>
-        <option value="iodoTMT (C)">iodoTMT (C)</option>
-        <option value="iodoTMT (D)">iodoTMT (D)</option>
-        <option value="iodoTMT (E)">iodoTMT (E)</option>
-        <option value="iodoTMT (H)">iodoTMT (H)</option>
-        <option value="iodoTMT (K)">iodoTMT (K)</option>
-        <option value="iodoTMT6plex (C)">iodoTMT6plex (C)</option>
-        <option value="iodoTMT6plex (D)">iodoTMT6plex (D)</option>
-        <option value="iodoTMT6plex (E)">iodoTMT6plex (E)</option>
-        <option value="iodoTMT6plex (H)">iodoTMT6plex (H)</option>
-        <option value="iodoTMT6plex (K)">iodoTMT6plex (K)</option>
-        <option value="IodoU-AMP (F)">IodoU-AMP (F)</option>
-        <option value="IodoU-AMP (W)">IodoU-AMP (W)</option>
-        <option value="IodoU-AMP (Y)">IodoU-AMP (Y)</option>
-        <option value="ISD_z+2_ion (N-term)">ISD_z+2_ion (N-term)</option>
-        <option value="Isopropylphospho (S)">Isopropylphospho (S)</option>
-        <option value="Isopropylphospho (T)">Isopropylphospho (T)</option>
-        <option value="Isopropylphospho (Y)">Isopropylphospho (Y)</option>
-        <option value="iTRAQ4plex (C)">iTRAQ4plex (C)</option>
-        <option value="iTRAQ4plex (H)">iTRAQ4plex (H)</option>
-        <option value="iTRAQ4plex (K)">iTRAQ4plex (K)</option>
-        <option value="iTRAQ4plex (N-term)">iTRAQ4plex (N-term)</option>
-        <option value="iTRAQ4plex (Protein N-term)">iTRAQ4plex (Protein N-term)</option>
-        <option value="iTRAQ4plex (S)">iTRAQ4plex (S)</option>
-        <option value="iTRAQ4plex (T)">iTRAQ4plex (T)</option>
-        <option value="iTRAQ4plex (Y)">iTRAQ4plex (Y)</option>
-        <option value="iTRAQ4plex114 (C)">iTRAQ4plex114 (C)</option>
-        <option value="iTRAQ4plex114 (K)">iTRAQ4plex114 (K)</option>
-        <option value="iTRAQ4plex114 (N-term)">iTRAQ4plex114 (N-term)</option>
-        <option value="iTRAQ4plex114 (Y)">iTRAQ4plex114 (Y)</option>
-        <option value="iTRAQ4plex115 (C)">iTRAQ4plex115 (C)</option>
-        <option value="iTRAQ4plex115 (K)">iTRAQ4plex115 (K)</option>
-        <option value="iTRAQ4plex115 (N-term)">iTRAQ4plex115 (N-term)</option>
-        <option value="iTRAQ4plex115 (Y)">iTRAQ4plex115 (Y)</option>
-        <option value="iTRAQ8plex (C)">iTRAQ8plex (C)</option>
-        <option value="iTRAQ8plex (H)">iTRAQ8plex (H)</option>
-        <option value="iTRAQ8plex (K)">iTRAQ8plex (K)</option>
-        <option value="iTRAQ8plex (N-term)">iTRAQ8plex (N-term)</option>
-        <option value="iTRAQ8plex (Protein N-term)">iTRAQ8plex (Protein N-term)</option>
-        <option value="iTRAQ8plex (S)">iTRAQ8plex (S)</option>
-        <option value="iTRAQ8plex (T)">iTRAQ8plex (T)</option>
-        <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
-        <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
-        <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
-        <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
-        <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
-        <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
-        <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
-        <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
-        <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
-        <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
-        <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
-        <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
-        <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
-        <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
-        <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
-        <option value="Label:13C(5)15N(1) (E)">Label:13C(5)15N(1) (E)</option>
-        <option value="Label:13C(5)15N(1) (M)">Label:13C(5)15N(1) (M)</option>
-        <option value="Label:13C(5)15N(1) (P)">Label:13C(5)15N(1) (P)</option>
-        <option value="Label:13C(5)15N(1) (V)">Label:13C(5)15N(1) (V)</option>
-        <option value="Label:13C(6) (I)">Label:13C(6) (I)</option>
-        <option value="Label:13C(6) (K)">Label:13C(6) (K)</option>
-        <option value="Label:13C(6) (L)">Label:13C(6) (L)</option>
-        <option value="Label:13C(6) (R)">Label:13C(6) (R)</option>
-        <option value="Label:13C(6)+Acetyl (K)">Label:13C(6)+Acetyl (K)</option>
-        <option value="Label:13C(6)+Dimethyl (K)">Label:13C(6)+Dimethyl (K)</option>
-        <option value="Label:13C(6)+GG (K)">Label:13C(6)+GG (K)</option>
-        <option value="Label:13C(6)15N(1) (I)">Label:13C(6)15N(1) (I)</option>
-        <option value="Label:13C(6)15N(1) (L)">Label:13C(6)15N(1) (L)</option>
-        <option value="Label:13C(6)15N(2) (K)">Label:13C(6)15N(2) (K)</option>
-        <option value="Label:13C(6)15N(2)+Acetyl (K)">Label:13C(6)15N(2)+Acetyl (K)</option>
-        <option value="Label:13C(6)15N(2)+Dimethyl (K)">Label:13C(6)15N(2)+Dimethyl (K)</option>
-        <option value="Label:13C(6)15N(2)+GG (K)">Label:13C(6)15N(2)+GG (K)</option>
-        <option value="Label:13C(6)15N(4) (R)">Label:13C(6)15N(4) (R)</option>
-        <option value="Label:13C(6)15N(4)+Dimethyl (R)">Label:13C(6)15N(4)+Dimethyl (R)</option>
-        <option value="Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R)">Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R)</option>
-        <option value="Label:13C(6)15N(4)+Methyl (R)">Label:13C(6)15N(4)+Methyl (R)</option>
-        <option value="Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R)">Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R)</option>
-        <option value="Label:13C(9) (F)">Label:13C(9) (F)</option>
-        <option value="Label:13C(9) (Y)">Label:13C(9) (Y)</option>
-        <option value="Label:13C(9)+Phospho (Y)">Label:13C(9)+Phospho (Y)</option>
-        <option value="Label:13C(9)15N(1) (F)">Label:13C(9)15N(1) (F)</option>
-        <option value="Label:15N(1) (A)">Label:15N(1) (A)</option>
-        <option value="Label:15N(1) (C)">Label:15N(1) (C)</option>
-        <option value="Label:15N(1) (D)">Label:15N(1) (D)</option>
-        <option value="Label:15N(1) (E)">Label:15N(1) (E)</option>
-        <option value="Label:15N(1) (F)">Label:15N(1) (F)</option>
-        <option value="Label:15N(1) (G)">Label:15N(1) (G)</option>
-        <option value="Label:15N(1) (I)">Label:15N(1) (I)</option>
-        <option value="Label:15N(1) (L)">Label:15N(1) (L)</option>
-        <option value="Label:15N(1) (M)">Label:15N(1) (M)</option>
-        <option value="Label:15N(1) (P)">Label:15N(1) (P)</option>
-        <option value="Label:15N(1) (S)">Label:15N(1) (S)</option>
-        <option value="Label:15N(1) (T)">Label:15N(1) (T)</option>
-        <option value="Label:15N(1) (V)">Label:15N(1) (V)</option>
-        <option value="Label:15N(1) (Y)">Label:15N(1) (Y)</option>
-        <option value="Label:15N(2) (K)">Label:15N(2) (K)</option>
-        <option value="Label:15N(2) (N)">Label:15N(2) (N)</option>
-        <option value="Label:15N(2) (Q)">Label:15N(2) (Q)</option>
-        <option value="Label:15N(2) (W)">Label:15N(2) (W)</option>
-        <option value="Label:15N(2)2H(9) (K)">Label:15N(2)2H(9) (K)</option>
-        <option value="Label:15N(3) (H)">Label:15N(3) (H)</option>
-        <option value="Label:15N(4) (R)">Label:15N(4) (R)</option>
-        <option value="Label:18O(1) (C-term)">Label:18O(1) (C-term)</option>
-        <option value="Label:18O(1) (S)">Label:18O(1) (S)</option>
-        <option value="Label:18O(1) (T)">Label:18O(1) (T)</option>
-        <option value="Label:18O(1) (Y)">Label:18O(1) (Y)</option>
-        <option value="Label:18O(2) (C-term)">Label:18O(2) (C-term)</option>
-        <option value="Label:2H(10) (L)">Label:2H(10) (L)</option>
-        <option value="Label:2H(3) (L)">Label:2H(3) (L)</option>
-        <option value="Label:2H(3) (M)">Label:2H(3) (M)</option>
-        <option value="Label:2H(3)+Oxidation (M)">Label:2H(3)+Oxidation (M)</option>
-        <option value="Label:2H(4) (A)">Label:2H(4) (A)</option>
-        <option value="Label:2H(4) (F)">Label:2H(4) (F)</option>
-        <option value="Label:2H(4) (K)">Label:2H(4) (K)</option>
-        <option value="Label:2H(4) (U)">Label:2H(4) (U)</option>
-        <option value="Label:2H(4) (Y)">Label:2H(4) (Y)</option>
-        <option value="Label:2H(4)+Acetyl (K)">Label:2H(4)+Acetyl (K)</option>
-        <option value="Label:2H(4)+GG (K)">Label:2H(4)+GG (K)</option>
-        <option value="Label:2H(4)13C(1) (R)">Label:2H(4)13C(1) (R)</option>
-        <option value="Label:2H(6)15N(1) (P)">Label:2H(6)15N(1) (P)</option>
-        <option value="Label:2H(7)15N(4) (R)">Label:2H(7)15N(4) (R)</option>
-        <option value="Label:2H(9)13C(6)15N(2) (K)">Label:2H(9)13C(6)15N(2) (K)</option>
-        <option value="lapachenole (C)">lapachenole (C)</option>
-        <option value="Leu-&gt;MetOx (L)">Leu-&gt;MetOx (L)</option>
-        <option value="LG-anhydrolactam (K)">LG-anhydrolactam (K)</option>
-        <option value="LG-anhydrolactam (N-term)">LG-anhydrolactam (N-term)</option>
-        <option value="LG-anhyropyrrole (K)">LG-anhyropyrrole (K)</option>
-        <option value="LG-anhyropyrrole (N-term)">LG-anhyropyrrole (N-term)</option>
-        <option value="LG-Hlactam-K (K)">LG-Hlactam-K (K)</option>
-        <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
-        <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
-        <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
-        <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
-        <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
-        <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
-        <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
-        <option value="Lipoyl (K)">Lipoyl (K)</option>
-        <option value="LRGG (K)">LRGG (K)</option>
-        <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
-        <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
-        <option value="Lys (N-term)">Lys (N-term)</option>
-        <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
-        <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
-        <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
-        <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
-        <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
-        <option value="Lys-&gt;Asp (K)">Lys-&gt;Asp (K)</option>
-        <option value="Lys-&gt;CamCys (K)">Lys-&gt;CamCys (K)</option>
-        <option value="Lys-&gt;Cys (K)">Lys-&gt;Cys (K)</option>
-        <option value="Lys-&gt;Gln (K)">Lys-&gt;Gln (K)</option>
-        <option value="Lys-&gt;Glu (K)">Lys-&gt;Glu (K)</option>
-        <option value="Lys-&gt;Gly (K)">Lys-&gt;Gly (K)</option>
-        <option value="Lys-&gt;His (K)">Lys-&gt;His (K)</option>
-        <option value="Lys-&gt;Met (K)">Lys-&gt;Met (K)</option>
-        <option value="Lys-&gt;MetOx (K)">Lys-&gt;MetOx (K)</option>
-        <option value="Lys-&gt;Phe (K)">Lys-&gt;Phe (K)</option>
-        <option value="Lys-&gt;Pro (K)">Lys-&gt;Pro (K)</option>
-        <option value="Lys-&gt;Ser (K)">Lys-&gt;Ser (K)</option>
-        <option value="Lys-&gt;Thr (K)">Lys-&gt;Thr (K)</option>
-        <option value="Lys-&gt;Trp (K)">Lys-&gt;Trp (K)</option>
-        <option value="Lys-&gt;Tyr (K)">Lys-&gt;Tyr (K)</option>
-        <option value="Lys-&gt;Val (K)">Lys-&gt;Val (K)</option>
-        <option value="Lys-&gt;Xle (K)">Lys-&gt;Xle (K)</option>
-        <option value="Lys-loss (Protein C-term K)">Lys-loss (Protein C-term K)</option>
-        <option value="Lysbiotinhydrazide (K)">Lysbiotinhydrazide (K)</option>
-        <option value="maleimide (C)">maleimide (C)</option>
-        <option value="maleimide (K)">maleimide (K)</option>
-        <option value="Maleimide-PEO2-Biotin (C)">Maleimide-PEO2-Biotin (C)</option>
-        <option value="maleimide3 (C)">maleimide3 (C)</option>
-        <option value="maleimide3 (K)">maleimide3 (K)</option>
-        <option value="maleimide5 (C)">maleimide5 (C)</option>
-        <option value="maleimide5 (K)">maleimide5 (K)</option>
-        <option value="Malonyl (C)">Malonyl (C)</option>
-        <option value="Malonyl (K)">Malonyl (K)</option>
-        <option value="Malonyl (S)">Malonyl (S)</option>
-        <option value="MDCC (C)">MDCC (C)</option>
-        <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
-        <option value="Menadione (C)">Menadione (C)</option>
-        <option value="Menadione (K)">Menadione (K)</option>
-        <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
-        <option value="Menadione-HQ (K)">Menadione-HQ (K)</option>
-        <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
-        <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
-        <option value="MesitylOxide (H)">MesitylOxide (H)</option>
-        <option value="MesitylOxide (K)">MesitylOxide (K)</option>
-        <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
-        <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
-        <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
-        <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
-        <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
-        <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
-        <option value="Met-&gt;AspSA (M)">Met-&gt;AspSA (M)</option>
-        <option value="Met-&gt;Cys (M)">Met-&gt;Cys (M)</option>
-        <option value="Met-&gt;Gln (M)">Met-&gt;Gln (M)</option>
-        <option value="Met-&gt;Glu (M)">Met-&gt;Glu (M)</option>
-        <option value="Met-&gt;Gly (M)">Met-&gt;Gly (M)</option>
-        <option value="Met-&gt;His (M)">Met-&gt;His (M)</option>
-        <option value="Met-&gt;Hpg (M)">Met-&gt;Hpg (M)</option>
-        <option value="Met-&gt;Hse (C-term M)">Met-&gt;Hse (C-term M)</option>
-        <option value="Met-&gt;Hsl (C-term M)">Met-&gt;Hsl (C-term M)</option>
-        <option value="Met-&gt;Lys (M)">Met-&gt;Lys (M)</option>
-        <option value="Met-&gt;Phe (M)">Met-&gt;Phe (M)</option>
-        <option value="Met-&gt;Pro (M)">Met-&gt;Pro (M)</option>
-        <option value="Met-&gt;Ser (M)">Met-&gt;Ser (M)</option>
-        <option value="Met-&gt;Thr (M)">Met-&gt;Thr (M)</option>
-        <option value="Met-&gt;Trp (M)">Met-&gt;Trp (M)</option>
-        <option value="Met-&gt;Tyr (M)">Met-&gt;Tyr (M)</option>
-        <option value="Met-&gt;Val (M)">Met-&gt;Val (M)</option>
-        <option value="Met-&gt;Xle (M)">Met-&gt;Xle (M)</option>
-        <option value="Met-loss (Protein N-term M)">Met-loss (Protein N-term M)</option>
-        <option value="Met-loss+Acetyl (Protein N-term M)">Met-loss+Acetyl (Protein N-term M)</option>
-        <option value="Methamidophos-O (C)">Methamidophos-O (C)</option>
-        <option value="Methamidophos-O (H)">Methamidophos-O (H)</option>
-        <option value="Methamidophos-O (K)">Methamidophos-O (K)</option>
-        <option value="Methamidophos-O (S)">Methamidophos-O (S)</option>
-        <option value="Methamidophos-O (T)">Methamidophos-O (T)</option>
-        <option value="Methamidophos-O (Y)">Methamidophos-O (Y)</option>
-        <option value="Methamidophos-S (C)">Methamidophos-S (C)</option>
-        <option value="Methamidophos-S (H)">Methamidophos-S (H)</option>
-        <option value="Methamidophos-S (K)">Methamidophos-S (K)</option>
-        <option value="Methamidophos-S (S)">Methamidophos-S (S)</option>
-        <option value="Methamidophos-S (T)">Methamidophos-S (T)</option>
-        <option value="Methamidophos-S (Y)">Methamidophos-S (Y)</option>
-        <option value="Methyl (C)">Methyl (C)</option>
-        <option value="Methyl (C-term)">Methyl (C-term)</option>
-        <option value="Methyl (D)">Methyl (D)</option>
-        <option value="Methyl (E)">Methyl (E)</option>
-        <option value="Methyl (H)">Methyl (H)</option>
-        <option value="Methyl (I)">Methyl (I)</option>
-        <option value="Methyl (K)">Methyl (K)</option>
-        <option value="Methyl (L)">Methyl (L)</option>
-        <option value="Methyl (N)">Methyl (N)</option>
-        <option value="Methyl (N-term)">Methyl (N-term)</option>
-        <option value="Methyl (Protein N-term)">Methyl (Protein N-term)</option>
-        <option value="Methyl (Q)">Methyl (Q)</option>
-        <option value="Methyl (R)">Methyl (R)</option>
-        <option value="Methyl (S)">Methyl (S)</option>
-        <option value="Methyl (T)">Methyl (T)</option>
-        <option value="Methyl+Acetyl:2H(3) (K)">Methyl+Acetyl:2H(3) (K)</option>
-        <option value="Methyl+Deamidated (N)">Methyl+Deamidated (N)</option>
-        <option value="Methyl+Deamidated (Q)">Methyl+Deamidated (Q)</option>
-        <option value="Methyl-PEO12-Maleimide (C)">Methyl-PEO12-Maleimide (C)</option>
-        <option value="Methyl:2H(2) (K)">Methyl:2H(2) (K)</option>
-        <option value="Methyl:2H(2) (N-term)">Methyl:2H(2) (N-term)</option>
-        <option value="Methyl:2H(2)13C (C)">Methyl:2H(2)13C (C)</option>
-        <option value="Methyl:2H(2)13C (C-term)">Methyl:2H(2)13C (C-term)</option>
-        <option value="Methyl:2H(2)13C (D)">Methyl:2H(2)13C (D)</option>
-        <option value="Methyl:2H(2)13C (E)">Methyl:2H(2)13C (E)</option>
-        <option value="Methyl:2H(2)13C (H)">Methyl:2H(2)13C (H)</option>
-        <option value="Methyl:2H(2)13C (I)">Methyl:2H(2)13C (I)</option>
-        <option value="Methyl:2H(2)13C (K)">Methyl:2H(2)13C (K)</option>
-        <option value="Methyl:2H(2)13C (L)">Methyl:2H(2)13C (L)</option>
-        <option value="Methyl:2H(2)13C (N)">Methyl:2H(2)13C (N)</option>
-        <option value="Methyl:2H(2)13C (N-term)">Methyl:2H(2)13C (N-term)</option>
-        <option value="Methyl:2H(2)13C (Protein N-term)">Methyl:2H(2)13C (Protein N-term)</option>
-        <option value="Methyl:2H(2)13C (Q)">Methyl:2H(2)13C (Q)</option>
-        <option value="Methyl:2H(2)13C (R)">Methyl:2H(2)13C (R)</option>
-        <option value="Methyl:2H(2)13C (S)">Methyl:2H(2)13C (S)</option>
-        <option value="Methyl:2H(2)13C (T)">Methyl:2H(2)13C (T)</option>
-        <option value="Methyl:2H(3) (D)">Methyl:2H(3) (D)</option>
-        <option value="Methyl:2H(3) (E)">Methyl:2H(3) (E)</option>
-        <option value="Methyl:2H(3) (K)">Methyl:2H(3) (K)</option>
-        <option value="Methyl:2H(3) (R)">Methyl:2H(3) (R)</option>
-        <option value="Methyl:2H(3) (X)">Methyl:2H(3) (X)</option>
-        <option value="Methyl:2H(3)+Acetyl:2H(3) (K)">Methyl:2H(3)+Acetyl:2H(3) (K)</option>
-        <option value="Methyl:2H(3)13C(1) (K)">Methyl:2H(3)13C(1) (K)</option>
-        <option value="Methyl:2H(3)13C(1) (N-term)">Methyl:2H(3)13C(1) (N-term)</option>
-        <option value="Methyl:2H(3)13C(1) (R)">Methyl:2H(3)13C(1) (R)</option>
-        <option value="Methylamine (S)">Methylamine (S)</option>
-        <option value="Methylamine (T)">Methylamine (T)</option>
-        <option value="Methylmalonylation (S)">Methylmalonylation (S)</option>
-        <option value="methylol (K)">methylol (K)</option>
-        <option value="methylol (W)">methylol (W)</option>
-        <option value="methylol (Y)">methylol (Y)</option>
-        <option value="Methylphosphonate (S)">Methylphosphonate (S)</option>
-        <option value="Methylphosphonate (T)">Methylphosphonate (T)</option>
-        <option value="Methylphosphonate (Y)">Methylphosphonate (Y)</option>
-        <option value="Methylpyrroline (K)">Methylpyrroline (K)</option>
-        <option value="methylsulfonylethyl (C)">methylsulfonylethyl (C)</option>
-        <option value="methylsulfonylethyl (H)">methylsulfonylethyl (H)</option>
-        <option value="methylsulfonylethyl (K)">methylsulfonylethyl (K)</option>
-        <option value="Methylthio (C)">Methylthio (C)</option>
-        <option value="Methylthio (D)">Methylthio (D)</option>
-        <option value="Methylthio (K)">Methylthio (K)</option>
-        <option value="Methylthio (N)">Methylthio (N)</option>
-        <option value="Methylthio (N-term)">Methylthio (N-term)</option>
-        <option value="MG-H1 (R)">MG-H1 (R)</option>
-        <option value="Microcin (Protein C-term)">Microcin (Protein C-term)</option>
-        <option value="MicrocinC7 (Protein C-term)">MicrocinC7 (Protein C-term)</option>
-        <option value="MM-diphenylpentanone (C)">MM-diphenylpentanone (C)</option>
-        <option value="Molybdopterin (C)">Molybdopterin (C)</option>
-        <option value="MolybdopterinGD (C)">MolybdopterinGD (C)</option>
-        <option value="MolybdopterinGD (D)">MolybdopterinGD (D)</option>
-        <option value="MolybdopterinGD (U)">MolybdopterinGD (U)</option>
-        <option value="MolybdopterinGD+Delta:S(-1)Se(1) (C)">MolybdopterinGD+Delta:S(-1)Se(1) (C)</option>
-        <option value="monomethylphosphothione (C)">monomethylphosphothione (C)</option>
-        <option value="monomethylphosphothione (H)">monomethylphosphothione (H)</option>
-        <option value="monomethylphosphothione (K)">monomethylphosphothione (K)</option>
-        <option value="monomethylphosphothione (S)">monomethylphosphothione (S)</option>
-        <option value="monomethylphosphothione (T)">monomethylphosphothione (T)</option>
-        <option value="monomethylphosphothione (Y)">monomethylphosphothione (Y)</option>
-        <option value="mTRAQ (H)">mTRAQ (H)</option>
-        <option value="mTRAQ (K)">mTRAQ (K)</option>
-        <option value="mTRAQ (N-term)">mTRAQ (N-term)</option>
-        <option value="mTRAQ (S)">mTRAQ (S)</option>
-        <option value="mTRAQ (T)">mTRAQ (T)</option>
-        <option value="mTRAQ (Y)">mTRAQ (Y)</option>
-        <option value="mTRAQ:13C(3)15N(1) (H)">mTRAQ:13C(3)15N(1) (H)</option>
-        <option value="mTRAQ:13C(3)15N(1) (K)">mTRAQ:13C(3)15N(1) (K)</option>
-        <option value="mTRAQ:13C(3)15N(1) (N-term)">mTRAQ:13C(3)15N(1) (N-term)</option>
-        <option value="mTRAQ:13C(3)15N(1) (S)">mTRAQ:13C(3)15N(1) (S)</option>
-        <option value="mTRAQ:13C(3)15N(1) (T)">mTRAQ:13C(3)15N(1) (T)</option>
-        <option value="mTRAQ:13C(3)15N(1) (Y)">mTRAQ:13C(3)15N(1) (Y)</option>
-        <option value="mTRAQ:13C(6)15N(2) (H)">mTRAQ:13C(6)15N(2) (H)</option>
-        <option value="mTRAQ:13C(6)15N(2) (K)">mTRAQ:13C(6)15N(2) (K)</option>
-        <option value="mTRAQ:13C(6)15N(2) (N-term)">mTRAQ:13C(6)15N(2) (N-term)</option>
-        <option value="mTRAQ:13C(6)15N(2) (S)">mTRAQ:13C(6)15N(2) (S)</option>
-        <option value="mTRAQ:13C(6)15N(2) (T)">mTRAQ:13C(6)15N(2) (T)</option>
-        <option value="mTRAQ:13C(6)15N(2) (Y)">mTRAQ:13C(6)15N(2) (Y)</option>
-        <option value="MTSL (C)">MTSL (C)</option>
-        <option value="MurNAc (A)">MurNAc (A)</option>
-        <option value="Myristoleyl (Protein N-term G)">Myristoleyl (Protein N-term G)</option>
-        <option value="Myristoyl (C)">Myristoyl (C)</option>
-        <option value="Myristoyl (K)">Myristoyl (K)</option>
-        <option value="Myristoyl (N-term G)">Myristoyl (N-term G)</option>
-        <option value="Myristoyl+Delta:H(-4) (Protein N-term G)">Myristoyl+Delta:H(-4) (Protein N-term G)</option>
-        <option value="N-dimethylphosphate (S)">N-dimethylphosphate (S)</option>
-        <option value="NA-LNO2 (C)">NA-LNO2 (C)</option>
-        <option value="NA-LNO2 (H)">NA-LNO2 (H)</option>
-        <option value="NA-OA-NO2 (C)">NA-OA-NO2 (C)</option>
-        <option value="NA-OA-NO2 (H)">NA-OA-NO2 (H)</option>
-        <option value="NBS (W)">NBS (W)</option>
-        <option value="NBS:13C(6) (W)">NBS:13C(6) (W)</option>
-        <option value="NDA (K)">NDA (K)</option>
-        <option value="NDA (N-term)">NDA (N-term)</option>
-        <option value="NEIAA (C)">NEIAA (C)</option>
-        <option value="NEIAA (Y)">NEIAA (Y)</option>
-        <option value="NEIAA:2H(5) (C)">NEIAA:2H(5) (C)</option>
-        <option value="NEIAA:2H(5) (Y)">NEIAA:2H(5) (Y)</option>
-        <option value="NEM:2H(5) (C)">NEM:2H(5) (C)</option>
-        <option value="NEM:2H(5)+H2O (C)">NEM:2H(5)+H2O (C)</option>
-        <option value="NEMsulfur (C)">NEMsulfur (C)</option>
-        <option value="NEMsulfurWater (C)">NEMsulfurWater (C)</option>
-        <option value="Nethylmaleimide (C)">Nethylmaleimide (C)</option>
-        <option value="Nethylmaleimide+water (C)">Nethylmaleimide+water (C)</option>
-        <option value="Nethylmaleimide+water (K)">Nethylmaleimide+water (K)</option>
-        <option value="NeuAc (N)">NeuAc (N)</option>
-        <option value="NeuAc (S)">NeuAc (S)</option>
-        <option value="NeuAc (T)">NeuAc (T)</option>
-        <option value="NeuGc (N)">NeuGc (N)</option>
-        <option value="NeuGc (S)">NeuGc (S)</option>
-        <option value="NeuGc (T)">NeuGc (T)</option>
-        <option value="NHS-fluorescein (K)">NHS-fluorescein (K)</option>
-        <option value="NHS-LC-Biotin (K)">NHS-LC-Biotin (K)</option>
-        <option value="NHS-LC-Biotin (N-term)">NHS-LC-Biotin (N-term)</option>
-        <option value="NIC (K)">NIC (K)</option>
-        <option value="NIC (N-term)">NIC (N-term)</option>
-        <option value="NIPCAM (C)">NIPCAM (C)</option>
-        <option value="Nitrene (Y)">Nitrene (Y)</option>
-        <option value="Nitro (F)">Nitro (F)</option>
-        <option value="Nitro (W)">Nitro (W)</option>
-        <option value="Nitro (Y)">Nitro (Y)</option>
-        <option value="Nitrosyl (C)">Nitrosyl (C)</option>
-        <option value="Nitrosyl (Y)">Nitrosyl (Y)</option>
-        <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
-        <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
-        <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
-        <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
-        <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-        <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
-        <option value="NP40 (N-term)">NP40 (N-term)</option>
-        <option value="NQIGG (K)">NQIGG (K)</option>
-        <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
-        <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
-        <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
-        <option value="O-Et-N-diMePhospho (S)">O-Et-N-diMePhospho (S)</option>
-        <option value="O-Isopropylmethylphosphonate (S)">O-Isopropylmethylphosphonate (S)</option>
-        <option value="O-Isopropylmethylphosphonate (T)">O-Isopropylmethylphosphonate (T)</option>
-        <option value="O-Isopropylmethylphosphonate (Y)">O-Isopropylmethylphosphonate (Y)</option>
-        <option value="O-Methylphosphate (S)">O-Methylphosphate (S)</option>
-        <option value="O-Methylphosphate (T)">O-Methylphosphate (T)</option>
-        <option value="O-Methylphosphate (Y)">O-Methylphosphate (Y)</option>
-        <option value="O-pinacolylmethylphosphonate (H)">O-pinacolylmethylphosphonate (H)</option>
-        <option value="O-pinacolylmethylphosphonate (K)">O-pinacolylmethylphosphonate (K)</option>
-        <option value="O-pinacolylmethylphosphonate (S)">O-pinacolylmethylphosphonate (S)</option>
-        <option value="O-pinacolylmethylphosphonate (T)">O-pinacolylmethylphosphonate (T)</option>
-        <option value="O-pinacolylmethylphosphonate (Y)">O-pinacolylmethylphosphonate (Y)</option>
-        <option value="Octanoyl (C)">Octanoyl (C)</option>
-        <option value="Octanoyl (S)">Octanoyl (S)</option>
-        <option value="Octanoyl (T)">Octanoyl (T)</option>
-        <option value="OxArgBiotin (R)">OxArgBiotin (R)</option>
-        <option value="OxArgBiotinRed (R)">OxArgBiotinRed (R)</option>
-        <option value="Oxidation (C)">Oxidation (C)</option>
-        <option value="Oxidation (C-term G)">Oxidation (C-term G)</option>
-        <option value="Oxidation (D)">Oxidation (D)</option>
-        <option value="Oxidation (E)">Oxidation (E)</option>
-        <option value="Oxidation (F)">Oxidation (F)</option>
-        <option value="Oxidation (H)">Oxidation (H)</option>
-        <option value="Oxidation (I)">Oxidation (I)</option>
-        <option value="Oxidation (K)">Oxidation (K)</option>
-        <option value="Oxidation (L)">Oxidation (L)</option>
-        <option value="Oxidation (M)">Oxidation (M)</option>
-        <option value="Oxidation (N)">Oxidation (N)</option>
-        <option value="Oxidation (P)">Oxidation (P)</option>
-        <option value="Oxidation (Q)">Oxidation (Q)</option>
-        <option value="Oxidation (R)">Oxidation (R)</option>
-        <option value="Oxidation (S)">Oxidation (S)</option>
-        <option value="Oxidation (T)">Oxidation (T)</option>
-        <option value="Oxidation (U)">Oxidation (U)</option>
-        <option value="Oxidation (V)">Oxidation (V)</option>
-        <option value="Oxidation (W)">Oxidation (W)</option>
-        <option value="Oxidation (Y)">Oxidation (Y)</option>
-        <option value="Oxidation+NEM (C)">Oxidation+NEM (C)</option>
-        <option value="OxLysBiotin (K)">OxLysBiotin (K)</option>
-        <option value="OxLysBiotinRed (K)">OxLysBiotinRed (K)</option>
-        <option value="OxProBiotin (P)">OxProBiotin (P)</option>
-        <option value="OxProBiotinRed (P)">OxProBiotinRed (P)</option>
-        <option value="Palmitoleyl (C)">Palmitoleyl (C)</option>
-        <option value="Palmitoleyl (S)">Palmitoleyl (S)</option>
-        <option value="Palmitoleyl (T)">Palmitoleyl (T)</option>
-        <option value="Palmitoyl (C)">Palmitoyl (C)</option>
-        <option value="Palmitoyl (K)">Palmitoyl (K)</option>
-        <option value="Palmitoyl (Protein N-term)">Palmitoyl (Protein N-term)</option>
-        <option value="Palmitoyl (S)">Palmitoyl (S)</option>
-        <option value="Palmitoyl (T)">Palmitoyl (T)</option>
-        <option value="PEITC (C)">PEITC (C)</option>
-        <option value="PEITC (K)">PEITC (K)</option>
-        <option value="PEITC (N-term)">PEITC (N-term)</option>
-        <option value="Pent(1)HexNAc(1) (S)">Pent(1)HexNAc(1) (S)</option>
-        <option value="Pent(1)HexNAc(1) (T)">Pent(1)HexNAc(1) (T)</option>
-        <option value="Pent(2) (S)">Pent(2) (S)</option>
-        <option value="Pent(2) (T)">Pent(2) (T)</option>
-        <option value="Pentose (S)">Pentose (S)</option>
-        <option value="Pentose (T)">Pentose (T)</option>
-        <option value="Pentylamine (Q)">Pentylamine (Q)</option>
-        <option value="PEO-Iodoacetyl-LC-Biotin (C)">PEO-Iodoacetyl-LC-Biotin (C)</option>
-        <option value="PET (S)">PET (S)</option>
-        <option value="PET (T)">PET (T)</option>
-        <option value="Phe-&gt;Ala (F)">Phe-&gt;Ala (F)</option>
-        <option value="Phe-&gt;Arg (F)">Phe-&gt;Arg (F)</option>
-        <option value="Phe-&gt;Asn (F)">Phe-&gt;Asn (F)</option>
-        <option value="Phe-&gt;Asp (F)">Phe-&gt;Asp (F)</option>
-        <option value="Phe-&gt;CamCys (F)">Phe-&gt;CamCys (F)</option>
-        <option value="Phe-&gt;Cys (F)">Phe-&gt;Cys (F)</option>
-        <option value="Phe-&gt;Gln (F)">Phe-&gt;Gln (F)</option>
-        <option value="Phe-&gt;Glu (F)">Phe-&gt;Glu (F)</option>
-        <option value="Phe-&gt;Gly (F)">Phe-&gt;Gly (F)</option>
-        <option value="Phe-&gt;His (F)">Phe-&gt;His (F)</option>
-        <option value="Phe-&gt;Lys (F)">Phe-&gt;Lys (F)</option>
-        <option value="Phe-&gt;Met (F)">Phe-&gt;Met (F)</option>
-        <option value="Phe-&gt;Pro (F)">Phe-&gt;Pro (F)</option>
-        <option value="Phe-&gt;Ser (F)">Phe-&gt;Ser (F)</option>
-        <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
-        <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
-        <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
-        <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
-        <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
-        <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
-        <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
-        <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
-        <option value="Phospho (C)">Phospho (C)</option>
-        <option value="Phospho (D)">Phospho (D)</option>
-        <option value="Phospho (E)">Phospho (E)</option>
-        <option value="Phospho (H)">Phospho (H)</option>
-        <option value="Phospho (K)">Phospho (K)</option>
-        <option value="Phospho (R)">Phospho (R)</option>
-        <option value="Phospho (S)">Phospho (S)</option>
-        <option value="Phospho (T)">Phospho (T)</option>
-        <option value="Phospho (Y)">Phospho (Y)</option>
-        <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
-        <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
-        <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
-        <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
-        <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
-        <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
-        <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
-        <option value="Phosphogluconoylation (K)">Phosphogluconoylation (K)</option>
-        <option value="Phosphogluconoylation (N-term)">Phosphogluconoylation (N-term)</option>
-        <option value="Phosphoguanosine (H)">Phosphoguanosine (H)</option>
-        <option value="Phosphoguanosine (K)">Phosphoguanosine (K)</option>
-        <option value="PhosphoHex (S)">PhosphoHex (S)</option>
-        <option value="PhosphoHex (T)">PhosphoHex (T)</option>
-        <option value="PhosphoHex(2) (N)">PhosphoHex(2) (N)</option>
-        <option value="PhosphoHex(2) (S)">PhosphoHex(2) (S)</option>
-        <option value="PhosphoHex(2) (T)">PhosphoHex(2) (T)</option>
-        <option value="PhosphoHexNAc (S)">PhosphoHexNAc (S)</option>
-        <option value="PhosphoHexNAc (T)">PhosphoHexNAc (T)</option>
-        <option value="Phosphopantetheine (S)">Phosphopantetheine (S)</option>
-        <option value="Phosphopropargyl (S)">Phosphopropargyl (S)</option>
-        <option value="Phosphopropargyl (T)">Phosphopropargyl (T)</option>
-        <option value="Phosphopropargyl (Y)">Phosphopropargyl (Y)</option>
-        <option value="phosphoRibosyl (D)">phosphoRibosyl (D)</option>
-        <option value="phosphoRibosyl (E)">phosphoRibosyl (E)</option>
-        <option value="phosphoRibosyl (R)">phosphoRibosyl (R)</option>
-        <option value="PhosphoribosyldephosphoCoA (S)">PhosphoribosyldephosphoCoA (S)</option>
-        <option value="PhosphoUridine (H)">PhosphoUridine (H)</option>
-        <option value="PhosphoUridine (Y)">PhosphoUridine (Y)</option>
-        <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
-        <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
-        <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
-        <option value="Piperidine (K)">Piperidine (K)</option>
-        <option value="Piperidine (N-term)">Piperidine (N-term)</option>
-        <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
-        <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
-        <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
-        <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
-        <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
-        <option value="Pro-&gt;Gln (P)">Pro-&gt;Gln (P)</option>
-        <option value="Pro-&gt;Glu (P)">Pro-&gt;Glu (P)</option>
-        <option value="Pro-&gt;Gly (P)">Pro-&gt;Gly (P)</option>
-        <option value="Pro-&gt;HAVA (P)">Pro-&gt;HAVA (P)</option>
-        <option value="Pro-&gt;His (P)">Pro-&gt;His (P)</option>
-        <option value="Pro-&gt;Lys (P)">Pro-&gt;Lys (P)</option>
-        <option value="Pro-&gt;Met (P)">Pro-&gt;Met (P)</option>
-        <option value="Pro-&gt;Phe (P)">Pro-&gt;Phe (P)</option>
-        <option value="Pro-&gt;pyro-Glu (P)">Pro-&gt;pyro-Glu (P)</option>
-        <option value="Pro-&gt;Pyrrolidinone (P)">Pro-&gt;Pyrrolidinone (P)</option>
-        <option value="Pro-&gt;Pyrrolidone (P)">Pro-&gt;Pyrrolidone (P)</option>
-        <option value="Pro-&gt;Ser (P)">Pro-&gt;Ser (P)</option>
-        <option value="Pro-&gt;Thr (P)">Pro-&gt;Thr (P)</option>
-        <option value="Pro-&gt;Trp (P)">Pro-&gt;Trp (P)</option>
-        <option value="Pro-&gt;Tyr (P)">Pro-&gt;Tyr (P)</option>
-        <option value="Pro-&gt;Val (P)">Pro-&gt;Val (P)</option>
-        <option value="Pro-&gt;Xle (P)">Pro-&gt;Xle (P)</option>
-        <option value="probiotinhydrazide (P)">probiotinhydrazide (P)</option>
-        <option value="Propargylamine (C-term)">Propargylamine (C-term)</option>
-        <option value="Propargylamine (D)">Propargylamine (D)</option>
-        <option value="Propargylamine (E)">Propargylamine (E)</option>
-        <option value="Propionamide (C)">Propionamide (C)</option>
-        <option value="Propionamide (K)">Propionamide (K)</option>
-        <option value="Propionamide (N-term)">Propionamide (N-term)</option>
-        <option value="Propionamide:2H(3) (C)">Propionamide:2H(3) (C)</option>
-        <option value="Propionyl (K)">Propionyl (K)</option>
-        <option value="Propionyl (N-term)">Propionyl (N-term)</option>
-        <option value="Propionyl (Protein N-term)">Propionyl (Protein N-term)</option>
-        <option value="Propionyl (S)">Propionyl (S)</option>
-        <option value="Propionyl (T)">Propionyl (T)</option>
-        <option value="Propionyl:13C(3) (K)">Propionyl:13C(3) (K)</option>
-        <option value="Propionyl:13C(3) (N-term)">Propionyl:13C(3) (N-term)</option>
-        <option value="Propiophenone (C)">Propiophenone (C)</option>
-        <option value="Propiophenone (H)">Propiophenone (H)</option>
-        <option value="Propiophenone (K)">Propiophenone (K)</option>
-        <option value="Propiophenone (R)">Propiophenone (R)</option>
-        <option value="Propiophenone (S)">Propiophenone (S)</option>
-        <option value="Propiophenone (T)">Propiophenone (T)</option>
-        <option value="Propiophenone (W)">Propiophenone (W)</option>
-        <option value="Propyl (C-term)">Propyl (C-term)</option>
-        <option value="Propyl (D)">Propyl (D)</option>
-        <option value="Propyl (E)">Propyl (E)</option>
-        <option value="Propyl (K)">Propyl (K)</option>
-        <option value="Propyl (N-term)">Propyl (N-term)</option>
-        <option value="Propyl (Protein C-term)">Propyl (Protein C-term)</option>
-        <option value="Propyl:2H(6) (K)">Propyl:2H(6) (K)</option>
-        <option value="Propyl:2H(6) (N-term)">Propyl:2H(6) (N-term)</option>
-        <option value="PropylNAGthiazoline (C)">PropylNAGthiazoline (C)</option>
-        <option value="PS_Hapten (C)">PS_Hapten (C)</option>
-        <option value="PS_Hapten (H)">PS_Hapten (H)</option>
-        <option value="PS_Hapten (K)">PS_Hapten (K)</option>
-        <option value="pupylation (K)">pupylation (K)</option>
-        <option value="Puromycin (C-term)">Puromycin (C-term)</option>
-        <option value="PyMIC (N-term)">PyMIC (N-term)</option>
-        <option value="PyridoxalPhosphate (K)">PyridoxalPhosphate (K)</option>
-        <option value="PyridoxalPhosphateH2 (K)">PyridoxalPhosphateH2 (K)</option>
-        <option value="Pyridylacetyl (K)">Pyridylacetyl (K)</option>
-        <option value="Pyridylacetyl (N-term)">Pyridylacetyl (N-term)</option>
-        <option value="Pyridylethyl (C)">Pyridylethyl (C)</option>
-        <option value="Pyro-carbamidomethyl (N-term C)">Pyro-carbamidomethyl (N-term C)</option>
-        <option value="pyrophospho (S)">pyrophospho (S)</option>
-        <option value="pyrophospho (T)">pyrophospho (T)</option>
-        <option value="PyruvicAcidIminyl (K)">PyruvicAcidIminyl (K)</option>
-        <option value="PyruvicAcidIminyl (Protein N-term C)">PyruvicAcidIminyl (Protein N-term C)</option>
-        <option value="PyruvicAcidIminyl (Protein N-term V)">PyruvicAcidIminyl (Protein N-term V)</option>
-        <option value="QAT (C)">QAT (C)</option>
-        <option value="QAT:2H(3) (C)">QAT:2H(3) (C)</option>
-        <option value="QEQTGG (K)">QEQTGG (K)</option>
-        <option value="QQQTGG (K)">QQQTGG (K)</option>
-        <option value="QTGG (K)">QTGG (K)</option>
-        <option value="Quinone (W)">Quinone (W)</option>
-        <option value="Quinone (Y)">Quinone (Y)</option>
-        <option value="Retinylidene (K)">Retinylidene (K)</option>
-        <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
-        <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
-        <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-        <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-        <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-        <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-        <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-        <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-        <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-        <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-        <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
-        <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
-        <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
-        <option value="Saligenin (H)">Saligenin (H)</option>
-        <option value="Saligenin (K)">Saligenin (K)</option>
-        <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
-        <option value="Ser-&gt;Arg (S)">Ser-&gt;Arg (S)</option>
-        <option value="Ser-&gt;Asn (S)">Ser-&gt;Asn (S)</option>
-        <option value="Ser-&gt;Asp (S)">Ser-&gt;Asp (S)</option>
-        <option value="Ser-&gt;Cys (S)">Ser-&gt;Cys (S)</option>
-        <option value="Ser-&gt;Gln (S)">Ser-&gt;Gln (S)</option>
-        <option value="Ser-&gt;Glu (S)">Ser-&gt;Glu (S)</option>
-        <option value="Ser-&gt;Gly (S)">Ser-&gt;Gly (S)</option>
-        <option value="Ser-&gt;His (S)">Ser-&gt;His (S)</option>
-        <option value="Ser-&gt;LacticAcid (Protein N-term S)">Ser-&gt;LacticAcid (Protein N-term S)</option>
-        <option value="Ser-&gt;Lys (S)">Ser-&gt;Lys (S)</option>
-        <option value="Ser-&gt;Met (S)">Ser-&gt;Met (S)</option>
-        <option value="Ser-&gt;Phe (S)">Ser-&gt;Phe (S)</option>
-        <option value="Ser-&gt;Pro (S)">Ser-&gt;Pro (S)</option>
-        <option value="Ser-&gt;Thr (S)">Ser-&gt;Thr (S)</option>
-        <option value="Ser-&gt;Trp (S)">Ser-&gt;Trp (S)</option>
-        <option value="Ser-&gt;Tyr (S)">Ser-&gt;Tyr (S)</option>
-        <option value="Ser-&gt;Val (S)">Ser-&gt;Val (S)</option>
-        <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
-        <option value="serotonylation (Q)">serotonylation (Q)</option>
-        <option value="shTMT (K)">shTMT (K)</option>
-        <option value="shTMT (N-term)">shTMT (N-term)</option>
-        <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
-        <option value="SMA (K)">SMA (K)</option>
-        <option value="SMA (N-term)">SMA (N-term)</option>
-        <option value="spermidine (Q)">spermidine (Q)</option>
-        <option value="spermine (Q)">spermine (Q)</option>
-        <option value="SPITC (K)">SPITC (K)</option>
-        <option value="SPITC (N-term)">SPITC (N-term)</option>
-        <option value="SPITC:13C(6) (K)">SPITC:13C(6) (K)</option>
-        <option value="SPITC:13C(6) (N-term)">SPITC:13C(6) (N-term)</option>
-        <option value="Succinyl (K)">Succinyl (K)</option>
-        <option value="Succinyl (N-term)">Succinyl (N-term)</option>
-        <option value="Succinyl (Protein N-term)">Succinyl (Protein N-term)</option>
-        <option value="Succinyl:13C(4) (K)">Succinyl:13C(4) (K)</option>
-        <option value="Succinyl:13C(4) (N-term)">Succinyl:13C(4) (N-term)</option>
-        <option value="Succinyl:2H(4) (K)">Succinyl:2H(4) (K)</option>
-        <option value="Succinyl:2H(4) (N-term)">Succinyl:2H(4) (N-term)</option>
-        <option value="SulfanilicAcid (C-term)">SulfanilicAcid (C-term)</option>
-        <option value="SulfanilicAcid (D)">SulfanilicAcid (D)</option>
-        <option value="SulfanilicAcid (E)">SulfanilicAcid (E)</option>
-        <option value="SulfanilicAcid:13C(6) (C-term)">SulfanilicAcid:13C(6) (C-term)</option>
-        <option value="SulfanilicAcid:13C(6) (D)">SulfanilicAcid:13C(6) (D)</option>
-        <option value="SulfanilicAcid:13C(6) (E)">SulfanilicAcid:13C(6) (E)</option>
-        <option value="Sulfide (C)">Sulfide (C)</option>
-        <option value="Sulfide (D)">Sulfide (D)</option>
-        <option value="Sulfide (W)">Sulfide (W)</option>
-        <option value="Sulfo (C)">Sulfo (C)</option>
-        <option value="Sulfo (S)">Sulfo (S)</option>
-        <option value="Sulfo (T)">Sulfo (T)</option>
-        <option value="Sulfo (Y)">Sulfo (Y)</option>
-        <option value="sulfo+amino (Y)">sulfo+amino (Y)</option>
-        <option value="Sulfo-NHS-LC-LC-Biotin (K)">Sulfo-NHS-LC-LC-Biotin (K)</option>
-        <option value="Sulfo-NHS-LC-LC-Biotin (N-term)">Sulfo-NHS-LC-LC-Biotin (N-term)</option>
-        <option value="SulfoGMBS (C)">SulfoGMBS (C)</option>
-        <option value="SulfurDioxide (C)">SulfurDioxide (C)</option>
-        <option value="SUMO2135 (K)">SUMO2135 (K)</option>
-        <option value="SUMO3549 (K)">SUMO3549 (K)</option>
-        <option value="TAMRA-FP (S)">TAMRA-FP (S)</option>
-        <option value="TAMRA-FP (Y)">TAMRA-FP (Y)</option>
-        <option value="Thiadiazole (C)">Thiadiazole (C)</option>
-        <option value="Thiazolidine (C)">Thiazolidine (C)</option>
-        <option value="Thiazolidine (F)">Thiazolidine (F)</option>
-        <option value="Thiazolidine (H)">Thiazolidine (H)</option>
-        <option value="Thiazolidine (K)">Thiazolidine (K)</option>
-        <option value="Thiazolidine (Protein N-term)">Thiazolidine (Protein N-term)</option>
-        <option value="Thiazolidine (R)">Thiazolidine (R)</option>
-        <option value="Thiazolidine (W)">Thiazolidine (W)</option>
-        <option value="Thiazolidine (Y)">Thiazolidine (Y)</option>
-        <option value="thioacylPA (K)">thioacylPA (K)</option>
-        <option value="Thiophos-S-S-biotin (S)">Thiophos-S-S-biotin (S)</option>
-        <option value="Thiophos-S-S-biotin (T)">Thiophos-S-S-biotin (T)</option>
-        <option value="Thiophos-S-S-biotin (Y)">Thiophos-S-S-biotin (Y)</option>
-        <option value="Thiophospho (S)">Thiophospho (S)</option>
-        <option value="Thiophospho (T)">Thiophospho (T)</option>
-        <option value="Thiophospho (Y)">Thiophospho (Y)</option>
-        <option value="Thr-&gt;Ala (T)">Thr-&gt;Ala (T)</option>
-        <option value="Thr-&gt;Arg (T)">Thr-&gt;Arg (T)</option>
-        <option value="Thr-&gt;Asn (T)">Thr-&gt;Asn (T)</option>
-        <option value="Thr-&gt;Asp (T)">Thr-&gt;Asp (T)</option>
-        <option value="Thr-&gt;Cys (T)">Thr-&gt;Cys (T)</option>
-        <option value="Thr-&gt;Gln (T)">Thr-&gt;Gln (T)</option>
-        <option value="Thr-&gt;Glu (T)">Thr-&gt;Glu (T)</option>
-        <option value="Thr-&gt;Gly (T)">Thr-&gt;Gly (T)</option>
-        <option value="Thr-&gt;His (T)">Thr-&gt;His (T)</option>
-        <option value="Thr-&gt;Lys (T)">Thr-&gt;Lys (T)</option>
-        <option value="Thr-&gt;Met (T)">Thr-&gt;Met (T)</option>
-        <option value="Thr-&gt;Phe (T)">Thr-&gt;Phe (T)</option>
-        <option value="Thr-&gt;Pro (T)">Thr-&gt;Pro (T)</option>
-        <option value="Thr-&gt;Ser (T)">Thr-&gt;Ser (T)</option>
-        <option value="Thr-&gt;Trp (T)">Thr-&gt;Trp (T)</option>
-        <option value="Thr-&gt;Tyr (T)">Thr-&gt;Tyr (T)</option>
-        <option value="Thr-&gt;Val (T)">Thr-&gt;Val (T)</option>
-        <option value="Thr-&gt;Xle (T)">Thr-&gt;Xle (T)</option>
-        <option value="Thrbiotinhydrazide (T)">Thrbiotinhydrazide (T)</option>
-        <option value="Thyroxine (Y)">Thyroxine (Y)</option>
-        <option value="TMAB (K)">TMAB (K)</option>
-        <option value="TMAB (N-term)">TMAB (N-term)</option>
-        <option value="TMAB:2H(9) (K)">TMAB:2H(9) (K)</option>
-        <option value="TMAB:2H(9) (N-term)">TMAB:2H(9) (N-term)</option>
-        <option value="TMPP-Ac (K)">TMPP-Ac (K)</option>
-        <option value="TMPP-Ac (N-term)">TMPP-Ac (N-term)</option>
-        <option value="TMPP-Ac (Y)">TMPP-Ac (Y)</option>
-        <option value="TMPP-Ac:13C(9) (K)">TMPP-Ac:13C(9) (K)</option>
-        <option value="TMPP-Ac:13C(9) (N-term)">TMPP-Ac:13C(9) (N-term)</option>
-        <option value="TMPP-Ac:13C(9) (Y)">TMPP-Ac:13C(9) (Y)</option>
-        <option value="TMT (H)">TMT (H)</option>
-        <option value="TMT (K)">TMT (K)</option>
-        <option value="TMT (N-term)">TMT (N-term)</option>
-        <option value="TMT (Protein N-term)">TMT (Protein N-term)</option>
-        <option value="TMT (S)">TMT (S)</option>
-        <option value="TMT (T)">TMT (T)</option>
-        <option value="TMT2plex (H)">TMT2plex (H)</option>
-        <option value="TMT2plex (K)">TMT2plex (K)</option>
-        <option value="TMT2plex (N-term)">TMT2plex (N-term)</option>
-        <option value="TMT2plex (Protein N-term)">TMT2plex (Protein N-term)</option>
-        <option value="TMT2plex (S)">TMT2plex (S)</option>
-        <option value="TMT2plex (T)">TMT2plex (T)</option>
-        <option value="TMT6plex (H)">TMT6plex (H)</option>
-        <option value="TMT6plex (K)">TMT6plex (K)</option>
-        <option value="TMT6plex (N-term)">TMT6plex (N-term)</option>
-        <option value="TMT6plex (Protein N-term)">TMT6plex (Protein N-term)</option>
-        <option value="TMT6plex (S)">TMT6plex (S)</option>
-        <option value="TMT6plex (T)">TMT6plex (T)</option>
-        <option value="TMTpro (H)">TMTpro (H)</option>
-        <option value="TMTpro (K)">TMTpro (K)</option>
-        <option value="TMTpro (N-term)">TMTpro (N-term)</option>
-        <option value="TMTpro (Protein N-term)">TMTpro (Protein N-term)</option>
-        <option value="TMTpro (S)">TMTpro (S)</option>
-        <option value="TMTpro (T)">TMTpro (T)</option>
-        <option value="TMTpro_zero (H)">TMTpro_zero (H)</option>
-        <option value="TMTpro_zero (K)">TMTpro_zero (K)</option>
-        <option value="TMTpro_zero (N-term)">TMTpro_zero (N-term)</option>
-        <option value="TMTpro_zero (Protein N-term)">TMTpro_zero (Protein N-term)</option>
-        <option value="TMTpro_zero (S)">TMTpro_zero (S)</option>
-        <option value="TMTpro_zero (T)">TMTpro_zero (T)</option>
-        <option value="TNBS (K)">TNBS (K)</option>
-        <option value="TNBS (N-term)">TNBS (N-term)</option>
-        <option value="trifluoro (L)">trifluoro (L)</option>
-        <option value="Triiodo (Y)">Triiodo (Y)</option>
-        <option value="Triiodothyronine (Y)">Triiodothyronine (Y)</option>
-        <option value="Trimethyl (K)">Trimethyl (K)</option>
-        <option value="Trimethyl (Protein N-term A)">Trimethyl (Protein N-term A)</option>
-        <option value="Trimethyl (R)">Trimethyl (R)</option>
-        <option value="Trimethyl:13C(3)2H(9) (K)">Trimethyl:13C(3)2H(9) (K)</option>
-        <option value="Trimethyl:13C(3)2H(9) (R)">Trimethyl:13C(3)2H(9) (R)</option>
-        <option value="Trimethyl:2H(9) (K)">Trimethyl:2H(9) (K)</option>
-        <option value="Trimethyl:2H(9) (R)">Trimethyl:2H(9) (R)</option>
-        <option value="Trioxidation (C)">Trioxidation (C)</option>
-        <option value="Trioxidation (F)">Trioxidation (F)</option>
-        <option value="Trioxidation (W)">Trioxidation (W)</option>
-        <option value="Trioxidation (Y)">Trioxidation (Y)</option>
-        <option value="Tripalmitate (Protein N-term C)">Tripalmitate (Protein N-term C)</option>
-        <option value="Tris (N)">Tris (N)</option>
-        <option value="Triton (C-term)">Triton (C-term)</option>
-        <option value="Triton (N-term)">Triton (N-term)</option>
-        <option value="Trp-&gt;Ala (W)">Trp-&gt;Ala (W)</option>
-        <option value="Trp-&gt;Arg (W)">Trp-&gt;Arg (W)</option>
-        <option value="Trp-&gt;Asn (W)">Trp-&gt;Asn (W)</option>
-        <option value="Trp-&gt;Asp (W)">Trp-&gt;Asp (W)</option>
-        <option value="Trp-&gt;Cys (W)">Trp-&gt;Cys (W)</option>
-        <option value="Trp-&gt;Gln (W)">Trp-&gt;Gln (W)</option>
-        <option value="Trp-&gt;Glu (W)">Trp-&gt;Glu (W)</option>
-        <option value="Trp-&gt;Gly (W)">Trp-&gt;Gly (W)</option>
-        <option value="Trp-&gt;His (W)">Trp-&gt;His (W)</option>
-        <option value="Trp-&gt;Hydroxykynurenin (W)">Trp-&gt;Hydroxykynurenin (W)</option>
-        <option value="Trp-&gt;Kynurenin (W)">Trp-&gt;Kynurenin (W)</option>
-        <option value="Trp-&gt;Lys (W)">Trp-&gt;Lys (W)</option>
-        <option value="Trp-&gt;Met (W)">Trp-&gt;Met (W)</option>
-        <option value="Trp-&gt;Oxolactone (W)">Trp-&gt;Oxolactone (W)</option>
-        <option value="Trp-&gt;Phe (W)">Trp-&gt;Phe (W)</option>
-        <option value="Trp-&gt;Pro (W)">Trp-&gt;Pro (W)</option>
-        <option value="Trp-&gt;Ser (W)">Trp-&gt;Ser (W)</option>
-        <option value="Trp-&gt;Thr (W)">Trp-&gt;Thr (W)</option>
-        <option value="Trp-&gt;Tyr (W)">Trp-&gt;Tyr (W)</option>
-        <option value="Trp-&gt;Val (W)">Trp-&gt;Val (W)</option>
-        <option value="Trp-&gt;Xle (W)">Trp-&gt;Xle (W)</option>
-        <option value="Tween20 (N-term)">Tween20 (N-term)</option>
-        <option value="Tween80 (C-term)">Tween80 (C-term)</option>
-        <option value="Tyr-&gt;Ala (Y)">Tyr-&gt;Ala (Y)</option>
-        <option value="Tyr-&gt;Arg (Y)">Tyr-&gt;Arg (Y)</option>
-        <option value="Tyr-&gt;Asn (Y)">Tyr-&gt;Asn (Y)</option>
-        <option value="Tyr-&gt;Asp (Y)">Tyr-&gt;Asp (Y)</option>
-        <option value="Tyr-&gt;Cys (Y)">Tyr-&gt;Cys (Y)</option>
-        <option value="Tyr-&gt;Dha (Y)">Tyr-&gt;Dha (Y)</option>
-        <option value="Tyr-&gt;Gln (Y)">Tyr-&gt;Gln (Y)</option>
-        <option value="Tyr-&gt;Glu (Y)">Tyr-&gt;Glu (Y)</option>
-        <option value="Tyr-&gt;Gly (Y)">Tyr-&gt;Gly (Y)</option>
-        <option value="Tyr-&gt;His (Y)">Tyr-&gt;His (Y)</option>
-        <option value="Tyr-&gt;Lys (Y)">Tyr-&gt;Lys (Y)</option>
-        <option value="Tyr-&gt;Met (Y)">Tyr-&gt;Met (Y)</option>
-        <option value="Tyr-&gt;Phe (Y)">Tyr-&gt;Phe (Y)</option>
-        <option value="Tyr-&gt;Pro (Y)">Tyr-&gt;Pro (Y)</option>
-        <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
-        <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
-        <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
-        <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
-        <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-        <option value="Ub-amide (C)">Ub-amide (C)</option>
-        <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
-        <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
-        <option value="Ub-VME (C)">Ub-VME (C)</option>
-        <option value="UgiJoullie (D)">UgiJoullie (D)</option>
-        <option value="UgiJoullie (E)">UgiJoullie (E)</option>
-        <option value="UgiJoullieProGly (D)">UgiJoullieProGly (D)</option>
-        <option value="UgiJoullieProGly (E)">UgiJoullieProGly (E)</option>
-        <option value="UgiJoullieProGlyProGly (D)">UgiJoullieProGlyProGly (D)</option>
-        <option value="UgiJoullieProGlyProGly (E)">UgiJoullieProGlyProGly (E)</option>
-        <option value="Unknown:162 (C-term)">Unknown:162 (C-term)</option>
-        <option value="Unknown:162 (D)">Unknown:162 (D)</option>
-        <option value="Unknown:162 (E)">Unknown:162 (E)</option>
-        <option value="Unknown:162 (N-term)">Unknown:162 (N-term)</option>
-        <option value="Unknown:177 (C-term)">Unknown:177 (C-term)</option>
-        <option value="Unknown:177 (D)">Unknown:177 (D)</option>
-        <option value="Unknown:177 (E)">Unknown:177 (E)</option>
-        <option value="Unknown:177 (N-term)">Unknown:177 (N-term)</option>
-        <option value="Unknown:210 (C-term)">Unknown:210 (C-term)</option>
-        <option value="Unknown:210 (D)">Unknown:210 (D)</option>
-        <option value="Unknown:210 (E)">Unknown:210 (E)</option>
-        <option value="Unknown:210 (N-term)">Unknown:210 (N-term)</option>
-        <option value="Unknown:216 (C-term)">Unknown:216 (C-term)</option>
-        <option value="Unknown:216 (D)">Unknown:216 (D)</option>
-        <option value="Unknown:216 (E)">Unknown:216 (E)</option>
-        <option value="Unknown:216 (N-term)">Unknown:216 (N-term)</option>
-        <option value="Unknown:234 (C-term)">Unknown:234 (C-term)</option>
-        <option value="Unknown:234 (D)">Unknown:234 (D)</option>
-        <option value="Unknown:234 (E)">Unknown:234 (E)</option>
-        <option value="Unknown:234 (N-term)">Unknown:234 (N-term)</option>
-        <option value="Unknown:248 (C-term)">Unknown:248 (C-term)</option>
-        <option value="Unknown:248 (D)">Unknown:248 (D)</option>
-        <option value="Unknown:248 (E)">Unknown:248 (E)</option>
-        <option value="Unknown:248 (N-term)">Unknown:248 (N-term)</option>
-        <option value="Unknown:250 (C-term)">Unknown:250 (C-term)</option>
-        <option value="Unknown:250 (D)">Unknown:250 (D)</option>
-        <option value="Unknown:250 (E)">Unknown:250 (E)</option>
-        <option value="Unknown:250 (N-term)">Unknown:250 (N-term)</option>
-        <option value="Unknown:302 (C-term)">Unknown:302 (C-term)</option>
-        <option value="Unknown:302 (D)">Unknown:302 (D)</option>
-        <option value="Unknown:302 (E)">Unknown:302 (E)</option>
-        <option value="Unknown:302 (N-term)">Unknown:302 (N-term)</option>
-        <option value="Unknown:306 (C-term)">Unknown:306 (C-term)</option>
-        <option value="Unknown:306 (D)">Unknown:306 (D)</option>
-        <option value="Unknown:306 (E)">Unknown:306 (E)</option>
-        <option value="Unknown:306 (N-term)">Unknown:306 (N-term)</option>
-        <option value="Unknown:420 (C-term)">Unknown:420 (C-term)</option>
-        <option value="Unknown:420 (N-term)">Unknown:420 (N-term)</option>
-        <option value="Val-&gt;Ala (V)">Val-&gt;Ala (V)</option>
-        <option value="Val-&gt;Arg (V)">Val-&gt;Arg (V)</option>
-        <option value="Val-&gt;Asn (V)">Val-&gt;Asn (V)</option>
-        <option value="Val-&gt;Asp (V)">Val-&gt;Asp (V)</option>
-        <option value="Val-&gt;Cys (V)">Val-&gt;Cys (V)</option>
-        <option value="Val-&gt;Gln (V)">Val-&gt;Gln (V)</option>
-        <option value="Val-&gt;Glu (V)">Val-&gt;Glu (V)</option>
-        <option value="Val-&gt;Gly (V)">Val-&gt;Gly (V)</option>
-        <option value="Val-&gt;His (V)">Val-&gt;His (V)</option>
-        <option value="Val-&gt;Lys (V)">Val-&gt;Lys (V)</option>
-        <option value="Val-&gt;Met (V)">Val-&gt;Met (V)</option>
-        <option value="Val-&gt;Phe (V)">Val-&gt;Phe (V)</option>
-        <option value="Val-&gt;Pro (V)">Val-&gt;Pro (V)</option>
-        <option value="Val-&gt;Ser (V)">Val-&gt;Ser (V)</option>
-        <option value="Val-&gt;Thr (V)">Val-&gt;Thr (V)</option>
-        <option value="Val-&gt;Trp (V)">Val-&gt;Trp (V)</option>
-        <option value="Val-&gt;Tyr (V)">Val-&gt;Tyr (V)</option>
-        <option value="Val-&gt;Xle (V)">Val-&gt;Xle (V)</option>
-        <option value="VFQQQTGG (K)">VFQQQTGG (K)</option>
-        <option value="VIEVYQEQTGG (K)">VIEVYQEQTGG (K)</option>
-        <option value="Withaferin (C)">Withaferin (C)</option>
-        <option value="Xle-&gt;Ala (I)">Xle-&gt;Ala (I)</option>
-        <option value="Xle-&gt;Ala (L)">Xle-&gt;Ala (L)</option>
-        <option value="Xle-&gt;Arg (I)">Xle-&gt;Arg (I)</option>
-        <option value="Xle-&gt;Arg (L)">Xle-&gt;Arg (L)</option>
-        <option value="Xle-&gt;Asn (I)">Xle-&gt;Asn (I)</option>
-        <option value="Xle-&gt;Asn (L)">Xle-&gt;Asn (L)</option>
-        <option value="Xle-&gt;Asp (I)">Xle-&gt;Asp (I)</option>
-        <option value="Xle-&gt;Asp (L)">Xle-&gt;Asp (L)</option>
-        <option value="Xle-&gt;Cys (I)">Xle-&gt;Cys (I)</option>
-        <option value="Xle-&gt;Cys (L)">Xle-&gt;Cys (L)</option>
-        <option value="Xle-&gt;Gln (I)">Xle-&gt;Gln (I)</option>
-        <option value="Xle-&gt;Gln (L)">Xle-&gt;Gln (L)</option>
-        <option value="Xle-&gt;Glu (I)">Xle-&gt;Glu (I)</option>
-        <option value="Xle-&gt;Glu (L)">Xle-&gt;Glu (L)</option>
-        <option value="Xle-&gt;Gly (I)">Xle-&gt;Gly (I)</option>
-        <option value="Xle-&gt;Gly (L)">Xle-&gt;Gly (L)</option>
-        <option value="Xle-&gt;His (I)">Xle-&gt;His (I)</option>
-        <option value="Xle-&gt;His (L)">Xle-&gt;His (L)</option>
-        <option value="Xle-&gt;Lys (I)">Xle-&gt;Lys (I)</option>
-        <option value="Xle-&gt;Lys (L)">Xle-&gt;Lys (L)</option>
-        <option value="Xle-&gt;Met (I)">Xle-&gt;Met (I)</option>
-        <option value="Xle-&gt;Met (L)">Xle-&gt;Met (L)</option>
-        <option value="Xle-&gt;Phe (I)">Xle-&gt;Phe (I)</option>
-        <option value="Xle-&gt;Phe (L)">Xle-&gt;Phe (L)</option>
-        <option value="Xle-&gt;Pro (I)">Xle-&gt;Pro (I)</option>
-        <option value="Xle-&gt;Pro (L)">Xle-&gt;Pro (L)</option>
-        <option value="Xle-&gt;Ser (I)">Xle-&gt;Ser (I)</option>
-        <option value="Xle-&gt;Ser (L)">Xle-&gt;Ser (L)</option>
-        <option value="Xle-&gt;Thr (I)">Xle-&gt;Thr (I)</option>
-        <option value="Xle-&gt;Thr (L)">Xle-&gt;Thr (L)</option>
-        <option value="Xle-&gt;Trp (I)">Xle-&gt;Trp (I)</option>
-        <option value="Xle-&gt;Trp (L)">Xle-&gt;Trp (L)</option>
-        <option value="Xle-&gt;Tyr (I)">Xle-&gt;Tyr (I)</option>
-        <option value="Xle-&gt;Tyr (L)">Xle-&gt;Tyr (L)</option>
-        <option value="Xle-&gt;Val (I)">Xle-&gt;Val (I)</option>
-        <option value="Xle-&gt;Val (L)">Xle-&gt;Val (L)</option>
-        <option value="Xlink:B10621 (C)">Xlink:B10621 (C)</option>
-        <option value="Xlink:BMOE (C)">Xlink:BMOE (C)</option>
-        <option value="Xlink:BS2G[113] (K)">Xlink:BS2G[113] (K)</option>
-        <option value="Xlink:BS2G[113] (Protein N-term)">Xlink:BS2G[113] (Protein N-term)</option>
-        <option value="Xlink:BS2G[114] (K)">Xlink:BS2G[114] (K)</option>
-        <option value="Xlink:BS2G[114] (Protein N-term)">Xlink:BS2G[114] (Protein N-term)</option>
-        <option value="Xlink:BS2G[217] (K)">Xlink:BS2G[217] (K)</option>
-        <option value="Xlink:BS2G[217] (Protein N-term)">Xlink:BS2G[217] (Protein N-term)</option>
-        <option value="Xlink:BS2G[96] (K)">Xlink:BS2G[96] (K)</option>
-        <option value="Xlink:BS2G[96] (Protein N-term)">Xlink:BS2G[96] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[111] (K)">Xlink:BuUrBu[111] (K)</option>
-        <option value="Xlink:BuUrBu[111] (Protein N-term)">Xlink:BuUrBu[111] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[196] (K)">Xlink:BuUrBu[196] (K)</option>
-        <option value="Xlink:BuUrBu[196] (Protein N-term)">Xlink:BuUrBu[196] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[213] (K)">Xlink:BuUrBu[213] (K)</option>
-        <option value="Xlink:BuUrBu[213] (Protein N-term)">Xlink:BuUrBu[213] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[214] (K)">Xlink:BuUrBu[214] (K)</option>
-        <option value="Xlink:BuUrBu[214] (Protein N-term)">Xlink:BuUrBu[214] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[317] (K)">Xlink:BuUrBu[317] (K)</option>
-        <option value="Xlink:BuUrBu[317] (Protein N-term)">Xlink:BuUrBu[317] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[85] (K)">Xlink:BuUrBu[85] (K)</option>
-        <option value="Xlink:BuUrBu[85] (Protein N-term)">Xlink:BuUrBu[85] (Protein N-term)</option>
-        <option value="Xlink:DFDNB (K)">Xlink:DFDNB (K)</option>
-        <option value="Xlink:DFDNB (N)">Xlink:DFDNB (N)</option>
-        <option value="Xlink:DFDNB (Q)">Xlink:DFDNB (Q)</option>
-        <option value="Xlink:DFDNB (R)">Xlink:DFDNB (R)</option>
-        <option value="Xlink:DMP[122] (K)">Xlink:DMP[122] (K)</option>
-        <option value="Xlink:DMP[122] (Protein N-term)">Xlink:DMP[122] (Protein N-term)</option>
-        <option value="Xlink:DMP[139] (K)">Xlink:DMP[139] (K)</option>
-        <option value="Xlink:DMP[139] (Protein N-term)">Xlink:DMP[139] (Protein N-term)</option>
-        <option value="Xlink:DMP[140] (K)">Xlink:DMP[140] (K)</option>
-        <option value="Xlink:DMP[140] (Protein N-term)">Xlink:DMP[140] (Protein N-term)</option>
-        <option value="Xlink:DMP[154] (K)">Xlink:DMP[154] (K)</option>
-        <option value="Xlink:DMP[154] (Protein N-term)">Xlink:DMP[154] (Protein N-term)</option>
-        <option value="Xlink:DSS[138] (K)">Xlink:DSS[138] (K)</option>
-        <option value="Xlink:DSS[138] (Protein N-term)">Xlink:DSS[138] (Protein N-term)</option>
-        <option value="Xlink:DSS[155] (K)">Xlink:DSS[155] (K)</option>
-        <option value="Xlink:DSS[155] (Protein N-term)">Xlink:DSS[155] (Protein N-term)</option>
-        <option value="Xlink:DSS[156] (K)">Xlink:DSS[156] (K)</option>
-        <option value="Xlink:DSS[156] (Protein N-term)">Xlink:DSS[156] (Protein N-term)</option>
-        <option value="Xlink:DSS[259] (K)">Xlink:DSS[259] (K)</option>
-        <option value="Xlink:DSS[259] (Protein N-term)">Xlink:DSS[259] (Protein N-term)</option>
-        <option value="Xlink:DSSO[104] (K)">Xlink:DSSO[104] (K)</option>
-        <option value="Xlink:DSSO[104] (Protein N-term)">Xlink:DSSO[104] (Protein N-term)</option>
-        <option value="Xlink:DSSO[158] (K)">Xlink:DSSO[158] (K)</option>
-        <option value="Xlink:DSSO[158] (Protein N-term)">Xlink:DSSO[158] (Protein N-term)</option>
-        <option value="Xlink:DSSO[175] (K)">Xlink:DSSO[175] (K)</option>
-        <option value="Xlink:DSSO[175] (Protein N-term)">Xlink:DSSO[175] (Protein N-term)</option>
-        <option value="Xlink:DSSO[176] (K)">Xlink:DSSO[176] (K)</option>
-        <option value="Xlink:DSSO[176] (Protein N-term)">Xlink:DSSO[176] (Protein N-term)</option>
-        <option value="Xlink:DSSO[279] (K)">Xlink:DSSO[279] (K)</option>
-        <option value="Xlink:DSSO[279] (Protein N-term)">Xlink:DSSO[279] (Protein N-term)</option>
-        <option value="Xlink:DSSO[54] (K)">Xlink:DSSO[54] (K)</option>
-        <option value="Xlink:DSSO[54] (Protein N-term)">Xlink:DSSO[54] (Protein N-term)</option>
-        <option value="Xlink:DSSO[86] (K)">Xlink:DSSO[86] (K)</option>
-        <option value="Xlink:DSSO[86] (Protein N-term)">Xlink:DSSO[86] (Protein N-term)</option>
-        <option value="Xlink:DST[114] (K)">Xlink:DST[114] (K)</option>
-        <option value="Xlink:DST[114] (Protein N-term)">Xlink:DST[114] (Protein N-term)</option>
-        <option value="Xlink:DST[132] (K)">Xlink:DST[132] (K)</option>
-        <option value="Xlink:DST[132] (Protein N-term)">Xlink:DST[132] (Protein N-term)</option>
-        <option value="Xlink:DST[56] (K)">Xlink:DST[56] (K)</option>
-        <option value="Xlink:DST[56] (Protein N-term)">Xlink:DST[56] (Protein N-term)</option>
-        <option value="Xlink:DTBP[172] (K)">Xlink:DTBP[172] (K)</option>
-        <option value="Xlink:DTBP[172] (Protein N-term)">Xlink:DTBP[172] (Protein N-term)</option>
-        <option value="Xlink:DTBP[87] (K)">Xlink:DTBP[87] (K)</option>
-        <option value="Xlink:DTBP[87] (Protein N-term)">Xlink:DTBP[87] (Protein N-term)</option>
-        <option value="Xlink:DTSSP[174] (K)">Xlink:DTSSP[174] (K)</option>
-        <option value="Xlink:DTSSP[174] (Protein N-term)">Xlink:DTSSP[174] (Protein N-term)</option>
-        <option value="Xlink:DTSSP[192] (K)">Xlink:DTSSP[192] (K)</option>
-        <option value="Xlink:DTSSP[192] (Protein N-term)">Xlink:DTSSP[192] (Protein N-term)</option>
-        <option value="Xlink:DTSSP[88] (K)">Xlink:DTSSP[88] (K)</option>
-        <option value="Xlink:DTSSP[88] (Protein N-term)">Xlink:DTSSP[88] (Protein N-term)</option>
-        <option value="Xlink:EGS[115] (K)">Xlink:EGS[115] (K)</option>
-        <option value="Xlink:EGS[115] (Protein N-term)">Xlink:EGS[115] (Protein N-term)</option>
-        <option value="Xlink:EGS[226] (K)">Xlink:EGS[226] (K)</option>
-        <option value="Xlink:EGS[226] (Protein N-term)">Xlink:EGS[226] (Protein N-term)</option>
-        <option value="Xlink:EGS[244] (K)">Xlink:EGS[244] (K)</option>
-        <option value="Xlink:EGS[244] (Protein N-term)">Xlink:EGS[244] (Protein N-term)</option>
-        <option value="Xlink:SMCC[219] (C)">Xlink:SMCC[219] (C)</option>
-        <option value="Xlink:SMCC[219] (K)">Xlink:SMCC[219] (K)</option>
-        <option value="Xlink:SMCC[219] (Protein N-term)">Xlink:SMCC[219] (Protein N-term)</option>
-        <option value="Xlink:SMCC[237] (C)">Xlink:SMCC[237] (C)</option>
-        <option value="Xlink:SMCC[237] (K)">Xlink:SMCC[237] (K)</option>
-        <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
-        <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
-        <option value="ZGB (K)">ZGB (K)</option>
-        <option value="ZGB (N-term)">ZGB (N-term)</option>
-        <option value="ZQG (K)">ZQG (K)</option>
-        <expand macro="list_string_san" name="fixed_modifications"/>
-      </param>
-      <param name="variable_modifications" argument="-algorithm:variable_modifications" multiple="true" type="select" optional="true" label="variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
-        <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
-        <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
-        <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
-        <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
-        <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
-        <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
-        <option value="2-succinyl (C)">2-succinyl (C)</option>
-        <option value="2HPG (R)">2HPG (R)</option>
-        <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
-        <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
-        <option value="3sulfo (N-term)">3sulfo (N-term)</option>
-        <option value="4-ONE (C)">4-ONE (C)</option>
-        <option value="4-ONE (H)">4-ONE (H)</option>
-        <option value="4-ONE (K)">4-ONE (K)</option>
-        <option value="4-ONE+Delta:H(-2)O(-1) (C)">4-ONE+Delta:H(-2)O(-1) (C)</option>
-        <option value="4-ONE+Delta:H(-2)O(-1) (H)">4-ONE+Delta:H(-2)O(-1) (H)</option>
-        <option value="4-ONE+Delta:H(-2)O(-1) (K)">4-ONE+Delta:H(-2)O(-1) (K)</option>
-        <option value="4AcAllylGal (C)">4AcAllylGal (C)</option>
-        <option value="a-type-ion (C-term)">a-type-ion (C-term)</option>
-        <option value="AccQTag (K)">AccQTag (K)</option>
-        <option value="AccQTag (N-term)">AccQTag (N-term)</option>
-        <option value="Acetyl (C)">Acetyl (C)</option>
-        <option value="Acetyl (H)">Acetyl (H)</option>
-        <option value="Acetyl (K)">Acetyl (K)</option>
-        <option value="Acetyl (N-term)">Acetyl (N-term)</option>
-        <option value="Acetyl (Protein N-term)">Acetyl (Protein N-term)</option>
-        <option value="Acetyl (R)">Acetyl (R)</option>
-        <option value="Acetyl (S)">Acetyl (S)</option>
-        <option value="Acetyl (T)">Acetyl (T)</option>
-        <option value="Acetyl (Y)">Acetyl (Y)</option>
-        <option value="Acetyl:13C(2) (K)">Acetyl:13C(2) (K)</option>
-        <option value="Acetyl:13C(2) (Protein N-term)">Acetyl:13C(2) (Protein N-term)</option>
-        <option value="Acetyl:2H(3) (H)">Acetyl:2H(3) (H)</option>
-        <option value="Acetyl:2H(3) (K)">Acetyl:2H(3) (K)</option>
-        <option value="Acetyl:2H(3) (N-term)">Acetyl:2H(3) (N-term)</option>
-        <option value="Acetyl:2H(3) (Protein N-term)">Acetyl:2H(3) (Protein N-term)</option>
-        <option value="Acetyl:2H(3) (S)">Acetyl:2H(3) (S)</option>
-        <option value="Acetyl:2H(3) (T)">Acetyl:2H(3) (T)</option>
-        <option value="Acetyl:2H(3) (Y)">Acetyl:2H(3) (Y)</option>
-        <option value="Acetyldeoxyhypusine (K)">Acetyldeoxyhypusine (K)</option>
-        <option value="Acetylhypusine (K)">Acetylhypusine (K)</option>
-        <option value="ADP-Ribosyl (C)">ADP-Ribosyl (C)</option>
-        <option value="ADP-Ribosyl (D)">ADP-Ribosyl (D)</option>
-        <option value="ADP-Ribosyl (E)">ADP-Ribosyl (E)</option>
-        <option value="ADP-Ribosyl (K)">ADP-Ribosyl (K)</option>
-        <option value="ADP-Ribosyl (N)">ADP-Ribosyl (N)</option>
-        <option value="ADP-Ribosyl (R)">ADP-Ribosyl (R)</option>
-        <option value="ADP-Ribosyl (S)">ADP-Ribosyl (S)</option>
-        <option value="ADP-Ribosyl (T)">ADP-Ribosyl (T)</option>
-        <option value="AEBS (H)">AEBS (H)</option>
-        <option value="AEBS (K)">AEBS (K)</option>
-        <option value="AEBS (Protein N-term)">AEBS (Protein N-term)</option>
-        <option value="AEBS (S)">AEBS (S)</option>
-        <option value="AEBS (Y)">AEBS (Y)</option>
-        <option value="AEC-MAEC (S)">AEC-MAEC (S)</option>
-        <option value="AEC-MAEC (T)">AEC-MAEC (T)</option>
-        <option value="AEC-MAEC:2H(4) (S)">AEC-MAEC:2H(4) (S)</option>
-        <option value="AEC-MAEC:2H(4) (T)">AEC-MAEC:2H(4) (T)</option>
-        <option value="AFB1_Dialdehyde (K)">AFB1_Dialdehyde (K)</option>
-        <option value="AHA-Alkyne (M)">AHA-Alkyne (M)</option>
-        <option value="AHA-Alkyne-KDDDD (M)">AHA-Alkyne-KDDDD (M)</option>
-        <option value="AHA-SS (M)">AHA-SS (M)</option>
-        <option value="AHA-SS_CAM (M)">AHA-SS_CAM (M)</option>
-        <option value="Ahx2+Hsl (C-term)">Ahx2+Hsl (C-term)</option>
-        <option value="Ala-&gt;Arg (A)">Ala-&gt;Arg (A)</option>
-        <option value="Ala-&gt;Asn (A)">Ala-&gt;Asn (A)</option>
-        <option value="Ala-&gt;Asp (A)">Ala-&gt;Asp (A)</option>
-        <option value="Ala-&gt;Cys (A)">Ala-&gt;Cys (A)</option>
-        <option value="Ala-&gt;Gln (A)">Ala-&gt;Gln (A)</option>
-        <option value="Ala-&gt;Glu (A)">Ala-&gt;Glu (A)</option>
-        <option value="Ala-&gt;Gly (A)">Ala-&gt;Gly (A)</option>
-        <option value="Ala-&gt;His (A)">Ala-&gt;His (A)</option>
-        <option value="Ala-&gt;Lys (A)">Ala-&gt;Lys (A)</option>
-        <option value="Ala-&gt;Met (A)">Ala-&gt;Met (A)</option>
-        <option value="Ala-&gt;Phe (A)">Ala-&gt;Phe (A)</option>
-        <option value="Ala-&gt;Pro (A)">Ala-&gt;Pro (A)</option>
-        <option value="Ala-&gt;Ser (A)">Ala-&gt;Ser (A)</option>
-        <option value="Ala-&gt;Thr (A)">Ala-&gt;Thr (A)</option>
-        <option value="Ala-&gt;Trp (A)">Ala-&gt;Trp (A)</option>
-        <option value="Ala-&gt;Tyr (A)">Ala-&gt;Tyr (A)</option>
-        <option value="Ala-&gt;Val (A)">Ala-&gt;Val (A)</option>
-        <option value="Ala-&gt;Xle (A)">Ala-&gt;Xle (A)</option>
-        <option value="Amidated (C-term)">Amidated (C-term)</option>
-        <option value="Amidated (Protein C-term)">Amidated (Protein C-term)</option>
-        <option value="Amidine (K)">Amidine (K)</option>
-        <option value="Amidine (N-term)">Amidine (N-term)</option>
-        <option value="Amidino (C)">Amidino (C)</option>
-        <option value="Amino (Y)">Amino (Y)</option>
-        <option value="Ammonia-loss (N)">Ammonia-loss (N)</option>
-        <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
-        <option value="Ammonia-loss (Protein N-term S)">Ammonia-loss (Protein N-term S)</option>
-        <option value="Ammonia-loss (Protein N-term T)">Ammonia-loss (Protein N-term T)</option>
-        <option value="Ammonium (C-term)">Ammonium (C-term)</option>
-        <option value="Ammonium (D)">Ammonium (D)</option>
-        <option value="Ammonium (E)">Ammonium (E)</option>
-        <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
-        <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
-        <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
-        <option value="Archaeol (C)">Archaeol (C)</option>
-        <option value="Arg (N-term)">Arg (N-term)</option>
-        <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
-        <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
-        <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
-        <option value="Arg-&gt;Cys (R)">Arg-&gt;Cys (R)</option>
-        <option value="Arg-&gt;Gln (R)">Arg-&gt;Gln (R)</option>
-        <option value="Arg-&gt;Glu (R)">Arg-&gt;Glu (R)</option>
-        <option value="Arg-&gt;GluSA (R)">Arg-&gt;GluSA (R)</option>
-        <option value="Arg-&gt;Gly (R)">Arg-&gt;Gly (R)</option>
-        <option value="Arg-&gt;His (R)">Arg-&gt;His (R)</option>
-        <option value="Arg-&gt;Lys (R)">Arg-&gt;Lys (R)</option>
-        <option value="Arg-&gt;Met (R)">Arg-&gt;Met (R)</option>
-        <option value="Arg-&gt;Npo (R)">Arg-&gt;Npo (R)</option>
-        <option value="Arg-&gt;Orn (R)">Arg-&gt;Orn (R)</option>
-        <option value="Arg-&gt;Phe (R)">Arg-&gt;Phe (R)</option>
-        <option value="Arg-&gt;Pro (R)">Arg-&gt;Pro (R)</option>
-        <option value="Arg-&gt;Ser (R)">Arg-&gt;Ser (R)</option>
-        <option value="Arg-&gt;Thr (R)">Arg-&gt;Thr (R)</option>
-        <option value="Arg-&gt;Trp (R)">Arg-&gt;Trp (R)</option>
-        <option value="Arg-&gt;Tyr (R)">Arg-&gt;Tyr (R)</option>
-        <option value="Arg-&gt;Val (R)">Arg-&gt;Val (R)</option>
-        <option value="Arg-&gt;Xle (R)">Arg-&gt;Xle (R)</option>
-        <option value="Arg-loss (C-term R)">Arg-loss (C-term R)</option>
-        <option value="Arg2PG (R)">Arg2PG (R)</option>
-        <option value="Argbiotinhydrazide (R)">Argbiotinhydrazide (R)</option>
-        <option value="AROD (C)">AROD (C)</option>
-        <option value="Asn-&gt;Ala (N)">Asn-&gt;Ala (N)</option>
-        <option value="Asn-&gt;Arg (N)">Asn-&gt;Arg (N)</option>
-        <option value="Asn-&gt;Asp (N)">Asn-&gt;Asp (N)</option>
-        <option value="Asn-&gt;Cys (N)">Asn-&gt;Cys (N)</option>
-        <option value="Asn-&gt;Gln (N)">Asn-&gt;Gln (N)</option>
-        <option value="Asn-&gt;Glu (N)">Asn-&gt;Glu (N)</option>
-        <option value="Asn-&gt;Gly (N)">Asn-&gt;Gly (N)</option>
-        <option value="Asn-&gt;His (N)">Asn-&gt;His (N)</option>
-        <option value="Asn-&gt;Lys (N)">Asn-&gt;Lys (N)</option>
-        <option value="Asn-&gt;Met (N)">Asn-&gt;Met (N)</option>
-        <option value="Asn-&gt;Phe (N)">Asn-&gt;Phe (N)</option>
-        <option value="Asn-&gt;Pro (N)">Asn-&gt;Pro (N)</option>
-        <option value="Asn-&gt;Ser (N)">Asn-&gt;Ser (N)</option>
-        <option value="Asn-&gt;Thr (N)">Asn-&gt;Thr (N)</option>
-        <option value="Asn-&gt;Trp (N)">Asn-&gt;Trp (N)</option>
-        <option value="Asn-&gt;Tyr (N)">Asn-&gt;Tyr (N)</option>
-        <option value="Asn-&gt;Val (N)">Asn-&gt;Val (N)</option>
-        <option value="Asn-&gt;Xle (N)">Asn-&gt;Xle (N)</option>
-        <option value="Asp-&gt;Ala (D)">Asp-&gt;Ala (D)</option>
-        <option value="Asp-&gt;Arg (D)">Asp-&gt;Arg (D)</option>
-        <option value="Asp-&gt;Asn (D)">Asp-&gt;Asn (D)</option>
-        <option value="Asp-&gt;Cys (D)">Asp-&gt;Cys (D)</option>
-        <option value="Asp-&gt;Gln (D)">Asp-&gt;Gln (D)</option>
-        <option value="Asp-&gt;Glu (D)">Asp-&gt;Glu (D)</option>
-        <option value="Asp-&gt;Gly (D)">Asp-&gt;Gly (D)</option>
-        <option value="Asp-&gt;His (D)">Asp-&gt;His (D)</option>
-        <option value="Asp-&gt;Lys (D)">Asp-&gt;Lys (D)</option>
-        <option value="Asp-&gt;Met (D)">Asp-&gt;Met (D)</option>
-        <option value="Asp-&gt;Phe (D)">Asp-&gt;Phe (D)</option>
-        <option value="Asp-&gt;Pro (D)">Asp-&gt;Pro (D)</option>
-        <option value="Asp-&gt;Ser (D)">Asp-&gt;Ser (D)</option>
-        <option value="Asp-&gt;Thr (D)">Asp-&gt;Thr (D)</option>
-        <option value="Asp-&gt;Trp (D)">Asp-&gt;Trp (D)</option>
-        <option value="Asp-&gt;Tyr (D)">Asp-&gt;Tyr (D)</option>
-        <option value="Asp-&gt;Val (D)">Asp-&gt;Val (D)</option>
-        <option value="Asp-&gt;Xle (D)">Asp-&gt;Xle (D)</option>
-        <option value="Aspartylurea (H)">Aspartylurea (H)</option>
-        <option value="Atto495Maleimide (C)">Atto495Maleimide (C)</option>
-        <option value="AzidoF (F)">AzidoF (F)</option>
-        <option value="azole (C)">azole (C)</option>
-        <option value="azole (S)">azole (S)</option>
-        <option value="Bacillosamine (N)">Bacillosamine (N)</option>
-        <option value="BADGE (C)">BADGE (C)</option>
-        <option value="BDMAPP (H)">BDMAPP (H)</option>
-        <option value="BDMAPP (K)">BDMAPP (K)</option>
-        <option value="BDMAPP (Protein N-term)">BDMAPP (Protein N-term)</option>
-        <option value="BDMAPP (W)">BDMAPP (W)</option>
-        <option value="BDMAPP (Y)">BDMAPP (Y)</option>
-        <option value="BEMAD_C (C)">BEMAD_C (C)</option>
-        <option value="BEMAD_C:2H(6) (C)">BEMAD_C:2H(6) (C)</option>
-        <option value="BEMAD_ST (S)">BEMAD_ST (S)</option>
-        <option value="BEMAD_ST (T)">BEMAD_ST (T)</option>
-        <option value="BEMAD_ST:2H(6) (S)">BEMAD_ST:2H(6) (S)</option>
-        <option value="BEMAD_ST:2H(6) (T)">BEMAD_ST:2H(6) (T)</option>
-        <option value="Benzoyl (K)">Benzoyl (K)</option>
-        <option value="Benzoyl (N-term)">Benzoyl (N-term)</option>
-        <option value="benzylguanidine (K)">benzylguanidine (K)</option>
-        <option value="betaFNA (C)">betaFNA (C)</option>
-        <option value="betaFNA (K)">betaFNA (K)</option>
-        <option value="BHT (C)">BHT (C)</option>
-        <option value="BHT (H)">BHT (H)</option>
-        <option value="BHT (K)">BHT (K)</option>
-        <option value="BHTOH (C)">BHTOH (C)</option>
-        <option value="BHTOH (H)">BHTOH (H)</option>
-        <option value="BHTOH (K)">BHTOH (K)</option>
-        <option value="Biotin (K)">Biotin (K)</option>
-        <option value="Biotin (N-term)">Biotin (N-term)</option>
-        <option value="Biotin-HPDP (C)">Biotin-HPDP (C)</option>
-        <option value="Biotin-PEG-PRA (M)">Biotin-PEG-PRA (M)</option>
-        <option value="Biotin-PEO-Amine (D)">Biotin-PEO-Amine (D)</option>
-        <option value="Biotin-PEO-Amine (E)">Biotin-PEO-Amine (E)</option>
-        <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
-        <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
-        <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
-        <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
-        <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
-        <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
-        <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
-        <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
-        <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
-        <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
-        <option value="Biotin:Thermo-21328 (K)">Biotin:Thermo-21328 (K)</option>
-        <option value="Biotin:Thermo-21328 (N-term)">Biotin:Thermo-21328 (N-term)</option>
-        <option value="Biotin:Thermo-21330 (K)">Biotin:Thermo-21330 (K)</option>
-        <option value="Biotin:Thermo-21330 (N-term)">Biotin:Thermo-21330 (N-term)</option>
-        <option value="Biotin:Thermo-21345 (Q)">Biotin:Thermo-21345 (Q)</option>
-        <option value="Biotin:Thermo-21360 (X)">Biotin:Thermo-21360 (X)</option>
-        <option value="Biotin:Thermo-21901+2H2O (C)">Biotin:Thermo-21901+2H2O (C)</option>
-        <option value="Biotin:Thermo-21901+H2O (C)">Biotin:Thermo-21901+H2O (C)</option>
-        <option value="Biotin:Thermo-21911 (C)">Biotin:Thermo-21911 (C)</option>
-        <option value="Biotin:Thermo-33033 (X)">Biotin:Thermo-33033 (X)</option>
-        <option value="Biotin:Thermo-33033-H (X)">Biotin:Thermo-33033-H (X)</option>
-        <option value="Biotin:Thermo-88310 (K)">Biotin:Thermo-88310 (K)</option>
-        <option value="Biotin:Thermo-88317 (S)">Biotin:Thermo-88317 (S)</option>
-        <option value="Biotin:Thermo-88317 (Y)">Biotin:Thermo-88317 (Y)</option>
-        <option value="biotinAcrolein298 (C)">biotinAcrolein298 (C)</option>
-        <option value="biotinAcrolein298 (H)">biotinAcrolein298 (H)</option>
-        <option value="biotinAcrolein298 (K)">biotinAcrolein298 (K)</option>
-        <option value="biotinAcrolein298 (Protein N-term)">biotinAcrolein298 (Protein N-term)</option>
-        <option value="BisANS (K)">BisANS (K)</option>
-        <option value="bisANS-sulfonates (K)">bisANS-sulfonates (K)</option>
-        <option value="bisANS-sulfonates (S)">bisANS-sulfonates (S)</option>
-        <option value="bisANS-sulfonates (T)">bisANS-sulfonates (T)</option>
-        <option value="BITC (C)">BITC (C)</option>
-        <option value="BITC (K)">BITC (K)</option>
-        <option value="BITC (N-term)">BITC (N-term)</option>
-        <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
-        <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-        <option value="Bodipy (C)">Bodipy (C)</option>
-        <option value="Brij35 (N-term)">Brij35 (N-term)</option>
-        <option value="Brij58 (N-term)">Brij58 (N-term)</option>
-        <option value="Bromo (F)">Bromo (F)</option>
-        <option value="Bromo (H)">Bromo (H)</option>
-        <option value="Bromo (W)">Bromo (W)</option>
-        <option value="Bromo (Y)">Bromo (Y)</option>
-        <option value="Bromobimane (C)">Bromobimane (C)</option>
-        <option value="Butyryl (K)">Butyryl (K)</option>
-        <option value="C8-QAT (K)">C8-QAT (K)</option>
-        <option value="C8-QAT (N-term)">C8-QAT (N-term)</option>
-        <option value="CAF (N-term)">CAF (N-term)</option>
-        <option value="CAMthiopropanoyl (K)">CAMthiopropanoyl (K)</option>
-        <option value="CAMthiopropanoyl (Protein N-term)">CAMthiopropanoyl (Protein N-term)</option>
-        <option value="Can-FP-biotin (S)">Can-FP-biotin (S)</option>
-        <option value="Can-FP-biotin (T)">Can-FP-biotin (T)</option>
-        <option value="Can-FP-biotin (Y)">Can-FP-biotin (Y)</option>
-        <option value="Carbamidomethyl (C)">Carbamidomethyl (C)</option>
-        <option value="Carbamidomethyl (D)">Carbamidomethyl (D)</option>
-        <option value="Carbamidomethyl (E)">Carbamidomethyl (E)</option>
-        <option value="Carbamidomethyl (H)">Carbamidomethyl (H)</option>
-        <option value="Carbamidomethyl (K)">Carbamidomethyl (K)</option>
-        <option value="Carbamidomethyl (M)">Carbamidomethyl (M)</option>
-        <option value="Carbamidomethyl (N-term)">Carbamidomethyl (N-term)</option>
-        <option value="Carbamidomethyl (S)">Carbamidomethyl (S)</option>
-        <option value="Carbamidomethyl (T)">Carbamidomethyl (T)</option>
-        <option value="Carbamidomethyl (U)">Carbamidomethyl (U)</option>
-        <option value="Carbamidomethyl (Y)">Carbamidomethyl (Y)</option>
-        <option value="CarbamidomethylDTT (C)">CarbamidomethylDTT (C)</option>
-        <option value="Carbamyl (C)">Carbamyl (C)</option>
-        <option value="Carbamyl (K)">Carbamyl (K)</option>
-        <option value="Carbamyl (M)">Carbamyl (M)</option>
-        <option value="Carbamyl (N-term)">Carbamyl (N-term)</option>
-        <option value="Carbamyl (Protein N-term)">Carbamyl (Protein N-term)</option>
-        <option value="Carbamyl (R)">Carbamyl (R)</option>
-        <option value="Carbamyl (S)">Carbamyl (S)</option>
-        <option value="Carbamyl (T)">Carbamyl (T)</option>
-        <option value="Carbamyl (Y)">Carbamyl (Y)</option>
-        <option value="Carbofuran (S)">Carbofuran (S)</option>
-        <option value="Carbonyl (A)">Carbonyl (A)</option>
-        <option value="Carbonyl (E)">Carbonyl (E)</option>
-        <option value="Carbonyl (I)">Carbonyl (I)</option>
-        <option value="Carbonyl (L)">Carbonyl (L)</option>
-        <option value="Carbonyl (Q)">Carbonyl (Q)</option>
-        <option value="Carbonyl (R)">Carbonyl (R)</option>
-        <option value="Carbonyl (S)">Carbonyl (S)</option>
-        <option value="Carbonyl (V)">Carbonyl (V)</option>
-        <option value="Carboxy (D)">Carboxy (D)</option>
-        <option value="Carboxy (E)">Carboxy (E)</option>
-        <option value="Carboxy (K)">Carboxy (K)</option>
-        <option value="Carboxy (Protein N-term M)">Carboxy (Protein N-term M)</option>
-        <option value="Carboxy (W)">Carboxy (W)</option>
-        <option value="Carboxy-&gt;Thiocarboxy (Protein C-term G)">Carboxy-&gt;Thiocarboxy (Protein C-term G)</option>
-        <option value="Carboxyethyl (H)">Carboxyethyl (H)</option>
-        <option value="Carboxyethyl (K)">Carboxyethyl (K)</option>
-        <option value="Carboxyethylpyrrole (K)">Carboxyethylpyrrole (K)</option>
-        <option value="Carboxymethyl (C)">Carboxymethyl (C)</option>
-        <option value="Carboxymethyl (K)">Carboxymethyl (K)</option>
-        <option value="Carboxymethyl (N-term)">Carboxymethyl (N-term)</option>
-        <option value="Carboxymethyl (U)">Carboxymethyl (U)</option>
-        <option value="Carboxymethyl (W)">Carboxymethyl (W)</option>
-        <option value="Carboxymethyl:13C(2) (C)">Carboxymethyl:13C(2) (C)</option>
-        <option value="CarboxymethylDMAP (N-term)">CarboxymethylDMAP (N-term)</option>
-        <option value="CarboxymethylDTT (C)">CarboxymethylDTT (C)</option>
-        <option value="Cation:Ag (C-term)">Cation:Ag (C-term)</option>
-        <option value="Cation:Ag (D)">Cation:Ag (D)</option>
-        <option value="Cation:Ag (E)">Cation:Ag (E)</option>
-        <option value="Cation:Al[III] (C-term)">Cation:Al[III] (C-term)</option>
-        <option value="Cation:Al[III] (D)">Cation:Al[III] (D)</option>
-        <option value="Cation:Al[III] (E)">Cation:Al[III] (E)</option>
-        <option value="Cation:Ca[II] (C-term)">Cation:Ca[II] (C-term)</option>
-        <option value="Cation:Ca[II] (D)">Cation:Ca[II] (D)</option>
-        <option value="Cation:Ca[II] (E)">Cation:Ca[II] (E)</option>
-        <option value="Cation:Cu[I] (C-term)">Cation:Cu[I] (C-term)</option>
-        <option value="Cation:Cu[I] (D)">Cation:Cu[I] (D)</option>
-        <option value="Cation:Cu[I] (E)">Cation:Cu[I] (E)</option>
-        <option value="Cation:Cu[I] (H)">Cation:Cu[I] (H)</option>
-        <option value="Cation:Fe[II] (C-term)">Cation:Fe[II] (C-term)</option>
-        <option value="Cation:Fe[II] (D)">Cation:Fe[II] (D)</option>
-        <option value="Cation:Fe[II] (E)">Cation:Fe[II] (E)</option>
-        <option value="Cation:Fe[III] (C-term)">Cation:Fe[III] (C-term)</option>
-        <option value="Cation:Fe[III] (D)">Cation:Fe[III] (D)</option>
-        <option value="Cation:Fe[III] (E)">Cation:Fe[III] (E)</option>
-        <option value="Cation:K (C-term)">Cation:K (C-term)</option>
-        <option value="Cation:K (D)">Cation:K (D)</option>
-        <option value="Cation:K (E)">Cation:K (E)</option>
-        <option value="Cation:Li (C-term)">Cation:Li (C-term)</option>
-        <option value="Cation:Li (D)">Cation:Li (D)</option>
-        <option value="Cation:Li (E)">Cation:Li (E)</option>
-        <option value="Cation:Mg[II] (C-term)">Cation:Mg[II] (C-term)</option>
-        <option value="Cation:Mg[II] (D)">Cation:Mg[II] (D)</option>
-        <option value="Cation:Mg[II] (E)">Cation:Mg[II] (E)</option>
-        <option value="Cation:Na (C-term)">Cation:Na (C-term)</option>
-        <option value="Cation:Na (D)">Cation:Na (D)</option>
-        <option value="Cation:Na (E)">Cation:Na (E)</option>
-        <option value="Cation:Ni[II] (C-term)">Cation:Ni[II] (C-term)</option>
-        <option value="Cation:Ni[II] (D)">Cation:Ni[II] (D)</option>
-        <option value="Cation:Ni[II] (E)">Cation:Ni[II] (E)</option>
-        <option value="Cation:Zn[II] (C-term)">Cation:Zn[II] (C-term)</option>
-        <option value="Cation:Zn[II] (D)">Cation:Zn[II] (D)</option>
-        <option value="Cation:Zn[II] (E)">Cation:Zn[II] (E)</option>
-        <option value="Cation:Zn[II] (H)">Cation:Zn[II] (H)</option>
-        <option value="cGMP (C)">cGMP (C)</option>
-        <option value="cGMP (S)">cGMP (S)</option>
-        <option value="cGMP+RMP-loss (C)">cGMP+RMP-loss (C)</option>
-        <option value="cGMP+RMP-loss (S)">cGMP+RMP-loss (S)</option>
-        <option value="CHDH (D)">CHDH (D)</option>
-        <option value="Chlorination (W)">Chlorination (W)</option>
-        <option value="Chlorination (Y)">Chlorination (Y)</option>
-        <option value="Cholesterol (Protein C-term)">Cholesterol (Protein C-term)</option>
-        <option value="CIGG (K)">CIGG (K)</option>
-        <option value="CLIP_TRAQ_2 (K)">CLIP_TRAQ_2 (K)</option>
-        <option value="CLIP_TRAQ_2 (N-term)">CLIP_TRAQ_2 (N-term)</option>
-        <option value="CLIP_TRAQ_2 (Y)">CLIP_TRAQ_2 (Y)</option>
-        <option value="CLIP_TRAQ_3 (K)">CLIP_TRAQ_3 (K)</option>
-        <option value="CLIP_TRAQ_3 (N-term)">CLIP_TRAQ_3 (N-term)</option>
-        <option value="CLIP_TRAQ_3 (Y)">CLIP_TRAQ_3 (Y)</option>
-        <option value="CLIP_TRAQ_4 (K)">CLIP_TRAQ_4 (K)</option>
-        <option value="CLIP_TRAQ_4 (N-term)">CLIP_TRAQ_4 (N-term)</option>
-        <option value="CLIP_TRAQ_4 (Y)">CLIP_TRAQ_4 (Y)</option>
-        <option value="CoenzymeA (C)">CoenzymeA (C)</option>
-        <option value="Cresylphosphate (H)">Cresylphosphate (H)</option>
-        <option value="Cresylphosphate (K)">Cresylphosphate (K)</option>
-        <option value="Cresylphosphate (R)">Cresylphosphate (R)</option>
-        <option value="Cresylphosphate (S)">Cresylphosphate (S)</option>
-        <option value="Cresylphosphate (T)">Cresylphosphate (T)</option>
-        <option value="Cresylphosphate (Y)">Cresylphosphate (Y)</option>
-        <option value="CresylSaligeninPhosphate (H)">CresylSaligeninPhosphate (H)</option>
-        <option value="CresylSaligeninPhosphate (K)">CresylSaligeninPhosphate (K)</option>
-        <option value="CresylSaligeninPhosphate (R)">CresylSaligeninPhosphate (R)</option>
-        <option value="CresylSaligeninPhosphate (S)">CresylSaligeninPhosphate (S)</option>
-        <option value="CresylSaligeninPhosphate (T)">CresylSaligeninPhosphate (T)</option>
-        <option value="CresylSaligeninPhosphate (Y)">CresylSaligeninPhosphate (Y)</option>
-        <option value="Crotonaldehyde (C)">Crotonaldehyde (C)</option>
-        <option value="Crotonaldehyde (H)">Crotonaldehyde (H)</option>
-        <option value="Crotonaldehyde (K)">Crotonaldehyde (K)</option>
-        <option value="Crotonyl (K)">Crotonyl (K)</option>
-        <option value="CuSMo (C)">CuSMo (C)</option>
-        <option value="CUSTOM0 (A)">CUSTOM0 (A)</option>
-        <option value="CUSTOM0 (C)">CUSTOM0 (C)</option>
-        <option value="CUSTOM0 (C-term)">CUSTOM0 (C-term)</option>
-        <option value="CUSTOM0 (D)">CUSTOM0 (D)</option>
-        <option value="CUSTOM0 (E)">CUSTOM0 (E)</option>
-        <option value="CUSTOM0 (F)">CUSTOM0 (F)</option>
-        <option value="CUSTOM0 (G)">CUSTOM0 (G)</option>
-        <option value="CUSTOM0 (H)">CUSTOM0 (H)</option>
-        <option value="CUSTOM0 (I)">CUSTOM0 (I)</option>
-        <option value="CUSTOM0 (K)">CUSTOM0 (K)</option>
-        <option value="CUSTOM0 (L)">CUSTOM0 (L)</option>
-        <option value="CUSTOM0 (M)">CUSTOM0 (M)</option>
-        <option value="CUSTOM0 (N)">CUSTOM0 (N)</option>
-        <option value="CUSTOM0 (N-term)">CUSTOM0 (N-term)</option>
-        <option value="CUSTOM0 (P)">CUSTOM0 (P)</option>
-        <option value="CUSTOM0 (Q)">CUSTOM0 (Q)</option>
-        <option value="CUSTOM0 (R)">CUSTOM0 (R)</option>
-        <option value="CUSTOM0 (S)">CUSTOM0 (S)</option>
-        <option value="CUSTOM0 (T)">CUSTOM0 (T)</option>
-        <option value="CUSTOM0 (V)">CUSTOM0 (V)</option>
-        <option value="CUSTOM0 (W)">CUSTOM0 (W)</option>
-        <option value="CUSTOM0 (Y)">CUSTOM0 (Y)</option>
-        <option value="CUSTOM1 (A)">CUSTOM1 (A)</option>
-        <option value="CUSTOM1 (C)">CUSTOM1 (C)</option>
-        <option value="CUSTOM1 (C-term)">CUSTOM1 (C-term)</option>
-        <option value="CUSTOM1 (D)">CUSTOM1 (D)</option>
-        <option value="CUSTOM1 (E)">CUSTOM1 (E)</option>
-        <option value="CUSTOM1 (F)">CUSTOM1 (F)</option>
-        <option value="CUSTOM1 (G)">CUSTOM1 (G)</option>
-        <option value="CUSTOM1 (H)">CUSTOM1 (H)</option>
-        <option value="CUSTOM1 (I)">CUSTOM1 (I)</option>
-        <option value="CUSTOM1 (K)">CUSTOM1 (K)</option>
-        <option value="CUSTOM1 (L)">CUSTOM1 (L)</option>
-        <option value="CUSTOM1 (M)">CUSTOM1 (M)</option>
-        <option value="CUSTOM1 (N)">CUSTOM1 (N)</option>
-        <option value="CUSTOM1 (N-term)">CUSTOM1 (N-term)</option>
-        <option value="CUSTOM1 (P)">CUSTOM1 (P)</option>
-        <option value="CUSTOM1 (Q)">CUSTOM1 (Q)</option>
-        <option value="CUSTOM1 (R)">CUSTOM1 (R)</option>
-        <option value="CUSTOM1 (S)">CUSTOM1 (S)</option>
-        <option value="CUSTOM1 (T)">CUSTOM1 (T)</option>
-        <option value="CUSTOM1 (V)">CUSTOM1 (V)</option>
-        <option value="CUSTOM1 (W)">CUSTOM1 (W)</option>
-        <option value="CUSTOM1 (Y)">CUSTOM1 (Y)</option>
-        <option value="CUSTOM2 (A)">CUSTOM2 (A)</option>
-        <option value="CUSTOM2 (C)">CUSTOM2 (C)</option>
-        <option value="CUSTOM2 (C-term)">CUSTOM2 (C-term)</option>
-        <option value="CUSTOM2 (D)">CUSTOM2 (D)</option>
-        <option value="CUSTOM2 (E)">CUSTOM2 (E)</option>
-        <option value="CUSTOM2 (F)">CUSTOM2 (F)</option>
-        <option value="CUSTOM2 (G)">CUSTOM2 (G)</option>
-        <option value="CUSTOM2 (H)">CUSTOM2 (H)</option>
-        <option value="CUSTOM2 (I)">CUSTOM2 (I)</option>
-        <option value="CUSTOM2 (K)">CUSTOM2 (K)</option>
-        <option value="CUSTOM2 (L)">CUSTOM2 (L)</option>
-        <option value="CUSTOM2 (M)">CUSTOM2 (M)</option>
-        <option value="CUSTOM2 (N)">CUSTOM2 (N)</option>
-        <option value="CUSTOM2 (N-term)">CUSTOM2 (N-term)</option>
-        <option value="CUSTOM2 (P)">CUSTOM2 (P)</option>
-        <option value="CUSTOM2 (Q)">CUSTOM2 (Q)</option>
-        <option value="CUSTOM2 (R)">CUSTOM2 (R)</option>
-        <option value="CUSTOM2 (S)">CUSTOM2 (S)</option>
-        <option value="CUSTOM2 (T)">CUSTOM2 (T)</option>
-        <option value="CUSTOM2 (V)">CUSTOM2 (V)</option>
-        <option value="CUSTOM2 (W)">CUSTOM2 (W)</option>
-        <option value="CUSTOM2 (Y)">CUSTOM2 (Y)</option>
-        <option value="CUSTOM3 (A)">CUSTOM3 (A)</option>
-        <option value="CUSTOM3 (C)">CUSTOM3 (C)</option>
-        <option value="CUSTOM3 (C-term)">CUSTOM3 (C-term)</option>
-        <option value="CUSTOM3 (D)">CUSTOM3 (D)</option>
-        <option value="CUSTOM3 (E)">CUSTOM3 (E)</option>
-        <option value="CUSTOM3 (F)">CUSTOM3 (F)</option>
-        <option value="CUSTOM3 (G)">CUSTOM3 (G)</option>
-        <option value="CUSTOM3 (H)">CUSTOM3 (H)</option>
-        <option value="CUSTOM3 (I)">CUSTOM3 (I)</option>
-        <option value="CUSTOM3 (K)">CUSTOM3 (K)</option>
-        <option value="CUSTOM3 (L)">CUSTOM3 (L)</option>
-        <option value="CUSTOM3 (M)">CUSTOM3 (M)</option>
-        <option value="CUSTOM3 (N)">CUSTOM3 (N)</option>
-        <option value="CUSTOM3 (N-term)">CUSTOM3 (N-term)</option>
-        <option value="CUSTOM3 (P)">CUSTOM3 (P)</option>
-        <option value="CUSTOM3 (Q)">CUSTOM3 (Q)</option>
-        <option value="CUSTOM3 (R)">CUSTOM3 (R)</option>
-        <option value="CUSTOM3 (S)">CUSTOM3 (S)</option>
-        <option value="CUSTOM3 (T)">CUSTOM3 (T)</option>
-        <option value="CUSTOM3 (V)">CUSTOM3 (V)</option>
-        <option value="CUSTOM3 (W)">CUSTOM3 (W)</option>
-        <option value="CUSTOM3 (Y)">CUSTOM3 (Y)</option>
-        <option value="CUSTOM4 (A)">CUSTOM4 (A)</option>
-        <option value="CUSTOM4 (C)">CUSTOM4 (C)</option>
-        <option value="CUSTOM4 (C-term)">CUSTOM4 (C-term)</option>
-        <option value="CUSTOM4 (D)">CUSTOM4 (D)</option>
-        <option value="CUSTOM4 (E)">CUSTOM4 (E)</option>
-        <option value="CUSTOM4 (F)">CUSTOM4 (F)</option>
-        <option value="CUSTOM4 (G)">CUSTOM4 (G)</option>
-        <option value="CUSTOM4 (H)">CUSTOM4 (H)</option>
-        <option value="CUSTOM4 (I)">CUSTOM4 (I)</option>
-        <option value="CUSTOM4 (K)">CUSTOM4 (K)</option>
-        <option value="CUSTOM4 (L)">CUSTOM4 (L)</option>
-        <option value="CUSTOM4 (M)">CUSTOM4 (M)</option>
-        <option value="CUSTOM4 (N)">CUSTOM4 (N)</option>
-        <option value="CUSTOM4 (N-term)">CUSTOM4 (N-term)</option>
-        <option value="CUSTOM4 (P)">CUSTOM4 (P)</option>
-        <option value="CUSTOM4 (Q)">CUSTOM4 (Q)</option>
-        <option value="CUSTOM4 (R)">CUSTOM4 (R)</option>
-        <option value="CUSTOM4 (S)">CUSTOM4 (S)</option>
-        <option value="CUSTOM4 (T)">CUSTOM4 (T)</option>
-        <option value="CUSTOM4 (V)">CUSTOM4 (V)</option>
-        <option value="CUSTOM4 (W)">CUSTOM4 (W)</option>
-        <option value="CUSTOM4 (Y)">CUSTOM4 (Y)</option>
-        <option value="CUSTOM5 (A)">CUSTOM5 (A)</option>
-        <option value="CUSTOM5 (C)">CUSTOM5 (C)</option>
-        <option value="CUSTOM5 (C-term)">CUSTOM5 (C-term)</option>
-        <option value="CUSTOM5 (D)">CUSTOM5 (D)</option>
-        <option value="CUSTOM5 (E)">CUSTOM5 (E)</option>
-        <option value="CUSTOM5 (F)">CUSTOM5 (F)</option>
-        <option value="CUSTOM5 (G)">CUSTOM5 (G)</option>
-        <option value="CUSTOM5 (H)">CUSTOM5 (H)</option>
-        <option value="CUSTOM5 (I)">CUSTOM5 (I)</option>
-        <option value="CUSTOM5 (K)">CUSTOM5 (K)</option>
-        <option value="CUSTOM5 (L)">CUSTOM5 (L)</option>
-        <option value="CUSTOM5 (M)">CUSTOM5 (M)</option>
-        <option value="CUSTOM5 (N)">CUSTOM5 (N)</option>
-        <option value="CUSTOM5 (N-term)">CUSTOM5 (N-term)</option>
-        <option value="CUSTOM5 (P)">CUSTOM5 (P)</option>
-        <option value="CUSTOM5 (Q)">CUSTOM5 (Q)</option>
-        <option value="CUSTOM5 (R)">CUSTOM5 (R)</option>
-        <option value="CUSTOM5 (S)">CUSTOM5 (S)</option>
-        <option value="CUSTOM5 (T)">CUSTOM5 (T)</option>
-        <option value="CUSTOM5 (V)">CUSTOM5 (V)</option>
-        <option value="CUSTOM5 (W)">CUSTOM5 (W)</option>
-        <option value="CUSTOM5 (Y)">CUSTOM5 (Y)</option>
-        <option value="CUSTOM6 (A)">CUSTOM6 (A)</option>
-        <option value="CUSTOM6 (C)">CUSTOM6 (C)</option>
-        <option value="CUSTOM6 (C-term)">CUSTOM6 (C-term)</option>
-        <option value="CUSTOM6 (D)">CUSTOM6 (D)</option>
-        <option value="CUSTOM6 (E)">CUSTOM6 (E)</option>
-        <option value="CUSTOM6 (F)">CUSTOM6 (F)</option>
-        <option value="CUSTOM6 (G)">CUSTOM6 (G)</option>
-        <option value="CUSTOM6 (H)">CUSTOM6 (H)</option>
-        <option value="CUSTOM6 (I)">CUSTOM6 (I)</option>
-        <option value="CUSTOM6 (K)">CUSTOM6 (K)</option>
-        <option value="CUSTOM6 (L)">CUSTOM6 (L)</option>
-        <option value="CUSTOM6 (M)">CUSTOM6 (M)</option>
-        <option value="CUSTOM6 (N)">CUSTOM6 (N)</option>
-        <option value="CUSTOM6 (N-term)">CUSTOM6 (N-term)</option>
-        <option value="CUSTOM6 (P)">CUSTOM6 (P)</option>
-        <option value="CUSTOM6 (Q)">CUSTOM6 (Q)</option>
-        <option value="CUSTOM6 (R)">CUSTOM6 (R)</option>
-        <option value="CUSTOM6 (S)">CUSTOM6 (S)</option>
-        <option value="CUSTOM6 (T)">CUSTOM6 (T)</option>
-        <option value="CUSTOM6 (V)">CUSTOM6 (V)</option>
-        <option value="CUSTOM6 (W)">CUSTOM6 (W)</option>
-        <option value="CUSTOM6 (Y)">CUSTOM6 (Y)</option>
-        <option value="CUSTOM7 (A)">CUSTOM7 (A)</option>
-        <option value="CUSTOM7 (C)">CUSTOM7 (C)</option>
-        <option value="CUSTOM7 (C-term)">CUSTOM7 (C-term)</option>
-        <option value="CUSTOM7 (D)">CUSTOM7 (D)</option>
-        <option value="CUSTOM7 (E)">CUSTOM7 (E)</option>
-        <option value="CUSTOM7 (F)">CUSTOM7 (F)</option>
-        <option value="CUSTOM7 (G)">CUSTOM7 (G)</option>
-        <option value="CUSTOM7 (H)">CUSTOM7 (H)</option>
-        <option value="CUSTOM7 (I)">CUSTOM7 (I)</option>
-        <option value="CUSTOM7 (K)">CUSTOM7 (K)</option>
-        <option value="CUSTOM7 (L)">CUSTOM7 (L)</option>
-        <option value="CUSTOM7 (M)">CUSTOM7 (M)</option>
-        <option value="CUSTOM7 (N)">CUSTOM7 (N)</option>
-        <option value="CUSTOM7 (N-term)">CUSTOM7 (N-term)</option>
-        <option value="CUSTOM7 (P)">CUSTOM7 (P)</option>
-        <option value="CUSTOM7 (Q)">CUSTOM7 (Q)</option>
-        <option value="CUSTOM7 (R)">CUSTOM7 (R)</option>
-        <option value="CUSTOM7 (S)">CUSTOM7 (S)</option>
-        <option value="CUSTOM7 (T)">CUSTOM7 (T)</option>
-        <option value="CUSTOM7 (V)">CUSTOM7 (V)</option>
-        <option value="CUSTOM7 (W)">CUSTOM7 (W)</option>
-        <option value="CUSTOM7 (Y)">CUSTOM7 (Y)</option>
-        <option value="CUSTOM8 (A)">CUSTOM8 (A)</option>
-        <option value="CUSTOM8 (C)">CUSTOM8 (C)</option>
-        <option value="CUSTOM8 (C-term)">CUSTOM8 (C-term)</option>
-        <option value="CUSTOM8 (D)">CUSTOM8 (D)</option>
-        <option value="CUSTOM8 (E)">CUSTOM8 (E)</option>
-        <option value="CUSTOM8 (F)">CUSTOM8 (F)</option>
-        <option value="CUSTOM8 (G)">CUSTOM8 (G)</option>
-        <option value="CUSTOM8 (H)">CUSTOM8 (H)</option>
-        <option value="CUSTOM8 (I)">CUSTOM8 (I)</option>
-        <option value="CUSTOM8 (K)">CUSTOM8 (K)</option>
-        <option value="CUSTOM8 (L)">CUSTOM8 (L)</option>
-        <option value="CUSTOM8 (M)">CUSTOM8 (M)</option>
-        <option value="CUSTOM8 (N)">CUSTOM8 (N)</option>
-        <option value="CUSTOM8 (N-term)">CUSTOM8 (N-term)</option>
-        <option value="CUSTOM8 (P)">CUSTOM8 (P)</option>
-        <option value="CUSTOM8 (Q)">CUSTOM8 (Q)</option>
-        <option value="CUSTOM8 (R)">CUSTOM8 (R)</option>
-        <option value="CUSTOM8 (S)">CUSTOM8 (S)</option>
-        <option value="CUSTOM8 (T)">CUSTOM8 (T)</option>
-        <option value="CUSTOM8 (V)">CUSTOM8 (V)</option>
-        <option value="CUSTOM8 (W)">CUSTOM8 (W)</option>
-        <option value="CUSTOM8 (Y)">CUSTOM8 (Y)</option>
-        <option value="CUSTOM9 (A)">CUSTOM9 (A)</option>
-        <option value="CUSTOM9 (C)">CUSTOM9 (C)</option>
-        <option value="CUSTOM9 (C-term)">CUSTOM9 (C-term)</option>
-        <option value="CUSTOM9 (D)">CUSTOM9 (D)</option>
-        <option value="CUSTOM9 (E)">CUSTOM9 (E)</option>
-        <option value="CUSTOM9 (F)">CUSTOM9 (F)</option>
-        <option value="CUSTOM9 (G)">CUSTOM9 (G)</option>
-        <option value="CUSTOM9 (H)">CUSTOM9 (H)</option>
-        <option value="CUSTOM9 (I)">CUSTOM9 (I)</option>
-        <option value="CUSTOM9 (K)">CUSTOM9 (K)</option>
-        <option value="CUSTOM9 (L)">CUSTOM9 (L)</option>
-        <option value="CUSTOM9 (M)">CUSTOM9 (M)</option>
-        <option value="CUSTOM9 (N)">CUSTOM9 (N)</option>
-        <option value="CUSTOM9 (N-term)">CUSTOM9 (N-term)</option>
-        <option value="CUSTOM9 (P)">CUSTOM9 (P)</option>
-        <option value="CUSTOM9 (Q)">CUSTOM9 (Q)</option>
-        <option value="CUSTOM9 (R)">CUSTOM9 (R)</option>
-        <option value="CUSTOM9 (S)">CUSTOM9 (S)</option>
-        <option value="CUSTOM9 (T)">CUSTOM9 (T)</option>
-        <option value="CUSTOM9 (V)">CUSTOM9 (V)</option>
-        <option value="CUSTOM9 (W)">CUSTOM9 (W)</option>
-        <option value="CUSTOM9 (Y)">CUSTOM9 (Y)</option>
-        <option value="Cy3-maleimide (C)">Cy3-maleimide (C)</option>
-        <option value="Cy3b-maleimide (C)">Cy3b-maleimide (C)</option>
-        <option value="Cyano (C)">Cyano (C)</option>
-        <option value="CyDye-Cy3 (C)">CyDye-Cy3 (C)</option>
-        <option value="CyDye-Cy5 (C)">CyDye-Cy5 (C)</option>
-        <option value="Cys-&gt;Ala (C)">Cys-&gt;Ala (C)</option>
-        <option value="Cys-&gt;Arg (C)">Cys-&gt;Arg (C)</option>
-        <option value="Cys-&gt;Asn (C)">Cys-&gt;Asn (C)</option>
-        <option value="Cys-&gt;Asp (C)">Cys-&gt;Asp (C)</option>
-        <option value="Cys-&gt;CamSec (C)">Cys-&gt;CamSec (C)</option>
-        <option value="Cys-&gt;Dha (C)">Cys-&gt;Dha (C)</option>
-        <option value="Cys-&gt;ethylaminoAla (C)">Cys-&gt;ethylaminoAla (C)</option>
-        <option value="Cys-&gt;Gln (C)">Cys-&gt;Gln (C)</option>
-        <option value="Cys-&gt;Glu (C)">Cys-&gt;Glu (C)</option>
-        <option value="Cys-&gt;Gly (C)">Cys-&gt;Gly (C)</option>
-        <option value="Cys-&gt;His (C)">Cys-&gt;His (C)</option>
-        <option value="Cys-&gt;Lys (C)">Cys-&gt;Lys (C)</option>
-        <option value="Cys-&gt;Met (C)">Cys-&gt;Met (C)</option>
-        <option value="Cys-&gt;methylaminoAla (C)">Cys-&gt;methylaminoAla (C)</option>
-        <option value="Cys-&gt;Oxoalanine (C)">Cys-&gt;Oxoalanine (C)</option>
-        <option value="Cys-&gt;Phe (C)">Cys-&gt;Phe (C)</option>
-        <option value="Cys-&gt;Pro (C)">Cys-&gt;Pro (C)</option>
-        <option value="Cys-&gt;PyruvicAcid (Protein N-term C)">Cys-&gt;PyruvicAcid (Protein N-term C)</option>
-        <option value="Cys-&gt;SecNEM (C)">Cys-&gt;SecNEM (C)</option>
-        <option value="Cys-&gt;SecNEM:2H(5) (C)">Cys-&gt;SecNEM:2H(5) (C)</option>
-        <option value="Cys-&gt;Ser (C)">Cys-&gt;Ser (C)</option>
-        <option value="Cys-&gt;Thr (C)">Cys-&gt;Thr (C)</option>
-        <option value="Cys-&gt;Trp (C)">Cys-&gt;Trp (C)</option>
-        <option value="Cys-&gt;Tyr (C)">Cys-&gt;Tyr (C)</option>
-        <option value="Cys-&gt;Val (C)">Cys-&gt;Val (C)</option>
-        <option value="Cys-&gt;Xle (C)">Cys-&gt;Xle (C)</option>
-        <option value="Cysteinyl (C)">Cysteinyl (C)</option>
-        <option value="cysTMT (C)">cysTMT (C)</option>
-        <option value="cysTMT6plex (C)">cysTMT6plex (C)</option>
-        <option value="Cytopiloyne (C)">Cytopiloyne (C)</option>
-        <option value="Cytopiloyne (K)">Cytopiloyne (K)</option>
-        <option value="Cytopiloyne (N-term)">Cytopiloyne (N-term)</option>
-        <option value="Cytopiloyne (P)">Cytopiloyne (P)</option>
-        <option value="Cytopiloyne (R)">Cytopiloyne (R)</option>
-        <option value="Cytopiloyne (S)">Cytopiloyne (S)</option>
-        <option value="Cytopiloyne (Y)">Cytopiloyne (Y)</option>
-        <option value="Cytopiloyne+water (C)">Cytopiloyne+water (C)</option>
-        <option value="Cytopiloyne+water (K)">Cytopiloyne+water (K)</option>
-        <option value="Cytopiloyne+water (N-term)">Cytopiloyne+water (N-term)</option>
-        <option value="Cytopiloyne+water (R)">Cytopiloyne+water (R)</option>
-        <option value="Cytopiloyne+water (S)">Cytopiloyne+water (S)</option>
-        <option value="Cytopiloyne+water (T)">Cytopiloyne+water (T)</option>
-        <option value="Cytopiloyne+water (Y)">Cytopiloyne+water (Y)</option>
-        <option value="DAET (S)">DAET (S)</option>
-        <option value="DAET (T)">DAET (T)</option>
-        <option value="Dansyl (K)">Dansyl (K)</option>
-        <option value="Dansyl (N-term)">Dansyl (N-term)</option>
-        <option value="Dap-DSP (A)">Dap-DSP (A)</option>
-        <option value="Dap-DSP (E)">Dap-DSP (E)</option>
-        <option value="Dap-DSP (K)">Dap-DSP (K)</option>
-        <option value="Deamidated (N)">Deamidated (N)</option>
-        <option value="Deamidated (Protein N-term F)">Deamidated (Protein N-term F)</option>
-        <option value="Deamidated (Q)">Deamidated (Q)</option>
-        <option value="Deamidated (R)">Deamidated (R)</option>
-        <option value="Deamidated:18O(1) (N)">Deamidated:18O(1) (N)</option>
-        <option value="Deamidated:18O(1) (Q)">Deamidated:18O(1) (Q)</option>
-        <option value="Decanoyl (S)">Decanoyl (S)</option>
-        <option value="Decanoyl (T)">Decanoyl (T)</option>
-        <option value="Decarboxylation (D)">Decarboxylation (D)</option>
-        <option value="Decarboxylation (E)">Decarboxylation (E)</option>
-        <option value="DEDGFLYMVYASQETFG (K)">DEDGFLYMVYASQETFG (K)</option>
-        <option value="Dehydrated (D)">Dehydrated (D)</option>
-        <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
-        <option value="Dehydrated (Protein C-term N)">Dehydrated (Protein C-term N)</option>
-        <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
-        <option value="Dehydrated (S)">Dehydrated (S)</option>
-        <option value="Dehydrated (T)">Dehydrated (T)</option>
-        <option value="Dehydrated (Y)">Dehydrated (Y)</option>
-        <option value="Dehydro (C)">Dehydro (C)</option>
-        <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
-        <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-        <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
-        <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
-        <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
-        <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
-        <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
-        <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
-        <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
-        <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
-        <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
-        <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-        <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
-        <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
-        <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
-        <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
-        <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
-        <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
-        <option value="Delta:H(4)C(3) (K)">Delta:H(4)C(3) (K)</option>
-        <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
-        <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
-        <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
-        <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
-        <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
-        <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
-        <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
-        <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
-        <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
-        <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
-        <option value="Delta:H(6)C(3)O(1) (K)">Delta:H(6)C(3)O(1) (K)</option>
-        <option value="Delta:H(6)C(3)O(1) (Protein N-term)">Delta:H(6)C(3)O(1) (Protein N-term)</option>
-        <option value="Delta:H(6)C(6)O(1) (K)">Delta:H(6)C(6)O(1) (K)</option>
-        <option value="Delta:H(6)C(7)O(4) (R)">Delta:H(6)C(7)O(4) (R)</option>
-        <option value="Delta:H(8)C(6)O(1) (K)">Delta:H(8)C(6)O(1) (K)</option>
-        <option value="Delta:H(8)C(6)O(1) (Protein N-term)">Delta:H(8)C(6)O(1) (Protein N-term)</option>
-        <option value="Delta:H(8)C(6)O(2) (K)">Delta:H(8)C(6)O(2) (K)</option>
-        <option value="Delta:Hg(1) (C)">Delta:Hg(1) (C)</option>
-        <option value="Delta:O(4) (W)">Delta:O(4) (W)</option>
-        <option value="Delta:S(-1)Se(1) (C)">Delta:S(-1)Se(1) (C)</option>
-        <option value="Delta:S(-1)Se(1) (M)">Delta:S(-1)Se(1) (M)</option>
-        <option value="Delta:Se(1) (C)">Delta:Se(1) (C)</option>
-        <option value="Deoxy (D)">Deoxy (D)</option>
-        <option value="Deoxy (S)">Deoxy (S)</option>
-        <option value="Deoxy (T)">Deoxy (T)</option>
-        <option value="Deoxyhypusine (K)">Deoxyhypusine (K)</option>
-        <option value="Deoxyhypusine (Q)">Deoxyhypusine (Q)</option>
-        <option value="DeStreak (C)">DeStreak (C)</option>
-        <option value="Dethiomethyl (M)">Dethiomethyl (M)</option>
-        <option value="dHex (N)">dHex (N)</option>
-        <option value="dHex (S)">dHex (S)</option>
-        <option value="dHex (T)">dHex (T)</option>
-        <option value="dHex(1)Hex(1) (S)">dHex(1)Hex(1) (S)</option>
-        <option value="dHex(1)Hex(1) (T)">dHex(1)Hex(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexA(1)HexNAc(3) (S)">dHex(1)Hex(1)HexA(1)HexNAc(3) (S)</option>
-        <option value="dHex(1)Hex(1)HexA(1)HexNAc(3) (T)">dHex(1)Hex(1)HexA(1)HexNAc(3) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)Kdn(1) (S)">dHex(1)Hex(1)HexNAc(1)Kdn(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)Kdn(1) (T)">dHex(1)Hex(1)HexNAc(1)Kdn(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(1)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(1)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3) (S)">dHex(1)Hex(1)HexNAc(3) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3) (T)">dHex(1)Hex(1)HexNAc(3) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(1)HexNAc(4) (S)">dHex(1)Hex(1)HexNAc(4) (S)</option>
-        <option value="dHex(1)Hex(1)HexNAc(4) (T)">dHex(1)Hex(1)HexNAc(4) (T)</option>
-        <option value="dHex(1)Hex(2) (S)">dHex(1)Hex(2) (S)</option>
-        <option value="dHex(1)Hex(2) (T)">dHex(1)Hex(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexA(1) (S)">dHex(1)Hex(2)HexA(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexA(1) (T)">dHex(1)Hex(2)HexA(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(1) (S)">dHex(1)Hex(2)HexA(1)HexNAc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(1) (T)">dHex(1)Hex(2)HexA(1)HexNAc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (S)">dHex(1)Hex(2)HexA(1)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (T)">dHex(1)Hex(2)HexA(1)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1) (S)">dHex(1)Hex(2)HexNAc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1) (T)">dHex(1)Hex(2)HexNAc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)Pent(1) (N)">dHex(1)Hex(2)HexNAc(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3) (N)">dHex(1)Hex(2)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3) (S)">dHex(1)Hex(2)HexNAc(3) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3) (T)">dHex(1)Hex(2)HexNAc(3) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4) (N)">dHex(1)Hex(2)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4) (S)">dHex(1)Hex(2)HexNAc(4) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4) (T)">dHex(1)Hex(2)HexNAc(4) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-        <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-        <option value="dHex(1)Hex(3) (S)">dHex(1)Hex(3) (S)</option>
-        <option value="dHex(1)Hex(3) (T)">dHex(1)Hex(3) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(2) (S)">dHex(1)Hex(3)HexA(1)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(2) (T)">dHex(1)Hex(3)HexA(1)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexA(2)HexNAc(2) (S)">dHex(1)Hex(3)HexA(2)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(3)HexA(2)HexNAc(2) (T)">dHex(1)Hex(3)HexA(2)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(1) (S)">dHex(1)Hex(3)HexNAc(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(1) (T)">dHex(1)Hex(3)HexNAc(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2) (N)">dHex(1)Hex(3)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2) (S)">dHex(1)Hex(3)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2) (T)">dHex(1)Hex(3)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)Pent(1) (N)">dHex(1)Hex(3)HexNAc(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3) (N)">dHex(1)Hex(3)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3) (S)">dHex(1)Hex(3)HexNAc(3) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3) (T)">dHex(1)Hex(3)HexNAc(3) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Pent(1) (N)">dHex(1)Hex(3)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Pent(2) (N)">dHex(1)Hex(3)HexNAc(3)Pent(2) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Pent(3) (N)">dHex(1)Hex(3)HexNAc(3)Pent(3) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4) (N)">dHex(1)Hex(3)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4) (S)">dHex(1)Hex(3)HexNAc(4) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4) (T)">dHex(1)Hex(3)HexNAc(4) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)Pent(1) (N)">dHex(1)Hex(3)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)Pent(2) (N)">dHex(1)Hex(3)HexNAc(4)Pent(2) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)Pent(3) (N)">dHex(1)Hex(3)HexNAc(4)Pent(3) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5) (N)">dHex(1)Hex(3)HexNAc(5) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5) (S)">dHex(1)Hex(3)HexNAc(5) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5) (T)">dHex(1)Hex(3)HexNAc(5) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(5)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(5)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(6) (N)">dHex(1)Hex(3)HexNAc(6) (N)</option>
-        <option value="dHex(1)Hex(3)HexNAc(6) (S)">dHex(1)Hex(3)HexNAc(6) (S)</option>
-        <option value="dHex(1)Hex(3)HexNAc(6) (T)">dHex(1)Hex(3)HexNAc(6) (T)</option>
-        <option value="dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4) (S)">dHex(1)Hex(4) (S)</option>
-        <option value="dHex(1)Hex(4) (T)">dHex(1)Hex(4) (T)</option>
-        <option value="dHex(1)Hex(4)HexA(1) (S)">dHex(1)Hex(4)HexA(1) (S)</option>
-        <option value="dHex(1)Hex(4)HexA(1) (T)">dHex(1)Hex(4)HexA(1) (T)</option>
-        <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (S)">dHex(1)Hex(4)HexA(1)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (T)">dHex(1)Hex(4)HexA(1)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(1)Pent(1) (N)">dHex(1)Hex(4)HexNAc(1)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(2) (N)">dHex(1)Hex(4)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(2) (S)">dHex(1)Hex(4)HexNAc(2) (S)</option>
-        <option value="dHex(1)Hex(4)HexNAc(2) (T)">dHex(1)Hex(4)HexNAc(2) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(2)Pent(1) (N)">dHex(1)Hex(4)HexNAc(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3) (N)">dHex(1)Hex(4)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)Pent(1) (N)">dHex(1)Hex(4)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4) (N)">dHex(1)Hex(4)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4) (S)">dHex(1)Hex(4)HexNAc(4) (S)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4) (T)">dHex(1)Hex(4)HexNAc(4) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)Pent(1) (N)">dHex(1)Hex(4)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(5) (N)">dHex(1)Hex(4)HexNAc(5) (N)</option>
-        <option value="dHex(1)Hex(4)HexNAc(5)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(5)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5) (S)">dHex(1)Hex(5) (S)</option>
-        <option value="dHex(1)Hex(5) (T)">dHex(1)Hex(5) (T)</option>
-        <option value="dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N)">dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(2) (N)">dHex(1)Hex(5)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(2)Pent(1) (N)">dHex(1)Hex(5)HexNAc(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3) (N)">dHex(1)Hex(5)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4) (N)">dHex(1)Hex(5)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N)">dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N)">dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)Pent(1) (N)">dHex(1)Hex(5)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(4)Sulf(2) (N)">dHex(1)Hex(5)HexNAc(4)Sulf(2) (N)</option>
-        <option value="dHex(1)Hex(5)HexNAc(5) (N)">dHex(1)Hex(5)HexNAc(5) (N)</option>
-        <option value="dHex(1)Hex(6) (S)">dHex(1)Hex(6) (S)</option>
-        <option value="dHex(1)Hex(6) (T)">dHex(1)Hex(6) (T)</option>
-        <option value="dHex(1)Hex(6)HexNAc(2) (N)">dHex(1)Hex(6)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(6)HexNAc(3) (N)">dHex(1)Hex(6)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(6)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(6)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(6)HexNAc(4) (N)">dHex(1)Hex(6)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(2) (N)">dHex(1)Hex(7)HexNAc(2) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(3) (N)">dHex(1)Hex(7)HexNAc(3) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(3)Phos(1) (N)">dHex(1)Hex(7)HexNAc(3)Phos(1) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)</option>
-        <option value="dHex(1)Hex(7)HexNAc(4) (N)">dHex(1)Hex(7)HexNAc(4) (N)</option>
-        <option value="dHex(1)Hex(8)HexNAc(2) (N)">dHex(1)Hex(8)HexNAc(2) (N)</option>
-        <option value="dHex(1)HexNAc(3) (S)">dHex(1)HexNAc(3) (S)</option>
-        <option value="dHex(1)HexNAc(3) (T)">dHex(1)HexNAc(3) (T)</option>
-        <option value="dHex(1)HexNAc(4) (S)">dHex(1)HexNAc(4) (S)</option>
-        <option value="dHex(1)HexNAc(4) (T)">dHex(1)HexNAc(4) (T)</option>
-        <option value="dHex(1)HexNAc(5) (S)">dHex(1)HexNAc(5) (S)</option>
-        <option value="dHex(1)HexNAc(5) (T)">dHex(1)HexNAc(5) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(1)Kdn(1) (S)">dHex(2)Hex(1)HexNAc(1)Kdn(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(1)Kdn(1) (T)">dHex(2)Hex(1)HexNAc(1)Kdn(1) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(2)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(2)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)NeuAc(1) (S)">dHex(2)Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)NeuAc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(3) (S)">dHex(2)Hex(1)HexNAc(3) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(3) (T)">dHex(2)Hex(1)HexNAc(3) (T)</option>
-        <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2) (S)">dHex(2)Hex(2) (S)</option>
-        <option value="dHex(2)Hex(2) (T)">dHex(2)Hex(2) (T)</option>
-        <option value="dHex(2)Hex(2)HexA(1) (S)">dHex(2)Hex(2)HexA(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexA(1) (T)">dHex(2)Hex(2)HexA(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexA(1)HexNAc(1) (S)">dHex(2)Hex(2)HexA(1)HexNAc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexA(1)HexNAc(1) (T)">dHex(2)Hex(2)HexA(1)HexNAc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(1) (S)">dHex(2)Hex(2)HexNAc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(1) (T)">dHex(2)Hex(2)HexNAc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2) (N)">dHex(2)Hex(2)HexNAc(2) (N)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2) (S)">dHex(2)Hex(2)HexNAc(2) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2) (T)">dHex(2)Hex(2)HexNAc(2) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(2)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(2)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(2)Sulf(2) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(2)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(2)Sulf(2) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3) (N)">dHex(2)Hex(2)HexNAc(3) (N)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3) (S)">dHex(2)Hex(2)HexNAc(3) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3) (T)">dHex(2)Hex(2)HexNAc(3) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)NeuAc(1) (S)">dHex(2)Hex(2)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(2)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)NeuGc(1) (S)">dHex(2)Hex(2)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)NeuGc(1) (T)">dHex(2)Hex(2)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(4) (S)">dHex(2)Hex(2)HexNAc(4) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(4) (T)">dHex(2)Hex(2)HexNAc(4) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(5) (S)">dHex(2)Hex(2)HexNAc(5) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(5) (T)">dHex(2)Hex(2)HexNAc(5) (T)</option>
-        <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3) (S)">dHex(2)Hex(3) (S)</option>
-        <option value="dHex(2)Hex(3) (T)">dHex(2)Hex(3) (T)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(1)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(1)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(1)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2) (N)">dHex(2)Hex(3)HexNAc(2) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2) (S)">dHex(2)Hex(3)HexNAc(2) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2) (T)">dHex(2)Hex(3)HexNAc(2) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(3)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(3)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3) (N)">dHex(2)Hex(3)HexNAc(3) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3) (S)">dHex(2)Hex(3)HexNAc(3) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3) (T)">dHex(2)Hex(3)HexNAc(3) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)Pent(1) (N)">dHex(2)Hex(3)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)Pent(2) (N)">dHex(2)Hex(3)HexNAc(3)Pent(2) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4) (N)">dHex(2)Hex(3)HexNAc(4) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4) (S)">dHex(2)Hex(3)HexNAc(4) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4) (T)">dHex(2)Hex(3)HexNAc(4) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4)Pent(1) (N)">dHex(2)Hex(3)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(4)Pent(2) (N)">dHex(2)Hex(3)HexNAc(4)Pent(2) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(5) (N)">dHex(2)Hex(3)HexNAc(5) (N)</option>
-        <option value="dHex(2)Hex(3)HexNAc(5) (S)">dHex(2)Hex(3)HexNAc(5) (S)</option>
-        <option value="dHex(2)Hex(3)HexNAc(5) (T)">dHex(2)Hex(3)HexNAc(5) (T)</option>
-        <option value="dHex(2)Hex(3)HexNAc(6) (N)">dHex(2)Hex(3)HexNAc(6) (N)</option>
-        <option value="dHex(2)Hex(4) (S)">dHex(2)Hex(4) (S)</option>
-        <option value="dHex(2)Hex(4) (T)">dHex(2)Hex(4) (T)</option>
-        <option value="dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="dHex(2)Hex(4)HexNAc(1) (S)">dHex(2)Hex(4)HexNAc(1) (S)</option>
-        <option value="dHex(2)Hex(4)HexNAc(1) (T)">dHex(2)Hex(4)HexNAc(1) (T)</option>
-        <option value="dHex(2)Hex(4)HexNAc(2) (N)">dHex(2)Hex(4)HexNAc(2) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(2) (S)">dHex(2)Hex(4)HexNAc(2) (S)</option>
-        <option value="dHex(2)Hex(4)HexNAc(2) (T)">dHex(2)Hex(4)HexNAc(2) (T)</option>
-        <option value="dHex(2)Hex(4)HexNAc(3) (N)">dHex(2)Hex(4)HexNAc(3) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(3)Pent(1) (N)">dHex(2)Hex(4)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4) (N)">dHex(2)Hex(4)HexNAc(4) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4) (S)">dHex(2)Hex(4)HexNAc(4) (S)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4) (T)">dHex(2)Hex(4)HexNAc(4) (T)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4)Pent(1) (N)">dHex(2)Hex(4)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(2)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(5) (N)">dHex(2)Hex(4)HexNAc(5) (N)</option>
-        <option value="dHex(2)Hex(4)HexNAc(5) (S)">dHex(2)Hex(4)HexNAc(5) (S)</option>
-        <option value="dHex(2)Hex(4)HexNAc(5) (T)">dHex(2)Hex(4)HexNAc(5) (T)</option>
-        <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (S)">dHex(2)Hex(5)HexNAc(2)Me(1) (S)</option>
-        <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (T)">dHex(2)Hex(5)HexNAc(2)Me(1) (T)</option>
-        <option value="dHex(2)Hex(5)HexNAc(3)Pent(1) (N)">dHex(2)Hex(5)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(2)Hex(5)HexNAc(4) (N)">dHex(2)Hex(5)HexNAc(4) (N)</option>
-        <option value="dHex(2)HexNAc(2)Kdn(1) (S)">dHex(2)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(2)HexNAc(2)Kdn(1) (T)">dHex(2)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(2)HexNAc(5) (S)">dHex(2)HexNAc(5) (S)</option>
-        <option value="dHex(2)HexNAc(5) (T)">dHex(2)HexNAc(5) (T)</option>
-        <option value="dHex(2)HexNAc(7) (S)">dHex(2)HexNAc(7) (S)</option>
-        <option value="dHex(2)HexNAc(7) (T)">dHex(2)HexNAc(7) (T)</option>
-        <option value="dHex(3)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(3)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(3)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(3)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(3)Hex(1)HexNAc(3)Kdn(1) (S)">dHex(3)Hex(1)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(3)Hex(1)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(1)HexNAc(3)Kdn(1) (T)</option>
-        <option value="dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(2) (S)">dHex(3)Hex(2)HexNAc(2) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(2) (T)">dHex(3)Hex(2)HexNAc(2) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(3)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(3) (S)">dHex(3)Hex(2)HexNAc(3) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(3) (T)">dHex(3)Hex(2)HexNAc(3) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (S)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(4) (S)">dHex(3)Hex(2)HexNAc(4) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(4) (T)">dHex(3)Hex(2)HexNAc(4) (T)</option>
-        <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-        <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(1) (S)">dHex(3)Hex(3)HexNAc(1) (S)</option>
-        <option value="dHex(3)Hex(3)HexNAc(1) (T)">dHex(3)Hex(3)HexNAc(1) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(2) (S)">dHex(3)Hex(3)HexNAc(2) (S)</option>
-        <option value="dHex(3)Hex(3)HexNAc(2) (T)">dHex(3)Hex(3)HexNAc(2) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3) (S)">dHex(3)Hex(3)HexNAc(3) (S)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3) (T)">dHex(3)Hex(3)HexNAc(3) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="dHex(3)Hex(3)HexNAc(3)Pent(1) (N)">dHex(3)Hex(3)HexNAc(3)Pent(1) (N)</option>
-        <option value="dHex(3)Hex(3)HexNAc(4) (N)">dHex(3)Hex(3)HexNAc(4) (N)</option>
-        <option value="dHex(3)Hex(3)HexNAc(4)Pent(1) (N)">dHex(3)Hex(3)HexNAc(4)Pent(1) (N)</option>
-        <option value="dHex(3)Hex(4)HexNAc(4) (N)">dHex(3)Hex(4)HexNAc(4) (N)</option>
-        <option value="dHex(3)Hex(4)HexNAc(4) (S)">dHex(3)Hex(4)HexNAc(4) (S)</option>
-        <option value="dHex(3)Hex(4)HexNAc(4) (T)">dHex(3)Hex(4)HexNAc(4) (T)</option>
-        <option value="dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-        <option value="dHex(3)HexNAc(3)Kdn(1) (S)">dHex(3)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(3)HexNAc(3)Kdn(1) (T)">dHex(3)HexNAc(3)Kdn(1) (T)</option>
-        <option value="dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)">dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)</option>
-        <option value="dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)">dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)</option>
-        <option value="dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)">dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)">dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)</option>
-        <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-        <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-        <option value="dHex(4)Hex(2)HexNAc(3) (S)">dHex(4)Hex(2)HexNAc(3) (S)</option>
-        <option value="dHex(4)Hex(2)HexNAc(3) (T)">dHex(4)Hex(2)HexNAc(3) (T)</option>
-        <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="dHex(4)Hex(3)HexNAc(3) (S)">dHex(4)Hex(3)HexNAc(3) (S)</option>
-        <option value="dHex(4)Hex(3)HexNAc(3) (T)">dHex(4)Hex(3)HexNAc(3) (T)</option>
-        <option value="dHex(4)HexNAc(3)Kdn(1) (S)">dHex(4)HexNAc(3)Kdn(1) (S)</option>
-        <option value="dHex(4)HexNAc(3)Kdn(1) (T)">dHex(4)HexNAc(3)Kdn(1) (T)</option>
-        <option value="DHP (C)">DHP (C)</option>
-        <option value="Diacylglycerol (C)">Diacylglycerol (C)</option>
-        <option value="DiART6plex (K)">DiART6plex (K)</option>
-        <option value="DiART6plex (N-term)">DiART6plex (N-term)</option>
-        <option value="DiART6plex (Protein N-term)">DiART6plex (Protein N-term)</option>
-        <option value="DiART6plex (Y)">DiART6plex (Y)</option>
-        <option value="DiART6plex115 (K)">DiART6plex115 (K)</option>
-        <option value="DiART6plex115 (N-term)">DiART6plex115 (N-term)</option>
-        <option value="DiART6plex115 (Protein N-term)">DiART6plex115 (Protein N-term)</option>
-        <option value="DiART6plex115 (Y)">DiART6plex115 (Y)</option>
-        <option value="DiART6plex116/119 (K)">DiART6plex116/119 (K)</option>
-        <option value="DiART6plex116/119 (N-term)">DiART6plex116/119 (N-term)</option>
-        <option value="DiART6plex116/119 (Protein N-term)">DiART6plex116/119 (Protein N-term)</option>
-        <option value="DiART6plex116/119 (Y)">DiART6plex116/119 (Y)</option>
-        <option value="DiART6plex117 (K)">DiART6plex117 (K)</option>
-        <option value="DiART6plex117 (N-term)">DiART6plex117 (N-term)</option>
-        <option value="DiART6plex117 (Protein N-term)">DiART6plex117 (Protein N-term)</option>
-        <option value="DiART6plex117 (Y)">DiART6plex117 (Y)</option>
-        <option value="DiART6plex118 (K)">DiART6plex118 (K)</option>
-        <option value="DiART6plex118 (N-term)">DiART6plex118 (N-term)</option>
-        <option value="DiART6plex118 (Protein N-term)">DiART6plex118 (Protein N-term)</option>
-        <option value="DiART6plex118 (Y)">DiART6plex118 (Y)</option>
-        <option value="Dibromo (Y)">Dibromo (Y)</option>
-        <option value="Dicarbamidomethyl (C)">Dicarbamidomethyl (C)</option>
-        <option value="Dicarbamidomethyl (H)">Dicarbamidomethyl (H)</option>
-        <option value="Dicarbamidomethyl (K)">Dicarbamidomethyl (K)</option>
-        <option value="Dicarbamidomethyl (N-term)">Dicarbamidomethyl (N-term)</option>
-        <option value="Dicarbamidomethyl (R)">Dicarbamidomethyl (R)</option>
-        <option value="dichlorination (C)">dichlorination (C)</option>
-        <option value="dichlorination (Y)">dichlorination (Y)</option>
-        <option value="Didehydro (C-term K)">Didehydro (C-term K)</option>
-        <option value="Didehydro (S)">Didehydro (S)</option>
-        <option value="Didehydro (T)">Didehydro (T)</option>
-        <option value="Didehydro (Y)">Didehydro (Y)</option>
-        <option value="Didehydroretinylidene (K)">Didehydroretinylidene (K)</option>
-        <option value="Diethyl (K)">Diethyl (K)</option>
-        <option value="Diethyl (N-term)">Diethyl (N-term)</option>
-        <option value="Diethylphosphate (C)">Diethylphosphate (C)</option>
-        <option value="Diethylphosphate (H)">Diethylphosphate (H)</option>
-        <option value="Diethylphosphate (K)">Diethylphosphate (K)</option>
-        <option value="Diethylphosphate (N-term)">Diethylphosphate (N-term)</option>
-        <option value="Diethylphosphate (S)">Diethylphosphate (S)</option>
-        <option value="Diethylphosphate (T)">Diethylphosphate (T)</option>
-        <option value="Diethylphosphate (Y)">Diethylphosphate (Y)</option>
-        <option value="Diethylphosphothione (C)">Diethylphosphothione (C)</option>
-        <option value="Diethylphosphothione (H)">Diethylphosphothione (H)</option>
-        <option value="Diethylphosphothione (K)">Diethylphosphothione (K)</option>
-        <option value="Diethylphosphothione (S)">Diethylphosphothione (S)</option>
-        <option value="Diethylphosphothione (T)">Diethylphosphothione (T)</option>
-        <option value="Diethylphosphothione (Y)">Diethylphosphothione (Y)</option>
-        <option value="Difuran (Y)">Difuran (Y)</option>
-        <option value="Dihydroxyimidazolidine (R)">Dihydroxyimidazolidine (R)</option>
-        <option value="Diiodo (H)">Diiodo (H)</option>
-        <option value="Diiodo (Y)">Diiodo (Y)</option>
-        <option value="Diironsubcluster (C)">Diironsubcluster (C)</option>
-        <option value="Diisopropylphosphate (K)">Diisopropylphosphate (K)</option>
-        <option value="Diisopropylphosphate (N-term)">Diisopropylphosphate (N-term)</option>
-        <option value="Diisopropylphosphate (S)">Diisopropylphosphate (S)</option>
-        <option value="Diisopropylphosphate (T)">Diisopropylphosphate (T)</option>
-        <option value="Diisopropylphosphate (Y)">Diisopropylphosphate (Y)</option>
-        <option value="DiLeu4plex (K)">DiLeu4plex (K)</option>
-        <option value="DiLeu4plex (N-term)">DiLeu4plex (N-term)</option>
-        <option value="DiLeu4plex (Y)">DiLeu4plex (Y)</option>
-        <option value="DiLeu4plex115 (K)">DiLeu4plex115 (K)</option>
-        <option value="DiLeu4plex115 (N-term)">DiLeu4plex115 (N-term)</option>
-        <option value="DiLeu4plex115 (Y)">DiLeu4plex115 (Y)</option>
-        <option value="DiLeu4plex117 (K)">DiLeu4plex117 (K)</option>
-        <option value="DiLeu4plex117 (N-term)">DiLeu4plex117 (N-term)</option>
-        <option value="DiLeu4plex117 (Y)">DiLeu4plex117 (Y)</option>
-        <option value="DiLeu4plex118 (K)">DiLeu4plex118 (K)</option>
-        <option value="DiLeu4plex118 (N-term)">DiLeu4plex118 (N-term)</option>
-        <option value="DiLeu4plex118 (Y)">DiLeu4plex118 (Y)</option>
-        <option value="Dimethyl (K)">Dimethyl (K)</option>
-        <option value="Dimethyl (N)">Dimethyl (N)</option>
-        <option value="Dimethyl (N-term)">Dimethyl (N-term)</option>
-        <option value="Dimethyl (Protein N-term P)">Dimethyl (Protein N-term P)</option>
-        <option value="Dimethyl (Protein N-term)">Dimethyl (Protein N-term)</option>
-        <option value="Dimethyl (R)">Dimethyl (R)</option>
-        <option value="Dimethyl:2H(2)13C (K)">Dimethyl:2H(2)13C (K)</option>
-        <option value="Dimethyl:2H(2)13C (N)">Dimethyl:2H(2)13C (N)</option>
-        <option value="Dimethyl:2H(2)13C (N-term)">Dimethyl:2H(2)13C (N-term)</option>
-        <option value="Dimethyl:2H(2)13C (Protein N-term P)">Dimethyl:2H(2)13C (Protein N-term P)</option>
-        <option value="Dimethyl:2H(2)13C (R)">Dimethyl:2H(2)13C (R)</option>
-        <option value="Dimethyl:2H(4) (K)">Dimethyl:2H(4) (K)</option>
-        <option value="Dimethyl:2H(4) (N-term)">Dimethyl:2H(4) (N-term)</option>
-        <option value="Dimethyl:2H(4) (Protein N-term)">Dimethyl:2H(4) (Protein N-term)</option>
-        <option value="Dimethyl:2H(4) (R)">Dimethyl:2H(4) (R)</option>
-        <option value="Dimethyl:2H(4)13C(2) (K)">Dimethyl:2H(4)13C(2) (K)</option>
-        <option value="Dimethyl:2H(4)13C(2) (N-term)">Dimethyl:2H(4)13C(2) (N-term)</option>
-        <option value="Dimethyl:2H(4)13C(2) (Protein N-term)">Dimethyl:2H(4)13C(2) (Protein N-term)</option>
-        <option value="Dimethyl:2H(4)13C(2) (R)">Dimethyl:2H(4)13C(2) (R)</option>
-        <option value="Dimethyl:2H(6) (K)">Dimethyl:2H(6) (K)</option>
-        <option value="Dimethyl:2H(6) (N-term)">Dimethyl:2H(6) (N-term)</option>
-        <option value="Dimethyl:2H(6) (R)">Dimethyl:2H(6) (R)</option>
-        <option value="Dimethyl:2H(6)13C(2) (K)">Dimethyl:2H(6)13C(2) (K)</option>
-        <option value="Dimethyl:2H(6)13C(2) (N-term)">Dimethyl:2H(6)13C(2) (N-term)</option>
-        <option value="Dimethyl:2H(6)13C(2) (Protein N-term)">Dimethyl:2H(6)13C(2) (Protein N-term)</option>
-        <option value="Dimethyl:2H(6)13C(2) (R)">Dimethyl:2H(6)13C(2) (R)</option>
-        <option value="DimethylamineGMBS (C)">DimethylamineGMBS (C)</option>
-        <option value="Dimethylaminoethyl (C)">Dimethylaminoethyl (C)</option>
-        <option value="DimethylArsino (C)">DimethylArsino (C)</option>
-        <option value="Dimethylphosphothione (C)">Dimethylphosphothione (C)</option>
-        <option value="Dimethylphosphothione (H)">Dimethylphosphothione (H)</option>
-        <option value="Dimethylphosphothione (K)">Dimethylphosphothione (K)</option>
-        <option value="Dimethylphosphothione (S)">Dimethylphosphothione (S)</option>
-        <option value="Dimethylphosphothione (T)">Dimethylphosphothione (T)</option>
-        <option value="Dimethylphosphothione (Y)">Dimethylphosphothione (Y)</option>
-        <option value="DimethylpyrroleAdduct (K)">DimethylpyrroleAdduct (K)</option>
-        <option value="Dioxidation (C)">Dioxidation (C)</option>
-        <option value="Dioxidation (E)">Dioxidation (E)</option>
-        <option value="Dioxidation (F)">Dioxidation (F)</option>
-        <option value="Dioxidation (I)">Dioxidation (I)</option>
-        <option value="Dioxidation (K)">Dioxidation (K)</option>
-        <option value="Dioxidation (L)">Dioxidation (L)</option>
-        <option value="Dioxidation (M)">Dioxidation (M)</option>
-        <option value="Dioxidation (P)">Dioxidation (P)</option>
-        <option value="Dioxidation (R)">Dioxidation (R)</option>
-        <option value="Dioxidation (U)">Dioxidation (U)</option>
-        <option value="Dioxidation (V)">Dioxidation (V)</option>
-        <option value="Dioxidation (W)">Dioxidation (W)</option>
-        <option value="Dioxidation (Y)">Dioxidation (Y)</option>
-        <option value="Diphthamide (H)">Diphthamide (H)</option>
-        <option value="Dipyridyl (C)">Dipyridyl (C)</option>
-        <option value="Dipyrrolylmethanemethyl (C)">Dipyrrolylmethanemethyl (C)</option>
-        <option value="DMPO (C)">DMPO (C)</option>
-        <option value="DMPO (H)">DMPO (H)</option>
-        <option value="DMPO (Y)">DMPO (Y)</option>
-        <option value="DNCB_hapten (C)">DNCB_hapten (C)</option>
-        <option value="DNCB_hapten (H)">DNCB_hapten (H)</option>
-        <option value="DNCB_hapten (K)">DNCB_hapten (K)</option>
-        <option value="DNCB_hapten (Y)">DNCB_hapten (Y)</option>
-        <option value="dNIC (K)">dNIC (K)</option>
-        <option value="dNIC (N-term)">dNIC (N-term)</option>
-        <option value="DNPS (C)">DNPS (C)</option>
-        <option value="DNPS (W)">DNPS (W)</option>
-        <option value="DTT (C)">DTT (C)</option>
-        <option value="DyLight-maleimide (C)">DyLight-maleimide (C)</option>
-        <option value="DYn-2 (C)">DYn-2 (C)</option>
-        <option value="EDEDTIDVFQQQTGG (K)">EDEDTIDVFQQQTGG (K)</option>
-        <option value="EDT-iodoacetyl-PEO-biotin (S)">EDT-iodoacetyl-PEO-biotin (S)</option>
-        <option value="EDT-iodoacetyl-PEO-biotin (T)">EDT-iodoacetyl-PEO-biotin (T)</option>
-        <option value="EDT-maleimide-PEO-biotin (S)">EDT-maleimide-PEO-biotin (S)</option>
-        <option value="EDT-maleimide-PEO-biotin (T)">EDT-maleimide-PEO-biotin (T)</option>
-        <option value="EEEDVIEVYQEQTGG (K)">EEEDVIEVYQEQTGG (K)</option>
-        <option value="EGCG1 (C)">EGCG1 (C)</option>
-        <option value="EGCG2 (C)">EGCG2 (C)</option>
-        <option value="EHD-diphenylpentanone (C)">EHD-diphenylpentanone (C)</option>
-        <option value="EHD-diphenylpentanone (M)">EHD-diphenylpentanone (M)</option>
-        <option value="EQAT (C)">EQAT (C)</option>
-        <option value="EQAT:2H(5) (C)">EQAT:2H(5) (C)</option>
-        <option value="EQIGG (K)">EQIGG (K)</option>
-        <option value="ESP (K)">ESP (K)</option>
-        <option value="ESP (N-term)">ESP (N-term)</option>
-        <option value="ESP:2H(10) (K)">ESP:2H(10) (K)</option>
-        <option value="ESP:2H(10) (N-term)">ESP:2H(10) (N-term)</option>
-        <option value="Ethanedithiol (S)">Ethanedithiol (S)</option>
-        <option value="Ethanedithiol (T)">Ethanedithiol (T)</option>
-        <option value="Ethanolamine (C)">Ethanolamine (C)</option>
-        <option value="Ethanolamine (C-term)">Ethanolamine (C-term)</option>
-        <option value="Ethanolamine (D)">Ethanolamine (D)</option>
-        <option value="Ethanolamine (E)">Ethanolamine (E)</option>
-        <option value="Ethanolyl (C)">Ethanolyl (C)</option>
-        <option value="Ethanolyl (K)">Ethanolyl (K)</option>
-        <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-        <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
-        <option value="Ethyl (C-term)">Ethyl (C-term)</option>
-        <option value="Ethyl (D)">Ethyl (D)</option>
-        <option value="Ethyl (E)">Ethyl (E)</option>
-        <option value="Ethyl (K)">Ethyl (K)</option>
-        <option value="Ethyl (N-term)">Ethyl (N-term)</option>
-        <option value="Ethyl (Protein N-term)">Ethyl (Protein N-term)</option>
-        <option value="Ethyl+Deamidated (N)">Ethyl+Deamidated (N)</option>
-        <option value="Ethyl+Deamidated (Q)">Ethyl+Deamidated (Q)</option>
-        <option value="ethylamino (S)">ethylamino (S)</option>
-        <option value="ethylamino (T)">ethylamino (T)</option>
-        <option value="Ethylphosphate (K)">Ethylphosphate (K)</option>
-        <option value="Ethylphosphate (N-term)">Ethylphosphate (N-term)</option>
-        <option value="Ethylphosphate (S)">Ethylphosphate (S)</option>
-        <option value="Ethylphosphate (T)">Ethylphosphate (T)</option>
-        <option value="Ethylphosphate (Y)">Ethylphosphate (Y)</option>
-        <option value="ethylsulfonylethyl (C)">ethylsulfonylethyl (C)</option>
-        <option value="ethylsulfonylethyl (H)">ethylsulfonylethyl (H)</option>
-        <option value="ethylsulfonylethyl (K)">ethylsulfonylethyl (K)</option>
-        <option value="ExacTagAmine (K)">ExacTagAmine (K)</option>
-        <option value="ExacTagThiol (C)">ExacTagThiol (C)</option>
-        <option value="FAD (C)">FAD (C)</option>
-        <option value="FAD (H)">FAD (H)</option>
-        <option value="FAD (Y)">FAD (Y)</option>
-        <option value="Farnesyl (C)">Farnesyl (C)</option>
-        <option value="Fluorescein (C)">Fluorescein (C)</option>
-        <option value="Fluorescein-tyramine (Y)">Fluorescein-tyramine (Y)</option>
-        <option value="Fluoro (A)">Fluoro (A)</option>
-        <option value="Fluoro (F)">Fluoro (F)</option>
-        <option value="Fluoro (W)">Fluoro (W)</option>
-        <option value="Fluoro (Y)">Fluoro (Y)</option>
-        <option value="FMN (S)">FMN (S)</option>
-        <option value="FMN (T)">FMN (T)</option>
-        <option value="FMNC (C)">FMNC (C)</option>
-        <option value="FMNH (C)">FMNH (C)</option>
-        <option value="FMNH (H)">FMNH (H)</option>
-        <option value="FNEM (C)">FNEM (C)</option>
-        <option value="Formyl (K)">Formyl (K)</option>
-        <option value="Formyl (N-term)">Formyl (N-term)</option>
-        <option value="Formyl (Protein N-term)">Formyl (Protein N-term)</option>
-        <option value="Formyl (S)">Formyl (S)</option>
-        <option value="Formyl (T)">Formyl (T)</option>
-        <option value="Formylasparagine (H)">Formylasparagine (H)</option>
-        <option value="FormylMet (Protein N-term)">FormylMet (Protein N-term)</option>
-        <option value="FP-Biotin (K)">FP-Biotin (K)</option>
-        <option value="FP-Biotin (S)">FP-Biotin (S)</option>
-        <option value="FP-Biotin (T)">FP-Biotin (T)</option>
-        <option value="FP-Biotin (Y)">FP-Biotin (Y)</option>
-        <option value="FTC (C)">FTC (C)</option>
-        <option value="FTC (K)">FTC (K)</option>
-        <option value="FTC (P)">FTC (P)</option>
-        <option value="FTC (R)">FTC (R)</option>
-        <option value="FTC (S)">FTC (S)</option>
-        <option value="Furan (Y)">Furan (Y)</option>
-        <option value="G-H1 (R)">G-H1 (R)</option>
-        <option value="Galactosyl (K)">Galactosyl (K)</option>
-        <option value="Galactosyl (N-term)">Galactosyl (N-term)</option>
-        <option value="GEE (Q)">GEE (Q)</option>
-        <option value="GeranylGeranyl (C)">GeranylGeranyl (C)</option>
-        <option value="GG (C)">GG (C)</option>
-        <option value="GG (K)">GG (K)</option>
-        <option value="GG (Protein N-term)">GG (Protein N-term)</option>
-        <option value="GG (S)">GG (S)</option>
-        <option value="GG (T)">GG (T)</option>
-        <option value="GGQ (K)">GGQ (K)</option>
-        <option value="GIST-Quat (K)">GIST-Quat (K)</option>
-        <option value="GIST-Quat (N-term)">GIST-Quat (N-term)</option>
-        <option value="GIST-Quat:2H(3) (K)">GIST-Quat:2H(3) (K)</option>
-        <option value="GIST-Quat:2H(3) (N-term)">GIST-Quat:2H(3) (N-term)</option>
-        <option value="GIST-Quat:2H(6) (K)">GIST-Quat:2H(6) (K)</option>
-        <option value="GIST-Quat:2H(6) (N-term)">GIST-Quat:2H(6) (N-term)</option>
-        <option value="GIST-Quat:2H(9) (K)">GIST-Quat:2H(9) (K)</option>
-        <option value="GIST-Quat:2H(9) (N-term)">GIST-Quat:2H(9) (N-term)</option>
-        <option value="Gln-&gt;Ala (Q)">Gln-&gt;Ala (Q)</option>
-        <option value="Gln-&gt;Arg (Q)">Gln-&gt;Arg (Q)</option>
-        <option value="Gln-&gt;Asn (Q)">Gln-&gt;Asn (Q)</option>
-        <option value="Gln-&gt;Asp (Q)">Gln-&gt;Asp (Q)</option>
-        <option value="Gln-&gt;Cys (Q)">Gln-&gt;Cys (Q)</option>
-        <option value="Gln-&gt;Glu (Q)">Gln-&gt;Glu (Q)</option>
-        <option value="Gln-&gt;Gly (Q)">Gln-&gt;Gly (Q)</option>
-        <option value="Gln-&gt;His (Q)">Gln-&gt;His (Q)</option>
-        <option value="Gln-&gt;Lys (Q)">Gln-&gt;Lys (Q)</option>
-        <option value="Gln-&gt;Met (Q)">Gln-&gt;Met (Q)</option>
-        <option value="Gln-&gt;Phe (Q)">Gln-&gt;Phe (Q)</option>
-        <option value="Gln-&gt;Pro (Q)">Gln-&gt;Pro (Q)</option>
-        <option value="Gln-&gt;pyro-Glu (N-term Q)">Gln-&gt;pyro-Glu (N-term Q)</option>
-        <option value="Gln-&gt;Ser (Q)">Gln-&gt;Ser (Q)</option>
-        <option value="Gln-&gt;Thr (Q)">Gln-&gt;Thr (Q)</option>
-        <option value="Gln-&gt;Trp (Q)">Gln-&gt;Trp (Q)</option>
-        <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
-        <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
-        <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
-        <option value="Glu (E)">Glu (E)</option>
-        <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
-        <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
-        <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
-        <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
-        <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
-        <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
-        <option value="Glu-&gt;Gln (E)">Glu-&gt;Gln (E)</option>
-        <option value="Glu-&gt;Gly (E)">Glu-&gt;Gly (E)</option>
-        <option value="Glu-&gt;His (E)">Glu-&gt;His (E)</option>
-        <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
-        <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
-        <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
-        <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
-        <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
-        <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
-        <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
-        <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
-        <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
-        <option value="Glu-&gt;Val (E)">Glu-&gt;Val (E)</option>
-        <option value="Glu-&gt;Xle (E)">Glu-&gt;Xle (E)</option>
-        <option value="glucosone (R)">glucosone (R)</option>
-        <option value="Glucosylgalactosyl (K)">Glucosylgalactosyl (K)</option>
-        <option value="Glucuronyl (Protein N-term)">Glucuronyl (Protein N-term)</option>
-        <option value="Glucuronyl (S)">Glucuronyl (S)</option>
-        <option value="Glucuronyl (T)">Glucuronyl (T)</option>
-        <option value="GluGlu (E)">GluGlu (E)</option>
-        <option value="GluGlu (Protein C-term)">GluGlu (Protein C-term)</option>
-        <option value="GluGluGlu (E)">GluGluGlu (E)</option>
-        <option value="GluGluGlu (Protein C-term)">GluGluGlu (Protein C-term)</option>
-        <option value="GluGluGluGlu (E)">GluGluGluGlu (E)</option>
-        <option value="GluGluGluGlu (Protein C-term)">GluGluGluGlu (Protein C-term)</option>
-        <option value="Gluratylation (K)">Gluratylation (K)</option>
-        <option value="Glutathione (C)">Glutathione (C)</option>
-        <option value="Gly (K)">Gly (K)</option>
-        <option value="Gly (S)">Gly (S)</option>
-        <option value="Gly (T)">Gly (T)</option>
-        <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
-        <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
-        <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
-        <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
-        <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
-        <option value="Gly-&gt;Gln (G)">Gly-&gt;Gln (G)</option>
-        <option value="Gly-&gt;Glu (G)">Gly-&gt;Glu (G)</option>
-        <option value="Gly-&gt;His (G)">Gly-&gt;His (G)</option>
-        <option value="Gly-&gt;Lys (G)">Gly-&gt;Lys (G)</option>
-        <option value="Gly-&gt;Met (G)">Gly-&gt;Met (G)</option>
-        <option value="Gly-&gt;Phe (G)">Gly-&gt;Phe (G)</option>
-        <option value="Gly-&gt;Pro (G)">Gly-&gt;Pro (G)</option>
-        <option value="Gly-&gt;Ser (G)">Gly-&gt;Ser (G)</option>
-        <option value="Gly-&gt;Thr (G)">Gly-&gt;Thr (G)</option>
-        <option value="Gly-&gt;Trp (G)">Gly-&gt;Trp (G)</option>
-        <option value="Gly-&gt;Tyr (G)">Gly-&gt;Tyr (G)</option>
-        <option value="Gly-&gt;Val (G)">Gly-&gt;Val (G)</option>
-        <option value="Gly-&gt;Xle (G)">Gly-&gt;Xle (G)</option>
-        <option value="Gly-loss+Amide (C-term G)">Gly-loss+Amide (C-term G)</option>
-        <option value="Glycerophospho (S)">Glycerophospho (S)</option>
-        <option value="GlycerylPE (E)">GlycerylPE (E)</option>
-        <option value="glycidamide (K)">glycidamide (K)</option>
-        <option value="glycidamide (N-term)">glycidamide (N-term)</option>
-        <option value="Glycosyl (P)">Glycosyl (P)</option>
-        <option value="glyoxalAGE (R)">glyoxalAGE (R)</option>
-        <option value="GNLLFLACYCIGG (K)">GNLLFLACYCIGG (K)</option>
-        <option value="GPIanchor (Protein C-term)">GPIanchor (Protein C-term)</option>
-        <option value="Guanidinyl (K)">Guanidinyl (K)</option>
-        <option value="Guanidinyl (N-term)">Guanidinyl (N-term)</option>
-        <option value="Haloxon (C)">Haloxon (C)</option>
-        <option value="Haloxon (H)">Haloxon (H)</option>
-        <option value="Haloxon (K)">Haloxon (K)</option>
-        <option value="Haloxon (S)">Haloxon (S)</option>
-        <option value="Haloxon (T)">Haloxon (T)</option>
-        <option value="Haloxon (Y)">Haloxon (Y)</option>
-        <option value="HCysteinyl (C)">HCysteinyl (C)</option>
-        <option value="HCysThiolactone (K)">HCysThiolactone (K)</option>
-        <option value="Heme (C)">Heme (C)</option>
-        <option value="Heme (H)">Heme (H)</option>
-        <option value="Hep (K)">Hep (K)</option>
-        <option value="Hep (N)">Hep (N)</option>
-        <option value="Hep (Q)">Hep (Q)</option>
-        <option value="Hep (R)">Hep (R)</option>
-        <option value="Hep (S)">Hep (S)</option>
-        <option value="Hep (T)">Hep (T)</option>
-        <option value="Hex (C)">Hex (C)</option>
-        <option value="Hex (K)">Hex (K)</option>
-        <option value="Hex (N)">Hex (N)</option>
-        <option value="Hex (N-term)">Hex (N-term)</option>
-        <option value="Hex (R)">Hex (R)</option>
-        <option value="Hex (S)">Hex (S)</option>
-        <option value="Hex (T)">Hex (T)</option>
-        <option value="Hex (W)">Hex (W)</option>
-        <option value="Hex (Y)">Hex (Y)</option>
-        <option value="Hex(1)HexA(1) (S)">Hex(1)HexA(1) (S)</option>
-        <option value="Hex(1)HexA(1) (T)">Hex(1)HexA(1) (T)</option>
-        <option value="Hex(1)HexA(1)HexNAc(1) (S)">Hex(1)HexA(1)HexNAc(1) (S)</option>
-        <option value="Hex(1)HexA(1)HexNAc(1) (T)">Hex(1)HexA(1)HexNAc(1) (T)</option>
-        <option value="Hex(1)HexA(1)HexNAc(2) (S)">Hex(1)HexA(1)HexNAc(2) (S)</option>
-        <option value="Hex(1)HexA(1)HexNAc(2) (T)">Hex(1)HexA(1)HexNAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(1) (N)">Hex(1)HexNAc(1) (N)</option>
-        <option value="Hex(1)HexNAc(1) (S)">Hex(1)HexNAc(1) (S)</option>
-        <option value="Hex(1)HexNAc(1) (T)">Hex(1)HexNAc(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1) (N)">Hex(1)HexNAc(1)dHex(1) (N)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1) (S)">Hex(1)HexNAc(1)dHex(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1) (T)">Hex(1)HexNAc(1)dHex(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1)Me(1) (S)">Hex(1)HexNAc(1)dHex(1)Me(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1)Me(1) (T)">Hex(1)HexNAc(1)dHex(1)Me(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1)Me(2) (S)">Hex(1)HexNAc(1)dHex(1)Me(2) (S)</option>
-        <option value="Hex(1)HexNAc(1)dHex(1)Me(2) (T)">Hex(1)HexNAc(1)dHex(1)Me(2) (T)</option>
-        <option value="Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S)">Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T)">Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1) (N)">Hex(1)HexNAc(1)NeuAc(1) (N)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1) (S)">Hex(1)HexNAc(1)NeuAc(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1) (T)">Hex(1)HexNAc(1)NeuAc(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S)">Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T)">Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S)">Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T)">Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T)">Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2) (N)">Hex(1)HexNAc(1)NeuAc(2) (N)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2) (S)">Hex(1)HexNAc(1)NeuAc(2) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2) (T)">Hex(1)HexNAc(1)NeuAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S)">Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T)">Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S)">Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T)">Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(3) (S)">Hex(1)HexNAc(1)NeuAc(3) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuAc(3) (T)">Hex(1)HexNAc(1)NeuAc(3) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(1) (S)">Hex(1)HexNAc(1)NeuGc(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(1) (T)">Hex(1)HexNAc(1)NeuGc(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(2) (S)">Hex(1)HexNAc(1)NeuGc(2) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(2) (T)">Hex(1)HexNAc(1)NeuGc(2) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(3) (S)">Hex(1)HexNAc(1)NeuGc(3) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(3) (T)">Hex(1)HexNAc(1)NeuGc(3) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(4) (S)">Hex(1)HexNAc(1)NeuGc(4) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(4) (T)">Hex(1)HexNAc(1)NeuGc(4) (T)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(5) (S)">Hex(1)HexNAc(1)NeuGc(5) (S)</option>
-        <option value="Hex(1)HexNAc(1)NeuGc(5) (T)">Hex(1)HexNAc(1)NeuGc(5) (T)</option>
-        <option value="Hex(1)HexNAc(1)Phos(1) (S)">Hex(1)HexNAc(1)Phos(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)Phos(1) (T)">Hex(1)HexNAc(1)Phos(1) (T)</option>
-        <option value="Hex(1)HexNAc(1)Sulf(1) (S)">Hex(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(1)Sulf(1) (T)">Hex(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(2) (N)">Hex(1)HexNAc(2) (N)</option>
-        <option value="Hex(1)HexNAc(2) (S)">Hex(1)HexNAc(2) (S)</option>
-        <option value="Hex(1)HexNAc(2) (T)">Hex(1)HexNAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(2)dHex(1) (N)">Hex(1)HexNAc(2)dHex(1) (N)</option>
-        <option value="Hex(1)HexNAc(2)dHex(1) (S)">Hex(1)HexNAc(2)dHex(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)dHex(1) (T)">Hex(1)HexNAc(2)dHex(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)dHex(1)Pent(1) (N)">Hex(1)HexNAc(2)dHex(1)Pent(1) (N)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2) (N)">Hex(1)HexNAc(2)dHex(2) (N)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2) (S)">Hex(1)HexNAc(2)dHex(2) (S)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2) (T)">Hex(1)HexNAc(2)dHex(2) (T)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(1) (S)">Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(1) (T)">Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(2) (S)">Hex(1)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(2) (T)">Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T)">Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)NeuGc(1) (S)">Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)NeuGc(1) (T)">Hex(1)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="Hex(1)HexNAc(2)Pent(1) (N)">Hex(1)HexNAc(2)Pent(1) (N)</option>
-        <option value="Hex(1)HexNAc(2)Sulf(1) (S)">Hex(1)HexNAc(2)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(2)Sulf(1) (T)">Hex(1)HexNAc(2)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(3) (S)">Hex(1)HexNAc(3) (S)</option>
-        <option value="Hex(1)HexNAc(3) (T)">Hex(1)HexNAc(3) (T)</option>
-        <option value="Hex(1)HexNAc(3)NeuAc(1) (S)">Hex(1)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="Hex(1)HexNAc(3)NeuAc(1) (T)">Hex(1)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="Hex(1)HexNAc(3)NeuAc(2) (S)">Hex(1)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="Hex(1)HexNAc(3)NeuAc(2) (T)">Hex(1)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="Hex(1)HexNAc(3)NeuGc(1) (S)">Hex(1)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="Hex(1)HexNAc(3)NeuGc(1) (T)">Hex(1)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="Hex(1)HexNAc(3)Sulf(1) (S)">Hex(1)HexNAc(3)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(3)Sulf(1) (T)">Hex(1)HexNAc(3)Sulf(1) (T)</option>
-        <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)</option>
-        <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)</option>
-        <option value="Hex(1)NeuAc(1) (S)">Hex(1)NeuAc(1) (S)</option>
-        <option value="Hex(1)NeuAc(1) (T)">Hex(1)NeuAc(1) (T)</option>
-        <option value="Hex(1)NeuAc(1)Pent(1) (S)">Hex(1)NeuAc(1)Pent(1) (S)</option>
-        <option value="Hex(1)NeuAc(1)Pent(1) (T)">Hex(1)NeuAc(1)Pent(1) (T)</option>
-        <option value="Hex(1)NeuGc(1) (S)">Hex(1)NeuGc(1) (S)</option>
-        <option value="Hex(1)NeuGc(1) (T)">Hex(1)NeuGc(1) (T)</option>
-        <option value="Hex(1)Pent(1) (S)">Hex(1)Pent(1) (S)</option>
-        <option value="Hex(1)Pent(1) (T)">Hex(1)Pent(1) (T)</option>
-        <option value="Hex(1)Pent(2) (S)">Hex(1)Pent(2) (S)</option>
-        <option value="Hex(1)Pent(2) (T)">Hex(1)Pent(2) (T)</option>
-        <option value="Hex(1)Pent(2)Me(1) (S)">Hex(1)Pent(2)Me(1) (S)</option>
-        <option value="Hex(1)Pent(2)Me(1) (T)">Hex(1)Pent(2)Me(1) (T)</option>
-        <option value="Hex(1)Pent(3) (S)">Hex(1)Pent(3) (S)</option>
-        <option value="Hex(1)Pent(3) (T)">Hex(1)Pent(3) (T)</option>
-        <option value="Hex(1)Pent(3)Me(1) (S)">Hex(1)Pent(3)Me(1) (S)</option>
-        <option value="Hex(1)Pent(3)Me(1) (T)">Hex(1)Pent(3)Me(1) (T)</option>
-        <option value="Hex(10)HexNAc(1) (N)">Hex(10)HexNAc(1) (N)</option>
-        <option value="Hex(10)Phos(3) (S)">Hex(10)Phos(3) (S)</option>
-        <option value="Hex(10)Phos(3) (T)">Hex(10)Phos(3) (T)</option>
-        <option value="Hex(2) (K)">Hex(2) (K)</option>
-        <option value="Hex(2) (R)">Hex(2) (R)</option>
-        <option value="Hex(2) (S)">Hex(2) (S)</option>
-        <option value="Hex(2) (T)">Hex(2) (T)</option>
-        <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)Pent(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)Pent(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(1) (N)">Hex(2)HexNAc(1) (N)</option>
-        <option value="Hex(2)HexNAc(1) (S)">Hex(2)HexNAc(1) (S)</option>
-        <option value="Hex(2)HexNAc(1) (T)">Hex(2)HexNAc(1) (T)</option>
-        <option value="Hex(2)HexNAc(1)Me(1) (S)">Hex(2)HexNAc(1)Me(1) (S)</option>
-        <option value="Hex(2)HexNAc(1)Me(1) (T)">Hex(2)HexNAc(1)Me(1) (T)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(1) (S)">Hex(2)HexNAc(1)NeuGc(1) (S)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(1) (T)">Hex(2)HexNAc(1)NeuGc(1) (T)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(2) (S)">Hex(2)HexNAc(1)NeuGc(2) (S)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(2) (T)">Hex(2)HexNAc(1)NeuGc(2) (T)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(3) (S)">Hex(2)HexNAc(1)NeuGc(3) (S)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(3) (T)">Hex(2)HexNAc(1)NeuGc(3) (T)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(4) (S)">Hex(2)HexNAc(1)NeuGc(4) (S)</option>
-        <option value="Hex(2)HexNAc(1)NeuGc(4) (T)">Hex(2)HexNAc(1)NeuGc(4) (T)</option>
-        <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (S)">Hex(2)HexNAc(1)Pent(1)HexA(1) (S)</option>
-        <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (T)">Hex(2)HexNAc(1)Pent(1)HexA(1) (T)</option>
-        <option value="Hex(2)HexNAc(1)Sulf(1) (S)">Hex(2)HexNAc(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(1)Sulf(1) (T)">Hex(2)HexNAc(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(2) (N)">Hex(2)HexNAc(2) (N)</option>
-        <option value="Hex(2)HexNAc(2) (S)">Hex(2)HexNAc(2) (S)</option>
-        <option value="Hex(2)HexNAc(2) (T)">Hex(2)HexNAc(2) (T)</option>
-        <option value="Hex(2)HexNAc(2)dHex(1) (N)">Hex(2)HexNAc(2)dHex(1) (N)</option>
-        <option value="Hex(2)HexNAc(2)dHex(1) (S)">Hex(2)HexNAc(2)dHex(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)dHex(1) (T)">Hex(2)HexNAc(2)dHex(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1) (N)">Hex(2)HexNAc(2)NeuAc(1) (N)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1) (S)">Hex(2)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1) (T)">Hex(2)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(2) (S)">Hex(2)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(2) (T)">Hex(2)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)NeuGc(1) (S)">Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)NeuGc(1) (T)">Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-        <option value="Hex(2)HexNAc(2)Pent(1) (N)">Hex(2)HexNAc(2)Pent(1) (N)</option>
-        <option value="Hex(2)HexNAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(3) (N)">Hex(2)HexNAc(3) (N)</option>
-        <option value="Hex(2)HexNAc(3) (S)">Hex(2)HexNAc(3) (S)</option>
-        <option value="Hex(2)HexNAc(3) (T)">Hex(2)HexNAc(3) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(2) (S)">Hex(2)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(2) (T)">Hex(2)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(3) (S)">Hex(2)HexNAc(3)NeuAc(3) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuAc(3) (T)">Hex(2)HexNAc(3)NeuAc(3) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(1) (T)">Hex(2)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(2) (S)">Hex(2)HexNAc(3)NeuGc(2) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(2) (T)">Hex(2)HexNAc(3)NeuGc(2) (T)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(3) (S)">Hex(2)HexNAc(3)NeuGc(3) (S)</option>
-        <option value="Hex(2)HexNAc(3)NeuGc(3) (T)">Hex(2)HexNAc(3)NeuGc(3) (T)</option>
-        <option value="Hex(2)HexNAc(3)Sulf(1) (S)">Hex(2)HexNAc(3)Sulf(1) (S)</option>
-        <option value="Hex(2)HexNAc(3)Sulf(1) (T)">Hex(2)HexNAc(3)Sulf(1) (T)</option>
-        <option value="Hex(2)HexNAc(4) (N)">Hex(2)HexNAc(4) (N)</option>
-        <option value="Hex(2)HexNAc(4) (S)">Hex(2)HexNAc(4) (S)</option>
-        <option value="Hex(2)HexNAc(4) (T)">Hex(2)HexNAc(4) (T)</option>
-        <option value="Hex(2)HexNAc(4)NeuAc(1) (S)">Hex(2)HexNAc(4)NeuAc(1) (S)</option>
-        <option value="Hex(2)HexNAc(4)NeuAc(1) (T)">Hex(2)HexNAc(4)NeuAc(1) (T)</option>
-        <option value="Hex(2)HexNAc(5) (S)">Hex(2)HexNAc(5) (S)</option>
-        <option value="Hex(2)HexNAc(5) (T)">Hex(2)HexNAc(5) (T)</option>
-        <option value="Hex(2)NeuAc(1) (S)">Hex(2)NeuAc(1) (S)</option>
-        <option value="Hex(2)NeuAc(1) (T)">Hex(2)NeuAc(1) (T)</option>
-        <option value="Hex(2)Pent(2) (S)">Hex(2)Pent(2) (S)</option>
-        <option value="Hex(2)Pent(2) (T)">Hex(2)Pent(2) (T)</option>
-        <option value="Hex(2)Pent(2)Me(1) (S)">Hex(2)Pent(2)Me(1) (S)</option>
-        <option value="Hex(2)Pent(2)Me(1) (T)">Hex(2)Pent(2)Me(1) (T)</option>
-        <option value="Hex(2)Sulf(1) (S)">Hex(2)Sulf(1) (S)</option>
-        <option value="Hex(2)Sulf(1) (T)">Hex(2)Sulf(1) (T)</option>
-        <option value="Hex(3) (N)">Hex(3) (N)</option>
-        <option value="Hex(3) (S)">Hex(3) (S)</option>
-        <option value="Hex(3) (T)">Hex(3) (T)</option>
-        <option value="Hex(3)HexNAc(1) (N)">Hex(3)HexNAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(1) (S)">Hex(3)HexNAc(1) (S)</option>
-        <option value="Hex(3)HexNAc(1) (T)">Hex(3)HexNAc(1) (T)</option>
-        <option value="Hex(3)HexNAc(1)HexA(1) (S)">Hex(3)HexNAc(1)HexA(1) (S)</option>
-        <option value="Hex(3)HexNAc(1)HexA(1) (T)">Hex(3)HexNAc(1)HexA(1) (T)</option>
-        <option value="Hex(3)HexNAc(1)Me(1) (S)">Hex(3)HexNAc(1)Me(1) (S)</option>
-        <option value="Hex(3)HexNAc(1)Me(1) (T)">Hex(3)HexNAc(1)Me(1) (T)</option>
-        <option value="Hex(3)HexNAc(1)Pent(1) (N)">Hex(3)HexNAc(1)Pent(1) (N)</option>
-        <option value="Hex(3)HexNAc(2) (N)">Hex(3)HexNAc(2) (N)</option>
-        <option value="Hex(3)HexNAc(2) (S)">Hex(3)HexNAc(2) (S)</option>
-        <option value="Hex(3)HexNAc(2) (T)">Hex(3)HexNAc(2) (T)</option>
-        <option value="Hex(3)HexNAc(2)NeuAc(1) (N)">Hex(3)HexNAc(2)NeuAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(2)NeuAc(2) (S)">Hex(3)HexNAc(2)NeuAc(2) (S)</option>
-        <option value="Hex(3)HexNAc(2)NeuAc(2) (T)">Hex(3)HexNAc(2)NeuAc(2) (T)</option>
-        <option value="Hex(3)HexNAc(2)Pent(1) (N)">Hex(3)HexNAc(2)Pent(1) (N)</option>
-        <option value="Hex(3)HexNAc(2)Phos(1) (N)">Hex(3)HexNAc(2)Phos(1) (N)</option>
-        <option value="Hex(3)HexNAc(3) (N)">Hex(3)HexNAc(3) (N)</option>
-        <option value="Hex(3)HexNAc(3) (S)">Hex(3)HexNAc(3) (S)</option>
-        <option value="Hex(3)HexNAc(3) (T)">Hex(3)HexNAc(3) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(1) (S)">Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(1) (T)">Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(2) (S)">Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(2) (T)">Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(3) (S)">Hex(3)HexNAc(3)NeuAc(3) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuAc(3) (T)">Hex(3)HexNAc(3)NeuAc(3) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuGc(1) (S)">Hex(3)HexNAc(3)NeuGc(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuGc(1) (T)">Hex(3)HexNAc(3)NeuGc(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)</option>
-        <option value="Hex(3)HexNAc(3)Pent(1) (N)">Hex(3)HexNAc(3)Pent(1) (N)</option>
-        <option value="Hex(3)HexNAc(3)Sulf(1) (N)">Hex(3)HexNAc(3)Sulf(1) (N)</option>
-        <option value="Hex(3)HexNAc(3)Sulf(1) (S)">Hex(3)HexNAc(3)Sulf(1) (S)</option>
-        <option value="Hex(3)HexNAc(3)Sulf(1) (T)">Hex(3)HexNAc(3)Sulf(1) (T)</option>
-        <option value="Hex(3)HexNAc(4) (N)">Hex(3)HexNAc(4) (N)</option>
-        <option value="Hex(3)HexNAc(4) (S)">Hex(3)HexNAc(4) (S)</option>
-        <option value="Hex(3)HexNAc(4) (T)">Hex(3)HexNAc(4) (T)</option>
-        <option value="Hex(3)HexNAc(4)NeuAc(1) (N)">Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(4)NeuAc(2) (N)">Hex(3)HexNAc(4)NeuAc(2) (N)</option>
-        <option value="Hex(3)HexNAc(4)Pent(1) (N)">Hex(3)HexNAc(4)Pent(1) (N)</option>
-        <option value="Hex(3)HexNAc(4)Sulf(1) (N)">Hex(3)HexNAc(4)Sulf(1) (N)</option>
-        <option value="Hex(3)HexNAc(5) (N)">Hex(3)HexNAc(5) (N)</option>
-        <option value="Hex(3)HexNAc(5) (S)">Hex(3)HexNAc(5) (S)</option>
-        <option value="Hex(3)HexNAc(5) (T)">Hex(3)HexNAc(5) (T)</option>
-        <option value="Hex(3)HexNAc(5)NeuAc(1) (N)">Hex(3)HexNAc(5)NeuAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(5)Sulf(1) (N)">Hex(3)HexNAc(5)Sulf(1) (N)</option>
-        <option value="Hex(3)HexNAc(6) (N)">Hex(3)HexNAc(6) (N)</option>
-        <option value="Hex(3)HexNAc(6) (S)">Hex(3)HexNAc(6) (S)</option>
-        <option value="Hex(3)HexNAc(6) (T)">Hex(3)HexNAc(6) (T)</option>
-        <option value="Hex(3)HexNAc(6)NeuAc(1) (N)">Hex(3)HexNAc(6)NeuAc(1) (N)</option>
-        <option value="Hex(3)HexNAc(6)Sulf(1) (N)">Hex(3)HexNAc(6)Sulf(1) (N)</option>
-        <option value="Hex(3)HexNAc(6)Sulf(2) (N)">Hex(3)HexNAc(6)Sulf(2) (N)</option>
-        <option value="Hex(3)HexNAc(7) (N)">Hex(3)HexNAc(7) (N)</option>
-        <option value="Hex(3)HexNAc(7)Sulf(1) (N)">Hex(3)HexNAc(7)Sulf(1) (N)</option>
-        <option value="Hex(4) (S)">Hex(4) (S)</option>
-        <option value="Hex(4) (T)">Hex(4) (T)</option>
-        <option value="Hex(4)HexA(1) (S)">Hex(4)HexA(1) (S)</option>
-        <option value="Hex(4)HexA(1) (T)">Hex(4)HexA(1) (T)</option>
-        <option value="Hex(4)HexA(1)HexNAc(1) (S)">Hex(4)HexA(1)HexNAc(1) (S)</option>
-        <option value="Hex(4)HexA(1)HexNAc(1) (T)">Hex(4)HexA(1)HexNAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(1) (N)">Hex(4)HexNAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(1) (S)">Hex(4)HexNAc(1) (S)</option>
-        <option value="Hex(4)HexNAc(1) (T)">Hex(4)HexNAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(2) (N)">Hex(4)HexNAc(2) (N)</option>
-        <option value="Hex(4)HexNAc(2)NeuAc(1) (N)">Hex(4)HexNAc(2)NeuAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(2)NeuAc(1) (S)">Hex(4)HexNAc(2)NeuAc(1) (S)</option>
-        <option value="Hex(4)HexNAc(2)NeuAc(1) (T)">Hex(4)HexNAc(2)NeuAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(2)Pent(1) (N)">Hex(4)HexNAc(2)Pent(1) (N)</option>
-        <option value="Hex(4)HexNAc(3) (N)">Hex(4)HexNAc(3) (N)</option>
-        <option value="Hex(4)HexNAc(3) (S)">Hex(4)HexNAc(3) (S)</option>
-        <option value="Hex(4)HexNAc(3) (T)">Hex(4)HexNAc(3) (T)</option>
-        <option value="Hex(4)HexNAc(3)NeuAc(1) (N)">Hex(4)HexNAc(3)NeuAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(3)NeuAc(1) (S)">Hex(4)HexNAc(3)NeuAc(1) (S)</option>
-        <option value="Hex(4)HexNAc(3)NeuAc(1) (T)">Hex(4)HexNAc(3)NeuAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(3)NeuAc(2) (N)">Hex(4)HexNAc(3)NeuAc(2) (N)</option>
-        <option value="Hex(4)HexNAc(3)NeuGc(1) (N)">Hex(4)HexNAc(3)NeuGc(1) (N)</option>
-        <option value="Hex(4)HexNAc(3)Pent(1) (N)">Hex(4)HexNAc(3)Pent(1) (N)</option>
-        <option value="Hex(4)HexNAc(4) (N)">Hex(4)HexNAc(4) (N)</option>
-        <option value="Hex(4)HexNAc(4) (S)">Hex(4)HexNAc(4) (S)</option>
-        <option value="Hex(4)HexNAc(4) (T)">Hex(4)HexNAc(4) (T)</option>
-        <option value="Hex(4)HexNAc(4)Me(2)Pent(1) (N)">Hex(4)HexNAc(4)Me(2)Pent(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1) (N)">Hex(4)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1) (S)">Hex(4)HexNAc(4)NeuAc(1) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1) (T)">Hex(4)HexNAc(4)NeuAc(1) (T)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1) (N)">Hex(4)HexNAc(4)NeuGc(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1) (S)">Hex(4)HexNAc(4)NeuGc(1) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1) (T)">Hex(4)HexNAc(4)NeuGc(1) (T)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)</option>
-        <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)</option>
-        <option value="Hex(4)HexNAc(4)Pent(1) (N)">Hex(4)HexNAc(4)Pent(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)Sulf(1) (N)">Hex(4)HexNAc(4)Sulf(1) (N)</option>
-        <option value="Hex(4)HexNAc(4)Sulf(2) (S)">Hex(4)HexNAc(4)Sulf(2) (S)</option>
-        <option value="Hex(4)HexNAc(4)Sulf(2) (T)">Hex(4)HexNAc(4)Sulf(2) (T)</option>
-        <option value="Hex(4)HexNAc(5) (N)">Hex(4)HexNAc(5) (N)</option>
-        <option value="Hex(4)HexNAc(5)NeuAc(1) (N)">Hex(4)HexNAc(5)NeuAc(1) (N)</option>
-        <option value="Hex(4)HexNAc(5)Sulf(1) (N)">Hex(4)HexNAc(5)Sulf(1) (N)</option>
-        <option value="Hex(4)HexNAc(6) (N)">Hex(4)HexNAc(6) (N)</option>
-        <option value="Hex(4)Phos(1) (S)">Hex(4)Phos(1) (S)</option>
-        <option value="Hex(4)Phos(1) (T)">Hex(4)Phos(1) (T)</option>
-        <option value="Hex(5) (S)">Hex(5) (S)</option>
-        <option value="Hex(5) (T)">Hex(5) (T)</option>
-        <option value="Hex(5)HexA(1) (S)">Hex(5)HexA(1) (S)</option>
-        <option value="Hex(5)HexA(1) (T)">Hex(5)HexA(1) (T)</option>
-        <option value="Hex(5)HexNAc(1) (N)">Hex(5)HexNAc(1) (N)</option>
-        <option value="Hex(5)HexNAc(1) (S)">Hex(5)HexNAc(1) (S)</option>
-        <option value="Hex(5)HexNAc(1) (T)">Hex(5)HexNAc(1) (T)</option>
-        <option value="Hex(5)HexNAc(2) (N)">Hex(5)HexNAc(2) (N)</option>
-        <option value="Hex(5)HexNAc(2)Phos(1) (N)">Hex(5)HexNAc(2)Phos(1) (N)</option>
-        <option value="Hex(5)HexNAc(3) (N)">Hex(5)HexNAc(3) (N)</option>
-        <option value="Hex(5)HexNAc(3)Pent(1) (N)">Hex(5)HexNAc(3)Pent(1) (N)</option>
-        <option value="Hex(5)HexNAc(4) (N)">Hex(5)HexNAc(4) (N)</option>
-        <option value="Hex(5)HexNAc(4) (S)">Hex(5)HexNAc(4) (S)</option>
-        <option value="Hex(5)HexNAc(4) (T)">Hex(5)HexNAc(4) (T)</option>
-        <option value="Hex(5)HexNAc(4)Me(2)Pent(1) (N)">Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(1) (N)">Hex(5)HexNAc(4)NeuAc(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuAc(2) (N)">Hex(5)HexNAc(4)NeuAc(2) (N)</option>
-        <option value="Hex(5)HexNAc(4)NeuGc(1) (N)">Hex(5)HexNAc(4)NeuGc(1) (N)</option>
-        <option value="Hex(5)HexNAc(4)Sulf(1) (N)">Hex(5)HexNAc(4)Sulf(1) (N)</option>
-        <option value="Hex(5)HexNAc(5) (N)">Hex(5)HexNAc(5) (N)</option>
-        <option value="Hex(5)HexNAc(5) (S)">Hex(5)HexNAc(5) (S)</option>
-        <option value="Hex(5)HexNAc(5) (T)">Hex(5)HexNAc(5) (T)</option>
-        <option value="Hex(5)Phos(1) (S)">Hex(5)Phos(1) (S)</option>
-        <option value="Hex(5)Phos(1) (T)">Hex(5)Phos(1) (T)</option>
-        <option value="Hex(5)Phos(3) (S)">Hex(5)Phos(3) (S)</option>
-        <option value="Hex(5)Phos(3) (T)">Hex(5)Phos(3) (T)</option>
-        <option value="Hex(6)HexNAc(1) (N)">Hex(6)HexNAc(1) (N)</option>
-        <option value="Hex(6)HexNAc(2) (N)">Hex(6)HexNAc(2) (N)</option>
-        <option value="Hex(6)HexNAc(2)Phos(1) (N)">Hex(6)HexNAc(2)Phos(1) (N)</option>
-        <option value="Hex(6)HexNAc(3) (N)">Hex(6)HexNAc(3) (N)</option>
-        <option value="Hex(6)HexNAc(3)Phos(1) (N)">Hex(6)HexNAc(3)Phos(1) (N)</option>
-        <option value="Hex(6)HexNAc(4) (N)">Hex(6)HexNAc(4) (N)</option>
-        <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
-        <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
-        <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
-        <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
-        <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
-        <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
-        <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
-        <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
-        <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
-        <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
-        <option value="Hex(7)HexNAc(2) (N)">Hex(7)HexNAc(2) (N)</option>
-        <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
-        <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
-        <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
-        <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
-        <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
-        <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
-        <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
-        <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
-        <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
-        <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
-        <option value="Hex(8)Phos(3) (T)">Hex(8)Phos(3) (T)</option>
-        <option value="Hex(9) (N)">Hex(9) (N)</option>
-        <option value="Hex(9)HexNAc(1) (N)">Hex(9)HexNAc(1) (N)</option>
-        <option value="Hex(9)HexNAc(2) (N)">Hex(9)HexNAc(2) (N)</option>
-        <option value="Hex(9)Phos(3) (S)">Hex(9)Phos(3) (S)</option>
-        <option value="Hex(9)Phos(3) (T)">Hex(9)Phos(3) (T)</option>
-        <option value="HexA(2)HexNAc(3) (S)">HexA(2)HexNAc(3) (S)</option>
-        <option value="HexA(2)HexNAc(3) (T)">HexA(2)HexNAc(3) (T)</option>
-        <option value="HexN (K)">HexN (K)</option>
-        <option value="HexN (N)">HexN (N)</option>
-        <option value="HexN (S)">HexN (S)</option>
-        <option value="HexN (T)">HexN (T)</option>
-        <option value="HexN (W)">HexN (W)</option>
-        <option value="HexNAc (C)">HexNAc (C)</option>
-        <option value="HexNAc (N)">HexNAc (N)</option>
-        <option value="HexNAc (S)">HexNAc (S)</option>
-        <option value="HexNAc (T)">HexNAc (T)</option>
-        <option value="HexNAc(1)dHex(1) (N)">HexNAc(1)dHex(1) (N)</option>
-        <option value="HexNAc(1)dHex(1) (S)">HexNAc(1)dHex(1) (S)</option>
-        <option value="HexNAc(1)dHex(1) (T)">HexNAc(1)dHex(1) (T)</option>
-        <option value="HexNAc(1)dHex(2) (N)">HexNAc(1)dHex(2) (N)</option>
-        <option value="HexNAc(1)Kdn(2) (S)">HexNAc(1)Kdn(2) (S)</option>
-        <option value="HexNAc(1)Kdn(2) (T)">HexNAc(1)Kdn(2) (T)</option>
-        <option value="HexNAc(1)NeuAc(1) (S)">HexNAc(1)NeuAc(1) (S)</option>
-        <option value="HexNAc(1)NeuAc(1) (T)">HexNAc(1)NeuAc(1) (T)</option>
-        <option value="HexNAc(1)NeuGc(1) (S)">HexNAc(1)NeuGc(1) (S)</option>
-        <option value="HexNAc(1)NeuGc(1) (T)">HexNAc(1)NeuGc(1) (T)</option>
-        <option value="HexNAc(1)NeuGc(2) (S)">HexNAc(1)NeuGc(2) (S)</option>
-        <option value="HexNAc(1)NeuGc(2) (T)">HexNAc(1)NeuGc(2) (T)</option>
-        <option value="HexNAc(2) (N)">HexNAc(2) (N)</option>
-        <option value="HexNAc(2) (S)">HexNAc(2) (S)</option>
-        <option value="HexNAc(2) (T)">HexNAc(2) (T)</option>
-        <option value="HexNAc(2)dHex(1) (N)">HexNAc(2)dHex(1) (N)</option>
-        <option value="HexNAc(2)dHex(2) (N)">HexNAc(2)dHex(2) (N)</option>
-        <option value="HexNAc(2)NeuAc(1) (S)">HexNAc(2)NeuAc(1) (S)</option>
-        <option value="HexNAc(2)NeuAc(1) (T)">HexNAc(2)NeuAc(1) (T)</option>
-        <option value="HexNAc(2)NeuAc(1)Sulf(1) (S)">HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-        <option value="HexNAc(2)NeuAc(1)Sulf(1) (T)">HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-        <option value="HexNAc(2)NeuGc(1) (S)">HexNAc(2)NeuGc(1) (S)</option>
-        <option value="HexNAc(2)NeuGc(1) (T)">HexNAc(2)NeuGc(1) (T)</option>
-        <option value="HexNAc(2)Sulf(1) (S)">HexNAc(2)Sulf(1) (S)</option>
-        <option value="HexNAc(2)Sulf(1) (T)">HexNAc(2)Sulf(1) (T)</option>
-        <option value="HexNAc(3) (S)">HexNAc(3) (S)</option>
-        <option value="HexNAc(3) (T)">HexNAc(3) (T)</option>
-        <option value="HexNAc(3)Sulf(1) (S)">HexNAc(3)Sulf(1) (S)</option>
-        <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
-        <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
-        <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
-        <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
-        <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
-        <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
-        <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
-        <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
-        <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
-        <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
-        <option value="His-&gt;Gln (H)">His-&gt;Gln (H)</option>
-        <option value="His-&gt;Glu (H)">His-&gt;Glu (H)</option>
-        <option value="His-&gt;Gly (H)">His-&gt;Gly (H)</option>
-        <option value="His-&gt;Lys (H)">His-&gt;Lys (H)</option>
-        <option value="His-&gt;Met (H)">His-&gt;Met (H)</option>
-        <option value="His-&gt;Phe (H)">His-&gt;Phe (H)</option>
-        <option value="His-&gt;Pro (H)">His-&gt;Pro (H)</option>
-        <option value="His-&gt;Ser (H)">His-&gt;Ser (H)</option>
-        <option value="His-&gt;Thr (H)">His-&gt;Thr (H)</option>
-        <option value="His-&gt;Trp (H)">His-&gt;Trp (H)</option>
-        <option value="His-&gt;Tyr (H)">His-&gt;Tyr (H)</option>
-        <option value="His-&gt;Val (H)">His-&gt;Val (H)</option>
-        <option value="His-&gt;Xle (H)">His-&gt;Xle (H)</option>
-        <option value="HMVK (C)">HMVK (C)</option>
-        <option value="HN2_mustard (C)">HN2_mustard (C)</option>
-        <option value="HN2_mustard (H)">HN2_mustard (H)</option>
-        <option value="HN2_mustard (K)">HN2_mustard (K)</option>
-        <option value="HN3_mustard (C)">HN3_mustard (C)</option>
-        <option value="HN3_mustard (H)">HN3_mustard (H)</option>
-        <option value="HN3_mustard (K)">HN3_mustard (K)</option>
-        <option value="HNE (A)">HNE (A)</option>
-        <option value="HNE (C)">HNE (C)</option>
-        <option value="HNE (H)">HNE (H)</option>
-        <option value="HNE (K)">HNE (K)</option>
-        <option value="HNE (L)">HNE (L)</option>
-        <option value="HNE+Delta:H(2) (C)">HNE+Delta:H(2) (C)</option>
-        <option value="HNE+Delta:H(2) (H)">HNE+Delta:H(2) (H)</option>
-        <option value="HNE+Delta:H(2) (K)">HNE+Delta:H(2) (K)</option>
-        <option value="HNE-BAHAH (C)">HNE-BAHAH (C)</option>
-        <option value="HNE-BAHAH (H)">HNE-BAHAH (H)</option>
-        <option value="HNE-BAHAH (K)">HNE-BAHAH (K)</option>
-        <option value="HNE-Delta:H(2)O (C)">HNE-Delta:H(2)O (C)</option>
-        <option value="HNE-Delta:H(2)O (H)">HNE-Delta:H(2)O (H)</option>
-        <option value="HNE-Delta:H(2)O (K)">HNE-Delta:H(2)O (K)</option>
-        <option value="Homocysteic_acid (M)">Homocysteic_acid (M)</option>
-        <option value="HPG (R)">HPG (R)</option>
-        <option value="Hydroxamic_acid (D)">Hydroxamic_acid (D)</option>
-        <option value="Hydroxamic_acid (E)">Hydroxamic_acid (E)</option>
-        <option value="Hydroxycinnamyl (C)">Hydroxycinnamyl (C)</option>
-        <option value="Hydroxyfarnesyl (C)">Hydroxyfarnesyl (C)</option>
-        <option value="Hydroxyheme (E)">Hydroxyheme (E)</option>
-        <option value="hydroxyisobutyryl (K)">hydroxyisobutyryl (K)</option>
-        <option value="Hydroxymethyl (N)">Hydroxymethyl (N)</option>
-        <option value="HydroxymethylOP (K)">HydroxymethylOP (K)</option>
-        <option value="Hydroxytrimethyl (K)">Hydroxytrimethyl (K)</option>
-        <option value="Hypusine (K)">Hypusine (K)</option>
-        <option value="IASD (C)">IASD (C)</option>
-        <option value="IBTP (C)">IBTP (C)</option>
-        <option value="ICAT-C (C)">ICAT-C (C)</option>
-        <option value="ICAT-C:13C(9) (C)">ICAT-C:13C(9) (C)</option>
-        <option value="ICAT-D (C)">ICAT-D (C)</option>
-        <option value="ICAT-D:2H(8) (C)">ICAT-D:2H(8) (C)</option>
-        <option value="ICAT-G (C)">ICAT-G (C)</option>
-        <option value="ICAT-G:2H(8) (C)">ICAT-G:2H(8) (C)</option>
-        <option value="ICAT-H (C)">ICAT-H (C)</option>
-        <option value="ICAT-H:13C(6) (C)">ICAT-H:13C(6) (C)</option>
-        <option value="ICDID (C)">ICDID (C)</option>
-        <option value="ICDID:2H(6) (C)">ICDID:2H(6) (C)</option>
-        <option value="ICPL (K)">ICPL (K)</option>
-        <option value="ICPL (N-term)">ICPL (N-term)</option>
-        <option value="ICPL (Protein N-term)">ICPL (Protein N-term)</option>
-        <option value="ICPL:13C(6) (K)">ICPL:13C(6) (K)</option>
-        <option value="ICPL:13C(6) (N-term)">ICPL:13C(6) (N-term)</option>
-        <option value="ICPL:13C(6) (Protein N-term)">ICPL:13C(6) (Protein N-term)</option>
-        <option value="ICPL:13C(6)2H(4) (K)">ICPL:13C(6)2H(4) (K)</option>
-        <option value="ICPL:13C(6)2H(4) (N-term)">ICPL:13C(6)2H(4) (N-term)</option>
-        <option value="ICPL:13C(6)2H(4) (Protein N-term)">ICPL:13C(6)2H(4) (Protein N-term)</option>
-        <option value="ICPL:2H(4) (K)">ICPL:2H(4) (K)</option>
-        <option value="ICPL:2H(4) (N-term)">ICPL:2H(4) (N-term)</option>
-        <option value="ICPL:2H(4) (Protein N-term)">ICPL:2H(4) (Protein N-term)</option>
-        <option value="IDEnT (C)">IDEnT (C)</option>
-        <option value="IED-Biotin (C)">IED-Biotin (C)</option>
-        <option value="IGBP (C)">IGBP (C)</option>
-        <option value="IGBP:13C(2) (C)">IGBP:13C(2) (C)</option>
-        <option value="IMEHex(2)NeuAc(1) (K)">IMEHex(2)NeuAc(1) (K)</option>
-        <option value="IMID (K)">IMID (K)</option>
-        <option value="IMID:2H(4) (K)">IMID:2H(4) (K)</option>
-        <option value="Iminobiotin (K)">Iminobiotin (K)</option>
-        <option value="Iminobiotin (N-term)">Iminobiotin (N-term)</option>
-        <option value="Iodo (H)">Iodo (H)</option>
-        <option value="Iodo (Y)">Iodo (Y)</option>
-        <option value="Iodoacetanilide (C)">Iodoacetanilide (C)</option>
-        <option value="Iodoacetanilide (K)">Iodoacetanilide (K)</option>
-        <option value="Iodoacetanilide (N-term)">Iodoacetanilide (N-term)</option>
-        <option value="Iodoacetanilide:13C(6) (C)">Iodoacetanilide:13C(6) (C)</option>
-        <option value="Iodoacetanilide:13C(6) (K)">Iodoacetanilide:13C(6) (K)</option>
-        <option value="Iodoacetanilide:13C(6) (N-term)">Iodoacetanilide:13C(6) (N-term)</option>
-        <option value="iodoTMT (C)">iodoTMT (C)</option>
-        <option value="iodoTMT (D)">iodoTMT (D)</option>
-        <option value="iodoTMT (E)">iodoTMT (E)</option>
-        <option value="iodoTMT (H)">iodoTMT (H)</option>
-        <option value="iodoTMT (K)">iodoTMT (K)</option>
-        <option value="iodoTMT6plex (C)">iodoTMT6plex (C)</option>
-        <option value="iodoTMT6plex (D)">iodoTMT6plex (D)</option>
-        <option value="iodoTMT6plex (E)">iodoTMT6plex (E)</option>
-        <option value="iodoTMT6plex (H)">iodoTMT6plex (H)</option>
-        <option value="iodoTMT6plex (K)">iodoTMT6plex (K)</option>
-        <option value="IodoU-AMP (F)">IodoU-AMP (F)</option>
-        <option value="IodoU-AMP (W)">IodoU-AMP (W)</option>
-        <option value="IodoU-AMP (Y)">IodoU-AMP (Y)</option>
-        <option value="ISD_z+2_ion (N-term)">ISD_z+2_ion (N-term)</option>
-        <option value="Isopropylphospho (S)">Isopropylphospho (S)</option>
-        <option value="Isopropylphospho (T)">Isopropylphospho (T)</option>
-        <option value="Isopropylphospho (Y)">Isopropylphospho (Y)</option>
-        <option value="iTRAQ4plex (C)">iTRAQ4plex (C)</option>
-        <option value="iTRAQ4plex (H)">iTRAQ4plex (H)</option>
-        <option value="iTRAQ4plex (K)">iTRAQ4plex (K)</option>
-        <option value="iTRAQ4plex (N-term)">iTRAQ4plex (N-term)</option>
-        <option value="iTRAQ4plex (Protein N-term)">iTRAQ4plex (Protein N-term)</option>
-        <option value="iTRAQ4plex (S)">iTRAQ4plex (S)</option>
-        <option value="iTRAQ4plex (T)">iTRAQ4plex (T)</option>
-        <option value="iTRAQ4plex (Y)">iTRAQ4plex (Y)</option>
-        <option value="iTRAQ4plex114 (C)">iTRAQ4plex114 (C)</option>
-        <option value="iTRAQ4plex114 (K)">iTRAQ4plex114 (K)</option>
-        <option value="iTRAQ4plex114 (N-term)">iTRAQ4plex114 (N-term)</option>
-        <option value="iTRAQ4plex114 (Y)">iTRAQ4plex114 (Y)</option>
-        <option value="iTRAQ4plex115 (C)">iTRAQ4plex115 (C)</option>
-        <option value="iTRAQ4plex115 (K)">iTRAQ4plex115 (K)</option>
-        <option value="iTRAQ4plex115 (N-term)">iTRAQ4plex115 (N-term)</option>
-        <option value="iTRAQ4plex115 (Y)">iTRAQ4plex115 (Y)</option>
-        <option value="iTRAQ8plex (C)">iTRAQ8plex (C)</option>
-        <option value="iTRAQ8plex (H)">iTRAQ8plex (H)</option>
-        <option value="iTRAQ8plex (K)">iTRAQ8plex (K)</option>
-        <option value="iTRAQ8plex (N-term)">iTRAQ8plex (N-term)</option>
-        <option value="iTRAQ8plex (Protein N-term)">iTRAQ8plex (Protein N-term)</option>
-        <option value="iTRAQ8plex (S)">iTRAQ8plex (S)</option>
-        <option value="iTRAQ8plex (T)">iTRAQ8plex (T)</option>
-        <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
-        <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
-        <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
-        <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
-        <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
-        <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
-        <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
-        <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
-        <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
-        <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
-        <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
-        <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
-        <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
-        <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
-        <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
-        <option value="Label:13C(5)15N(1) (E)">Label:13C(5)15N(1) (E)</option>
-        <option value="Label:13C(5)15N(1) (M)">Label:13C(5)15N(1) (M)</option>
-        <option value="Label:13C(5)15N(1) (P)">Label:13C(5)15N(1) (P)</option>
-        <option value="Label:13C(5)15N(1) (V)">Label:13C(5)15N(1) (V)</option>
-        <option value="Label:13C(6) (I)">Label:13C(6) (I)</option>
-        <option value="Label:13C(6) (K)">Label:13C(6) (K)</option>
-        <option value="Label:13C(6) (L)">Label:13C(6) (L)</option>
-        <option value="Label:13C(6) (R)">Label:13C(6) (R)</option>
-        <option value="Label:13C(6)+Acetyl (K)">Label:13C(6)+Acetyl (K)</option>
-        <option value="Label:13C(6)+Dimethyl (K)">Label:13C(6)+Dimethyl (K)</option>
-        <option value="Label:13C(6)+GG (K)">Label:13C(6)+GG (K)</option>
-        <option value="Label:13C(6)15N(1) (I)">Label:13C(6)15N(1) (I)</option>
-        <option value="Label:13C(6)15N(1) (L)">Label:13C(6)15N(1) (L)</option>
-        <option value="Label:13C(6)15N(2) (K)">Label:13C(6)15N(2) (K)</option>
-        <option value="Label:13C(6)15N(2)+Acetyl (K)">Label:13C(6)15N(2)+Acetyl (K)</option>
-        <option value="Label:13C(6)15N(2)+Dimethyl (K)">Label:13C(6)15N(2)+Dimethyl (K)</option>
-        <option value="Label:13C(6)15N(2)+GG (K)">Label:13C(6)15N(2)+GG (K)</option>
-        <option value="Label:13C(6)15N(4) (R)">Label:13C(6)15N(4) (R)</option>
-        <option value="Label:13C(6)15N(4)+Dimethyl (R)">Label:13C(6)15N(4)+Dimethyl (R)</option>
-        <option value="Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R)">Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R)</option>
-        <option value="Label:13C(6)15N(4)+Methyl (R)">Label:13C(6)15N(4)+Methyl (R)</option>
-        <option value="Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R)">Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R)</option>
-        <option value="Label:13C(9) (F)">Label:13C(9) (F)</option>
-        <option value="Label:13C(9) (Y)">Label:13C(9) (Y)</option>
-        <option value="Label:13C(9)+Phospho (Y)">Label:13C(9)+Phospho (Y)</option>
-        <option value="Label:13C(9)15N(1) (F)">Label:13C(9)15N(1) (F)</option>
-        <option value="Label:15N(1) (A)">Label:15N(1) (A)</option>
-        <option value="Label:15N(1) (C)">Label:15N(1) (C)</option>
-        <option value="Label:15N(1) (D)">Label:15N(1) (D)</option>
-        <option value="Label:15N(1) (E)">Label:15N(1) (E)</option>
-        <option value="Label:15N(1) (F)">Label:15N(1) (F)</option>
-        <option value="Label:15N(1) (G)">Label:15N(1) (G)</option>
-        <option value="Label:15N(1) (I)">Label:15N(1) (I)</option>
-        <option value="Label:15N(1) (L)">Label:15N(1) (L)</option>
-        <option value="Label:15N(1) (M)">Label:15N(1) (M)</option>
-        <option value="Label:15N(1) (P)">Label:15N(1) (P)</option>
-        <option value="Label:15N(1) (S)">Label:15N(1) (S)</option>
-        <option value="Label:15N(1) (T)">Label:15N(1) (T)</option>
-        <option value="Label:15N(1) (V)">Label:15N(1) (V)</option>
-        <option value="Label:15N(1) (Y)">Label:15N(1) (Y)</option>
-        <option value="Label:15N(2) (K)">Label:15N(2) (K)</option>
-        <option value="Label:15N(2) (N)">Label:15N(2) (N)</option>
-        <option value="Label:15N(2) (Q)">Label:15N(2) (Q)</option>
-        <option value="Label:15N(2) (W)">Label:15N(2) (W)</option>
-        <option value="Label:15N(2)2H(9) (K)">Label:15N(2)2H(9) (K)</option>
-        <option value="Label:15N(3) (H)">Label:15N(3) (H)</option>
-        <option value="Label:15N(4) (R)">Label:15N(4) (R)</option>
-        <option value="Label:18O(1) (C-term)">Label:18O(1) (C-term)</option>
-        <option value="Label:18O(1) (S)">Label:18O(1) (S)</option>
-        <option value="Label:18O(1) (T)">Label:18O(1) (T)</option>
-        <option value="Label:18O(1) (Y)">Label:18O(1) (Y)</option>
-        <option value="Label:18O(2) (C-term)">Label:18O(2) (C-term)</option>
-        <option value="Label:2H(10) (L)">Label:2H(10) (L)</option>
-        <option value="Label:2H(3) (L)">Label:2H(3) (L)</option>
-        <option value="Label:2H(3) (M)">Label:2H(3) (M)</option>
-        <option value="Label:2H(3)+Oxidation (M)">Label:2H(3)+Oxidation (M)</option>
-        <option value="Label:2H(4) (A)">Label:2H(4) (A)</option>
-        <option value="Label:2H(4) (F)">Label:2H(4) (F)</option>
-        <option value="Label:2H(4) (K)">Label:2H(4) (K)</option>
-        <option value="Label:2H(4) (U)">Label:2H(4) (U)</option>
-        <option value="Label:2H(4) (Y)">Label:2H(4) (Y)</option>
-        <option value="Label:2H(4)+Acetyl (K)">Label:2H(4)+Acetyl (K)</option>
-        <option value="Label:2H(4)+GG (K)">Label:2H(4)+GG (K)</option>
-        <option value="Label:2H(4)13C(1) (R)">Label:2H(4)13C(1) (R)</option>
-        <option value="Label:2H(6)15N(1) (P)">Label:2H(6)15N(1) (P)</option>
-        <option value="Label:2H(7)15N(4) (R)">Label:2H(7)15N(4) (R)</option>
-        <option value="Label:2H(9)13C(6)15N(2) (K)">Label:2H(9)13C(6)15N(2) (K)</option>
-        <option value="lapachenole (C)">lapachenole (C)</option>
-        <option value="Leu-&gt;MetOx (L)">Leu-&gt;MetOx (L)</option>
-        <option value="LG-anhydrolactam (K)">LG-anhydrolactam (K)</option>
-        <option value="LG-anhydrolactam (N-term)">LG-anhydrolactam (N-term)</option>
-        <option value="LG-anhyropyrrole (K)">LG-anhyropyrrole (K)</option>
-        <option value="LG-anhyropyrrole (N-term)">LG-anhyropyrrole (N-term)</option>
-        <option value="LG-Hlactam-K (K)">LG-Hlactam-K (K)</option>
-        <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
-        <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
-        <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
-        <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
-        <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
-        <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
-        <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
-        <option value="Lipoyl (K)">Lipoyl (K)</option>
-        <option value="LRGG (K)">LRGG (K)</option>
-        <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
-        <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
-        <option value="Lys (N-term)">Lys (N-term)</option>
-        <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
-        <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
-        <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
-        <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
-        <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
-        <option value="Lys-&gt;Asp (K)">Lys-&gt;Asp (K)</option>
-        <option value="Lys-&gt;CamCys (K)">Lys-&gt;CamCys (K)</option>
-        <option value="Lys-&gt;Cys (K)">Lys-&gt;Cys (K)</option>
-        <option value="Lys-&gt;Gln (K)">Lys-&gt;Gln (K)</option>
-        <option value="Lys-&gt;Glu (K)">Lys-&gt;Glu (K)</option>
-        <option value="Lys-&gt;Gly (K)">Lys-&gt;Gly (K)</option>
-        <option value="Lys-&gt;His (K)">Lys-&gt;His (K)</option>
-        <option value="Lys-&gt;Met (K)">Lys-&gt;Met (K)</option>
-        <option value="Lys-&gt;MetOx (K)">Lys-&gt;MetOx (K)</option>
-        <option value="Lys-&gt;Phe (K)">Lys-&gt;Phe (K)</option>
-        <option value="Lys-&gt;Pro (K)">Lys-&gt;Pro (K)</option>
-        <option value="Lys-&gt;Ser (K)">Lys-&gt;Ser (K)</option>
-        <option value="Lys-&gt;Thr (K)">Lys-&gt;Thr (K)</option>
-        <option value="Lys-&gt;Trp (K)">Lys-&gt;Trp (K)</option>
-        <option value="Lys-&gt;Tyr (K)">Lys-&gt;Tyr (K)</option>
-        <option value="Lys-&gt;Val (K)">Lys-&gt;Val (K)</option>
-        <option value="Lys-&gt;Xle (K)">Lys-&gt;Xle (K)</option>
-        <option value="Lys-loss (Protein C-term K)">Lys-loss (Protein C-term K)</option>
-        <option value="Lysbiotinhydrazide (K)">Lysbiotinhydrazide (K)</option>
-        <option value="maleimide (C)">maleimide (C)</option>
-        <option value="maleimide (K)">maleimide (K)</option>
-        <option value="Maleimide-PEO2-Biotin (C)">Maleimide-PEO2-Biotin (C)</option>
-        <option value="maleimide3 (C)">maleimide3 (C)</option>
-        <option value="maleimide3 (K)">maleimide3 (K)</option>
-        <option value="maleimide5 (C)">maleimide5 (C)</option>
-        <option value="maleimide5 (K)">maleimide5 (K)</option>
-        <option value="Malonyl (C)">Malonyl (C)</option>
-        <option value="Malonyl (K)">Malonyl (K)</option>
-        <option value="Malonyl (S)">Malonyl (S)</option>
-        <option value="MDCC (C)">MDCC (C)</option>
-        <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
-        <option value="Menadione (C)">Menadione (C)</option>
-        <option value="Menadione (K)">Menadione (K)</option>
-        <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
-        <option value="Menadione-HQ (K)">Menadione-HQ (K)</option>
-        <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
-        <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
-        <option value="MesitylOxide (H)">MesitylOxide (H)</option>
-        <option value="MesitylOxide (K)">MesitylOxide (K)</option>
-        <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
-        <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
-        <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
-        <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
-        <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
-        <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
-        <option value="Met-&gt;AspSA (M)">Met-&gt;AspSA (M)</option>
-        <option value="Met-&gt;Cys (M)">Met-&gt;Cys (M)</option>
-        <option value="Met-&gt;Gln (M)">Met-&gt;Gln (M)</option>
-        <option value="Met-&gt;Glu (M)">Met-&gt;Glu (M)</option>
-        <option value="Met-&gt;Gly (M)">Met-&gt;Gly (M)</option>
-        <option value="Met-&gt;His (M)">Met-&gt;His (M)</option>
-        <option value="Met-&gt;Hpg (M)">Met-&gt;Hpg (M)</option>
-        <option value="Met-&gt;Hse (C-term M)">Met-&gt;Hse (C-term M)</option>
-        <option value="Met-&gt;Hsl (C-term M)">Met-&gt;Hsl (C-term M)</option>
-        <option value="Met-&gt;Lys (M)">Met-&gt;Lys (M)</option>
-        <option value="Met-&gt;Phe (M)">Met-&gt;Phe (M)</option>
-        <option value="Met-&gt;Pro (M)">Met-&gt;Pro (M)</option>
-        <option value="Met-&gt;Ser (M)">Met-&gt;Ser (M)</option>
-        <option value="Met-&gt;Thr (M)">Met-&gt;Thr (M)</option>
-        <option value="Met-&gt;Trp (M)">Met-&gt;Trp (M)</option>
-        <option value="Met-&gt;Tyr (M)">Met-&gt;Tyr (M)</option>
-        <option value="Met-&gt;Val (M)">Met-&gt;Val (M)</option>
-        <option value="Met-&gt;Xle (M)">Met-&gt;Xle (M)</option>
-        <option value="Met-loss (Protein N-term M)">Met-loss (Protein N-term M)</option>
-        <option value="Met-loss+Acetyl (Protein N-term M)">Met-loss+Acetyl (Protein N-term M)</option>
-        <option value="Methamidophos-O (C)">Methamidophos-O (C)</option>
-        <option value="Methamidophos-O (H)">Methamidophos-O (H)</option>
-        <option value="Methamidophos-O (K)">Methamidophos-O (K)</option>
-        <option value="Methamidophos-O (S)">Methamidophos-O (S)</option>
-        <option value="Methamidophos-O (T)">Methamidophos-O (T)</option>
-        <option value="Methamidophos-O (Y)">Methamidophos-O (Y)</option>
-        <option value="Methamidophos-S (C)">Methamidophos-S (C)</option>
-        <option value="Methamidophos-S (H)">Methamidophos-S (H)</option>
-        <option value="Methamidophos-S (K)">Methamidophos-S (K)</option>
-        <option value="Methamidophos-S (S)">Methamidophos-S (S)</option>
-        <option value="Methamidophos-S (T)">Methamidophos-S (T)</option>
-        <option value="Methamidophos-S (Y)">Methamidophos-S (Y)</option>
-        <option value="Methyl (C)">Methyl (C)</option>
-        <option value="Methyl (C-term)">Methyl (C-term)</option>
-        <option value="Methyl (D)">Methyl (D)</option>
-        <option value="Methyl (E)">Methyl (E)</option>
-        <option value="Methyl (H)">Methyl (H)</option>
-        <option value="Methyl (I)">Methyl (I)</option>
-        <option value="Methyl (K)">Methyl (K)</option>
-        <option value="Methyl (L)">Methyl (L)</option>
-        <option value="Methyl (N)">Methyl (N)</option>
-        <option value="Methyl (N-term)">Methyl (N-term)</option>
-        <option value="Methyl (Protein N-term)">Methyl (Protein N-term)</option>
-        <option value="Methyl (Q)">Methyl (Q)</option>
-        <option value="Methyl (R)">Methyl (R)</option>
-        <option value="Methyl (S)">Methyl (S)</option>
-        <option value="Methyl (T)">Methyl (T)</option>
-        <option value="Methyl+Acetyl:2H(3) (K)">Methyl+Acetyl:2H(3) (K)</option>
-        <option value="Methyl+Deamidated (N)">Methyl+Deamidated (N)</option>
-        <option value="Methyl+Deamidated (Q)">Methyl+Deamidated (Q)</option>
-        <option value="Methyl-PEO12-Maleimide (C)">Methyl-PEO12-Maleimide (C)</option>
-        <option value="Methyl:2H(2) (K)">Methyl:2H(2) (K)</option>
-        <option value="Methyl:2H(2) (N-term)">Methyl:2H(2) (N-term)</option>
-        <option value="Methyl:2H(2)13C (C)">Methyl:2H(2)13C (C)</option>
-        <option value="Methyl:2H(2)13C (C-term)">Methyl:2H(2)13C (C-term)</option>
-        <option value="Methyl:2H(2)13C (D)">Methyl:2H(2)13C (D)</option>
-        <option value="Methyl:2H(2)13C (E)">Methyl:2H(2)13C (E)</option>
-        <option value="Methyl:2H(2)13C (H)">Methyl:2H(2)13C (H)</option>
-        <option value="Methyl:2H(2)13C (I)">Methyl:2H(2)13C (I)</option>
-        <option value="Methyl:2H(2)13C (K)">Methyl:2H(2)13C (K)</option>
-        <option value="Methyl:2H(2)13C (L)">Methyl:2H(2)13C (L)</option>
-        <option value="Methyl:2H(2)13C (N)">Methyl:2H(2)13C (N)</option>
-        <option value="Methyl:2H(2)13C (N-term)">Methyl:2H(2)13C (N-term)</option>
-        <option value="Methyl:2H(2)13C (Protein N-term)">Methyl:2H(2)13C (Protein N-term)</option>
-        <option value="Methyl:2H(2)13C (Q)">Methyl:2H(2)13C (Q)</option>
-        <option value="Methyl:2H(2)13C (R)">Methyl:2H(2)13C (R)</option>
-        <option value="Methyl:2H(2)13C (S)">Methyl:2H(2)13C (S)</option>
-        <option value="Methyl:2H(2)13C (T)">Methyl:2H(2)13C (T)</option>
-        <option value="Methyl:2H(3) (D)">Methyl:2H(3) (D)</option>
-        <option value="Methyl:2H(3) (E)">Methyl:2H(3) (E)</option>
-        <option value="Methyl:2H(3) (K)">Methyl:2H(3) (K)</option>
-        <option value="Methyl:2H(3) (R)">Methyl:2H(3) (R)</option>
-        <option value="Methyl:2H(3) (X)">Methyl:2H(3) (X)</option>
-        <option value="Methyl:2H(3)+Acetyl:2H(3) (K)">Methyl:2H(3)+Acetyl:2H(3) (K)</option>
-        <option value="Methyl:2H(3)13C(1) (K)">Methyl:2H(3)13C(1) (K)</option>
-        <option value="Methyl:2H(3)13C(1) (N-term)">Methyl:2H(3)13C(1) (N-term)</option>
-        <option value="Methyl:2H(3)13C(1) (R)">Methyl:2H(3)13C(1) (R)</option>
-        <option value="Methylamine (S)">Methylamine (S)</option>
-        <option value="Methylamine (T)">Methylamine (T)</option>
-        <option value="Methylmalonylation (S)">Methylmalonylation (S)</option>
-        <option value="methylol (K)">methylol (K)</option>
-        <option value="methylol (W)">methylol (W)</option>
-        <option value="methylol (Y)">methylol (Y)</option>
-        <option value="Methylphosphonate (S)">Methylphosphonate (S)</option>
-        <option value="Methylphosphonate (T)">Methylphosphonate (T)</option>
-        <option value="Methylphosphonate (Y)">Methylphosphonate (Y)</option>
-        <option value="Methylpyrroline (K)">Methylpyrroline (K)</option>
-        <option value="methylsulfonylethyl (C)">methylsulfonylethyl (C)</option>
-        <option value="methylsulfonylethyl (H)">methylsulfonylethyl (H)</option>
-        <option value="methylsulfonylethyl (K)">methylsulfonylethyl (K)</option>
-        <option value="Methylthio (C)">Methylthio (C)</option>
-        <option value="Methylthio (D)">Methylthio (D)</option>
-        <option value="Methylthio (K)">Methylthio (K)</option>
-        <option value="Methylthio (N)">Methylthio (N)</option>
-        <option value="Methylthio (N-term)">Methylthio (N-term)</option>
-        <option value="MG-H1 (R)">MG-H1 (R)</option>
-        <option value="Microcin (Protein C-term)">Microcin (Protein C-term)</option>
-        <option value="MicrocinC7 (Protein C-term)">MicrocinC7 (Protein C-term)</option>
-        <option value="MM-diphenylpentanone (C)">MM-diphenylpentanone (C)</option>
-        <option value="Molybdopterin (C)">Molybdopterin (C)</option>
-        <option value="MolybdopterinGD (C)">MolybdopterinGD (C)</option>
-        <option value="MolybdopterinGD (D)">MolybdopterinGD (D)</option>
-        <option value="MolybdopterinGD (U)">MolybdopterinGD (U)</option>
-        <option value="MolybdopterinGD+Delta:S(-1)Se(1) (C)">MolybdopterinGD+Delta:S(-1)Se(1) (C)</option>
-        <option value="monomethylphosphothione (C)">monomethylphosphothione (C)</option>
-        <option value="monomethylphosphothione (H)">monomethylphosphothione (H)</option>
-        <option value="monomethylphosphothione (K)">monomethylphosphothione (K)</option>
-        <option value="monomethylphosphothione (S)">monomethylphosphothione (S)</option>
-        <option value="monomethylphosphothione (T)">monomethylphosphothione (T)</option>
-        <option value="monomethylphosphothione (Y)">monomethylphosphothione (Y)</option>
-        <option value="mTRAQ (H)">mTRAQ (H)</option>
-        <option value="mTRAQ (K)">mTRAQ (K)</option>
-        <option value="mTRAQ (N-term)">mTRAQ (N-term)</option>
-        <option value="mTRAQ (S)">mTRAQ (S)</option>
-        <option value="mTRAQ (T)">mTRAQ (T)</option>
-        <option value="mTRAQ (Y)">mTRAQ (Y)</option>
-        <option value="mTRAQ:13C(3)15N(1) (H)">mTRAQ:13C(3)15N(1) (H)</option>
-        <option value="mTRAQ:13C(3)15N(1) (K)">mTRAQ:13C(3)15N(1) (K)</option>
-        <option value="mTRAQ:13C(3)15N(1) (N-term)">mTRAQ:13C(3)15N(1) (N-term)</option>
-        <option value="mTRAQ:13C(3)15N(1) (S)">mTRAQ:13C(3)15N(1) (S)</option>
-        <option value="mTRAQ:13C(3)15N(1) (T)">mTRAQ:13C(3)15N(1) (T)</option>
-        <option value="mTRAQ:13C(3)15N(1) (Y)">mTRAQ:13C(3)15N(1) (Y)</option>
-        <option value="mTRAQ:13C(6)15N(2) (H)">mTRAQ:13C(6)15N(2) (H)</option>
-        <option value="mTRAQ:13C(6)15N(2) (K)">mTRAQ:13C(6)15N(2) (K)</option>
-        <option value="mTRAQ:13C(6)15N(2) (N-term)">mTRAQ:13C(6)15N(2) (N-term)</option>
-        <option value="mTRAQ:13C(6)15N(2) (S)">mTRAQ:13C(6)15N(2) (S)</option>
-        <option value="mTRAQ:13C(6)15N(2) (T)">mTRAQ:13C(6)15N(2) (T)</option>
-        <option value="mTRAQ:13C(6)15N(2) (Y)">mTRAQ:13C(6)15N(2) (Y)</option>
-        <option value="MTSL (C)">MTSL (C)</option>
-        <option value="MurNAc (A)">MurNAc (A)</option>
-        <option value="Myristoleyl (Protein N-term G)">Myristoleyl (Protein N-term G)</option>
-        <option value="Myristoyl (C)">Myristoyl (C)</option>
-        <option value="Myristoyl (K)">Myristoyl (K)</option>
-        <option value="Myristoyl (N-term G)">Myristoyl (N-term G)</option>
-        <option value="Myristoyl+Delta:H(-4) (Protein N-term G)">Myristoyl+Delta:H(-4) (Protein N-term G)</option>
-        <option value="N-dimethylphosphate (S)">N-dimethylphosphate (S)</option>
-        <option value="NA-LNO2 (C)">NA-LNO2 (C)</option>
-        <option value="NA-LNO2 (H)">NA-LNO2 (H)</option>
-        <option value="NA-OA-NO2 (C)">NA-OA-NO2 (C)</option>
-        <option value="NA-OA-NO2 (H)">NA-OA-NO2 (H)</option>
-        <option value="NBS (W)">NBS (W)</option>
-        <option value="NBS:13C(6) (W)">NBS:13C(6) (W)</option>
-        <option value="NDA (K)">NDA (K)</option>
-        <option value="NDA (N-term)">NDA (N-term)</option>
-        <option value="NEIAA (C)">NEIAA (C)</option>
-        <option value="NEIAA (Y)">NEIAA (Y)</option>
-        <option value="NEIAA:2H(5) (C)">NEIAA:2H(5) (C)</option>
-        <option value="NEIAA:2H(5) (Y)">NEIAA:2H(5) (Y)</option>
-        <option value="NEM:2H(5) (C)">NEM:2H(5) (C)</option>
-        <option value="NEM:2H(5)+H2O (C)">NEM:2H(5)+H2O (C)</option>
-        <option value="NEMsulfur (C)">NEMsulfur (C)</option>
-        <option value="NEMsulfurWater (C)">NEMsulfurWater (C)</option>
-        <option value="Nethylmaleimide (C)">Nethylmaleimide (C)</option>
-        <option value="Nethylmaleimide+water (C)">Nethylmaleimide+water (C)</option>
-        <option value="Nethylmaleimide+water (K)">Nethylmaleimide+water (K)</option>
-        <option value="NeuAc (N)">NeuAc (N)</option>
-        <option value="NeuAc (S)">NeuAc (S)</option>
-        <option value="NeuAc (T)">NeuAc (T)</option>
-        <option value="NeuGc (N)">NeuGc (N)</option>
-        <option value="NeuGc (S)">NeuGc (S)</option>
-        <option value="NeuGc (T)">NeuGc (T)</option>
-        <option value="NHS-fluorescein (K)">NHS-fluorescein (K)</option>
-        <option value="NHS-LC-Biotin (K)">NHS-LC-Biotin (K)</option>
-        <option value="NHS-LC-Biotin (N-term)">NHS-LC-Biotin (N-term)</option>
-        <option value="NIC (K)">NIC (K)</option>
-        <option value="NIC (N-term)">NIC (N-term)</option>
-        <option value="NIPCAM (C)">NIPCAM (C)</option>
-        <option value="Nitrene (Y)">Nitrene (Y)</option>
-        <option value="Nitro (F)">Nitro (F)</option>
-        <option value="Nitro (W)">Nitro (W)</option>
-        <option value="Nitro (Y)">Nitro (Y)</option>
-        <option value="Nitrosyl (C)">Nitrosyl (C)</option>
-        <option value="Nitrosyl (Y)">Nitrosyl (Y)</option>
-        <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
-        <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
-        <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
-        <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
-        <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-        <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
-        <option value="NP40 (N-term)">NP40 (N-term)</option>
-        <option value="NQIGG (K)">NQIGG (K)</option>
-        <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
-        <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
-        <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
-        <option value="O-Et-N-diMePhospho (S)">O-Et-N-diMePhospho (S)</option>
-        <option value="O-Isopropylmethylphosphonate (S)">O-Isopropylmethylphosphonate (S)</option>
-        <option value="O-Isopropylmethylphosphonate (T)">O-Isopropylmethylphosphonate (T)</option>
-        <option value="O-Isopropylmethylphosphonate (Y)">O-Isopropylmethylphosphonate (Y)</option>
-        <option value="O-Methylphosphate (S)">O-Methylphosphate (S)</option>
-        <option value="O-Methylphosphate (T)">O-Methylphosphate (T)</option>
-        <option value="O-Methylphosphate (Y)">O-Methylphosphate (Y)</option>
-        <option value="O-pinacolylmethylphosphonate (H)">O-pinacolylmethylphosphonate (H)</option>
-        <option value="O-pinacolylmethylphosphonate (K)">O-pinacolylmethylphosphonate (K)</option>
-        <option value="O-pinacolylmethylphosphonate (S)">O-pinacolylmethylphosphonate (S)</option>
-        <option value="O-pinacolylmethylphosphonate (T)">O-pinacolylmethylphosphonate (T)</option>
-        <option value="O-pinacolylmethylphosphonate (Y)">O-pinacolylmethylphosphonate (Y)</option>
-        <option value="Octanoyl (C)">Octanoyl (C)</option>
-        <option value="Octanoyl (S)">Octanoyl (S)</option>
-        <option value="Octanoyl (T)">Octanoyl (T)</option>
-        <option value="OxArgBiotin (R)">OxArgBiotin (R)</option>
-        <option value="OxArgBiotinRed (R)">OxArgBiotinRed (R)</option>
-        <option value="Oxidation (C)">Oxidation (C)</option>
-        <option value="Oxidation (C-term G)">Oxidation (C-term G)</option>
-        <option value="Oxidation (D)">Oxidation (D)</option>
-        <option value="Oxidation (E)">Oxidation (E)</option>
-        <option value="Oxidation (F)">Oxidation (F)</option>
-        <option value="Oxidation (H)">Oxidation (H)</option>
-        <option value="Oxidation (I)">Oxidation (I)</option>
-        <option value="Oxidation (K)">Oxidation (K)</option>
-        <option value="Oxidation (L)">Oxidation (L)</option>
-        <option value="Oxidation (M)">Oxidation (M)</option>
-        <option value="Oxidation (N)">Oxidation (N)</option>
-        <option value="Oxidation (P)">Oxidation (P)</option>
-        <option value="Oxidation (Q)">Oxidation (Q)</option>
-        <option value="Oxidation (R)">Oxidation (R)</option>
-        <option value="Oxidation (S)">Oxidation (S)</option>
-        <option value="Oxidation (T)">Oxidation (T)</option>
-        <option value="Oxidation (U)">Oxidation (U)</option>
-        <option value="Oxidation (V)">Oxidation (V)</option>
-        <option value="Oxidation (W)">Oxidation (W)</option>
-        <option value="Oxidation (Y)">Oxidation (Y)</option>
-        <option value="Oxidation+NEM (C)">Oxidation+NEM (C)</option>
-        <option value="OxLysBiotin (K)">OxLysBiotin (K)</option>
-        <option value="OxLysBiotinRed (K)">OxLysBiotinRed (K)</option>
-        <option value="OxProBiotin (P)">OxProBiotin (P)</option>
-        <option value="OxProBiotinRed (P)">OxProBiotinRed (P)</option>
-        <option value="Palmitoleyl (C)">Palmitoleyl (C)</option>
-        <option value="Palmitoleyl (S)">Palmitoleyl (S)</option>
-        <option value="Palmitoleyl (T)">Palmitoleyl (T)</option>
-        <option value="Palmitoyl (C)">Palmitoyl (C)</option>
-        <option value="Palmitoyl (K)">Palmitoyl (K)</option>
-        <option value="Palmitoyl (Protein N-term)">Palmitoyl (Protein N-term)</option>
-        <option value="Palmitoyl (S)">Palmitoyl (S)</option>
-        <option value="Palmitoyl (T)">Palmitoyl (T)</option>
-        <option value="PEITC (C)">PEITC (C)</option>
-        <option value="PEITC (K)">PEITC (K)</option>
-        <option value="PEITC (N-term)">PEITC (N-term)</option>
-        <option value="Pent(1)HexNAc(1) (S)">Pent(1)HexNAc(1) (S)</option>
-        <option value="Pent(1)HexNAc(1) (T)">Pent(1)HexNAc(1) (T)</option>
-        <option value="Pent(2) (S)">Pent(2) (S)</option>
-        <option value="Pent(2) (T)">Pent(2) (T)</option>
-        <option value="Pentose (S)">Pentose (S)</option>
-        <option value="Pentose (T)">Pentose (T)</option>
-        <option value="Pentylamine (Q)">Pentylamine (Q)</option>
-        <option value="PEO-Iodoacetyl-LC-Biotin (C)">PEO-Iodoacetyl-LC-Biotin (C)</option>
-        <option value="PET (S)">PET (S)</option>
-        <option value="PET (T)">PET (T)</option>
-        <option value="Phe-&gt;Ala (F)">Phe-&gt;Ala (F)</option>
-        <option value="Phe-&gt;Arg (F)">Phe-&gt;Arg (F)</option>
-        <option value="Phe-&gt;Asn (F)">Phe-&gt;Asn (F)</option>
-        <option value="Phe-&gt;Asp (F)">Phe-&gt;Asp (F)</option>
-        <option value="Phe-&gt;CamCys (F)">Phe-&gt;CamCys (F)</option>
-        <option value="Phe-&gt;Cys (F)">Phe-&gt;Cys (F)</option>
-        <option value="Phe-&gt;Gln (F)">Phe-&gt;Gln (F)</option>
-        <option value="Phe-&gt;Glu (F)">Phe-&gt;Glu (F)</option>
-        <option value="Phe-&gt;Gly (F)">Phe-&gt;Gly (F)</option>
-        <option value="Phe-&gt;His (F)">Phe-&gt;His (F)</option>
-        <option value="Phe-&gt;Lys (F)">Phe-&gt;Lys (F)</option>
-        <option value="Phe-&gt;Met (F)">Phe-&gt;Met (F)</option>
-        <option value="Phe-&gt;Pro (F)">Phe-&gt;Pro (F)</option>
-        <option value="Phe-&gt;Ser (F)">Phe-&gt;Ser (F)</option>
-        <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
-        <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
-        <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
-        <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
-        <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
-        <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
-        <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
-        <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
-        <option value="Phospho (C)">Phospho (C)</option>
-        <option value="Phospho (D)">Phospho (D)</option>
-        <option value="Phospho (E)">Phospho (E)</option>
-        <option value="Phospho (H)">Phospho (H)</option>
-        <option value="Phospho (K)">Phospho (K)</option>
-        <option value="Phospho (R)">Phospho (R)</option>
-        <option value="Phospho (S)">Phospho (S)</option>
-        <option value="Phospho (T)">Phospho (T)</option>
-        <option value="Phospho (Y)">Phospho (Y)</option>
-        <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
-        <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
-        <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
-        <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
-        <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
-        <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
-        <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
-        <option value="Phosphogluconoylation (K)">Phosphogluconoylation (K)</option>
-        <option value="Phosphogluconoylation (N-term)">Phosphogluconoylation (N-term)</option>
-        <option value="Phosphoguanosine (H)">Phosphoguanosine (H)</option>
-        <option value="Phosphoguanosine (K)">Phosphoguanosine (K)</option>
-        <option value="PhosphoHex (S)">PhosphoHex (S)</option>
-        <option value="PhosphoHex (T)">PhosphoHex (T)</option>
-        <option value="PhosphoHex(2) (N)">PhosphoHex(2) (N)</option>
-        <option value="PhosphoHex(2) (S)">PhosphoHex(2) (S)</option>
-        <option value="PhosphoHex(2) (T)">PhosphoHex(2) (T)</option>
-        <option value="PhosphoHexNAc (S)">PhosphoHexNAc (S)</option>
-        <option value="PhosphoHexNAc (T)">PhosphoHexNAc (T)</option>
-        <option value="Phosphopantetheine (S)">Phosphopantetheine (S)</option>
-        <option value="Phosphopropargyl (S)">Phosphopropargyl (S)</option>
-        <option value="Phosphopropargyl (T)">Phosphopropargyl (T)</option>
-        <option value="Phosphopropargyl (Y)">Phosphopropargyl (Y)</option>
-        <option value="phosphoRibosyl (D)">phosphoRibosyl (D)</option>
-        <option value="phosphoRibosyl (E)">phosphoRibosyl (E)</option>
-        <option value="phosphoRibosyl (R)">phosphoRibosyl (R)</option>
-        <option value="PhosphoribosyldephosphoCoA (S)">PhosphoribosyldephosphoCoA (S)</option>
-        <option value="PhosphoUridine (H)">PhosphoUridine (H)</option>
-        <option value="PhosphoUridine (Y)">PhosphoUridine (Y)</option>
-        <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
-        <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
-        <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
-        <option value="Piperidine (K)">Piperidine (K)</option>
-        <option value="Piperidine (N-term)">Piperidine (N-term)</option>
-        <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
-        <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
-        <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
-        <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
-        <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
-        <option value="Pro-&gt;Gln (P)">Pro-&gt;Gln (P)</option>
-        <option value="Pro-&gt;Glu (P)">Pro-&gt;Glu (P)</option>
-        <option value="Pro-&gt;Gly (P)">Pro-&gt;Gly (P)</option>
-        <option value="Pro-&gt;HAVA (P)">Pro-&gt;HAVA (P)</option>
-        <option value="Pro-&gt;His (P)">Pro-&gt;His (P)</option>
-        <option value="Pro-&gt;Lys (P)">Pro-&gt;Lys (P)</option>
-        <option value="Pro-&gt;Met (P)">Pro-&gt;Met (P)</option>
-        <option value="Pro-&gt;Phe (P)">Pro-&gt;Phe (P)</option>
-        <option value="Pro-&gt;pyro-Glu (P)">Pro-&gt;pyro-Glu (P)</option>
-        <option value="Pro-&gt;Pyrrolidinone (P)">Pro-&gt;Pyrrolidinone (P)</option>
-        <option value="Pro-&gt;Pyrrolidone (P)">Pro-&gt;Pyrrolidone (P)</option>
-        <option value="Pro-&gt;Ser (P)">Pro-&gt;Ser (P)</option>
-        <option value="Pro-&gt;Thr (P)">Pro-&gt;Thr (P)</option>
-        <option value="Pro-&gt;Trp (P)">Pro-&gt;Trp (P)</option>
-        <option value="Pro-&gt;Tyr (P)">Pro-&gt;Tyr (P)</option>
-        <option value="Pro-&gt;Val (P)">Pro-&gt;Val (P)</option>
-        <option value="Pro-&gt;Xle (P)">Pro-&gt;Xle (P)</option>
-        <option value="probiotinhydrazide (P)">probiotinhydrazide (P)</option>
-        <option value="Propargylamine (C-term)">Propargylamine (C-term)</option>
-        <option value="Propargylamine (D)">Propargylamine (D)</option>
-        <option value="Propargylamine (E)">Propargylamine (E)</option>
-        <option value="Propionamide (C)">Propionamide (C)</option>
-        <option value="Propionamide (K)">Propionamide (K)</option>
-        <option value="Propionamide (N-term)">Propionamide (N-term)</option>
-        <option value="Propionamide:2H(3) (C)">Propionamide:2H(3) (C)</option>
-        <option value="Propionyl (K)">Propionyl (K)</option>
-        <option value="Propionyl (N-term)">Propionyl (N-term)</option>
-        <option value="Propionyl (Protein N-term)">Propionyl (Protein N-term)</option>
-        <option value="Propionyl (S)">Propionyl (S)</option>
-        <option value="Propionyl (T)">Propionyl (T)</option>
-        <option value="Propionyl:13C(3) (K)">Propionyl:13C(3) (K)</option>
-        <option value="Propionyl:13C(3) (N-term)">Propionyl:13C(3) (N-term)</option>
-        <option value="Propiophenone (C)">Propiophenone (C)</option>
-        <option value="Propiophenone (H)">Propiophenone (H)</option>
-        <option value="Propiophenone (K)">Propiophenone (K)</option>
-        <option value="Propiophenone (R)">Propiophenone (R)</option>
-        <option value="Propiophenone (S)">Propiophenone (S)</option>
-        <option value="Propiophenone (T)">Propiophenone (T)</option>
-        <option value="Propiophenone (W)">Propiophenone (W)</option>
-        <option value="Propyl (C-term)">Propyl (C-term)</option>
-        <option value="Propyl (D)">Propyl (D)</option>
-        <option value="Propyl (E)">Propyl (E)</option>
-        <option value="Propyl (K)">Propyl (K)</option>
-        <option value="Propyl (N-term)">Propyl (N-term)</option>
-        <option value="Propyl (Protein C-term)">Propyl (Protein C-term)</option>
-        <option value="Propyl:2H(6) (K)">Propyl:2H(6) (K)</option>
-        <option value="Propyl:2H(6) (N-term)">Propyl:2H(6) (N-term)</option>
-        <option value="PropylNAGthiazoline (C)">PropylNAGthiazoline (C)</option>
-        <option value="PS_Hapten (C)">PS_Hapten (C)</option>
-        <option value="PS_Hapten (H)">PS_Hapten (H)</option>
-        <option value="PS_Hapten (K)">PS_Hapten (K)</option>
-        <option value="pupylation (K)">pupylation (K)</option>
-        <option value="Puromycin (C-term)">Puromycin (C-term)</option>
-        <option value="PyMIC (N-term)">PyMIC (N-term)</option>
-        <option value="PyridoxalPhosphate (K)">PyridoxalPhosphate (K)</option>
-        <option value="PyridoxalPhosphateH2 (K)">PyridoxalPhosphateH2 (K)</option>
-        <option value="Pyridylacetyl (K)">Pyridylacetyl (K)</option>
-        <option value="Pyridylacetyl (N-term)">Pyridylacetyl (N-term)</option>
-        <option value="Pyridylethyl (C)">Pyridylethyl (C)</option>
-        <option value="Pyro-carbamidomethyl (N-term C)">Pyro-carbamidomethyl (N-term C)</option>
-        <option value="pyrophospho (S)">pyrophospho (S)</option>
-        <option value="pyrophospho (T)">pyrophospho (T)</option>
-        <option value="PyruvicAcidIminyl (K)">PyruvicAcidIminyl (K)</option>
-        <option value="PyruvicAcidIminyl (Protein N-term C)">PyruvicAcidIminyl (Protein N-term C)</option>
-        <option value="PyruvicAcidIminyl (Protein N-term V)">PyruvicAcidIminyl (Protein N-term V)</option>
-        <option value="QAT (C)">QAT (C)</option>
-        <option value="QAT:2H(3) (C)">QAT:2H(3) (C)</option>
-        <option value="QEQTGG (K)">QEQTGG (K)</option>
-        <option value="QQQTGG (K)">QQQTGG (K)</option>
-        <option value="QTGG (K)">QTGG (K)</option>
-        <option value="Quinone (W)">Quinone (W)</option>
-        <option value="Quinone (Y)">Quinone (Y)</option>
-        <option value="Retinylidene (K)">Retinylidene (K)</option>
-        <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
-        <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
-        <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-        <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-        <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-        <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-        <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-        <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-        <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-        <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-        <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
-        <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
-        <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
-        <option value="Saligenin (H)">Saligenin (H)</option>
-        <option value="Saligenin (K)">Saligenin (K)</option>
-        <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
-        <option value="Ser-&gt;Arg (S)">Ser-&gt;Arg (S)</option>
-        <option value="Ser-&gt;Asn (S)">Ser-&gt;Asn (S)</option>
-        <option value="Ser-&gt;Asp (S)">Ser-&gt;Asp (S)</option>
-        <option value="Ser-&gt;Cys (S)">Ser-&gt;Cys (S)</option>
-        <option value="Ser-&gt;Gln (S)">Ser-&gt;Gln (S)</option>
-        <option value="Ser-&gt;Glu (S)">Ser-&gt;Glu (S)</option>
-        <option value="Ser-&gt;Gly (S)">Ser-&gt;Gly (S)</option>
-        <option value="Ser-&gt;His (S)">Ser-&gt;His (S)</option>
-        <option value="Ser-&gt;LacticAcid (Protein N-term S)">Ser-&gt;LacticAcid (Protein N-term S)</option>
-        <option value="Ser-&gt;Lys (S)">Ser-&gt;Lys (S)</option>
-        <option value="Ser-&gt;Met (S)">Ser-&gt;Met (S)</option>
-        <option value="Ser-&gt;Phe (S)">Ser-&gt;Phe (S)</option>
-        <option value="Ser-&gt;Pro (S)">Ser-&gt;Pro (S)</option>
-        <option value="Ser-&gt;Thr (S)">Ser-&gt;Thr (S)</option>
-        <option value="Ser-&gt;Trp (S)">Ser-&gt;Trp (S)</option>
-        <option value="Ser-&gt;Tyr (S)">Ser-&gt;Tyr (S)</option>
-        <option value="Ser-&gt;Val (S)">Ser-&gt;Val (S)</option>
-        <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
-        <option value="serotonylation (Q)">serotonylation (Q)</option>
-        <option value="shTMT (K)">shTMT (K)</option>
-        <option value="shTMT (N-term)">shTMT (N-term)</option>
-        <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
-        <option value="SMA (K)">SMA (K)</option>
-        <option value="SMA (N-term)">SMA (N-term)</option>
-        <option value="spermidine (Q)">spermidine (Q)</option>
-        <option value="spermine (Q)">spermine (Q)</option>
-        <option value="SPITC (K)">SPITC (K)</option>
-        <option value="SPITC (N-term)">SPITC (N-term)</option>
-        <option value="SPITC:13C(6) (K)">SPITC:13C(6) (K)</option>
-        <option value="SPITC:13C(6) (N-term)">SPITC:13C(6) (N-term)</option>
-        <option value="Succinyl (K)">Succinyl (K)</option>
-        <option value="Succinyl (N-term)">Succinyl (N-term)</option>
-        <option value="Succinyl (Protein N-term)">Succinyl (Protein N-term)</option>
-        <option value="Succinyl:13C(4) (K)">Succinyl:13C(4) (K)</option>
-        <option value="Succinyl:13C(4) (N-term)">Succinyl:13C(4) (N-term)</option>
-        <option value="Succinyl:2H(4) (K)">Succinyl:2H(4) (K)</option>
-        <option value="Succinyl:2H(4) (N-term)">Succinyl:2H(4) (N-term)</option>
-        <option value="SulfanilicAcid (C-term)">SulfanilicAcid (C-term)</option>
-        <option value="SulfanilicAcid (D)">SulfanilicAcid (D)</option>
-        <option value="SulfanilicAcid (E)">SulfanilicAcid (E)</option>
-        <option value="SulfanilicAcid:13C(6) (C-term)">SulfanilicAcid:13C(6) (C-term)</option>
-        <option value="SulfanilicAcid:13C(6) (D)">SulfanilicAcid:13C(6) (D)</option>
-        <option value="SulfanilicAcid:13C(6) (E)">SulfanilicAcid:13C(6) (E)</option>
-        <option value="Sulfide (C)">Sulfide (C)</option>
-        <option value="Sulfide (D)">Sulfide (D)</option>
-        <option value="Sulfide (W)">Sulfide (W)</option>
-        <option value="Sulfo (C)">Sulfo (C)</option>
-        <option value="Sulfo (S)">Sulfo (S)</option>
-        <option value="Sulfo (T)">Sulfo (T)</option>
-        <option value="Sulfo (Y)">Sulfo (Y)</option>
-        <option value="sulfo+amino (Y)">sulfo+amino (Y)</option>
-        <option value="Sulfo-NHS-LC-LC-Biotin (K)">Sulfo-NHS-LC-LC-Biotin (K)</option>
-        <option value="Sulfo-NHS-LC-LC-Biotin (N-term)">Sulfo-NHS-LC-LC-Biotin (N-term)</option>
-        <option value="SulfoGMBS (C)">SulfoGMBS (C)</option>
-        <option value="SulfurDioxide (C)">SulfurDioxide (C)</option>
-        <option value="SUMO2135 (K)">SUMO2135 (K)</option>
-        <option value="SUMO3549 (K)">SUMO3549 (K)</option>
-        <option value="TAMRA-FP (S)">TAMRA-FP (S)</option>
-        <option value="TAMRA-FP (Y)">TAMRA-FP (Y)</option>
-        <option value="Thiadiazole (C)">Thiadiazole (C)</option>
-        <option value="Thiazolidine (C)">Thiazolidine (C)</option>
-        <option value="Thiazolidine (F)">Thiazolidine (F)</option>
-        <option value="Thiazolidine (H)">Thiazolidine (H)</option>
-        <option value="Thiazolidine (K)">Thiazolidine (K)</option>
-        <option value="Thiazolidine (Protein N-term)">Thiazolidine (Protein N-term)</option>
-        <option value="Thiazolidine (R)">Thiazolidine (R)</option>
-        <option value="Thiazolidine (W)">Thiazolidine (W)</option>
-        <option value="Thiazolidine (Y)">Thiazolidine (Y)</option>
-        <option value="thioacylPA (K)">thioacylPA (K)</option>
-        <option value="Thiophos-S-S-biotin (S)">Thiophos-S-S-biotin (S)</option>
-        <option value="Thiophos-S-S-biotin (T)">Thiophos-S-S-biotin (T)</option>
-        <option value="Thiophos-S-S-biotin (Y)">Thiophos-S-S-biotin (Y)</option>
-        <option value="Thiophospho (S)">Thiophospho (S)</option>
-        <option value="Thiophospho (T)">Thiophospho (T)</option>
-        <option value="Thiophospho (Y)">Thiophospho (Y)</option>
-        <option value="Thr-&gt;Ala (T)">Thr-&gt;Ala (T)</option>
-        <option value="Thr-&gt;Arg (T)">Thr-&gt;Arg (T)</option>
-        <option value="Thr-&gt;Asn (T)">Thr-&gt;Asn (T)</option>
-        <option value="Thr-&gt;Asp (T)">Thr-&gt;Asp (T)</option>
-        <option value="Thr-&gt;Cys (T)">Thr-&gt;Cys (T)</option>
-        <option value="Thr-&gt;Gln (T)">Thr-&gt;Gln (T)</option>
-        <option value="Thr-&gt;Glu (T)">Thr-&gt;Glu (T)</option>
-        <option value="Thr-&gt;Gly (T)">Thr-&gt;Gly (T)</option>
-        <option value="Thr-&gt;His (T)">Thr-&gt;His (T)</option>
-        <option value="Thr-&gt;Lys (T)">Thr-&gt;Lys (T)</option>
-        <option value="Thr-&gt;Met (T)">Thr-&gt;Met (T)</option>
-        <option value="Thr-&gt;Phe (T)">Thr-&gt;Phe (T)</option>
-        <option value="Thr-&gt;Pro (T)">Thr-&gt;Pro (T)</option>
-        <option value="Thr-&gt;Ser (T)">Thr-&gt;Ser (T)</option>
-        <option value="Thr-&gt;Trp (T)">Thr-&gt;Trp (T)</option>
-        <option value="Thr-&gt;Tyr (T)">Thr-&gt;Tyr (T)</option>
-        <option value="Thr-&gt;Val (T)">Thr-&gt;Val (T)</option>
-        <option value="Thr-&gt;Xle (T)">Thr-&gt;Xle (T)</option>
-        <option value="Thrbiotinhydrazide (T)">Thrbiotinhydrazide (T)</option>
-        <option value="Thyroxine (Y)">Thyroxine (Y)</option>
-        <option value="TMAB (K)">TMAB (K)</option>
-        <option value="TMAB (N-term)">TMAB (N-term)</option>
-        <option value="TMAB:2H(9) (K)">TMAB:2H(9) (K)</option>
-        <option value="TMAB:2H(9) (N-term)">TMAB:2H(9) (N-term)</option>
-        <option value="TMPP-Ac (K)">TMPP-Ac (K)</option>
-        <option value="TMPP-Ac (N-term)">TMPP-Ac (N-term)</option>
-        <option value="TMPP-Ac (Y)">TMPP-Ac (Y)</option>
-        <option value="TMPP-Ac:13C(9) (K)">TMPP-Ac:13C(9) (K)</option>
-        <option value="TMPP-Ac:13C(9) (N-term)">TMPP-Ac:13C(9) (N-term)</option>
-        <option value="TMPP-Ac:13C(9) (Y)">TMPP-Ac:13C(9) (Y)</option>
-        <option value="TMT (H)">TMT (H)</option>
-        <option value="TMT (K)">TMT (K)</option>
-        <option value="TMT (N-term)">TMT (N-term)</option>
-        <option value="TMT (Protein N-term)">TMT (Protein N-term)</option>
-        <option value="TMT (S)">TMT (S)</option>
-        <option value="TMT (T)">TMT (T)</option>
-        <option value="TMT2plex (H)">TMT2plex (H)</option>
-        <option value="TMT2plex (K)">TMT2plex (K)</option>
-        <option value="TMT2plex (N-term)">TMT2plex (N-term)</option>
-        <option value="TMT2plex (Protein N-term)">TMT2plex (Protein N-term)</option>
-        <option value="TMT2plex (S)">TMT2plex (S)</option>
-        <option value="TMT2plex (T)">TMT2plex (T)</option>
-        <option value="TMT6plex (H)">TMT6plex (H)</option>
-        <option value="TMT6plex (K)">TMT6plex (K)</option>
-        <option value="TMT6plex (N-term)">TMT6plex (N-term)</option>
-        <option value="TMT6plex (Protein N-term)">TMT6plex (Protein N-term)</option>
-        <option value="TMT6plex (S)">TMT6plex (S)</option>
-        <option value="TMT6plex (T)">TMT6plex (T)</option>
-        <option value="TMTpro (H)">TMTpro (H)</option>
-        <option value="TMTpro (K)">TMTpro (K)</option>
-        <option value="TMTpro (N-term)">TMTpro (N-term)</option>
-        <option value="TMTpro (Protein N-term)">TMTpro (Protein N-term)</option>
-        <option value="TMTpro (S)">TMTpro (S)</option>
-        <option value="TMTpro (T)">TMTpro (T)</option>
-        <option value="TMTpro_zero (H)">TMTpro_zero (H)</option>
-        <option value="TMTpro_zero (K)">TMTpro_zero (K)</option>
-        <option value="TMTpro_zero (N-term)">TMTpro_zero (N-term)</option>
-        <option value="TMTpro_zero (Protein N-term)">TMTpro_zero (Protein N-term)</option>
-        <option value="TMTpro_zero (S)">TMTpro_zero (S)</option>
-        <option value="TMTpro_zero (T)">TMTpro_zero (T)</option>
-        <option value="TNBS (K)">TNBS (K)</option>
-        <option value="TNBS (N-term)">TNBS (N-term)</option>
-        <option value="trifluoro (L)">trifluoro (L)</option>
-        <option value="Triiodo (Y)">Triiodo (Y)</option>
-        <option value="Triiodothyronine (Y)">Triiodothyronine (Y)</option>
-        <option value="Trimethyl (K)">Trimethyl (K)</option>
-        <option value="Trimethyl (Protein N-term A)">Trimethyl (Protein N-term A)</option>
-        <option value="Trimethyl (R)">Trimethyl (R)</option>
-        <option value="Trimethyl:13C(3)2H(9) (K)">Trimethyl:13C(3)2H(9) (K)</option>
-        <option value="Trimethyl:13C(3)2H(9) (R)">Trimethyl:13C(3)2H(9) (R)</option>
-        <option value="Trimethyl:2H(9) (K)">Trimethyl:2H(9) (K)</option>
-        <option value="Trimethyl:2H(9) (R)">Trimethyl:2H(9) (R)</option>
-        <option value="Trioxidation (C)">Trioxidation (C)</option>
-        <option value="Trioxidation (F)">Trioxidation (F)</option>
-        <option value="Trioxidation (W)">Trioxidation (W)</option>
-        <option value="Trioxidation (Y)">Trioxidation (Y)</option>
-        <option value="Tripalmitate (Protein N-term C)">Tripalmitate (Protein N-term C)</option>
-        <option value="Tris (N)">Tris (N)</option>
-        <option value="Triton (C-term)">Triton (C-term)</option>
-        <option value="Triton (N-term)">Triton (N-term)</option>
-        <option value="Trp-&gt;Ala (W)">Trp-&gt;Ala (W)</option>
-        <option value="Trp-&gt;Arg (W)">Trp-&gt;Arg (W)</option>
-        <option value="Trp-&gt;Asn (W)">Trp-&gt;Asn (W)</option>
-        <option value="Trp-&gt;Asp (W)">Trp-&gt;Asp (W)</option>
-        <option value="Trp-&gt;Cys (W)">Trp-&gt;Cys (W)</option>
-        <option value="Trp-&gt;Gln (W)">Trp-&gt;Gln (W)</option>
-        <option value="Trp-&gt;Glu (W)">Trp-&gt;Glu (W)</option>
-        <option value="Trp-&gt;Gly (W)">Trp-&gt;Gly (W)</option>
-        <option value="Trp-&gt;His (W)">Trp-&gt;His (W)</option>
-        <option value="Trp-&gt;Hydroxykynurenin (W)">Trp-&gt;Hydroxykynurenin (W)</option>
-        <option value="Trp-&gt;Kynurenin (W)">Trp-&gt;Kynurenin (W)</option>
-        <option value="Trp-&gt;Lys (W)">Trp-&gt;Lys (W)</option>
-        <option value="Trp-&gt;Met (W)">Trp-&gt;Met (W)</option>
-        <option value="Trp-&gt;Oxolactone (W)">Trp-&gt;Oxolactone (W)</option>
-        <option value="Trp-&gt;Phe (W)">Trp-&gt;Phe (W)</option>
-        <option value="Trp-&gt;Pro (W)">Trp-&gt;Pro (W)</option>
-        <option value="Trp-&gt;Ser (W)">Trp-&gt;Ser (W)</option>
-        <option value="Trp-&gt;Thr (W)">Trp-&gt;Thr (W)</option>
-        <option value="Trp-&gt;Tyr (W)">Trp-&gt;Tyr (W)</option>
-        <option value="Trp-&gt;Val (W)">Trp-&gt;Val (W)</option>
-        <option value="Trp-&gt;Xle (W)">Trp-&gt;Xle (W)</option>
-        <option value="Tween20 (N-term)">Tween20 (N-term)</option>
-        <option value="Tween80 (C-term)">Tween80 (C-term)</option>
-        <option value="Tyr-&gt;Ala (Y)">Tyr-&gt;Ala (Y)</option>
-        <option value="Tyr-&gt;Arg (Y)">Tyr-&gt;Arg (Y)</option>
-        <option value="Tyr-&gt;Asn (Y)">Tyr-&gt;Asn (Y)</option>
-        <option value="Tyr-&gt;Asp (Y)">Tyr-&gt;Asp (Y)</option>
-        <option value="Tyr-&gt;Cys (Y)">Tyr-&gt;Cys (Y)</option>
-        <option value="Tyr-&gt;Dha (Y)">Tyr-&gt;Dha (Y)</option>
-        <option value="Tyr-&gt;Gln (Y)">Tyr-&gt;Gln (Y)</option>
-        <option value="Tyr-&gt;Glu (Y)">Tyr-&gt;Glu (Y)</option>
-        <option value="Tyr-&gt;Gly (Y)">Tyr-&gt;Gly (Y)</option>
-        <option value="Tyr-&gt;His (Y)">Tyr-&gt;His (Y)</option>
-        <option value="Tyr-&gt;Lys (Y)">Tyr-&gt;Lys (Y)</option>
-        <option value="Tyr-&gt;Met (Y)">Tyr-&gt;Met (Y)</option>
-        <option value="Tyr-&gt;Phe (Y)">Tyr-&gt;Phe (Y)</option>
-        <option value="Tyr-&gt;Pro (Y)">Tyr-&gt;Pro (Y)</option>
-        <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
-        <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
-        <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
-        <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
-        <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-        <option value="Ub-amide (C)">Ub-amide (C)</option>
-        <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
-        <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
-        <option value="Ub-VME (C)">Ub-VME (C)</option>
-        <option value="UgiJoullie (D)">UgiJoullie (D)</option>
-        <option value="UgiJoullie (E)">UgiJoullie (E)</option>
-        <option value="UgiJoullieProGly (D)">UgiJoullieProGly (D)</option>
-        <option value="UgiJoullieProGly (E)">UgiJoullieProGly (E)</option>
-        <option value="UgiJoullieProGlyProGly (D)">UgiJoullieProGlyProGly (D)</option>
-        <option value="UgiJoullieProGlyProGly (E)">UgiJoullieProGlyProGly (E)</option>
-        <option value="Unknown:162 (C-term)">Unknown:162 (C-term)</option>
-        <option value="Unknown:162 (D)">Unknown:162 (D)</option>
-        <option value="Unknown:162 (E)">Unknown:162 (E)</option>
-        <option value="Unknown:162 (N-term)">Unknown:162 (N-term)</option>
-        <option value="Unknown:177 (C-term)">Unknown:177 (C-term)</option>
-        <option value="Unknown:177 (D)">Unknown:177 (D)</option>
-        <option value="Unknown:177 (E)">Unknown:177 (E)</option>
-        <option value="Unknown:177 (N-term)">Unknown:177 (N-term)</option>
-        <option value="Unknown:210 (C-term)">Unknown:210 (C-term)</option>
-        <option value="Unknown:210 (D)">Unknown:210 (D)</option>
-        <option value="Unknown:210 (E)">Unknown:210 (E)</option>
-        <option value="Unknown:210 (N-term)">Unknown:210 (N-term)</option>
-        <option value="Unknown:216 (C-term)">Unknown:216 (C-term)</option>
-        <option value="Unknown:216 (D)">Unknown:216 (D)</option>
-        <option value="Unknown:216 (E)">Unknown:216 (E)</option>
-        <option value="Unknown:216 (N-term)">Unknown:216 (N-term)</option>
-        <option value="Unknown:234 (C-term)">Unknown:234 (C-term)</option>
-        <option value="Unknown:234 (D)">Unknown:234 (D)</option>
-        <option value="Unknown:234 (E)">Unknown:234 (E)</option>
-        <option value="Unknown:234 (N-term)">Unknown:234 (N-term)</option>
-        <option value="Unknown:248 (C-term)">Unknown:248 (C-term)</option>
-        <option value="Unknown:248 (D)">Unknown:248 (D)</option>
-        <option value="Unknown:248 (E)">Unknown:248 (E)</option>
-        <option value="Unknown:248 (N-term)">Unknown:248 (N-term)</option>
-        <option value="Unknown:250 (C-term)">Unknown:250 (C-term)</option>
-        <option value="Unknown:250 (D)">Unknown:250 (D)</option>
-        <option value="Unknown:250 (E)">Unknown:250 (E)</option>
-        <option value="Unknown:250 (N-term)">Unknown:250 (N-term)</option>
-        <option value="Unknown:302 (C-term)">Unknown:302 (C-term)</option>
-        <option value="Unknown:302 (D)">Unknown:302 (D)</option>
-        <option value="Unknown:302 (E)">Unknown:302 (E)</option>
-        <option value="Unknown:302 (N-term)">Unknown:302 (N-term)</option>
-        <option value="Unknown:306 (C-term)">Unknown:306 (C-term)</option>
-        <option value="Unknown:306 (D)">Unknown:306 (D)</option>
-        <option value="Unknown:306 (E)">Unknown:306 (E)</option>
-        <option value="Unknown:306 (N-term)">Unknown:306 (N-term)</option>
-        <option value="Unknown:420 (C-term)">Unknown:420 (C-term)</option>
-        <option value="Unknown:420 (N-term)">Unknown:420 (N-term)</option>
-        <option value="Val-&gt;Ala (V)">Val-&gt;Ala (V)</option>
-        <option value="Val-&gt;Arg (V)">Val-&gt;Arg (V)</option>
-        <option value="Val-&gt;Asn (V)">Val-&gt;Asn (V)</option>
-        <option value="Val-&gt;Asp (V)">Val-&gt;Asp (V)</option>
-        <option value="Val-&gt;Cys (V)">Val-&gt;Cys (V)</option>
-        <option value="Val-&gt;Gln (V)">Val-&gt;Gln (V)</option>
-        <option value="Val-&gt;Glu (V)">Val-&gt;Glu (V)</option>
-        <option value="Val-&gt;Gly (V)">Val-&gt;Gly (V)</option>
-        <option value="Val-&gt;His (V)">Val-&gt;His (V)</option>
-        <option value="Val-&gt;Lys (V)">Val-&gt;Lys (V)</option>
-        <option value="Val-&gt;Met (V)">Val-&gt;Met (V)</option>
-        <option value="Val-&gt;Phe (V)">Val-&gt;Phe (V)</option>
-        <option value="Val-&gt;Pro (V)">Val-&gt;Pro (V)</option>
-        <option value="Val-&gt;Ser (V)">Val-&gt;Ser (V)</option>
-        <option value="Val-&gt;Thr (V)">Val-&gt;Thr (V)</option>
-        <option value="Val-&gt;Trp (V)">Val-&gt;Trp (V)</option>
-        <option value="Val-&gt;Tyr (V)">Val-&gt;Tyr (V)</option>
-        <option value="Val-&gt;Xle (V)">Val-&gt;Xle (V)</option>
-        <option value="VFQQQTGG (K)">VFQQQTGG (K)</option>
-        <option value="VIEVYQEQTGG (K)">VIEVYQEQTGG (K)</option>
-        <option value="Withaferin (C)">Withaferin (C)</option>
-        <option value="Xle-&gt;Ala (I)">Xle-&gt;Ala (I)</option>
-        <option value="Xle-&gt;Ala (L)">Xle-&gt;Ala (L)</option>
-        <option value="Xle-&gt;Arg (I)">Xle-&gt;Arg (I)</option>
-        <option value="Xle-&gt;Arg (L)">Xle-&gt;Arg (L)</option>
-        <option value="Xle-&gt;Asn (I)">Xle-&gt;Asn (I)</option>
-        <option value="Xle-&gt;Asn (L)">Xle-&gt;Asn (L)</option>
-        <option value="Xle-&gt;Asp (I)">Xle-&gt;Asp (I)</option>
-        <option value="Xle-&gt;Asp (L)">Xle-&gt;Asp (L)</option>
-        <option value="Xle-&gt;Cys (I)">Xle-&gt;Cys (I)</option>
-        <option value="Xle-&gt;Cys (L)">Xle-&gt;Cys (L)</option>
-        <option value="Xle-&gt;Gln (I)">Xle-&gt;Gln (I)</option>
-        <option value="Xle-&gt;Gln (L)">Xle-&gt;Gln (L)</option>
-        <option value="Xle-&gt;Glu (I)">Xle-&gt;Glu (I)</option>
-        <option value="Xle-&gt;Glu (L)">Xle-&gt;Glu (L)</option>
-        <option value="Xle-&gt;Gly (I)">Xle-&gt;Gly (I)</option>
-        <option value="Xle-&gt;Gly (L)">Xle-&gt;Gly (L)</option>
-        <option value="Xle-&gt;His (I)">Xle-&gt;His (I)</option>
-        <option value="Xle-&gt;His (L)">Xle-&gt;His (L)</option>
-        <option value="Xle-&gt;Lys (I)">Xle-&gt;Lys (I)</option>
-        <option value="Xle-&gt;Lys (L)">Xle-&gt;Lys (L)</option>
-        <option value="Xle-&gt;Met (I)">Xle-&gt;Met (I)</option>
-        <option value="Xle-&gt;Met (L)">Xle-&gt;Met (L)</option>
-        <option value="Xle-&gt;Phe (I)">Xle-&gt;Phe (I)</option>
-        <option value="Xle-&gt;Phe (L)">Xle-&gt;Phe (L)</option>
-        <option value="Xle-&gt;Pro (I)">Xle-&gt;Pro (I)</option>
-        <option value="Xle-&gt;Pro (L)">Xle-&gt;Pro (L)</option>
-        <option value="Xle-&gt;Ser (I)">Xle-&gt;Ser (I)</option>
-        <option value="Xle-&gt;Ser (L)">Xle-&gt;Ser (L)</option>
-        <option value="Xle-&gt;Thr (I)">Xle-&gt;Thr (I)</option>
-        <option value="Xle-&gt;Thr (L)">Xle-&gt;Thr (L)</option>
-        <option value="Xle-&gt;Trp (I)">Xle-&gt;Trp (I)</option>
-        <option value="Xle-&gt;Trp (L)">Xle-&gt;Trp (L)</option>
-        <option value="Xle-&gt;Tyr (I)">Xle-&gt;Tyr (I)</option>
-        <option value="Xle-&gt;Tyr (L)">Xle-&gt;Tyr (L)</option>
-        <option value="Xle-&gt;Val (I)">Xle-&gt;Val (I)</option>
-        <option value="Xle-&gt;Val (L)">Xle-&gt;Val (L)</option>
-        <option value="Xlink:B10621 (C)">Xlink:B10621 (C)</option>
-        <option value="Xlink:BMOE (C)">Xlink:BMOE (C)</option>
-        <option value="Xlink:BS2G[113] (K)">Xlink:BS2G[113] (K)</option>
-        <option value="Xlink:BS2G[113] (Protein N-term)">Xlink:BS2G[113] (Protein N-term)</option>
-        <option value="Xlink:BS2G[114] (K)">Xlink:BS2G[114] (K)</option>
-        <option value="Xlink:BS2G[114] (Protein N-term)">Xlink:BS2G[114] (Protein N-term)</option>
-        <option value="Xlink:BS2G[217] (K)">Xlink:BS2G[217] (K)</option>
-        <option value="Xlink:BS2G[217] (Protein N-term)">Xlink:BS2G[217] (Protein N-term)</option>
-        <option value="Xlink:BS2G[96] (K)">Xlink:BS2G[96] (K)</option>
-        <option value="Xlink:BS2G[96] (Protein N-term)">Xlink:BS2G[96] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[111] (K)">Xlink:BuUrBu[111] (K)</option>
-        <option value="Xlink:BuUrBu[111] (Protein N-term)">Xlink:BuUrBu[111] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[196] (K)">Xlink:BuUrBu[196] (K)</option>
-        <option value="Xlink:BuUrBu[196] (Protein N-term)">Xlink:BuUrBu[196] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[213] (K)">Xlink:BuUrBu[213] (K)</option>
-        <option value="Xlink:BuUrBu[213] (Protein N-term)">Xlink:BuUrBu[213] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[214] (K)">Xlink:BuUrBu[214] (K)</option>
-        <option value="Xlink:BuUrBu[214] (Protein N-term)">Xlink:BuUrBu[214] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[317] (K)">Xlink:BuUrBu[317] (K)</option>
-        <option value="Xlink:BuUrBu[317] (Protein N-term)">Xlink:BuUrBu[317] (Protein N-term)</option>
-        <option value="Xlink:BuUrBu[85] (K)">Xlink:BuUrBu[85] (K)</option>
-        <option value="Xlink:BuUrBu[85] (Protein N-term)">Xlink:BuUrBu[85] (Protein N-term)</option>
-        <option value="Xlink:DFDNB (K)">Xlink:DFDNB (K)</option>
-        <option value="Xlink:DFDNB (N)">Xlink:DFDNB (N)</option>
-        <option value="Xlink:DFDNB (Q)">Xlink:DFDNB (Q)</option>
-        <option value="Xlink:DFDNB (R)">Xlink:DFDNB (R)</option>
-        <option value="Xlink:DMP[122] (K)">Xlink:DMP[122] (K)</option>
-        <option value="Xlink:DMP[122] (Protein N-term)">Xlink:DMP[122] (Protein N-term)</option>
-        <option value="Xlink:DMP[139] (K)">Xlink:DMP[139] (K)</option>
-        <option value="Xlink:DMP[139] (Protein N-term)">Xlink:DMP[139] (Protein N-term)</option>
-        <option value="Xlink:DMP[140] (K)">Xlink:DMP[140] (K)</option>
-        <option value="Xlink:DMP[140] (Protein N-term)">Xlink:DMP[140] (Protein N-term)</option>
-        <option value="Xlink:DMP[154] (K)">Xlink:DMP[154] (K)</option>
-        <option value="Xlink:DMP[154] (Protein N-term)">Xlink:DMP[154] (Protein N-term)</option>
-        <option value="Xlink:DSS[138] (K)">Xlink:DSS[138] (K)</option>
-        <option value="Xlink:DSS[138] (Protein N-term)">Xlink:DSS[138] (Protein N-term)</option>
-        <option value="Xlink:DSS[155] (K)">Xlink:DSS[155] (K)</option>
-        <option value="Xlink:DSS[155] (Protein N-term)">Xlink:DSS[155] (Protein N-term)</option>
-        <option value="Xlink:DSS[156] (K)">Xlink:DSS[156] (K)</option>
-        <option value="Xlink:DSS[156] (Protein N-term)">Xlink:DSS[156] (Protein N-term)</option>
-        <option value="Xlink:DSS[259] (K)">Xlink:DSS[259] (K)</option>
-        <option value="Xlink:DSS[259] (Protein N-term)">Xlink:DSS[259] (Protein N-term)</option>
-        <option value="Xlink:DSSO[104] (K)">Xlink:DSSO[104] (K)</option>
-        <option value="Xlink:DSSO[104] (Protein N-term)">Xlink:DSSO[104] (Protein N-term)</option>
-        <option value="Xlink:DSSO[158] (K)">Xlink:DSSO[158] (K)</option>
-        <option value="Xlink:DSSO[158] (Protein N-term)">Xlink:DSSO[158] (Protein N-term)</option>
-        <option value="Xlink:DSSO[175] (K)">Xlink:DSSO[175] (K)</option>
-        <option value="Xlink:DSSO[175] (Protein N-term)">Xlink:DSSO[175] (Protein N-term)</option>
-        <option value="Xlink:DSSO[176] (K)">Xlink:DSSO[176] (K)</option>
-        <option value="Xlink:DSSO[176] (Protein N-term)">Xlink:DSSO[176] (Protein N-term)</option>
-        <option value="Xlink:DSSO[279] (K)">Xlink:DSSO[279] (K)</option>
-        <option value="Xlink:DSSO[279] (Protein N-term)">Xlink:DSSO[279] (Protein N-term)</option>
-        <option value="Xlink:DSSO[54] (K)">Xlink:DSSO[54] (K)</option>
-        <option value="Xlink:DSSO[54] (Protein N-term)">Xlink:DSSO[54] (Protein N-term)</option>
-        <option value="Xlink:DSSO[86] (K)">Xlink:DSSO[86] (K)</option>
-        <option value="Xlink:DSSO[86] (Protein N-term)">Xlink:DSSO[86] (Protein N-term)</option>
-        <option value="Xlink:DST[114] (K)">Xlink:DST[114] (K)</option>
-        <option value="Xlink:DST[114] (Protein N-term)">Xlink:DST[114] (Protein N-term)</option>
-        <option value="Xlink:DST[132] (K)">Xlink:DST[132] (K)</option>
-        <option value="Xlink:DST[132] (Protein N-term)">Xlink:DST[132] (Protein N-term)</option>
-        <option value="Xlink:DST[56] (K)">Xlink:DST[56] (K)</option>
-        <option value="Xlink:DST[56] (Protein N-term)">Xlink:DST[56] (Protein N-term)</option>
-        <option value="Xlink:DTBP[172] (K)">Xlink:DTBP[172] (K)</option>
-        <option value="Xlink:DTBP[172] (Protein N-term)">Xlink:DTBP[172] (Protein N-term)</option>
-        <option value="Xlink:DTBP[87] (K)">Xlink:DTBP[87] (K)</option>
-        <option value="Xlink:DTBP[87] (Protein N-term)">Xlink:DTBP[87] (Protein N-term)</option>
-        <option value="Xlink:DTSSP[174] (K)">Xlink:DTSSP[174] (K)</option>
-        <option value="Xlink:DTSSP[174] (Protein N-term)">Xlink:DTSSP[174] (Protein N-term)</option>
-        <option value="Xlink:DTSSP[192] (K)">Xlink:DTSSP[192] (K)</option>
-        <option value="Xlink:DTSSP[192] (Protein N-term)">Xlink:DTSSP[192] (Protein N-term)</option>
-        <option value="Xlink:DTSSP[88] (K)">Xlink:DTSSP[88] (K)</option>
-        <option value="Xlink:DTSSP[88] (Protein N-term)">Xlink:DTSSP[88] (Protein N-term)</option>
-        <option value="Xlink:EGS[115] (K)">Xlink:EGS[115] (K)</option>
-        <option value="Xlink:EGS[115] (Protein N-term)">Xlink:EGS[115] (Protein N-term)</option>
-        <option value="Xlink:EGS[226] (K)">Xlink:EGS[226] (K)</option>
-        <option value="Xlink:EGS[226] (Protein N-term)">Xlink:EGS[226] (Protein N-term)</option>
-        <option value="Xlink:EGS[244] (K)">Xlink:EGS[244] (K)</option>
-        <option value="Xlink:EGS[244] (Protein N-term)">Xlink:EGS[244] (Protein N-term)</option>
-        <option value="Xlink:SMCC[219] (C)">Xlink:SMCC[219] (C)</option>
-        <option value="Xlink:SMCC[219] (K)">Xlink:SMCC[219] (K)</option>
-        <option value="Xlink:SMCC[219] (Protein N-term)">Xlink:SMCC[219] (Protein N-term)</option>
-        <option value="Xlink:SMCC[237] (C)">Xlink:SMCC[237] (C)</option>
-        <option value="Xlink:SMCC[237] (K)">Xlink:SMCC[237] (K)</option>
-        <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
-        <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
-        <option value="ZGB (K)">ZGB (K)</option>
-        <option value="ZGB (N-term)">ZGB (N-term)</option>
-        <option value="ZQG (K)">ZQG (K)</option>
-        <expand macro="list_string_san" name="variable_modifications"/>
-      </param>
-      <param name="residue_set" argument="-algorithm:residue_set" type="text" optional="true" value="Natural19WithoutI" label="The predefined amino acid set that should be used, see doc of ResidueDB for possible residue sets" help="">
-        <expand macro="list_string_san" name="residue_set"/>
-      </param>
-    </section>
-    <expand macro="adv_opts_macro">
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><!-- TOPP_CompNovoCID_1 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="CompNovoCID_1_input.mzML"/>
-      <output name="out" file="CompNovoCID_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <section name="algorithm">
-        <param name="max_number_aa_per_decomp" value="4"/>
-        <param name="tryptic_only" value="true"/>
-        <param name="precursor_mass_tolerance" value="0.3"/>
-        <param name="fragment_mass_tolerance" value="0.3"/>
-        <param name="max_number_pivot" value="9"/>
-        <param name="max_subscore_number" value="40"/>
-        <param name="decomp_weights_precision" value="0.01"/>
-        <param name="double_charged_iso_threshold" value="0.6"/>
-        <param name="max_mz" value="2000.0"/>
-        <param name="min_mz" value="200.0"/>
-        <param name="max_isotope_to_score" value="3"/>
-        <param name="max_decomp_weight" value="450.0"/>
-        <param name="max_isotope" value="3"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="estimate_precursor_mz" value="true"/>
-        <param name="number_of_prescoring_hits" value="250"/>
-        <param name="fixed_modifications"/>
-        <param name="variable_modifications"/>
-        <param name="residue_set" value="Natural19WithoutI"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
-  <help><![CDATA[Performs a de novo peptide identification using the CompNovo engine.
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_CompNovoCID.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/ConsensusID.xml b/tools/openms/ConsensusID.xml
index 12d15ceaf..a4309241a 100644
--- a/tools/openms/ConsensusID.xml
+++ b/tools/openms/ConsensusID.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [ID Processing]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="ConsensusID" name="ConsensusID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Computes a consensus of peptide identifications of several identification engines.</description>
+  <description>Computes a consensus of peptide identifications of several identification engines</description>
   <macros>
     <token name="@EXECUTABLE@">ConsensusID</token>
     <import>macros.xml</import>
@@ -17,9 +16,9 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir out &&
 
@@ -54,16 +53,16 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="consensusxml,featurexml,idxml" multiple="true" optional="false" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,featurexml,idxml" multiple="true" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="consensusxml,featurexml,idxml" multiple="false" optional="false" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,featurexml,idxml" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-rt_delta" type="float" optional="true" min="0.0" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help=""/>
-    <param argument="-mz_delta" type="float" optional="true" min="0.0" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help=""/>
+    <param argument="-rt_delta" type="float" min="0.0" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help=""/>
+    <param argument="-mz_delta" type="float" min="0.0" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help=""/>
     <param argument="-per_spectrum" type="boolean" truevalue="true" falsevalue="false" checked="false" label="(only idXML) if set, mapping will be done based on exact matching of originating mzml file and spectrum_ref" help=""/>
-    <param argument="-algorithm" type="select" optional="true" label="Algorithm used for consensus scoring" help="* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores.. * PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores.. * best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs.. * worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs.. * average:  For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs.. * ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types">
+    <param argument="-algorithm" type="select" label="Algorithm used for consensus scoring" help="* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores.. * PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores.. * best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs.. * worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs.. * average:  For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs.. * ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types">
       <option value="PEPMatrix" selected="true">PEPMatrix</option>
       <option value="PEPIons">PEPIons</option>
       <option value="best">best</option>
@@ -73,26 +72,26 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <expand macro="list_string_san" name="algorithm"/>
     </param>
     <section name="filter" title="Options for filtering peptide hits" help="" expanded="false">
-      <param name="considered_hits" argument="-filter:considered_hits" type="integer" optional="true" min="0" value="0" label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" help=""/>
-      <param name="min_support" argument="-filter:min_support" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" help=""/>
+      <param name="considered_hits" argument="-filter:considered_hits" type="integer" min="0" value="0" label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" help=""/>
+      <param name="min_support" argument="-filter:min_support" type="float" min="0.0" max="1.0" value="0.0" label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" help=""/>
       <param name="count_empty" argument="-filter:count_empty" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Count empty ID runs" help="(i.e. those containing no peptide hit for the current spectrum) when calculating 'min_support'?"/>
       <param name="keep_old_scores" argument="-filter:keep_old_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if set, keeps the original scores as user params" help=""/>
     </section>
     <section name="PEPIons" title="PEPIons algorithm parameters" help="" expanded="false">
-      <param name="mass_tolerance" argument="-PEPIons:mass_tolerance" type="float" optional="true" min="0.0" value="0.5" label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" help=""/>
-      <param name="min_shared" argument="-PEPIons:min_shared" type="integer" optional="true" min="1" value="2" label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" help=""/>
+      <param name="mass_tolerance" argument="-PEPIons:mass_tolerance" type="float" min="0.0" value="0.5" label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" help=""/>
+      <param name="min_shared" argument="-PEPIons:min_shared" type="integer" min="1" value="2" label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" help=""/>
     </section>
     <section name="PEPMatrix" title="PEPMatrix algorithm parameters" help="" expanded="false">
-      <param name="matrix" argument="-PEPMatrix:matrix" type="select" optional="true" label="Substitution matrix to use for alignment-based similarity scoring" help="">
+      <param name="matrix" argument="-PEPMatrix:matrix" type="select" label="Substitution matrix to use for alignment-based similarity scoring" help="">
         <option value="identity">identity</option>
         <option value="PAM30MS" selected="true">PAM30MS</option>
         <expand macro="list_string_san" name="matrix"/>
       </param>
-      <param name="penalty" argument="-PEPMatrix:penalty" type="integer" optional="true" min="1" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" help=""/>
+      <param name="penalty" argument="-PEPMatrix:penalty" type="integer" min="1" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -106,7 +105,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_ConsensusID_1 -->
+  <tests>
+    <!-- TOPP_ConsensusID_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -115,7 +115,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="ConsensusID_1_input.idXML"/>
       </conditional>
-      <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="ConsensusID_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
       <param name="per_spectrum" value="false"/>
@@ -140,6 +140,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ConsensusID_2 -->
     <test expect_num_outputs="2">
@@ -150,7 +153,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="ConsensusID_2_input.featureXML"/>
       </conditional>
-      <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="ConsensusID_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
       <param name="per_spectrum" value="false"/>
@@ -175,6 +178,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ConsensusID_3 -->
     <test expect_num_outputs="2">
@@ -185,7 +191,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="ConsensusID_3_input.consensusXML"/>
       </conditional>
-      <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="ConsensusID_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
       <param name="per_spectrum" value="false"/>
@@ -210,6 +216,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ConsensusID_4 -->
     <test expect_num_outputs="2">
@@ -220,7 +229,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="ConsensusID_1_input.idXML"/>
       </conditional>
-      <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="ConsensusID_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
       <param name="per_spectrum" value="false"/>
@@ -245,6 +254,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ConsensusID_5 -->
     <test expect_num_outputs="2">
@@ -255,7 +267,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="ConsensusID_1_input.idXML"/>
       </conditional>
-      <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="ConsensusID_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
       <param name="per_spectrum" value="false"/>
@@ -280,6 +292,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ConsensusID_6 -->
     <test expect_num_outputs="2">
@@ -290,7 +305,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="ConsensusID_1_input.idXML"/>
       </conditional>
-      <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="ConsensusID_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
       <param name="per_spectrum" value="false"/>
@@ -315,6 +330,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ConsensusID_7 -->
     <test expect_num_outputs="2">
@@ -325,7 +343,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="ConsensusID_6_input.idXML"/>
       </conditional>
-      <output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="ConsensusID_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
       <param name="per_spectrum" value="true"/>
@@ -350,6 +368,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ConsensusID_8 -->
     <test expect_num_outputs="2">
@@ -360,7 +381,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="ConsensusID_8_input.idXML"/>
       </conditional>
-      <output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="ConsensusID_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
       <param name="per_spectrum" value="true"/>
@@ -385,11 +406,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Computes a consensus of peptide identifications of several identification engines.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ConsensusID.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ConsensusID.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/ConsensusMapNormalizer.xml b/tools/openms/ConsensusMapNormalizer.xml
index df3fc689d..31d77d83b 100644
--- a/tools/openms/ConsensusMapNormalizer.xml
+++ b/tools/openms/ConsensusMapNormalizer.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Map Alignment]-->
+<!--Proposed Tool Section: [Quantitation]-->
 <tool id="ConsensusMapNormalizer" name="ConsensusMapNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Normalizes maps of one consensusXML file</description>
   <macros>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,15 +38,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml" optional="false" label="input file" help=" select consensusxml data sets(s)"/>
-    <param argument="-algorithm_type" type="select" optional="true" label="The normalization algorithm that is applied" help="'robust_regression' scales each map by a fator computed from the ratios of non-differential background features (as determined by the ratio_threshold parameter), 'quantile' performs quantile normalization, 'median' scales all maps to the same median intensity, 'median_shift' shifts the median instead of scaling (WARNING: if you have regular, log-normal MS data, 'median_shift' is probably the wrong choice. Use only if you know what you're doing!)">
+    <param argument="-in" type="data" format="consensusxml" label="input file" help=" select consensusxml data sets(s)"/>
+    <param argument="-algorithm_type" type="select" label="The normalization algorithm that is applied" help="'robust_regression' scales each map by a fator computed from the ratios of non-differential background features (as determined by the ratio_threshold parameter), 'quantile' performs quantile normalization, 'median' scales all maps to the same median intensity, 'median_shift' shifts the median instead of scaling (WARNING: if you have regular, log-normal MS data, 'median_shift' is probably the wrong choice. Use only if you know what you're doing!)">
       <option value="robust_regression" selected="true">robust_regression</option>
       <option value="median">median</option>
       <option value="median_shift">median_shift</option>
       <option value="quantile">quantile</option>
       <expand macro="list_string_san" name="algorithm_type"/>
     </param>
-    <param argument="-ratio_threshold" type="float" optional="true" min="0.001" max="1.0" value="0.67" label="Only for 'robust_regression': the parameter is used to distinguish between non-outliers (ratio_threshold &lt; intensity ratio &lt; 1/ratio_threshold) and outliers" help=""/>
+    <param argument="-ratio_threshold" type="float" min="0.001" max="1.0" value="0.67" label="Only for 'robust_regression': the parameter is used to distinguish between non-outliers (ratio_threshold &lt; intensity ratio &lt; 1/ratio_threshold) and outliers" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-accession_filter" type="text" optional="true" value="" label="Use only features with accessions (partially) matching this regular expression for computing the normalization factors" help="Useful, e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used">
         <expand macro="list_string_san" name="accession_filter"/>
@@ -56,7 +55,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <expand macro="list_string_san" name="description_filter"/>
       </param>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -70,7 +69,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_ConsensusMapNormalizer_1 -->
+  <tests>
+    <!-- TOPP_ConsensusMapNormalizer_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="accession_filter" value=""/>
@@ -79,7 +79,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/>
-      <output name="out" file="ConsensusMapNormalizer_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="ConsensusMapNormalizer_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="algorithm_type" value="robust_regression"/>
       <param name="ratio_threshold" value="0.67"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -88,11 +88,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Normalizes maps of one consensusXML file
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ConsensusMapNormalizer.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ConsensusMapNormalizer.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/CruxAdapter.xml b/tools/openms/CruxAdapter.xml
deleted file mode 100644
index 211d35f9b..000000000
--- a/tools/openms/CruxAdapter.xml
+++ /dev/null
@@ -1,192 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
-<tool id="CruxAdapter" name="CruxAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Identifies MS/MS spectra using Crux.</description>
-  <macros>
-    <token name="@EXECUTABLE@">CruxAdapter</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-mkdir out &&
-mkdir database &&
-ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in
-'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
--out
-'out/output.${gxy2omsext("idxml")}'
--database
-'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
-
-## Postprocessing
-&& mv 'out/output.${gxy2omsext("idxml")}' '$out'
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"crux_executable": "crux", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
-  </configfiles>
-  <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
-    <param argument="-database" type="data" format="fasta" optional="false" label="FASTA file" help=" select fasta data sets(s)"/>
-    <param argument="-extra_index_args" type="text" optional="true" value="" label="Extra arguments to be passed to tide-index" help="">
-      <expand macro="list_string_san" name="extra_index_args"/>
-    </param>
-    <param argument="-extra_search_args" type="text" optional="true" value="" label="Extra arguments to be passed to tide-search" help="">
-      <expand macro="list_string_san" name="extra_search_args"/>
-    </param>
-    <param argument="-extra_percolator_args" type="text" optional="true" value="" label="Extra arguments to be passed to percolato" help="">
-      <expand macro="list_string_san" name="extra_percolator_args"/>
-    </param>
-    <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (Crux parameter: peptide_mass_tolerance)" help=""/>
-    <param argument="-precursor_mass_units" type="select" optional="true" label="Unit of precursor mass tolerance (amu, m/z or ppm)" help="">
-      <option value="mass">mass</option>
-      <option value="mz">mz</option>
-      <option value="ppm" selected="true">ppm</option>
-      <expand macro="list_string_san" name="precursor_mass_units"/>
-    </param>
-    <param argument="-fragment_bin_offset" type="float" optional="true" value="0.0" label="In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0" help="(i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da)"/>
-    <param argument="-fragment_bin_width" type="float" optional="true" value="0.02" label="Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized" help="This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended"/>
-    <param argument="-isotope_error" type="text" optional="true" value="" label="List of positive, non-zero integers" help="">
-      <expand macro="list_string_san" name="isotope_error"/>
-    </param>
-    <param argument="-run_percolator" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to run percolator after tide-search" help=""/>
-    <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
-      <option value="custom-enzyme">custom-enzyme</option>
-      <option value="pepsin-a">pepsin-a</option>
-      <option value="cyanogen-bromide">cyanogen-bromide</option>
-      <option value="clostripain">clostripain</option>
-      <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
-      <option value="no-enzyme">no-enzyme</option>
-      <option value="arg-c">arg-c</option>
-      <option value="asp-n">asp-n</option>
-      <option value="iodosobenzoate">iodosobenzoate</option>
-      <option value="staph-protease">staph-protease</option>
-      <option value="proline-endopeptidase">proline-endopeptidase</option>
-      <option value="glu-c">glu-c</option>
-      <option value="elastase">elastase</option>
-      <option value="chymotrypsin">chymotrypsin</option>
-      <option value="lys-c">lys-c</option>
-      <option value="lys-n">lys-n</option>
-      <option value="trypsin/p">trypsin/p</option>
-      <option value="trypsin" selected="true">trypsin</option>
-      <expand macro="list_string_san" name="enzyme"/>
-    </param>
-    <param argument="-digestion" type="select" optional="true" label="Full, partial or non specific digestion" help="">
-      <option value="full-digest" selected="true">full-digest</option>
-      <option value="partial-digest">partial-digest</option>
-      <option value="non-specific-digest">non-specific-digest</option>
-      <expand macro="list_string_san" name="digestion"/>
-    </param>
-    <param argument="-allowed_missed_cleavages" type="integer" optional="true" value="0" label="Number of possible cleavage sites missed by the enzyme, maximum value is 5; for enzyme search" help=""/>
-    <param argument="-decoy_format" type="select" optional="true" label="Decoy generation method either by reversing the sequence or shuffling it" help="">
-      <option value="none">none</option>
-      <option value="shuffle" selected="true">shuffle</option>
-      <option value="peptide-reverse">peptide-reverse</option>
-      <option value="protein-reverse">protein-reverse</option>
-      <expand macro="list_string_san" name="decoy_format"/>
-    </param>
-    <param argument="-keep_terminal_aminos" type="select" optional="true" label="Whether to keep N and C terminal in place or also shuffled / reversed" help="">
-      <option value="N">N</option>
-      <option value="C">C</option>
-      <option value="NC" selected="true">NC</option>
-      <option value="none">none</option>
-      <expand macro="list_string_san" name="keep_terminal_aminos"/>
-    </param>
-    <param argument="-cterm_modifications" type="text" optional="true" value="" label="Specifies C-terminal static and variable mass modifications on peptides" help="Specify a comma-separated list of C-terminal modification sequences of the form: X+21.9819 Default = &lt;empty&gt;">
-      <expand macro="list_string_san" name="cterm_modifications"/>
-    </param>
-    <param argument="-nterm_modifications" type="text" optional="true" value="" label="Specifies N-terminal static and variable mass modifications on peptides" help="Specify a comma-separated list of N-terminal modification sequences of the form: 1E-18.0106,C-17.0265 Default = &lt;empty&gt;">
-      <expand macro="list_string_san" name="nterm_modifications"/>
-    </param>
-    <param argument="-modifications" type="text" optional="true" value="" label="Expression for static and variable mass modifications to include" help="Specify a comma-separated list of modification sequences of the form: C+57.02146,2M+15.9949,1STY+79.966331,... Default = C+57.02146">
-      <expand macro="list_string_san" name="modifications"/>
-    </param>
-    <param argument="-test_fdr" type="float" optional="true" value="0.01" label="False discovery rate threshold used in selecting hyperparameters during internal cross-validation and for reporting the final results" help=""/>
-    <param argument="-train_fdr" type="float" optional="true" value="0.01" label="False discovery rate threshold to define positive examples in training" help=""/>
-    <expand macro="adv_opts_macro">
-      <param argument="-custom_enzyme" type="text" optional="true" value="" label="Specify rules for in silico digestion of protein sequences" help="Overrides the enzyme option. Two lists of residues are given enclosed in square brackets or curly braces and separated by a |. The first list contains residues required/prohibited before the cleavage site and the second list is residues after the cleavage site.  ">
-        <expand macro="list_string_san" name="custom_enzyme"/>
-      </param>
-      <param argument="-decoy_prefix" type="text" optional="true" value="decoy_" label="Specifies the prefix of the protein names that indicate a decoy" help="">
-        <expand macro="list_string_san" name="decoy_prefix"/>
-      </param>
-      <param argument="-deisotope" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Deisotope spectra before searching" help=""/>
-      <param argument="-report_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include decoys in the final reported dataset" help=""/>
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><!-- TOPP_CruxAdapter_1 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="custom_enzyme" value=""/>
-        <param name="decoy_prefix" value="decoy_"/>
-        <param name="deisotope" value="false"/>
-        <param name="report_decoys" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="spectra_comet.mzML"/>
-      <output name="out" file="CruxAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <param name="database" value="proteins.fasta"/>
-      <param name="extra_index_args" value=""/>
-      <param name="extra_search_args" value=""/>
-      <param name="extra_percolator_args" value=""/>
-      <param name="precursor_mass_tolerance" value="10.0"/>
-      <param name="precursor_mass_units" value="ppm"/>
-      <param name="fragment_bin_offset" value="0.0"/>
-      <param name="fragment_bin_width" value="0.02"/>
-      <param name="isotope_error" value=""/>
-      <param name="run_percolator" value="false"/>
-      <param name="enzyme" value="trypsin"/>
-      <param name="digestion" value="full-digest"/>
-      <param name="allowed_missed_cleavages" value="0"/>
-      <param name="decoy_format" value="peptide-reverse"/>
-      <param name="keep_terminal_aminos" value="NC"/>
-      <param name="cterm_modifications" value=""/>
-      <param name="nterm_modifications" value=""/>
-      <param name="modifications" value=""/>
-      <param name="test_fdr" value="0.01"/>
-      <param name="train_fdr" value="0.01"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
-  <help><![CDATA[Identifies MS/MS spectra using Crux.
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_CruxAdapter.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/DTAExtractor.xml b/tools/openms/DTAExtractor.xml
index 06f2b030c..3232b31d9 100644
--- a/tools/openms/DTAExtractor.xml
+++ b/tools/openms/DTAExtractor.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [File Handling]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="DTAExtractor" name="DTAExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Extracts spectra of an MS run file to several files in DTA format.</description>
+  <description>Extracts spectra of an MS run file to several files in DTA format</description>
   <macros>
     <token name="@EXECUTABLE@">DTAExtractor</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 
 ## Main program call
 
@@ -36,22 +35,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
-    <param argument="-out" type="text" optional="false" value="" label="base name of DTA output files (RT, m/z and extension are appended)" help="">
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-out" type="text" value="" label="base name of DTA output files (RT, m/z and extension are appended)" help="">
       <expand macro="list_string_san" name="out"/>
     </param>
-    <param argument="-mz" type="text" optional="true" value=":" label="m/z range of precursor peaks to extract" help="This option is ignored for MS level 1">
+    <param argument="-mz" type="text" value=":" label="m/z range of precursor peaks to extract" help="This option is ignored for MS level 1">
       <expand macro="list_string_san" name="mz"/>
     </param>
-    <param argument="-rt" type="text" optional="true" value=":" label="retention time range of spectra to extract" help="">
+    <param argument="-rt" type="text" value=":" label="retention time range of spectra to extract" help="">
       <expand macro="list_string_san" name="rt"/>
     </param>
-    <param argument="-level" type="text" optional="true" value="1,2,3" label="MS levels to extract" help="">
+    <param argument="-level" type="text" value="1,2,3" label="MS levels to extract" help="">
       <expand macro="list_string_san" name="level"/>
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -67,7 +66,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_DTAExtractor_1 -->
+  <tests>
+    <!-- TOPP_DTAExtractor_1 -->
     <test expect_num_outputs="1">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -84,6 +84,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_DTAExtractor_2 -->
     <test expect_num_outputs="1">
@@ -102,6 +105,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_DTAExtractor_3 -->
     <test expect_num_outputs="1">
@@ -120,11 +126,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Extracts spectra of an MS run file to several files in DTA format.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_DTAExtractor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DTAExtractor.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/DatabaseFilter.xml b/tools/openms/DatabaseFilter.xml
index 0e3590270..0a1d712ef 100644
--- a/tools/openms/DatabaseFilter.xml
+++ b/tools/openms/DatabaseFilter.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="DatabaseFilter" name="DatabaseFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Filters a protein database (FASTA format) based on identified proteins</description>
   <macros>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir id &&
-ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
+cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -43,16 +42,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="fasta" optional="false" label="Input FASTA file, containing a database" help=" select fasta data sets(s)"/>
-    <param argument="-id" type="data" format="idxml,mzid" optional="false" label="Input file containing identified peptides and proteins" help=" select idxml,mzid data sets(s)"/>
-    <param argument="-method" type="select" optional="true" label="Switch between white-/blacklisting" help="">
+    <param argument="-in" type="data" format="fasta" label="Input FASTA file, containing a database" help=" select fasta data sets(s)"/>
+    <param argument="-id" type="data" format="idxml,mzid" label="Input file containing identified peptides and proteins" help=" select idxml,mzid data sets(s)"/>
+    <param argument="-method" type="select" label="Switch between white-/blacklisting" help="">
       <option value="whitelist" selected="true">whitelist</option>
       <option value="blacklist">blacklist</option>
       <expand macro="list_string_san" name="method"/>
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -66,7 +65,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_DatabaseFilter_1 -->
+  <tests>
+    <!-- TOPP_DatabaseFilter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -75,15 +75,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="in" value="DatabaseFilter_1.fasta"/>
       <param name="id" value="DatabaseFilter_1.idXML"/>
       <param name="method" value="whitelist"/>
-      <output name="out" file="DatabaseFilter_1_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
+      <output name="out" value="DatabaseFilter_1_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_DatabaseFilter_2 -->
+    <!-- TOPP_DatabaseFilter_2 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -92,15 +95,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="in" value="DatabaseFilter_1.fasta"/>
       <param name="id" value="DatabaseFilter_1.idXML"/>
       <param name="method" value="blacklist"/>
-      <output name="out" file="DatabaseFilter_2_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
+      <output name="out" value="DatabaseFilter_2_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_DatabaseFilter_3 -->
+    <!-- TOPP_DatabaseFilter_3 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -109,15 +115,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="in" value="DatabaseFilter_3.fasta"/>
       <param name="id" value="DatabaseFilter_3.mzid"/>
       <param name="method" value="whitelist"/>
-      <output name="out" file="DatabaseFilter_3_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
+      <output name="out" value="DatabaseFilter_3_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_DatabaseFilter_4 -->
+    <!-- TOPP_DatabaseFilter_4 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -126,18 +135,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="in" value="DatabaseFilter_3.fasta"/>
       <param name="id" value="DatabaseFilter_3.mzid"/>
       <param name="method" value="blacklist"/>
-      <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
+      <output name="out" value="DatabaseFilter_4_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Filters a protein database (FASTA format) based on identified proteins
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_DatabaseFilter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DatabaseFilter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/DatabaseSuitability.xml b/tools/openms/DatabaseSuitability.xml
index a256a17e9..f255fabfe 100644
--- a/tools/openms/DatabaseSuitability.xml
+++ b/tools/openms/DatabaseSuitability.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Quality Control]-->
 <tool id="DatabaseSuitability" name="DatabaseSuitability" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra.</description>
+  <description>Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra</description>
   <macros>
     <token name="@EXECUTABLE@">DatabaseSuitability</token>
     <import>macros.xml</import>
@@ -15,15 +14,15 @@
 
 ## Preprocessing
 mkdir in_id &&
-ln -s '$in_id' 'in_id/${re.sub("[^\w\-_]", "_", $in_id.element_identifier)}.$gxy2omsext($in_id.ext)' &&
+cp '$in_id' 'in_id/${re.sub("[^\w\-_]", "_", $in_id.element_identifier)}.$gxy2omsext($in_id.ext)' &&
 mkdir in_spec &&
-ln -s '$in_spec' 'in_spec/${re.sub("[^\w\-_]", "_", $in_spec.element_identifier)}.$gxy2omsext($in_spec.ext)' &&
+cp '$in_spec' 'in_spec/${re.sub("[^\w\-_]", "_", $in_spec.element_identifier)}.$gxy2omsext($in_spec.ext)' &&
 mkdir in_novo &&
-ln -s '$in_novo' 'in_novo/${re.sub("[^\w\-_]", "_", $in_novo.element_identifier)}.$gxy2omsext($in_novo.ext)' &&
+cp '$in_novo' 'in_novo/${re.sub("[^\w\-_]", "_", $in_novo.element_identifier)}.$gxy2omsext($in_novo.ext)' &&
 mkdir database &&
-ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
 mkdir novo_database &&
-ln -s '$novo_database' 'novo_database/${re.sub("[^\w\-_]", "_", $novo_database.element_identifier)}.$gxy2omsext($novo_database.ext)' &&
+cp '$novo_database' 'novo_database/${re.sub("[^\w\-_]", "_", $novo_database.element_identifier)}.$gxy2omsext($novo_database.ext)' &&
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
 #end if
@@ -64,24 +63,24 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in_id" type="data" format="idxml" optional="false" label="Input idXML file from a peptide identification search with a combined database" help="PeptideIndexer is needed, FDR is forbidden select idxml data sets(s)"/>
-    <param argument="-in_spec" type="data" format="mzml" optional="false" label="Input MzML file used for the peptide identification" help=" select mzml data sets(s)"/>
-    <param argument="-in_novo" type="data" format="idxml" optional="false" label="Input idXML file containing de novo peptides (unfiltered)" help=" select idxml data sets(s)"/>
-    <param argument="-database" type="data" format="fasta" optional="false" label="Input FASTA file of the database in question" help=" select fasta data sets(s)"/>
-    <param argument="-novo_database" type="data" format="fasta" optional="false" label="Input deNovo sequences derived from MzML given in 'in_spec' concatenated to one FASTA entry" help=" select fasta data sets(s)"/>
+    <param argument="-in_id" type="data" format="idxml" label="Input idXML file from a peptide identification search with a combined database" help="PeptideIndexer is needed, FDR is forbidden select idxml data sets(s)"/>
+    <param argument="-in_spec" type="data" format="mzml" label="Input MzML file used for the peptide identification" help=" select mzml data sets(s)"/>
+    <param argument="-in_novo" type="data" format="idxml" label="Input idXML file containing de novo peptides (unfiltered)" help=" select idxml data sets(s)"/>
+    <param argument="-database" type="data" format="fasta" label="Input FASTA file of the database in question" help=" select fasta data sets(s)"/>
+    <param argument="-novo_database" type="data" format="fasta" label="Input deNovo sequences derived from MzML given in 'in_spec' concatenated to one FASTA entry" help=" select fasta data sets(s)"/>
     <section name="algorithm" title="Parameter section for the suitability calculation algorithm" help="" expanded="false">
       <param name="no_rerank" argument="-algorithm:no_rerank" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if you want to disable re-ranking" help="Cases, where a de novo peptide scores just higher than the database peptide, are overlooked and counted as a de novo hit. This might underestimate the database quality"/>
-      <param name="reranking_cutoff_percentile" argument="-algorithm:reranking_cutoff_percentile" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Swap a top-scoring deNovo hit with a lower scoring DB hit if their xcorr score difference is in the given percentile of all score differences between the first two decoy hits of a PSM" help="The lower the value the lower the decoy cut-off will be. Therefore it will be harder for a lower scoring DB hit to be re-ranked to the top"/>
-      <param name="FDR" argument="-algorithm:FDR" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Filter peptide hits based on this q-value" help="(e.g., 0.05 = 5 % FDR)"/>
-      <param name="number_of_subsampled_runs" argument="-algorithm:number_of_subsampled_runs" type="integer" optional="true" min="0" value="1" label="Controls how many runs should be done for calculating corrected suitability" help="(0 : number of runs will be estimated automaticly) ATTENTION: For each run a seperate ID-search is performed. This can result in some serious run time"/>
+      <param name="reranking_cutoff_percentile" argument="-algorithm:reranking_cutoff_percentile" type="float" min="0.0" max="1.0" value="0.01" label="Swap a top-scoring deNovo hit with a lower scoring DB hit if their xcorr score difference is in the given percentile of all score differences between the first two decoy hits of a PSM" help="The lower the value the lower the decoy cut-off will be. Therefore it will be harder for a lower scoring DB hit to be re-ranked to the top"/>
+      <param name="FDR" argument="-algorithm:FDR" type="float" min="0.0" max="1.0" value="0.01" label="Filter peptide hits based on this q-value" help="(e.g., 0.05 = 5 % FDR)"/>
+      <param name="number_of_subsampled_runs" argument="-algorithm:number_of_subsampled_runs" type="integer" min="0" value="1" label="Controls how many runs should be done for calculating corrected suitability" help="(0 : number of runs will be estimated automaticly) ATTENTION: For each run a seperate ID-search is performed. This can result in some serious run time"/>
       <param name="keep_search_files" argument="-algorithm:keep_search_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you wish to keep the files used by and produced by the internal ID search" help=""/>
       <param name="disable_correction" argument="-algorithm:disable_correction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag to disable the calculation of the corrected suitability" help=""/>
       <param name="force" argument="-algorithm:force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag to enforce re-ranking when no cross correlation score is present" help="For re-ranking the default score found at each peptide hit is used. Use with care!"/>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-novo_threshold" type="float" optional="true" min="0.0" value="60.0" label="Minimum score a de novo sequence has to have to be defined as 'correct'" help="The default of 60 is proven to be a good estimate for sequences generated by Novor"/>
+      <param argument="-novo_threshold" type="float" min="0.0" value="60.0" label="Minimum score a de novo sequence has to have to be defined as 'correct'" help="The default of 60 is proven to be a good estimate for sequences generated by Novor"/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -101,7 +100,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_DatabaseSuitability_1 -->
+  <tests>
+    <!-- TOPP_DatabaseSuitability -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="novo_threshold" value="60.0"/>
@@ -113,7 +113,39 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
       <param name="database" value="DatabaseSuitability_database.fasta"/>
       <param name="novo_database" value="DatabaseSuitability_novo_database.FASTA"/>
-      <output name="out" file="DatabaseSuitability_out_1.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="DatabaseSuitability_out.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <section name="algorithm">
+        <param name="no_rerank" value="false"/>
+        <param name="reranking_cutoff_percentile" value="0.01"/>
+        <param name="FDR" value="0.01"/>
+        <param name="number_of_subsampled_runs" value="1"/>
+        <param name="keep_search_files" value="false"/>
+        <param name="disable_correction" value="true"/>
+        <param name="force" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_DatabaseSuitability_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="novo_threshold" value="60.0"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
+      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
+      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
+      <param name="database" value="DatabaseSuitability_database.fasta"/>
+      <param name="novo_database" value="DatabaseSuitability_novo_database.FASTA"/>
+      <output name="out" value="DatabaseSuitability_out_1.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <section name="algorithm">
         <param name="no_rerank" value="false"/>
         <param name="reranking_cutoff_percentile" value="0.01"/>
@@ -129,6 +161,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_DatabaseSuitability_2 -->
     <test expect_num_outputs="2">
@@ -142,7 +177,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
       <param name="database" value="DatabaseSuitability_database.fasta"/>
       <param name="novo_database" value="DatabaseSuitability_novo_database.FASTA"/>
-      <output name="out" file="DatabaseSuitability_out_2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="DatabaseSuitability_out_2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <section name="algorithm">
         <param name="no_rerank" value="false"/>
         <param name="reranking_cutoff_percentile" value="0.01"/>
@@ -158,6 +193,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_DatabaseSuitability_3 -->
     <test expect_num_outputs="2">
@@ -171,7 +209,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
       <param name="database" value="DatabaseSuitability_database.fasta"/>
       <param name="novo_database" value="DatabaseSuitability_novo_database.FASTA"/>
-      <output name="out" file="DatabaseSuitability_out_3.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="DatabaseSuitability_out_3.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <section name="algorithm">
         <param name="no_rerank" value="false"/>
         <param name="reranking_cutoff_percentile" value="0.5"/>
@@ -187,11 +225,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_DatabaseSuitability.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DatabaseSuitability.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/DeMeanderize.xml b/tools/openms/DeMeanderize.xml
index 8d74bc1c7..b57c9867b 100644
--- a/tools/openms/DeMeanderize.xml
+++ b/tools/openms/DeMeanderize.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Misc / Helpers]-->
 <tool id="DeMeanderize" name="DeMeanderize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Orders the spectra of MALDI spotting plates correctly.</description>
+  <description>Orders the spectra of MALDI spotting plates correctly</description>
   <macros>
     <token name="@EXECUTABLE@">DeMeanderize</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,12 +38,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input experiment file, containing the wrongly sorted spectra" help=" select mzml data sets(s)"/>
-    <param argument="-num_spots_per_row" type="integer" optional="true" min="1" value="48" label="Number of spots in one column, until next row is spotted" help=""/>
+    <param argument="-in" type="data" format="mzml" label="Input experiment file, containing the wrongly sorted spectra" help=" select mzml data sets(s)"/>
+    <param argument="-num_spots_per_row" type="integer" min="1" value="48" label="Number of spots in one column, until next row is spotted" help=""/>
     <expand macro="adv_opts_macro">
-      <param argument="-RT_distance" type="float" optional="true" min="0.0" value="1.0" label="RT distance between two spots which is used to calculated pseudo RT" help=""/>
+      <param argument="-RT_distance" type="float" min="0.0" value="1.0" label="RT distance between two spots which is used to calculated pseudo RT" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -58,15 +57,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- test with the output of a MSsimulator output generated by a test below -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="MSsimulator_MALDI.mzml"/>
-	<output name="out" ftype="mzml" value="DeMeanderize.mzml"/>
-  </test>
-</tests>
+  <tests/>
   <help><![CDATA[Orders the spectra of MALDI spotting plates correctly.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_DeMeanderize.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DeMeanderize.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/Decharger.xml b/tools/openms/Decharger.xml
deleted file mode 100644
index b421cc0ed..000000000
--- a/tools/openms/Decharger.xml
+++ /dev/null
@@ -1,161 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Quantitation]-->
-<tool id="Decharger" name="Decharger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Decharges and merges different feature charge variants of the same peptide.</description>
-  <macros>
-    <token name="@EXECUTABLE@">Decharger</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-mkdir out_cm &&
-#if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out_fm &&
-#end if
-#if "outpairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir outpairs &&
-#end if
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in
-'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
--out_cm
-'out_cm/output.${gxy2omsext("consensusxml")}'
-#if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out_fm
-  'out_fm/output.${gxy2omsext("featurexml")}'
-#end if
-#if "outpairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -outpairs
-  'outpairs/output.${gxy2omsext("consensusxml")}'
-#end if
-#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
-  | tee '$stdout'
-#end if
-
-## Postprocessing
-&& mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
-#if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out_fm/output.${gxy2omsext("featurexml")}' '$out_fm'
-#end if
-#if "outpairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'outpairs/output.${gxy2omsext("consensusxml")}' '$outpairs'
-#end if
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
-  </configfiles>
-  <inputs>
-    <param argument="-in" type="data" format="featurexml" optional="false" label="input file" help=" select featurexml data sets(s)"/>
-    <section name="algorithm" title="Feature decharging algorithm section" help="" expanded="false">
-      <section name="FeatureDeconvolution" title="" help="" expanded="false">
-        <param name="charge_min" argument="-algorithm:FeatureDeconvolution:charge_min" type="integer" optional="true" value="1" label="Minimal possible charge" help=""/>
-        <param name="charge_max" argument="-algorithm:FeatureDeconvolution:charge_max" type="integer" optional="true" value="10" label="Maximal possible charge" help=""/>
-        <param name="charge_span_max" argument="-algorithm:FeatureDeconvolution:charge_span_max" type="integer" optional="true" min="1" value="4" label="Maximal range of charges for a single analyte" help="i.e. observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge"/>
-        <param name="q_try" argument="-algorithm:FeatureDeconvolution:q_try" type="select" optional="true" label="Try different values of charge for each feature according to the above settings ('heuristic' [does not test all charges, just the likely ones] or 'all' ), or leave feature charge untouched ('feature')" help="">
-          <option value="feature" selected="true">feature</option>
-          <option value="heuristic">heuristic</option>
-          <option value="all">all</option>
-          <expand macro="list_string_san" name="q_try"/>
-        </param>
-        <param name="retention_max_diff" argument="-algorithm:FeatureDeconvolution:retention_max_diff" type="float" optional="true" value="1.0" label="Maximum allowed RT difference between any two features if their relation shall be determined" help=""/>
-        <param name="retention_max_diff_local" argument="-algorithm:FeatureDeconvolution:retention_max_diff_local" type="float" optional="true" value="1.0" label="Maximum allowed RT difference between between two co-features, after adduct shifts have been accounted for (if you do not have any adduct shifts, this value should be equal to 'retention_max_diff', otherwise it should be smaller!)" help=""/>
-        <param name="mass_max_diff" argument="-algorithm:FeatureDeconvolution:mass_max_diff" type="float" optional="true" value="0.5" label="Maximum allowed mass difference [in Th] for a single feature" help=""/>
-        <param name="potential_adducts" argument="-algorithm:FeatureDeconvolution:potential_adducts" type="text" optional="true" value="K:+:0.1" label="Adducts used to explain mass differences in format: 'Element:Charge(+/-):Probability[:RTShift[:Label]]'" help="i.e. the number of '+' or '-' indicate the charge, e.g. 'Ca:++:0.5' indicates +2. Probabilites have to be in (0,1]. RTShift param is optional and indicates the expected RT shift caused by this adduct, e.g. '(2)H4H-4:0:1:-3' indicates a 4 deuterium label, which causes early elution by 3 seconds. As a fifth parameter you can add a label which is tagged on every feature which has this adduct. This also determines the map number in the consensus file (space separated list, in order to allow for spaces in list items surround them by single quotes)">
-          <expand macro="list_string_val" name="potential_adducts"/>
-          <expand macro="list_string_san" name="potential_adducts"/>
-        </param>
-        <param name="max_neutrals" argument="-algorithm:FeatureDeconvolution:max_neutrals" type="integer" optional="true" value="0" label="Maximal number of neutral adducts(q=0) allowed" help="Add them in the 'potential_adducts' section!"/>
-        <param name="max_minority_bound" argument="-algorithm:FeatureDeconvolution:max_minority_bound" type="integer" optional="true" min="0" value="2" label="Maximum count of the least probable adduct (according to 'potential_adducts' param) within a charge variant" help="E.g. setting this to 2 will not allow an adduct composition of '1(H+),3(Na+)' if Na+ is the least probable adduct"/>
-        <param name="min_rt_overlap" argument="-algorithm:FeatureDeconvolution:min_rt_overlap" type="float" optional="true" min="0.0" max="1.0" value="0.66" label="Minimum overlap of the convex hull' RT intersection measured against the union from two features (if CHs are given)" help=""/>
-        <param name="intensity_filter" argument="-algorithm:FeatureDeconvolution:intensity_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable the intensity filter, which will only allow edges between two equally charged features if the intensity of the feature with less likely adducts is smaller than that of the other feature" help="It is not used for features of different charge"/>
-        <param name="negative_mode" argument="-algorithm:FeatureDeconvolution:negative_mode" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable negative ionization mode" help=""/>
-        <param name="default_map_label" argument="-algorithm:FeatureDeconvolution:default_map_label" type="text" optional="true" value="decharged features" label="Label of map in output consensus file where all features are put by default" help="">
-          <expand macro="list_string_san" name="default_map_label"/>
-        </param>
-        <param name="verbose_level" argument="-algorithm:FeatureDeconvolution:verbose_level" type="integer" optional="true" min="0" max="3" value="0" label="Amount of debug information given during processing" help=""/>
-      </section>
-    </section>
-    <expand macro="adv_opts_macro">
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="out_fm_FLAG">out_fm (output feature map)</option>
-      <option value="outpairs_FLAG">outpairs (output file)</option>
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml"/>
-    <data name="out_fm" label="${tool.name} on ${on_string}: out_fm" format="featurexml">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_fm_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="outpairs" label="${tool.name} on ${on_string}: outpairs" format="consensusxml">
-      <filter>OPTIONAL_OUTPUTS is not None and "outpairs_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><!-- TOPP_Decharger_1 -->
-    <test expect_num_outputs="4">
-      <section name="adv_opts">
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="Decharger_input.featureXML"/>
-      <output name="out_cm" file="Decharger_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
-      <output name="out_fm" file="Decharger_output_fm.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="outpairs" file="Decharger_output_pairs.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
-      <section name="algorithm">
-        <section name="FeatureDeconvolution">
-          <param name="charge_min" value="1"/>
-          <param name="charge_max" value="10"/>
-          <param name="charge_span_max" value="4"/>
-          <param name="q_try" value="feature"/>
-          <param name="retention_max_diff" value="1.0"/>
-          <param name="retention_max_diff_local" value="1.0"/>
-          <param name="mass_max_diff" value="0.1"/>
-          <param name="potential_adducts" value="&quot;H:+:0.7&quot; &quot;Na:+:0.1&quot; &quot;(2)H4H-4:0:0.1:-2:heavy&quot;"/>
-          <param name="max_neutrals" value="0"/>
-          <param name="max_minority_bound" value="2"/>
-          <param name="min_rt_overlap" value="0.66"/>
-          <param name="intensity_filter" value="false"/>
-          <param name="negative_mode" value="false"/>
-          <param name="default_map_label" value="decharged features"/>
-          <param name="verbose_level" value="0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG,outpairs_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
-  <help><![CDATA[Decharges and merges different feature charge variants of the same peptide.
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_Decharger.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/DecoyDatabase.xml b/tools/openms/DecoyDatabase.xml
index e67d39d6f..8837e991e 100644
--- a/tools/openms/DecoyDatabase.xml
+++ b/tools/openms/DecoyDatabase.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="DecoyDatabase" name="DecoyDatabase" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Create decoy sequence database from forward sequence database.</description>
+  <description>Create decoy sequence database from forward sequence database</description>
   <macros>
     <token name="@EXECUTABLE@">DecoyDatabase</token>
     <import>macros.xml</import>
@@ -17,9 +16,9 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir out &&
 
@@ -54,47 +53,50 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="fasta" multiple="true" optional="false" label="Input FASTA file(s), each containing a database" help="It is recommended to include a contaminant database as well select fasta data sets(s)"/>
+        <param argument="-in" type="data" format="fasta" multiple="true" label="Input FASTA file(s), each containing a database" help="It is recommended to include a contaminant database as well select fasta data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="fasta" multiple="false" optional="false" label="Input FASTA file(s), each containing a database" help="It is recommended to include a contaminant database as well select fasta data sets(s)"/>
+        <param argument="-in" type="data" format="fasta" label="Input FASTA file(s), each containing a database" help="It is recommended to include a contaminant database as well select fasta data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-decoy_string" type="text" optional="true" value="DECOY_" label="String that is combined with the accession of the protein identifier to indicate a decoy protein" help="">
+    <param argument="-decoy_string" type="text" value="DECOY_" label="String that is combined with the accession of the protein identifier to indicate a decoy protein" help="">
       <expand macro="list_string_san" name="decoy_string"/>
     </param>
-    <param argument="-decoy_string_position" type="select" optional="true" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="">
+    <param argument="-decoy_string_position" type="select" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="">
       <option value="prefix" selected="true">prefix</option>
       <option value="suffix">suffix</option>
       <expand macro="list_string_san" name="decoy_string_position"/>
     </param>
     <param argument="-only_decoy" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write only decoy proteins to the output database instead of a combined database" help=""/>
-    <param argument="-type" type="select" optional="true" label="Type of sequence" help="RNA sequences may contain modification codes, which will be handled correctly if this is set to 'RNA'">
+    <param argument="-type" type="select" label="Type of sequence" help="RNA sequences may contain modification codes, which will be handled correctly if this is set to 'RNA'">
       <option value="protein" selected="true">protein</option>
       <option value="RNA">RNA</option>
       <expand macro="list_string_san" name="type"/>
     </param>
-    <param argument="-method" type="select" optional="true" label="Method by which decoy sequences are generated from target sequences" help="Note that all sequences are shuffled using the same random seed, ensuring that identical sequences produce the same shuffled decoy sequences. Shuffled sequences that produce highly similar output sequences are shuffled again (see shuffle_sequence_identity_threshold)">
+    <param argument="-method" type="select" label="Method by which decoy sequences are generated from target sequences" help="Note that all sequences are shuffled using the same random seed, ensuring that identical sequences produce the same shuffled decoy sequences. Shuffled sequences that produce highly similar output sequences are shuffled again (see shuffle_sequence_identity_threshold)">
       <option value="reverse" selected="true">reverse</option>
       <option value="shuffle">shuffle</option>
       <expand macro="list_string_san" name="method"/>
     </param>
-    <param argument="-enzyme" type="select" optional="true" label="Enzyme used for the digestion of the sample" help="Only applicable if parameter 'type' is 'protein'">
-      <option value="Asp-N/B">Asp-N/B</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="Chymotrypsin">Chymotrypsin</option>
-      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
-      <option value="CNBr">CNBr</option>
-      <option value="2-iodobenzoate">2-iodobenzoate</option>
-      <option value="iodosobenzoate">iodosobenzoate</option>
+    <param argument="-enzyme" type="select" label="Enzyme used for the digestion of the sample" help="Only applicable if parameter 'type' is 'protein'">
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+      <option value="no cleavage">no cleavage</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
       <option value="Arg-C">Arg-C</option>
       <option value="Arg-C/P">Arg-C/P</option>
       <option value="Asp-N">Asp-N</option>
+      <option value="Asp-N/B">Asp-N/B</option>
+      <option value="Glu-C+P">Glu-C+P</option>
+      <option value="PepsinA + P">PepsinA + P</option>
       <option value="cyanogen-bromide">cyanogen-bromide</option>
       <option value="Clostripain/P">Clostripain/P</option>
       <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
-      <option value="no cleavage">no cleavage</option>
-      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
+      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+      <option value="CNBr">CNBr</option>
       <option value="Formic_acid">Formic_acid</option>
       <option value="Lys-C">Lys-C</option>
       <option value="Lys-N">Lys-N</option>
@@ -106,13 +108,10 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <option value="V8-E">V8-E</option>
       <option value="leukocyte elastase">leukocyte elastase</option>
       <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+      <option value="2-iodobenzoate">2-iodobenzoate</option>
+      <option value="iodosobenzoate">iodosobenzoate</option>
       <option value="staphylococcal protease/D">staphylococcal protease/D</option>
       <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
-      <option value="Glu-C+P">Glu-C+P</option>
-      <option value="PepsinA + P">PepsinA + P</option>
-      <option value="Trypsin" selected="true">Trypsin</option>
       <expand macro="list_string_san" name="enzyme"/>
     </param>
     <section name="Decoy" title="Decoy parameters section" help="" expanded="false">
@@ -123,13 +122,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <param name="keepPeptideCTerm" argument="-Decoy:keepPeptideCTerm" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to keep peptide C terminus constant when shuffling / reversing" help=""/>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-shuffle_max_attempts" type="integer" optional="true" value="30" label="shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm" help=""/>
-      <param argument="-shuffle_sequence_identity_threshold" type="float" optional="true" value="0.5" label="shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm" help="If the sequence identity is above this threshold, shuffling is repeated. In case of repeated failure, individual amino acids are 'mutated' to produce a different amino acid sequence"/>
-      <param argument="-seed" type="text" optional="true" value="1" label="Random number seed (use 'time' for system time)" help="">
+      <param argument="-shuffle_max_attempts" type="integer" value="30" label="shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm" help=""/>
+      <param argument="-shuffle_sequence_identity_threshold" type="float" value="0.5" label="shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm" help="If the sequence identity is above this threshold, shuffling is repeated. In case of repeated failure, individual amino acids are 'mutated' to produce a different amino acid sequence"/>
+      <param argument="-seed" type="text" value="1" label="Random number seed (use 'time' for system time)" help="">
         <expand macro="list_string_san" name="seed"/>
       </param>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -143,7 +142,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_DecoyDatabase_1 -->
+  <tests>
+    <!-- TOPP_DecoyDatabase_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="shuffle_max_attempts" value="30"/>
@@ -155,7 +155,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="DecoyDatabase_1.fasta"/>
       </conditional>
-      <output name="out" file="DecoyDatabase_1_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
+      <output name="out" value="DecoyDatabase_1_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
       <param name="decoy_string" value="DECOY_"/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="only_decoy" value="true"/>
@@ -173,8 +173,11 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_DecoyDatabase_2 -->
+    <!-- TOPP_DecoyDatabase_2 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="shuffle_max_attempts" value="30"/>
@@ -186,8 +189,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="DecoyDatabase_1.fasta"/>
       </conditional>
-      <output name="out" file="DecoyDatabase_2_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
-      <param name="decoy_string" value="blabla"/>
+      <output name="out" value="DecoyDatabase_2_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
+      <param name="decoy_string" value="DECOY_SEQ_"/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="only_decoy" value="false"/>
       <param name="type" value="protein"/>
@@ -204,8 +207,11 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_DecoyDatabase_3 -->
+    <!-- TOPP_DecoyDatabase_3 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="shuffle_max_attempts" value="30"/>
@@ -217,8 +223,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="DecoyDatabase_1.fasta"/>
       </conditional>
-      <output name="out" file="DecoyDatabase_3_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
-      <param name="decoy_string" value="blabla"/>
+      <output name="out" value="DecoyDatabase_3_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
+      <param name="decoy_string" value="DECOY_SEQ_"/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="only_decoy" value="false"/>
       <param name="type" value="protein"/>
@@ -235,8 +241,11 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_DecoyDatabase_4 -->
+    <!-- TOPP_DecoyDatabase_4 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="shuffle_max_attempts" value="30"/>
@@ -248,8 +257,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="DecoyDatabase_4.fasta"/>
       </conditional>
-      <output name="out" file="DecoyDatabase_4_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
-      <param name="decoy_string" value="blabla"/>
+      <output name="out" value="DecoyDatabase_4_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
+      <param name="decoy_string" value="DECOY_SEQ_"/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="only_decoy" value="false"/>
       <param name="type" value="RNA"/>
@@ -266,11 +275,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Create decoy sequence database from forward sequence database.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_DecoyDatabase.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DecoyDatabase.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/Digestor.xml b/tools/openms/Digestor.xml
index 3f6fa12c5..5acffe865 100644
--- a/tools/openms/Digestor.xml
+++ b/tools/openms/Digestor.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="Digestor" name="Digestor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Digests a protein database in-silico.</description>
+  <description>Digests a protein database in-silico</description>
   <macros>
     <token name="@EXECUTABLE@">Digestor</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,30 +38,37 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Set this if you cannot control the filename of 'out'" help="e.g., in TOPPAS">
+    <param argument="-in" type="data" format="fasta" label="input file" help=" select fasta data sets(s)"/>
+    <param argument="-out_type" type="select" label="Set this if you cannot control the filename of 'out'" help="e.g., in TOPPAS">
       <option value="fasta">fasta</option>
       <option value="idXML">idxml</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
-    <param argument="-min_length" type="integer" optional="true" value="6" label="Minimum length of peptide" help=""/>
-    <param argument="-max_length" type="integer" optional="true" value="40" label="Maximum length of peptide" help=""/>
-    <param argument="-enzyme" type="select" optional="true" label="The type of digestion enzyme" help="">
-      <option value="Arg-C/P">Arg-C/P</option>
-      <option value="Asp-N">Asp-N</option>
-      <option value="Asp-N/B">Asp-N/B</option>
-      <option value="Arg-C">Arg-C</option>
-      <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+    <param argument="-missed_cleavages" type="integer" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
+    <param argument="-min_length" type="integer" value="6" label="Minimum length of peptide" help=""/>
+    <param argument="-max_length" type="integer" value="40" label="Maximum length of peptide" help=""/>
+    <param argument="-enzyme" type="select" label="The type of digestion enzyme" help="">
       <option value="no cleavage">no cleavage</option>
       <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="V8-DE">V8-DE</option>
+      <option value="V8-E">V8-E</option>
+      <option value="leukocyte elastase">leukocyte elastase</option>
+      <option value="proline endopeptidase">proline endopeptidase</option>
+      <option value="staphylococcal protease/D">staphylococcal protease/D</option>
       <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
       <option value="Glu-C+P">Glu-C+P</option>
       <option value="PepsinA + P">PepsinA + P</option>
       <option value="cyanogen-bromide">cyanogen-bromide</option>
       <option value="Clostripain/P">Clostripain/P</option>
+      <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+      <option value="TrypChymo">TrypChymo</option>
+      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
+      <option value="Arg-C">Arg-C</option>
+      <option value="Arg-C/P">Arg-C/P</option>
+      <option value="Asp-N">Asp-N</option>
+      <option value="Asp-N/B">Asp-N/B</option>
       <option value="Asp-N_ambic">Asp-N_ambic</option>
       <option value="Chymotrypsin">Chymotrypsin</option>
       <option value="Chymotrypsin/P">Chymotrypsin/P</option>
@@ -72,26 +78,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Lys-N">Lys-N</option>
       <option value="Lys-C/P">Lys-C/P</option>
       <option value="PepsinA">PepsinA</option>
-      <option value="TrypChymo">TrypChymo</option>
-      <option value="Trypsin/P">Trypsin/P</option>
-      <option value="V8-DE">V8-DE</option>
-      <option value="V8-E">V8-E</option>
-      <option value="leukocyte elastase">leukocyte elastase</option>
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
       <option value="Alpha-lytic protease">Alpha-lytic protease</option>
       <option value="2-iodobenzoate">2-iodobenzoate</option>
       <option value="iodosobenzoate">iodosobenzoate</option>
-      <option value="staphylococcal protease/D">staphylococcal protease/D</option>
-      <option value="Trypsin" selected="true">Trypsin</option>
       <expand macro="list_string_san" name="enzyme"/>
     </param>
     <section name="FASTA" title="Options for FASTA output files" help="" expanded="false">
-      <param name="ID" argument="-FASTA:ID" type="select" optional="true" label="Identifier to use for each peptide: copy from parent protein (parent); a consecutive number (number); parent ID + consecutive number (both)" help="">
+      <param name="ID" argument="-FASTA:ID" type="select" label="Identifier to use for each peptide: copy from parent protein (parent); a consecutive number (number); parent ID + consecutive number (both)" help="">
         <option value="parent" selected="true">parent</option>
         <option value="number">number</option>
         <option value="both">both</option>
         <expand macro="list_string_san" name="ID"/>
       </param>
-      <param name="description" argument="-FASTA:description" type="select" optional="true" label="Keep or remove the (possibly lengthy) FASTA header description" help="Keeping it can increase resulting FASTA file significantly">
+      <param name="description" argument="-FASTA:description" type="select" label="Keep or remove the (possibly lengthy) FASTA header description" help="Keeping it can increase resulting FASTA file significantly">
         <option value="remove" selected="true">remove</option>
         <option value="keep">keep</option>
         <expand macro="list_string_san" name="description"/>
@@ -99,7 +99,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -117,16 +117,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- just using some random fasta, in contrast to DigestorMotif idXML/fasta output possible, testing for the non-default fasta option -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="fasta" value="random.fa"/>
-    <output name="out" ftype="fasta" value="Digestor.fasta"/>
-    <param name="out_type" value="fasta"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- just using some random fasta, in contrast to DigestorMotif idXML/fasta output possible, testing for the non-default fasta option -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="fasta" value="random.fa"/>
+      <output name="out" ftype="fasta" value="Digestor.fasta"/>
+      <param name="out_type" value="fasta"/>
+    </test>
+  </tests>
   <help><![CDATA[Digests a protein database in-silico.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_Digestor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_Digestor.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/DigestorMotif.xml b/tools/openms/DigestorMotif.xml
index 650ab6105..af1e314d4 100644
--- a/tools/openms/DigestorMotif.xml
+++ b/tools/openms/DigestorMotif.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="DigestorMotif" name="DigestorMotif" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>digests a protein database in-silico</description>
   <macros>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,53 +38,53 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="fasta" optional="false" label="FASTA input file" help=" select fasta data sets(s)"/>
-    <param argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="the number of allowed missed cleavages" help=""/>
-    <param argument="-mass_accuracy" type="integer" optional="true" value="1000" label="give your mass accuracy in pp" help=""/>
-    <param argument="-min_length" type="integer" optional="true" value="6" label="minimum length of peptide" help=""/>
-    <param argument="-out_option" type="integer" optional="true" value="1" label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" help=""/>
-    <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
-      <option value="Arg-C/P">Arg-C/P</option>
-      <option value="Asp-N">Asp-N</option>
-      <option value="Asp-N/B">Asp-N/B</option>
-      <option value="Arg-C">Arg-C</option>
+    <param argument="-in" type="data" format="fasta" label="FASTA input file" help=" select fasta data sets(s)"/>
+    <param argument="-missed_cleavages" type="integer" min="0" value="1" label="the number of allowed missed cleavages" help=""/>
+    <param argument="-mass_accuracy" type="integer" value="1000" label="give your mass accuracy in pp" help=""/>
+    <param argument="-min_length" type="integer" value="6" label="minimum length of peptide" help=""/>
+    <param argument="-out_option" type="integer" value="1" label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" help=""/>
+    <param argument="-enzyme" type="select" label="The enzyme used for peptide digestion" help="">
+      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="V8-DE">V8-DE</option>
+      <option value="V8-E">V8-E</option>
+      <option value="leukocyte elastase">leukocyte elastase</option>
+      <option value="proline endopeptidase">proline endopeptidase</option>
       <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
       <option value="Alpha-lytic protease">Alpha-lytic protease</option>
-      <option value="no cleavage">no cleavage</option>
-      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="2-iodobenzoate">2-iodobenzoate</option>
+      <option value="iodosobenzoate">iodosobenzoate</option>
+      <option value="staphylococcal protease/D">staphylococcal protease/D</option>
+      <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
       <option value="Glu-C+P">Glu-C+P</option>
       <option value="PepsinA + P">PepsinA + P</option>
       <option value="cyanogen-bromide">cyanogen-bromide</option>
       <option value="Clostripain/P">Clostripain/P</option>
       <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+      <option value="no cleavage">no cleavage</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
       <option value="Asp-N_ambic">Asp-N_ambic</option>
       <option value="Chymotrypsin">Chymotrypsin</option>
       <option value="Chymotrypsin/P">Chymotrypsin/P</option>
       <option value="CNBr">CNBr</option>
       <option value="Formic_acid">Formic_acid</option>
       <option value="Lys-C">Lys-C</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
+      <option value="Arg-C">Arg-C</option>
+      <option value="Arg-C/P">Arg-C/P</option>
+      <option value="Asp-N">Asp-N</option>
+      <option value="Asp-N/B">Asp-N/B</option>
       <option value="Lys-N">Lys-N</option>
       <option value="Lys-C/P">Lys-C/P</option>
       <option value="PepsinA">PepsinA</option>
       <option value="TrypChymo">TrypChymo</option>
-      <option value="Trypsin/P">Trypsin/P</option>
-      <option value="V8-DE">V8-DE</option>
-      <option value="V8-E">V8-E</option>
-      <option value="leukocyte elastase">leukocyte elastase</option>
-      <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="2-iodobenzoate">2-iodobenzoate</option>
-      <option value="iodosobenzoate">iodosobenzoate</option>
-      <option value="staphylococcal protease/D">staphylococcal protease/D</option>
-      <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
-      <option value="Trypsin" selected="true">Trypsin</option>
       <expand macro="list_string_san" name="enzyme"/>
     </param>
-    <param argument="-motif" type="text" optional="true" value="M" label="the motif for the restricted peptidome" help="">
+    <param argument="-motif" type="text" value="M" label="the motif for the restricted peptidome" help="">
       <expand macro="list_string_san" name="motif"/>
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -103,6 +102,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   <help><![CDATA[digests a protein database in-silico
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_DigestorMotif.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DigestorMotif.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/EICExtractor.xml b/tools/openms/EICExtractor.xml
index f901de19c..0f8dbd3d1 100644
--- a/tools/openms/EICExtractor.xml
+++ b/tools/openms/EICExtractor.xml
@@ -1,4 +1,3 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Quantitation]-->
 <tool id="EICExtractor" name="EICExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
@@ -17,21 +16,21 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 #if $in_header_cond.in_header:
   mkdir in_header_cond.in_header &&
   #if $in_header_cond.in_header_select == "no"
   mkdir ${' '.join(["'in_header_cond.in_header/%s'" % (i) for i, f in enumerate($in_header_cond.in_header) if f])} && 
-  ${' '.join(["ln -s '%s' 'in_header_cond.in_header/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_header_cond.in_header) if f])}
+  ${' '.join(["cp '%s' 'in_header_cond.in_header/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_header_cond.in_header) if f])}
   #else
-  ln -s '$in_header_cond.in_header' 'in_header_cond.in_header/${re.sub("[^\w\-_]", "_", $in_header_cond.in_header.element_identifier)}.$gxy2omsext($in_header_cond.in_header.ext)' &&
+  cp '$in_header_cond.in_header' 'in_header_cond.in_header/${re.sub("[^\w\-_]", "_", $in_header_cond.in_header.element_identifier)}.$gxy2omsext($in_header_cond.in_header.ext)' &&
   #end if
 #end if
 mkdir pos &&
-ln -s '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' &&
+cp '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' &&
 mkdir out &&
 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir auto_rt_out_debug_TIC &&
@@ -88,10 +87,10 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input raw data file" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" multiple="true" label="Input raw data file" help=" select mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input raw data file" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" label="Input raw data file" help=" select mzml data sets(s)"/>
       </when>
     </conditional>
     <conditional name="in_header_cond">
@@ -103,24 +102,24 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param argument="-in_header" type="data" format="txt" multiple="true" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in_header" type="data" format="txt" multiple="false" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/>
+        <param argument="-in_header" type="data" format="txt" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-pos" type="data" format="edta" optional="false" label="Input config file stating where to find signal" help=" select edta data sets(s)"/>
-    <param argument="-rt_tol" type="float" optional="true" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/>
-    <param argument="-mz_tol" type="float" optional="true" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/>
-    <param argument="-rt_collect" type="integer" optional="true" value="1" label="# of scans up &amp; down in RT from highest point for ppm estimation in result" help=""/>
+    <param argument="-pos" type="data" format="edta" label="Input config file stating where to find signal" help=" select edta data sets(s)"/>
+    <param argument="-rt_tol" type="float" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/>
+    <param argument="-mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/>
+    <param argument="-rt_collect" type="integer" value="1" label="# of scans up &amp; down in RT from highest point for ppm estimation in result" help=""/>
     <section name="auto_rt" title="Parameters for automatic detection of injection RT peaks (no need to specify them in 'pos' input file)" help="" expanded="false">
       <param name="enabled" argument="-auto_rt:enabled" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" help=""/>
-      <param name="FHWM" argument="-auto_rt:FHWM" type="float" optional="true" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]" help="Gaussian smoothing filter with this width is applied to TIC"/>
-      <param name="SNThreshold" argument="-auto_rt:SNThreshold" type="float" optional="true" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking" help="Higher thesholds will result in less peaks"/>
+      <param name="FHWM" argument="-auto_rt:FHWM" type="float" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]" help="Gaussian smoothing filter with this width is applied to TIC"/>
+      <param name="SNThreshold" argument="-auto_rt:SNThreshold" type="float" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking" help="Higher thesholds will result in less peaks"/>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-out_separator" type="text" optional="true" value="," label="Separator character for output CSV file" help="">
+      <param argument="-out_separator" type="text" value="," label="Separator character for output CSV file" help="">
         <expand macro="list_string_san" name="out_separator"/>
       </param>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -138,16 +137,18 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- just using some random test data -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" value="spectra.mzML"/>
-    <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/>
-    <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- just using some random test data -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" value="spectra.mzML"/>
+      <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/>
+      <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/>
+    </test>
+  </tests>
   <help><![CDATA[Extracts intensities from dedicates positions in a LC/MS map
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_EICExtractor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_EICExtractor.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/ERPairFinder.xml b/tools/openms/ERPairFinder.xml
index 8759ba340..e6a103a2a 100644
--- a/tools/openms/ERPairFinder.xml
+++ b/tools/openms/ERPairFinder.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Quantitation]-->
 <tool id="ERPairFinder" name="ERPairFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description>
+  <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans</description>
   <macros>
     <token name="@EXECUTABLE@">ERPairFinder</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir pair_in &&
-ln -s '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' &&
+cp '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' &&
 mkdir out &&
 #if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir feature_out &&
@@ -56,17 +55,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input mzML file containing the ER spectra" help=" select mzml data sets(s)"/>
-    <param argument="-pair_in" type="data" format="txt" optional="false" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help=" select txt data sets(s)"/>
-    <param argument="-precursor_mass_tolerance" type="float" optional="true" min="0.0" value="0.3" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help=""/>
+    <param argument="-in" type="data" format="mzml" label="Input mzML file containing the ER spectra" help=" select mzml data sets(s)"/>
+    <param argument="-pair_in" type="data" format="txt" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help=" select txt data sets(s)"/>
+    <param argument="-precursor_mass_tolerance" type="float" min="0.0" value="0.3" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help=""/>
     <expand macro="adv_opts_macro">
-      <param argument="-RT_tolerance" type="float" optional="true" min="1.0" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help=""/>
-      <param argument="-max_charge" type="integer" optional="true" min="1" value="3" label="Maximal charge state features should be search fo" help=""/>
-      <param argument="-intensity_threshold" type="float" optional="true" min="-1.0" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" help=""/>
-      <param argument="-max_isotope" type="integer" optional="true" min="2" value="3" label="Max isotope of the isotope distribution to be considered" help=""/>
-      <param argument="-expansion_range" type="float" optional="true" min="0.0" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th" help=""/>
+      <param argument="-RT_tolerance" type="float" min="1.0" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help=""/>
+      <param argument="-max_charge" type="integer" min="1" value="3" label="Maximal charge state features should be search fo" help=""/>
+      <param argument="-intensity_threshold" type="float" min="-1.0" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" help=""/>
+      <param argument="-max_isotope" type="integer" min="2" value="3" label="Max isotope of the isotope distribution to be considered" help=""/>
+      <param argument="-expansion_range" type="float" min="0.0" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -84,11 +83,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TODO -->
-</tests>
+  <tests>
+    <!-- TODO -->
+  </tests>
   <help><![CDATA[Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_ERPairFinder.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ERPairFinder.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/Epifany.xml b/tools/openms/Epifany.xml
index 1d006d275..b667797b2 100644
--- a/tools/openms/Epifany.xml
+++ b/tools/openms/Epifany.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="Epifany" name="Epifany" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Runs a Bayesian protein inference.</description>
+  <description>Runs a Bayesian protein inference</description>
   <macros>
     <token name="@EXECUTABLE@">Epifany</token>
     <import>macros.xml</import>
@@ -17,13 +16,13 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 #if $exp_design:
   mkdir exp_design &&
-  ln -s '$exp_design' 'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)' &&
+  cp '$exp_design' 'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)' &&
 #end if
 mkdir out &&
 
@@ -62,56 +61,57 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="false" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,idxml" multiple="true" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="consensusxml,idxml" multiple="false" optional="false" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,idxml" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/>
       </when>
     </conditional>
     <param argument="-exp_design" type="data" format="tabular" optional="true" label="(Currently unused) Input: experimental design" help=" select tabular data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output type: auto detected by file extension but can be overwritten here" help="">
+    <param argument="-out_type" type="select" label="Output type: auto detected by file extension but can be overwritten here" help="">
       <option value="consensusXML">consensusxml</option>
       <option value="idXML">idxml</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
     <param argument="-protein_fdr" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Additionally calculate the target-decoy FDR on protein-level based on the posteriors" help=""/>
-    <param argument="-greedy_group_resolution" type="select" optional="true" label="Post-process inference output with greedy resolution of shared peptides based on the parent protein probabilities" help="Also adds the resolved ambiguity groups to output">
+    <param argument="-greedy_group_resolution" type="select" label="Post-process inference output with greedy resolution of shared peptides based on the parent protein probabilities" help="Also adds the resolved ambiguity groups to output">
       <option value="none" selected="true">none</option>
       <option value="remove_associations_only">remove_associations_only</option>
       <option value="remove_proteins_wo_evidence">remove_proteins_wo_evidence</option>
       <expand macro="list_string_san" name="greedy_group_resolution"/>
     </param>
-    <param argument="-max_psms_extreme_probability" type="float" optional="true" value="1.0" label="Set PSMs with probability higher than this to this maximum probability" help=""/>
+    <param argument="-max_psms_extreme_probability" type="float" value="1.0" label="Set PSMs with probability higher than this to this maximum probability" help=""/>
     <section name="algorithm" title="Parameters for the Algorithm section" help="" expanded="false">
-      <param name="psm_probability_cutoff" argument="-algorithm:psm_probability_cutoff" type="float" optional="true" min="0.0" max="1.0" value="0.001" label="Remove PSMs with probabilities less than this cutoff" help=""/>
-      <param name="top_PSMs" argument="-algorithm:top_PSMs" type="integer" optional="true" min="0" value="1" label="Consider only top X PSMs per spectrum" help="0 considers all"/>
+      <param name="psm_probability_cutoff" argument="-algorithm:psm_probability_cutoff" type="float" min="0.0" max="1.0" value="0.001" label="Remove PSMs with probabilities less than this cutoff" help=""/>
+      <param name="top_PSMs" argument="-algorithm:top_PSMs" type="integer" min="0" value="1" label="Consider only top X PSMs per spectrum" help="0 considers all"/>
       <param name="keep_best_PSM_only" argument="-algorithm:keep_best_PSM_only" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Epifany uses the best PSM per peptide for inference" help="Discard the rest (true) or keepe.g. for quantification/reporting?"/>
       <param name="update_PSM_probabilities" argument="-algorithm:update_PSM_probabilities" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(Experimental:) Update PSM probabilities with their posteriors under consideration of the protein probabilities" help=""/>
       <param name="user_defined_priors" argument="-algorithm:user_defined_priors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="(Experimental:) Uses the current protein scores as user-defined priors" help=""/>
       <param name="annotate_group_probabilities" argument="-algorithm:annotate_group_probabilities" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Annotates group probabilities for indistinguishable protein groups (indistinguishable by experimentally observed PSMs)" help=""/>
       <param name="use_ids_outside_features" argument="-algorithm:use_ids_outside_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="(Only consensusXML) Also use IDs without associated features for inference?" help=""/>
       <section name="model_parameters" title="Model parameters for the Bayesian network" help="" expanded="false">
-        <param name="prot_prior" argument="-algorithm:model_parameters:prot_prior" type="float" optional="true" min="-1.0" max="1.0" value="-1.0" label="Protein prior probability ('gamma' parameter)" help="Negative values enable grid search for this param"/>
-        <param name="pep_emission" argument="-algorithm:model_parameters:pep_emission" type="float" optional="true" min="-1.0" max="1.0" value="-1.0" label="Peptide emission probability ('alpha' parameter)" help="Negative values enable grid search for this param"/>
-        <param name="pep_spurious_emission" argument="-algorithm:model_parameters:pep_spurious_emission" type="float" optional="true" min="-1.0" max="1.0" value="-1.0" label="Spurious peptide identification probability ('beta' parameter)" help="Usually much smaller than emission from proteins. Negative values enable grid search for this param"/>
-        <param name="pep_prior" argument="-algorithm:model_parameters:pep_prior" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="Peptide prior probability (experimental, should be covered by combinations of the other params)" help=""/>
+        <param name="prot_prior" argument="-algorithm:model_parameters:prot_prior" type="float" min="-1.0" max="1.0" value="-1.0" label="Protein prior probability ('gamma' parameter)" help="Negative values enable grid search for this param"/>
+        <param name="pep_emission" argument="-algorithm:model_parameters:pep_emission" type="float" min="-1.0" max="1.0" value="-1.0" label="Peptide emission probability ('alpha' parameter)" help="Negative values enable grid search for this param"/>
+        <param name="pep_spurious_emission" argument="-algorithm:model_parameters:pep_spurious_emission" type="float" min="-1.0" max="1.0" value="-1.0" label="Spurious peptide identification probability ('beta' parameter)" help="Usually much smaller than emission from proteins. Negative values enable grid search for this param"/>
+        <param name="pep_prior" argument="-algorithm:model_parameters:pep_prior" type="float" min="0.0" max="1.0" value="0.1" label="Peptide prior probability (experimental, should be covered by combinations of the other params)" help=""/>
         <param name="regularize" argument="-algorithm:model_parameters:regularize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Regularize the number of proteins that produce a peptide together (experimental, should be activated when using higher p-norms)" help=""/>
         <param name="extended_model" argument="-algorithm:model_parameters:extended_model" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Uses information from different peptidoforms also across runs (automatically activated if an experimental design is given!)" help=""/>
       </section>
       <section name="loopy_belief_propagation" title="Settings for the loopy belief propagation algorithm" help="" expanded="false">
-        <param name="scheduling_type" argument="-algorithm:loopy_belief_propagation:scheduling_type" type="select" optional="true" label="(Not used yet) How to pick the next message: priority = based on difference to last message (higher = more important)" help="fifo = first in first out. subtree = message passing follows a random spanning tree in each iteration">
+        <param name="scheduling_type" argument="-algorithm:loopy_belief_propagation:scheduling_type" type="select" label="(Not used yet) How to pick the next message: priority = based on difference to last message (higher = more important)" help="fifo = first in first out. subtree = message passing follows a random spanning tree in each iteration">
           <option value="priority" selected="true">priority</option>
           <option value="fifo">fifo</option>
           <option value="subtree">subtree</option>
           <expand macro="list_string_san" name="scheduling_type"/>
         </param>
-        <param name="convergence_threshold" argument="-algorithm:loopy_belief_propagation:convergence_threshold" type="float" optional="true" min="0.0" max="1.0" value="1e-05" label="Initial threshold under which MSE difference a message is considered to be converged" help=""/>
-        <param name="dampening_lambda" argument="-algorithm:loopy_belief_propagation:dampening_lambda" type="float" optional="true" min="0.0" max="0.49999" value="0.001" label="Initial value for how strongly should messages be updated in each step" help="0 = new message overwrites old completely (no dampening; only recommended for trees),0.5 = equal contribution of old and new message (stay below that),In-between it will be a convex combination of both. Prevents oscillations but hinders convergence"/>
-        <param name="max_nr_iterations" argument="-algorithm:loopy_belief_propagation:max_nr_iterations" type="integer" optional="true" value="2147483647" label="(Usually auto-determined by estimated but you can set a hard limit here)" help="If not all messages converge, how many iterations should be done at max per connected component?"/>
-        <param name="p_norm_inference" argument="-algorithm:loopy_belief_propagation:p_norm_inference" type="float" optional="true" value="1.0" label="P-norm used for marginalization of multidimensional factors" help="1 == sum-product inference (all configurations vote equally) (default),&lt;= 0 == infinity = max-product inference (only best configurations propagate)The higher the value the more important high probability configurations get"/>
+        <param name="convergence_threshold" argument="-algorithm:loopy_belief_propagation:convergence_threshold" type="float" min="0.0" max="1.0" value="1e-05" label="Initial threshold under which MSE difference a message is considered to be converged" help=""/>
+        <param name="dampening_lambda" argument="-algorithm:loopy_belief_propagation:dampening_lambda" type="float" min="0.0" max="0.49999" value="0.001" label="Initial value for how strongly should messages be updated in each step" help="0 = new message overwrites old completely (no dampening; only recommended for trees),0.5 = equal contribution of old and new message (stay below that),In-between it will be a convex combination of both. Prevents oscillations but hinders convergence"/>
+        <param name="max_nr_iterations" argument="-algorithm:loopy_belief_propagation:max_nr_iterations" type="integer" value="2147483647" label="(Usually auto-determined by estimated but you can set a hard limit here)" help="If not all messages converge, how many iterations should be done at max per connected component?"/>
+        <param name="p_norm_inference" argument="-algorithm:loopy_belief_propagation:p_norm_inference" type="float" value="1.0" label="P-norm used for marginalization of multidimensional factors" help="1 == sum-product inference (all configurations vote equally) (default),&lt;= 0 == infinity = max-product inference (only best configurations propagate)The higher the value the more important high probability configurations get"/>
       </section>
       <section name="param_optimize" title="Settings for the parameter optimization" help="" expanded="false">
-        <param name="aucweight" argument="-algorithm:param_optimize:aucweight" type="float" optional="true" min="0.0" max="1.0" value="0.3" label="How important is target decoy AUC vs calibration of the posteriors" help="0 = maximize calibration only, 1 = maximize AUC only, between = convex combination"/>
+        <param name="aucweight" argument="-algorithm:param_optimize:aucweight" type="float" min="0.0" max="1.0" value="0.3" label="How important is target decoy AUC vs calibration of the posteriors" help="0 = maximize calibration only, 1 = maximize AUC only, between = convex combination"/>
         <param name="conservative_fdr" argument="-algorithm:param_optimize:conservative_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use (D+1)/(T) instead of (D+1)/(T+D) for parameter estimation" help=""/>
         <param name="regularized_fdr" argument="-algorithm:param_optimize:regularized_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use a regularized FDR for proteins without unique peptides" help=""/>
       </section>
@@ -122,14 +122,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <param argument="-picked_decoy_string" type="text" optional="true" value="" label="If using picked protein FDRs, which decoy string was used" help="Leave blank for auto-detection">
         <expand macro="list_string_san" name="picked_decoy_string"/>
       </param>
-      <param argument="-picked_decoy_prefix" type="select" optional="true" label="If using picked protein FDRs, was the decoy string a prefix or suffix" help="Ignored during auto-detection">
+      <param argument="-picked_decoy_prefix" type="select" label="If using picked protein FDRs, was the decoy string a prefix or suffix" help="Ignored during auto-detection">
         <option value="prefix" selected="true">prefix</option>
         <option value="suffix">suffix</option>
         <expand macro="list_string_san" name="picked_decoy_prefix"/>
       </param>
-      <param argument="-min_psms_extreme_probability" type="float" optional="true" value="0.0" label="Set PSMs with probability lower than this to this minimum probability" help=""/>
+      <param argument="-min_psms_extreme_probability" type="float" value="0.0" label="Set PSMs with probability lower than this to this minimum probability" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -147,7 +147,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_Epifany_1 -->
+  <tests>
+    <!-- TOPP_Epifany_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="conservative_fdr" value="true"/>
@@ -161,7 +162,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="FidoAdapter_1_input.idXML"/>
       </conditional>
-      <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="Epifany_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="protein_fdr" value="false"/>
       <param name="greedy_group_resolution" value="none"/>
@@ -201,8 +202,11 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_Epifany_2 -->
+    <!-- TOPP_Epifany_2 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="conservative_fdr" value="true"/>
@@ -216,7 +220,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="Epifany_2_input.consensusXML"/>
       </conditional>
-      <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="Epifany_2_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="protein_fdr" value="false"/>
       <param name="greedy_group_resolution" value="none"/>
@@ -256,8 +260,11 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_Epifany_3 -->
+    <!-- TOPP_Epifany_3 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="conservative_fdr" value="true"/>
@@ -271,7 +278,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="Epifany_2_input.consensusXML"/>
       </conditional>
-      <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="Epifany_3_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="protein_fdr" value="false"/>
       <param name="greedy_group_resolution" value="none"/>
@@ -311,8 +318,11 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_Epifany_4 -->
+    <!-- TOPP_Epifany_4 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="conservative_fdr" value="true"/>
@@ -326,7 +336,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="FidoAdapter_1_input_singlerun.idXML"/>
       </conditional>
-      <output name="out" file="Epifany_4_out_singlerun.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="Epifany_4_out_singlerun.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="protein_fdr" value="false"/>
       <param name="greedy_group_resolution" value="remove_proteins_wo_evidence"/>
@@ -366,8 +376,11 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_Epifany_5 -->
+    <!-- TOPP_Epifany_5 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="conservative_fdr" value="true"/>
@@ -381,7 +394,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="FidoAdapter_1_input_singlerun.idXML"/>
       </conditional>
-      <output name="out" file="Epifany_4_out_singlerun_fdr.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="Epifany_4_out_singlerun_fdr.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="protein_fdr" value="true"/>
       <param name="greedy_group_resolution" value="remove_proteins_wo_evidence"/>
@@ -421,11 +434,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Runs a Bayesian protein inference.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_Epifany.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_Epifany.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/ExternalCalibration.xml b/tools/openms/ExternalCalibration.xml
index 7ff16e3e7..837f3c421 100644
--- a/tools/openms/ExternalCalibration.xml
+++ b/tools/openms/ExternalCalibration.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Mass Correction and Calibration]-->
 <tool id="ExternalCalibration" name="ExternalCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies an external mass recalibration.</description>
+  <description>Applies an external mass recalibration</description>
   <macros>
     <token name="@EXECUTABLE@">ExternalCalibration</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,16 +38,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input peak file" help=" select mzml data sets(s)"/>
-    <param argument="-offset" type="float" optional="true" value="0.0" label="Mass offset in ppm" help=""/>
-    <param argument="-slope" type="float" optional="true" value="0.0" label="Slope (dependent on m/z)" help=""/>
-    <param argument="-power" type="float" optional="true" value="0.0" label="Power (dependent on m/z)" help=""/>
-    <param argument="-ms_level" type="text" optional="true" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Scans with other levels remain unchanged (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-in" type="data" format="mzml" label="Input peak file" help=" select mzml data sets(s)"/>
+    <param argument="-offset" type="float" value="0.0" label="Mass offset in ppm" help=""/>
+    <param argument="-slope" type="float" value="0.0" label="Slope (dependent on m/z)" help=""/>
+    <param argument="-power" type="float" value="0.0" label="Power (dependent on m/z)" help=""/>
+    <param argument="-ms_level" type="text" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Scans with other levels remain unchanged (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_integer_valsan" name="ms_level"/>
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -62,14 +61,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_ExternalCalibration_1_MS1 -->
+  <tests>
+    <!-- TOPP_ExternalCalibration_1_MS1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ExternalCalibration_1_input.mzML"/>
-      <output name="out" file="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="offset" value="-5.5"/>
       <param name="slope" value="0.0001"/>
       <param name="power" value="0.0"/>
@@ -80,6 +80,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ExternalCalibration_2_MS2 -->
     <test expect_num_outputs="2">
@@ -88,7 +91,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ExternalCalibration_1_input.mzML"/>
-      <output name="out" file="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="offset" value="-5.5"/>
       <param name="slope" value="0.0001"/>
       <param name="power" value="0.0"/>
@@ -99,11 +102,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Applies an external mass recalibration.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ExternalCalibration.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ExternalCalibration.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FFEval.xml b/tools/openms/FFEval.xml
deleted file mode 100644
index fd330a9f5..000000000
--- a/tools/openms/FFEval.xml
+++ /dev/null
@@ -1,119 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
-<tool id="FFEval" name="FFEval" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Evaluation tool for feature detection algorithms.</description>
-  <macros>
-    <token name="@EXECUTABLE@">FFEval</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-mkdir truth &&
-ln -s '$truth' 'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)' &&
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out &&
-#end if
-#if $abort_reasons:
-  mkdir abort_reasons &&
-  ln -s '$abort_reasons' 'abort_reasons/${re.sub("[^\w\-_]", "_", $abort_reasons.element_identifier)}.$gxy2omsext($abort_reasons.ext)' &&
-#end if
-#if "out_roc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out_roc &&
-#end if
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in
-'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
--truth
-'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)'
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out
-  'out/output.${gxy2omsext("featurexml")}'
-#end if
-#if $abort_reasons:
-  -abort_reasons
-  'abort_reasons/${re.sub("[^\w\-_]", "_", $abort_reasons.element_identifier)}.$gxy2omsext($abort_reasons.ext)'
-#end if
-#if "out_roc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out_roc
-  'out_roc/output.${gxy2omsext("csv")}'
-#end if
-#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
-  | tee '$stdout'
-#end if
-
-## Postprocessing
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
-#end if
-#if "out_roc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out_roc/output.${gxy2omsext("csv")}' '$out_roc'
-#end if
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
-  </configfiles>
-  <inputs>
-    <param argument="-in" type="data" format="featurexml" optional="false" label="Feature input file, which contains the data to be tested against the truth file" help=" select featurexml data sets(s)"/>
-    <param argument="-truth" type="data" format="featurexml" optional="false" label="Truth feature file that defines what features should be found" help=" select featurexml data sets(s)"/>
-    <param argument="-rt_tol" type="float" optional="true" min="0.0" value="0.3" label="Allowed tolerance of RT relative to average feature RT span" help=""/>
-    <param argument="-rt_tol_abs" type="float" optional="true" min="-1.0" value="-1.0" label="Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero)" help=""/>
-    <param argument="-mz_tol" type="float" optional="true" min="0.0" value="0.25" label="Allowed tolerance in m/z (is divided by charge)" help=""/>
-    <param argument="-abort_reasons" type="data" format="featurexml" optional="true" label="Feature file containing seeds with abort reasons" help=" select featurexml data sets(s)"/>
-    <expand macro="adv_opts_macro">
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="out_FLAG">out (Feature output file)</option>
-      <option value="out_roc_FLAG">out_roc (If given, a ROC curve file is created (ROC points based on intensity threshold))</option>
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="out_roc" label="${tool.name} on ${on_string}: out_roc" format="csv">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_roc_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
-      <filter>OPTIONAL_OUTPUTS is None</filter>
-    </data>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><test expect_num_outputs="2"><!-- comparing an arbitarty FeatureFinder output with itself -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" value="FeatureFinderCentroided_1_output.featureXML"/>
-    <param name="truth" value="FeatureFinderCentroided_1_output.featureXML"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_FLAG,out_roc_FLAG"/>
-    <output name="out" value="FFEval.featureXML" compare="sim_size"/>
-	<output name="out_roc" value="FFEval_roc.csv" ftype="csv"/>
-  </test>
-</tests>
-  <help><![CDATA[Evaluation tool for feature detection algorithms.
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_FFEval.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/FalseDiscoveryRate.xml b/tools/openms/FalseDiscoveryRate.xml
index 97edc7235..0d7b8804f 100644
--- a/tools/openms/FalseDiscoveryRate.xml
+++ b/tools/openms/FalseDiscoveryRate.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [ID Processing]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
+  <description>Estimates the false discovery rate on peptide and protein level using decoy searches</description>
   <macros>
     <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,12 +38,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="idxml" optional="false" label="Identifications from searching a target-decoy database" help=" select idxml data sets(s)"/>
+    <param argument="-in" type="data" format="idxml" label="Identifications from searching a target-decoy database" help=" select idxml data sets(s)"/>
     <param argument="-PSM" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on PSM level" help=""/>
+    <param argument="-peptide" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform FDR calculation on peptide level and annotates it as meta value" help="(Note: if set, also calculates FDR/q-value on PSM level.)"/>
     <param argument="-protein" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on protein level" help=""/>
     <section name="FDR" title="FDR control" help="" expanded="false">
-      <param name="PSM" argument="-FDR:PSM" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Filter PSMs based on q-value" help="(e.g., 0.05 = 5% FDR, disabled for 1)"/>
-      <param name="protein" argument="-FDR:protein" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Filter proteins based on q-value" help="(e.g., 0.05 = 5% FDR, disabled for 1)"/>
+      <param name="PSM" argument="-FDR:PSM" type="float" min="0.0" max="1.0" value="1.0" label="Filter PSMs based on q-value" help="(e.g., 0.05 = 5% FDR, disabled for 1)"/>
+      <param name="protein" argument="-FDR:protein" type="float" min="0.0" max="1.0" value="1.0" label="Filter proteins based on q-value" help="(e.g., 0.05 = 5% FDR, disabled for 1)"/>
       <section name="cleanup" title="Cleanup references after FDR control" help="" expanded="false">
         <param name="remove_proteins_without_psms" argument="-FDR:cleanup:remove_proteins_without_psms" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove proteins without PSMs (due to being decoy or below PSM FDR threshold)" help=""/>
         <param name="remove_psms_without_proteins" argument="-FDR:cleanup:remove_psms_without_proteins" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove PSMs without proteins (due to being decoy or below protein FDR threshold)" help=""/>
@@ -62,7 +62,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -76,15 +76,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FalseDiscoveryRate_1 -->
+  <tests>
+    <!-- TOPP_FalseDiscoveryRate_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="PSM" value="true"/>
+      <param name="peptide" value="false"/>
       <param name="protein" value="false"/>
       <section name="FDR">
         <param name="PSM" value="1.0"/>
@@ -110,6 +112,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FalseDiscoveryRate_2 -->
     <test expect_num_outputs="2">
@@ -118,8 +123,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="PSM" value="true"/>
+      <param name="peptide" value="false"/>
       <param name="protein" value="false"/>
       <section name="FDR">
         <param name="PSM" value="1.0"/>
@@ -145,6 +151,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FalseDiscoveryRate_3 -->
     <test expect_num_outputs="2">
@@ -153,8 +162,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="PSM" value="true"/>
+      <param name="peptide" value="false"/>
       <param name="protein" value="false"/>
       <section name="FDR">
         <param name="PSM" value="1.0"/>
@@ -180,6 +190,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FalseDiscoveryRate_4 -->
     <test expect_num_outputs="2">
@@ -188,8 +201,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FalseDiscoveryRate_OMSSA_4.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="PSM" value="true"/>
+      <param name="peptide" value="false"/>
       <param name="protein" value="false"/>
       <section name="FDR">
         <param name="PSM" value="1.0"/>
@@ -215,6 +229,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FalseDiscoveryRate_5 -->
     <test expect_num_outputs="2">
@@ -223,8 +240,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FalseDiscoveryRate_5_input.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="PSM" value="false"/>
+      <param name="peptide" value="false"/>
       <param name="protein" value="true"/>
       <section name="FDR">
         <param name="PSM" value="1.0"/>
@@ -250,6 +268,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FalseDiscoveryRate_6 -->
     <test expect_num_outputs="2">
@@ -258,8 +279,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FalseDiscoveryRate_6_input.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="PSM" value="true"/>
+      <param name="peptide" value="false"/>
       <param name="protein" value="false"/>
       <section name="FDR">
         <param name="PSM" value="0.05"/>
@@ -285,6 +307,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FalseDiscoveryRate_7 -->
     <test expect_num_outputs="2">
@@ -293,8 +318,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FalseDiscoveryRate_7_input.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="PSM" value="false"/>
+      <param name="peptide" value="false"/>
       <param name="protein" value="true"/>
       <section name="FDR">
         <param name="PSM" value="1.0"/>
@@ -320,11 +346,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Estimates the false discovery rate on peptide and protein level using decoy searches.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FalseDiscoveryRate.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FalseDiscoveryRate.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FeatureFinderCentroided.xml b/tools/openms/FeatureFinderCentroided.xml
index e9b39589d..ef79b5886 100644
--- a/tools/openms/FeatureFinderCentroided.xml
+++ b/tools/openms/FeatureFinderCentroided.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Quantitation]-->
 <tool id="FeatureFinderCentroided" name="FeatureFinderCentroided" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Detects two-dimensional features in LC-MS data.</description>
+  <description>Detects two-dimensional features in LC-MS data</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderCentroided</token>
     <import>macros.xml</import>
@@ -15,11 +14,11 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if $seeds:
   mkdir seeds &&
-  ln -s '$seeds' 'seeds/${re.sub("[^\w\-_]", "_", $seeds.element_identifier)}.$gxy2omsext($seeds.ext)' &&
+  cp '$seeds' 'seeds/${re.sub("[^\w\-_]", "_", $seeds.element_identifier)}.$gxy2omsext($seeds.ext)' &&
 #end if
 #if "out_mzq_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_mzq &&
@@ -60,51 +59,51 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <param argument="-seeds" type="data" format="featurexml" optional="true" label="User specified seed list" help=" select featurexml data sets(s)"/>
     <section name="algorithm" title="Algorithm section" help="" expanded="false">
       <section name="debug" title="" help="" expanded="false">
-        <param name="pseudo_rt_shift" argument="-algorithm:debug:pseudo_rt_shift" type="float" optional="true" min="1.0" value="500.0" label="Pseudo RT shift used when" help=""/>
+        <param name="pseudo_rt_shift" argument="-algorithm:debug:pseudo_rt_shift" type="float" min="1.0" value="500.0" label="Pseudo RT shift used when" help=""/>
       </section>
       <section name="intensity" title="Settings for the calculation of a score indicating if a peak's intensity is significant in the local environment (between 0 and 1)" help="" expanded="false">
-        <param name="bins" argument="-algorithm:intensity:bins" type="integer" optional="true" min="1" value="10" label="Number of bins per dimension (RT and m/z)" help="The higher this value, the more local the intensity significance score is.. This parameter should be decreased, if the algorithm is used on small regions of a map"/>
+        <param name="bins" argument="-algorithm:intensity:bins" type="integer" min="1" value="10" label="Number of bins per dimension (RT and m/z)" help="The higher this value, the more local the intensity significance score is.. This parameter should be decreased, if the algorithm is used on small regions of a map"/>
       </section>
       <section name="mass_trace" title="Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1)" help="" expanded="false">
-        <param name="mz_tolerance" argument="-algorithm:mass_trace:mz_tolerance" type="float" optional="true" min="0.0" value="0.03" label="Tolerated m/z deviation of peaks belonging to the same mass trace" help="It should be larger than the m/z resolution of the instrument.. This value must be smaller than that 1/charge_high!"/>
-        <param name="min_spectra" argument="-algorithm:mass_trace:min_spectra" type="integer" optional="true" min="1" value="10" label="Number of spectra that have to show a similar peak mass in a mass trace" help=""/>
-        <param name="max_missing" argument="-algorithm:mass_trace:max_missing" type="integer" optional="true" min="0" value="1" label="Number of consecutive spectra where a high mass deviation or missing peak is acceptable" help="This parameter should be well below 'min_spectra'!"/>
-        <param name="slope_bound" argument="-algorithm:mass_trace:slope_bound" type="float" optional="true" min="0.0" value="0.1" label="The maximum slope of mass trace intensities when extending from the highest peak" help="This parameter is important to separate overlapping elution peaks.. It should be increased if feature elution profiles fluctuate a lot"/>
+        <param name="mz_tolerance" argument="-algorithm:mass_trace:mz_tolerance" type="float" min="0.0" value="0.03" label="Tolerated m/z deviation of peaks belonging to the same mass trace" help="It should be larger than the m/z resolution of the instrument.. This value must be smaller than that 1/charge_high!"/>
+        <param name="min_spectra" argument="-algorithm:mass_trace:min_spectra" type="integer" min="1" value="10" label="Number of spectra that have to show a similar peak mass in a mass trace" help=""/>
+        <param name="max_missing" argument="-algorithm:mass_trace:max_missing" type="integer" min="0" value="1" label="Number of consecutive spectra where a high mass deviation or missing peak is acceptable" help="This parameter should be well below 'min_spectra'!"/>
+        <param name="slope_bound" argument="-algorithm:mass_trace:slope_bound" type="float" min="0.0" value="0.1" label="The maximum slope of mass trace intensities when extending from the highest peak" help="This parameter is important to separate overlapping elution peaks.. It should be increased if feature elution profiles fluctuate a lot"/>
       </section>
       <section name="isotopic_pattern" title="Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1)" help="" expanded="false">
-        <param name="charge_low" argument="-algorithm:isotopic_pattern:charge_low" type="integer" optional="true" min="1" value="1" label="Lowest charge to search fo" help=""/>
-        <param name="charge_high" argument="-algorithm:isotopic_pattern:charge_high" type="integer" optional="true" min="1" value="4" label="Highest charge to search fo" help=""/>
-        <param name="mz_tolerance" argument="-algorithm:isotopic_pattern:mz_tolerance" type="float" optional="true" min="0.0" value="0.03" label="Tolerated m/z deviation from the theoretical isotopic pattern" help="It should be larger than the m/z resolution of the instrument.. This value must be smaller than that 1/charge_high!"/>
-        <param name="intensity_percentage" argument="-algorithm:isotopic_pattern:intensity_percentage" type="float" optional="true" min="0.0" max="100.0" value="10.0" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present" help=""/>
-        <param name="intensity_percentage_optional" argument="-algorithm:isotopic_pattern:intensity_percentage_optional" type="float" optional="true" min="0.0" max="100.0" value="0.1" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing" help=""/>
-        <param name="optional_fit_improvement" argument="-algorithm:isotopic_pattern:optional_fit_improvement" type="float" optional="true" min="0.0" max="100.0" value="2.0" label="Minimal percental improvement of isotope fit to allow leaving out an optional peak" help=""/>
-        <param name="mass_window_width" argument="-algorithm:isotopic_pattern:mass_window_width" type="float" optional="true" min="1.0" max="200.0" value="25.0" label="Window width in Dalton for precalculation of estimated isotope distributions" help=""/>
-        <param name="abundance_12C" argument="-algorithm:isotopic_pattern:abundance_12C" type="float" optional="true" min="0.0" max="100.0" value="98.93" label="Rel" help="abundance of the light carbon. Modify if labeled"/>
-        <param name="abundance_14N" argument="-algorithm:isotopic_pattern:abundance_14N" type="float" optional="true" min="0.0" max="100.0" value="99.632" label="Rel" help="abundance of the light nitrogen. Modify if labeled"/>
+        <param name="charge_low" argument="-algorithm:isotopic_pattern:charge_low" type="integer" min="1" value="1" label="Lowest charge to search fo" help=""/>
+        <param name="charge_high" argument="-algorithm:isotopic_pattern:charge_high" type="integer" min="1" value="4" label="Highest charge to search fo" help=""/>
+        <param name="mz_tolerance" argument="-algorithm:isotopic_pattern:mz_tolerance" type="float" min="0.0" value="0.03" label="Tolerated m/z deviation from the theoretical isotopic pattern" help="It should be larger than the m/z resolution of the instrument.. This value must be smaller than that 1/charge_high!"/>
+        <param name="intensity_percentage" argument="-algorithm:isotopic_pattern:intensity_percentage" type="float" min="0.0" max="100.0" value="10.0" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present" help=""/>
+        <param name="intensity_percentage_optional" argument="-algorithm:isotopic_pattern:intensity_percentage_optional" type="float" min="0.0" max="100.0" value="0.1" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing" help=""/>
+        <param name="optional_fit_improvement" argument="-algorithm:isotopic_pattern:optional_fit_improvement" type="float" min="0.0" max="100.0" value="2.0" label="Minimal percental improvement of isotope fit to allow leaving out an optional peak" help=""/>
+        <param name="mass_window_width" argument="-algorithm:isotopic_pattern:mass_window_width" type="float" min="1.0" max="200.0" value="25.0" label="Window width in Dalton for precalculation of estimated isotope distributions" help=""/>
+        <param name="abundance_12C" argument="-algorithm:isotopic_pattern:abundance_12C" type="float" min="0.0" max="100.0" value="98.93" label="Rel" help="abundance of the light carbon. Modify if labeled"/>
+        <param name="abundance_14N" argument="-algorithm:isotopic_pattern:abundance_14N" type="float" min="0.0" max="100.0" value="99.632" label="Rel" help="abundance of the light nitrogen. Modify if labeled"/>
       </section>
       <section name="seed" title="Settings that determine which peaks are considered a seed" help="" expanded="false">
-        <param name="min_score" argument="-algorithm:seed:min_score" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Minimum seed score a peak has to reach to be used as seed" help="The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.. If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score"/>
+        <param name="min_score" argument="-algorithm:seed:min_score" type="float" min="0.0" max="1.0" value="0.8" label="Minimum seed score a peak has to reach to be used as seed" help="The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.. If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score"/>
       </section>
       <section name="fit" title="Settings for the model fitting" help="" expanded="false">
-        <param name="max_iterations" argument="-algorithm:fit:max_iterations" type="integer" optional="true" min="1" value="500" label="Maximum number of iterations of the fit" help=""/>
+        <param name="max_iterations" argument="-algorithm:fit:max_iterations" type="integer" min="1" value="500" label="Maximum number of iterations of the fit" help=""/>
       </section>
       <section name="feature" title="Settings for the features (intensity, quality assessment, ...)" help="" expanded="false">
-        <param name="min_score" argument="-algorithm:feature:min_score" type="float" optional="true" min="0.0" max="1.0" value="0.7" label="Feature score threshold for a feature to be reported" help="The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks"/>
-        <param name="min_isotope_fit" argument="-algorithm:feature:min_isotope_fit" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Minimum isotope fit of the feature before model fitting" help=""/>
-        <param name="min_trace_score" argument="-algorithm:feature:min_trace_score" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Trace score threshold" help="Traces below this threshold are removed after the model fitting.. This parameter is important for features that overlap in m/z dimension"/>
-        <param name="min_rt_span" argument="-algorithm:feature:min_rt_span" type="float" optional="true" min="0.0" max="1.0" value="0.333" label="Minimum RT span in relation to extended area that has to remain after model fitting" help=""/>
-        <param name="max_rt_span" argument="-algorithm:feature:max_rt_span" type="float" optional="true" min="0.5" value="2.5" label="Maximum RT span in relation to extended area that the model is allowed to have" help=""/>
-        <param name="rt_shape" argument="-algorithm:feature:rt_shape" type="select" optional="true" label="Choose model used for RT profile fitting" help="If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used">
+        <param name="min_score" argument="-algorithm:feature:min_score" type="float" min="0.0" max="1.0" value="0.7" label="Feature score threshold for a feature to be reported" help="The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks"/>
+        <param name="min_isotope_fit" argument="-algorithm:feature:min_isotope_fit" type="float" min="0.0" max="1.0" value="0.8" label="Minimum isotope fit of the feature before model fitting" help=""/>
+        <param name="min_trace_score" argument="-algorithm:feature:min_trace_score" type="float" min="0.0" max="1.0" value="0.5" label="Trace score threshold" help="Traces below this threshold are removed after the model fitting.. This parameter is important for features that overlap in m/z dimension"/>
+        <param name="min_rt_span" argument="-algorithm:feature:min_rt_span" type="float" min="0.0" max="1.0" value="0.333" label="Minimum RT span in relation to extended area that has to remain after model fitting" help=""/>
+        <param name="max_rt_span" argument="-algorithm:feature:max_rt_span" type="float" min="0.5" value="2.5" label="Maximum RT span in relation to extended area that the model is allowed to have" help=""/>
+        <param name="rt_shape" argument="-algorithm:feature:rt_shape" type="select" label="Choose model used for RT profile fitting" help="If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used">
           <option value="symmetric" selected="true">symmetric</option>
           <option value="asymmetric">asymmetric</option>
           <expand macro="list_string_san" name="rt_shape"/>
         </param>
-        <param name="max_intersection" argument="-algorithm:feature:max_intersection" type="float" optional="true" min="0.0" max="1.0" value="0.35" label="Maximum allowed intersection of features" help=""/>
-        <param name="reported_mz" argument="-algorithm:feature:reported_mz" type="select" optional="true" label="The mass type that is reported for features" help="'maximum' returns the m/z value of the highest mass trace.. 'average' returns the intensity-weighted average m/z value of all contained peaks.. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model">
+        <param name="max_intersection" argument="-algorithm:feature:max_intersection" type="float" min="0.0" max="1.0" value="0.35" label="Maximum allowed intersection of features" help=""/>
+        <param name="reported_mz" argument="-algorithm:feature:reported_mz" type="select" label="The mass type that is reported for features" help="'maximum' returns the m/z value of the highest mass trace.. 'average' returns the intensity-weighted average m/z value of all contained peaks.. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model">
           <option value="maximum">maximum</option>
           <option value="average">average</option>
           <option value="monoisotopic" selected="true">monoisotopic</option>
@@ -112,14 +111,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         </param>
       </section>
       <section name="user-seed" title="Settings for user-specified seeds" help="" expanded="false">
-        <param name="rt_tolerance" argument="-algorithm:user-seed:rt_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Allowed RT deviation of seeds from the user-specified seed position" help=""/>
-        <param name="mz_tolerance" argument="-algorithm:user-seed:mz_tolerance" type="float" optional="true" min="0.0" value="1.1" label="Allowed m/z deviation of seeds from the user-specified seed position" help=""/>
-        <param name="min_score" argument="-algorithm:user-seed:min_score" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Overwrites 'seed:min_score' for user-specified seeds" help="The cutoff is typically a bit lower in this case"/>
+        <param name="rt_tolerance" argument="-algorithm:user-seed:rt_tolerance" type="float" min="0.0" value="5.0" label="Allowed RT deviation of seeds from the user-specified seed position" help=""/>
+        <param name="mz_tolerance" argument="-algorithm:user-seed:mz_tolerance" type="float" min="0.0" value="1.1" label="Allowed m/z deviation of seeds from the user-specified seed position" help=""/>
+        <param name="min_score" argument="-algorithm:user-seed:min_score" type="float" min="0.0" max="1.0" value="0.5" label="Overwrites 'seed:min_score' for user-specified seeds" help="The cutoff is typically a bit lower in this case"/>
       </section>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -137,7 +136,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FeatureFinderCentroided_1 -->
+  <tests>
+    <!-- TOPP_FeatureFinderCentroided_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -145,7 +145,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="pseudo_rt_shift" value="500.0"/>
       </section>
       <param name="in" value="FeatureFinderCentroided_1_input.mzML"/>
-      <output name="out" file="FeatureFinderCentroided_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderCentroided_1_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <section name="algorithm">
         <section name="intensity">
           <param name="bins" value="1"/>
@@ -195,11 +195,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Detects two-dimensional features in LC-MS data.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderCentroided.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderCentroided.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FeatureFinderIdentification.xml b/tools/openms/FeatureFinderIdentification.xml
index 721422f2e..7896f1fdb 100644
--- a/tools/openms/FeatureFinderIdentification.xml
+++ b/tools/openms/FeatureFinderIdentification.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Quantitation]-->
 <tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Detects features in MS1 data based on peptide identifications.</description>
+  <description>Detects features in MS1 data based on peptide identifications</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderIdentification</token>
     <import>macros.xml</import>
@@ -15,12 +14,12 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir id &&
-ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
+cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
 #if $id_ext:
   mkdir id_ext &&
-  ln -s '$id_ext' 'id_ext/${re.sub("[^\w\-_]", "_", $id_ext.element_identifier)}.$gxy2omsext($id_ext.ext)' &&
+  cp '$id_ext' 'id_ext/${re.sub("[^\w\-_]", "_", $id_ext.element_identifier)}.$gxy2omsext($id_ext.ext)' &&
 #end if
 mkdir out &&
 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
@@ -35,11 +34,13 @@ mkdir out &&
 #if "xval_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir svm_xval_out &&
 #end if
+## advanced options
   #if $adv_opts.candidates_in:
     mkdir adv_opts.candidates_in &&
-    ln -s '$adv_opts.candidates_in' 'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)' &&
+    cp '$adv_opts.candidates_in' 'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)' &&
   #end if
 
+
 ## Main program call
 
 set -o pipefail &&
@@ -72,10 +73,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   -svm:xval_out
   'svm_xval_out/output.${gxy2omsext("csv")}'
 #end if
+## advanced options
   #if $adv_opts.candidates_in:
     -candidates_in
     'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)'
   #end if
+
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
 #end if
@@ -102,73 +105,80 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/>
-    <param argument="-id" type="data" format="idxml" optional="false" label="Input file: Peptide identifications derived directly from 'in'" help=" select idxml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/>
+    <param argument="-id" type="data" format="idxml" label="Input file: Peptide identifications derived directly from 'in'" help=" select idxml data sets(s)"/>
     <param argument="-id_ext" type="data" format="idxml" optional="true" label="Input file: 'External' peptide identifications" help="(e.g. from aligned runs) select idxml data sets(s)"/>
     <param argument="-quantify_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether decoy peptides should be quantified (true) or skipped (false)" help=""/>
+    <param argument="-min_psm_cutoff" type="text" value="none" label="Minimum score for the best PSM of a spectrum to be used as seed" help="Use 'none' for no cutoff">
+      <expand macro="list_string_san" name="min_psm_cutoff"/>
+    </param>
+    <param argument="-add_mass_offset_peptides" type="float" min="0.0" value="0.0" label="If for every peptide (or seed) also an offset peptide is extracted (true)" help="Can be used to downstream to determine MBR false transfer rates. (0.0 = disabled)"/>
     <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false">
-      <param name="batch_size" argument="-extract:batch_size" type="integer" optional="true" min="1" value="5000" label="Nr of peptides used in each batch of chromatogram extraction" help="Smaller values decrease memory usage but increase runtime"/>
-      <param name="mz_window" argument="-extract:mz_window" type="float" optional="true" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/>
-      <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" optional="true" min="2" value="2" label="Number of isotopes to include in each peptide assay" help=""/>
-      <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/>
-      <param name="rt_quantile" argument="-extract:rt_quantile" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="Quantile of the RT deviations between aligned internal and external IDs to use for scaling the RT extraction window" help=""/>
-      <param name="rt_window" argument="-extract:rt_window" type="float" optional="true" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If set, this parameter takes precedence over 'extract:rt_quantile'"/>
+      <param name="batch_size" argument="-extract:batch_size" type="integer" min="1" value="5000" label="Nr of peptides used in each batch of chromatogram extraction" help="Smaller values decrease memory usage but increase runtime"/>
+      <param name="mz_window" argument="-extract:mz_window" type="float" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/>
+      <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" min="2" value="2" label="Number of isotopes to include in each peptide assay" help=""/>
+      <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/>
+      <param name="rt_quantile" argument="-extract:rt_quantile" type="float" min="0.0" max="1.0" value="0.95" label="Quantile of the RT deviations between aligned internal and external IDs to use for scaling the RT extraction window" help=""/>
+      <param name="rt_window" argument="-extract:rt_window" type="float" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If set, this parameter takes precedence over 'extract:rt_quantile'"/>
     </section>
     <section name="detect" title="Parameters for detecting features in extracted ion chromatograms" help="" expanded="false">
-      <param name="peak_width" argument="-detect:peak_width" type="float" optional="true" min="0.0" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
-      <param name="min_peak_width" argument="-detect:min_peak_width" type="float" optional="true" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
-      <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" optional="true" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/>
-      <param name="mapping_tolerance" argument="-detect:mapping_tolerance" type="float" optional="true" min="0.0" value="0.0" label="RT tolerance (plus/minus) for mapping peptide IDs to features" help="Absolute value in seconds if 1 or greater, else relative to the RT span of the feature"/>
+      <param name="peak_width" argument="-detect:peak_width" type="float" min="0.0" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
+      <param name="min_peak_width" argument="-detect:min_peak_width" type="float" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
+      <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/>
+      <param name="mapping_tolerance" argument="-detect:mapping_tolerance" type="float" min="0.0" value="0.0" label="RT tolerance (plus/minus) for mapping peptide IDs to features" help="Absolute value in seconds if 1 or greater, else relative to the RT span of the feature"/>
     </section>
     <section name="svm" title="Parameters for scoring features using a support vector machine (SVM)" help="" expanded="false">
-      <param name="samples" argument="-svm:samples" type="integer" optional="true" min="0" value="0" label="Number of observations to use for training ('0' for all)" help=""/>
+      <param name="samples" argument="-svm:samples" type="integer" min="0" value="0" label="Number of observations to use for training ('0' for all)" help=""/>
       <param name="no_selection" argument="-svm:no_selection" type="boolean" truevalue="true" falsevalue="false" checked="false" label="By default, roughly the same number of positive and negative observations, with the same intensity distribution, are selected for training" help="This aims to reduce biases, but also reduces the amount of training data. Set this flag to skip this procedure and consider all available observations (subject to 'svm:samples')"/>
-      <param name="kernel" argument="-svm:kernel" type="select" optional="true" label="SVM kernel" help="">
+      <param name="kernel" argument="-svm:kernel" type="select" label="SVM kernel" help="">
         <option value="RBF" selected="true">RBF</option>
         <option value="linear">linear</option>
         <expand macro="list_string_san" name="kernel"/>
       </param>
-      <param name="xval" argument="-svm:xval" type="integer" optional="true" min="1" value="5" label="Number of partitions for cross-validation (parameter optimization)" help=""/>
-      <param name="log2_C" argument="-svm:log2_C" type="text" optional="true" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0" label="Values to try for the SVM parameter 'C' during parameter optimization" help="A value 'x' is used as 'C = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="xval" argument="-svm:xval" type="integer" min="1" value="5" label="Number of partitions for cross-validation (parameter optimization)" help=""/>
+      <param name="log2_C" argument="-svm:log2_C" type="text" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0" label="Values to try for the SVM parameter 'C' during parameter optimization" help="A value 'x' is used as 'C = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_float_valsan" name="log2_C"/>
       </param>
-      <param name="log2_gamma" argument="-svm:log2_gamma" type="text" optional="true" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0" label="Values to try for the SVM parameter 'gamma' during parameter optimization (RBF kernel only)" help="A value 'x' is used as 'gamma = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="log2_gamma" argument="-svm:log2_gamma" type="text" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0" label="Values to try for the SVM parameter 'gamma' during parameter optimization (RBF kernel only)" help="A value 'x' is used as 'gamma = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_float_valsan" name="log2_gamma"/>
       </param>
-      <param name="epsilon" argument="-svm:epsilon" type="float" optional="true" min="0.0" value="0.001" label="Stopping criterion" help=""/>
-      <param name="cache_size" argument="-svm:cache_size" type="float" optional="true" min="1.0" value="100.0" label="Size of the kernel cache (in MB)" help=""/>
+      <param name="log2_p" argument="-svm:log2_p" type="text" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0" label="Values to try for the SVM parameter 'epsilon' during parameter optimization (epsilon-SVR only)" help="A value 'x' is used as 'epsilon = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+        <expand macro="list_float_valsan" name="log2_p"/>
+      </param>
+      <param name="epsilon" argument="-svm:epsilon" type="float" min="0.0" value="0.001" label="Stopping criterion" help=""/>
+      <param name="cache_size" argument="-svm:cache_size" type="float" min="1.0" value="100.0" label="Size of the kernel cache (in MB)" help=""/>
       <param name="no_shrinking" argument="-svm:no_shrinking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable the shrinking heuristics" help=""/>
-      <param name="predictors" argument="-svm:predictors" type="text" optional="true" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score" label="Names of OpenSWATH scores to use as predictors for the SVM (comma-separated list)" help="">
+      <param name="predictors" argument="-svm:predictors" type="text" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score" label="Names of OpenSWATH scores to use as predictors for the SVM (comma-separated list)" help="">
         <expand macro="list_string_san" name="predictors"/>
       </param>
-      <param name="min_prob" argument="-svm:min_prob" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum probability of correctness, as predicted by the SVM, required to retain a feature candidate" help=""/>
+      <param name="min_prob" argument="-svm:min_prob" type="float" min="0.0" max="1.0" value="0.0" label="Minimum probability of correctness, as predicted by the SVM, required to retain a feature candidate" help=""/>
     </section>
     <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false">
-      <param name="type" argument="-model:type" type="select" optional="true" label="Type of elution model to fit to features" help="">
+      <param name="type" argument="-model:type" type="select" label="Type of elution model to fit to features" help="">
         <option value="symmetric" selected="true">symmetric</option>
         <option value="asymmetric">asymmetric</option>
         <option value="none">none</option>
         <expand macro="list_string_san" name="type"/>
       </param>
-      <param name="add_zeros" argument="-model:add_zeros" type="float" optional="true" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/>
+      <param name="add_zeros" argument="-model:add_zeros" type="float" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/>
       <param name="unweighted_fit" argument="-model:unweighted_fit" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help=""/>
       <param name="no_imputation" argument="-model:no_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help=""/>
       <param name="each_trace" argument="-model:each_trace" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit elution model to each individual mass trace" help=""/>
       <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false">
-        <param name="min_area" argument="-model:check:min_area" type="float" optional="true" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/>
-        <param name="boundaries" argument="-model:check:boundaries" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help=""/>
-        <param name="width" argument="-model:check:width" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
-        <param name="asymmetry" argument="-model:check:asymmetry" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
+        <param name="min_area" argument="-model:check:min_area" type="float" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/>
+        <param name="boundaries" argument="-model:check:boundaries" type="float" min="0.0" max="1.0" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help=""/>
+        <param name="width" argument="-model:check:width" type="float" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
+        <param name="asymmetry" argument="-model:check:asymmetry" type="float" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
       </section>
     </section>
     <section name="EMGScoring" title="Parameters for fitting exp" help="mod. Gaussians to mass traces" expanded="false">
-      <param name="max_iteration" argument="-EMGScoring:max_iteration" type="integer" optional="true" min="1" value="100" label="Maximum number of iterations for EMG fitting" help=""/>
+      <param name="max_iteration" argument="-EMGScoring:max_iteration" type="integer" min="1" value="100" label="Maximum number of iterations for EMG fitting" help=""/>
       <param name="init_mom" argument="-EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Alternative initial parameters for fitting through method of moments" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-candidates_in" type="data" format="featurexml" optional="true" label="Input file: Feature candidates from a previous run" help="If set, only feature classification and elution model fitting are carried out, if enabled. Many parameters are ignored select featurexml data sets(s)"/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -198,7 +208,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FeatureFinderIdentification_1 -->
+  <tests>
+    <!-- TOPP_FeatureFinderIdentification_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -206,8 +217,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
       <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
-      <output name="out" file="FeatureFinderIdentification_1.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="quantify_decoys" value="false"/>
+      <param name="min_psm_cutoff" value="none"/>
+      <param name="add_mass_offset_peptides" value="0.0"/>
       <section name="extract">
         <param name="batch_size" value="5000"/>
         <param name="mz_window" value="0.1"/>
@@ -229,6 +242,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="xval" value="5"/>
         <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
         <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
+        <param name="log2_p" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0"/>
         <param name="epsilon" value="0.001"/>
         <param name="cache_size" value="100.0"/>
         <param name="no_shrinking" value="false"/>
@@ -258,6 +272,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureFinderIdentification_3 -->
     <test expect_num_outputs="2">
@@ -267,8 +284,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
       <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
-      <output name="out" file="FeatureFinderIdentification_3.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderIdentification_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="quantify_decoys" value="false"/>
+      <param name="min_psm_cutoff" value="none"/>
+      <param name="add_mass_offset_peptides" value="0.0"/>
       <section name="extract">
         <param name="batch_size" value="5000"/>
         <param name="mz_window" value="0.1"/>
@@ -290,6 +309,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="xval" value="5"/>
         <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
         <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
+        <param name="log2_p" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0"/>
         <param name="epsilon" value="0.001"/>
         <param name="cache_size" value="100.0"/>
         <param name="no_shrinking" value="false"/>
@@ -319,6 +339,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureFinderIdentification_5 -->
     <test expect_num_outputs="3">
@@ -328,9 +351,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
       <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
-      <output name="out" file="FeatureFinderIdentification_5.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="candidates_out" file="FeatureFinderIdentification_5_candidates.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="candidates_out" value="FeatureFinderIdentification_5_candidates.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="quantify_decoys" value="false"/>
+      <param name="min_psm_cutoff" value="none"/>
+      <param name="add_mass_offset_peptides" value="0.0"/>
       <section name="extract">
         <param name="batch_size" value="10"/>
         <param name="mz_window" value="0.1"/>
@@ -352,6 +377,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="xval" value="5"/>
         <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
         <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
+        <param name="log2_p" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0"/>
         <param name="epsilon" value="0.001"/>
         <param name="cache_size" value="100.0"/>
         <param name="no_shrinking" value="false"/>
@@ -381,11 +407,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Detects features in MS1 data based on peptide identifications.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderIdentification.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderIdentification.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FeatureFinderIsotopeWavelet.xml b/tools/openms/FeatureFinderIsotopeWavelet.xml
index 92d3e8db3..8e6c2e36c 100644
--- a/tools/openms/FeatureFinderIsotopeWavelet.xml
+++ b/tools/openms/FeatureFinderIsotopeWavelet.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Quantitation]-->
 <tool id="FeatureFinderIsotopeWavelet" name="FeatureFinderIsotopeWavelet" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Detects two-dimensional features in LC-MS data.</description>
+  <description>Detects two-dimensional features in LC-MS data</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderIsotopeWavelet</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,11 +38,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm section" help="" expanded="false">
-      <param name="max_charge" argument="-algorithm:max_charge" type="integer" optional="true" min="1" value="3" label="The maximal charge state to be considered" help=""/>
-      <param name="intensity_threshold" argument="-algorithm:intensity_threshold" type="float" optional="true" value="-1.0" label="The final threshold t' is build upon the formula: t' = av+t*sd, where t is the intensity_threshold, av the average intensity within the wavelet transformed signal and sd the standard deviation of the transform" help="If you set intensity_threshold=-1, t' will be zero.. As the 'optimal' value for this parameter is highly data dependent, we would recommend to start with -1, which will also extract features with very low signal-to-noise ratio. Subsequently, one might increase the threshold to find an optimized trade-off between false positives and true positives. Depending on the dynamic range of your spectra, suitable value ranges include: -1, [0:10], and if your data features even very high intensity values, t can also adopt values up to around 30. Please note that this parameter is not of an integer type, s.t. you can also use t:=0.1, e.g"/>
-      <param name="intensity_type" argument="-algorithm:intensity_type" type="select" optional="true" label="Determines the intensity type returned for the identified features" help="'ref' (default) returns the sum of the intensities of each isotopic peak within an isotope pattern. 'trans' refers to the intensity of the monoisotopic peak within the wavelet transform. 'corrected' refers also to the transformed intensity with an attempt to remove the effects of the convolution. While the latter ones might be preferable for qualitative analyses, 'ref' might be the best option to obtain quantitative results. Please note that intensity values might be spoiled (in particular for the option 'ref'), as soon as patterns overlap (see also the explanations given in the class documentation of FeatureFinderAlgorihtmIsotopeWavelet)">
+      <param name="max_charge" argument="-algorithm:max_charge" type="integer" min="1" value="3" label="The maximal charge state to be considered" help=""/>
+      <param name="intensity_threshold" argument="-algorithm:intensity_threshold" type="float" value="-1.0" label="The final threshold t' is build upon the formula: t' = av+t*sd, where t is the intensity_threshold, av the average intensity within the wavelet transformed signal and sd the standard deviation of the transform" help="If you set intensity_threshold=-1, t' will be zero.. As the 'optimal' value for this parameter is highly data dependent, we would recommend to start with -1, which will also extract features with very low signal-to-noise ratio. Subsequently, one might increase the threshold to find an optimized trade-off between false positives and true positives. Depending on the dynamic range of your spectra, suitable value ranges include: -1, [0:10], and if your data features even very high intensity values, t can also adopt values up to around 30. Please note that this parameter is not of an integer type, s.t. you can also use t:=0.1, e.g"/>
+      <param name="intensity_type" argument="-algorithm:intensity_type" type="select" label="Determines the intensity type returned for the identified features" help="'ref' (default) returns the sum of the intensities of each isotopic peak within an isotope pattern. 'trans' refers to the intensity of the monoisotopic peak within the wavelet transform. 'corrected' refers also to the transformed intensity with an attempt to remove the effects of the convolution. While the latter ones might be preferable for qualitative analyses, 'ref' might be the best option to obtain quantitative results. Please note that intensity values might be spoiled (in particular for the option 'ref'), as soon as patterns overlap (see also the explanations given in the class documentation of FeatureFinderAlgorihtmIsotopeWavelet)">
         <option value="ref" selected="true">ref</option>
         <option value="trans">trans</option>
         <option value="corrected">corrected</option>
@@ -52,13 +51,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="check_ppm" argument="-algorithm:check_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enables/disables a ppm test vs" help="the averagine model, i.e. potential peptide masses are checked for plausibility. In addition, a heuristic correcting potential mass shifts induced by the wavelet is applied"/>
       <param name="hr_data" argument="-algorithm:hr_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Must be true in case of high-resolution data" help="i.e. for spectra featuring large m/z-gaps (present in FTICR and Orbitrap data, e.g.). Please check a single MS scan out of your recording, if you are unsure"/>
       <section name="sweep_line" title="" help="" expanded="false">
-        <param name="rt_votes_cutoff" argument="-algorithm:sweep_line:rt_votes_cutoff" type="integer" optional="true" min="0" value="5" label="Defines the minimum number of subsequent scans where a pattern must occur to be considered as a feature" help=""/>
-        <param name="rt_interleave" argument="-algorithm:sweep_line:rt_interleave" type="integer" optional="true" min="0" value="1" label="Defines the maximum number of scans (w.r.t" help="rt_votes_cutoff) where an expected pattern is missing. There is usually no reason to change the default value"/>
+        <param name="rt_votes_cutoff" argument="-algorithm:sweep_line:rt_votes_cutoff" type="integer" min="0" value="5" label="Defines the minimum number of subsequent scans where a pattern must occur to be considered as a feature" help=""/>
+        <param name="rt_interleave" argument="-algorithm:sweep_line:rt_interleave" type="integer" min="0" value="1" label="Defines the maximum number of scans (w.r.t" help="rt_votes_cutoff) where an expected pattern is missing. There is usually no reason to change the default value"/>
       </section>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -72,15 +71,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!--just use the input of another FeatureFinder -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" value="FeatureFinderCentroided_1_input.mzML"/>
-    <output name="out" value="FeatureFinderIsotopeWavelet.featureXML" compare="sim_size"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!--just use the input of another FeatureFinder -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" value="FeatureFinderCentroided_1_input.mzML"/>
+      <output name="out" value="FeatureFinderIsotopeWavelet.featureXML" compare="sim_size"/>
+    </test>
+  </tests>
   <help><![CDATA[Detects two-dimensional features in LC-MS data.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderIsotopeWavelet.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderIsotopeWavelet.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FeatureFinderMRM.xml b/tools/openms/FeatureFinderMRM.xml
index 373f9853d..51c92b3ce 100644
--- a/tools/openms/FeatureFinderMRM.xml
+++ b/tools/openms/FeatureFinderMRM.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Quantitation]-->
 <tool id="FeatureFinderMRM" name="FeatureFinderMRM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Detects two-dimensional features in LC-MS data.</description>
+  <description>Detects two-dimensional features in LC-MS data</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderMRM</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,18 +38,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm section" help="" expanded="false">
-      <param name="min_rt_distance" argument="-algorithm:min_rt_distance" type="float" optional="true" min="0.0" value="10.0" label="Minimal distance of MRM features in seconds" help=""/>
-      <param name="min_num_peaks_per_feature" argument="-algorithm:min_num_peaks_per_feature" type="integer" optional="true" min="1" value="5" label="Minimal number of peaks which are needed for a single feature" help=""/>
-      <param name="min_signal_to_noise_ratio" argument="-algorithm:min_signal_to_noise_ratio" type="float" optional="true" min="0.0" value="2.0" label="Minimal S/N ratio a peak must have to be taken into account" help="Set to zero if the MRM-traces contains mostly signals, and no noise"/>
+      <param name="min_rt_distance" argument="-algorithm:min_rt_distance" type="float" min="0.0" value="10.0" label="Minimal distance of MRM features in seconds" help=""/>
+      <param name="min_num_peaks_per_feature" argument="-algorithm:min_num_peaks_per_feature" type="integer" min="1" value="5" label="Minimal number of peaks which are needed for a single feature" help=""/>
+      <param name="min_signal_to_noise_ratio" argument="-algorithm:min_signal_to_noise_ratio" type="float" min="0.0" value="2.0" label="Minimal S/N ratio a peak must have to be taken into account" help="Set to zero if the MRM-traces contains mostly signals, and no noise"/>
       <param name="write_debug_files" argument="-algorithm:write_debug_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, for each feature a plot will be created, in the subdirectory 'debug'" help=""/>
       <param name="resample_traces" argument="-algorithm:resample_traces" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension" help=""/>
       <param name="write_debuginfo" argument="-algorithm:write_debuginfo" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, debug messages are written, the output can be somewhat lengthy" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -64,14 +63,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FeatureFinderMRM_1 -->
+  <tests>
+    <!-- TOPP_FeatureFinderMRM_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMRM_1_input.mzML"/>
-      <output name="out" file="FeatureFinderMRM_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderMRM_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <section name="algorithm">
         <param name="min_rt_distance" value="10.0"/>
         <param name="min_num_peaks_per_feature" value="5"/>
@@ -86,11 +86,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Detects two-dimensional features in LC-MS data.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderMRM.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderMRM.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FeatureFinderMetabo.xml b/tools/openms/FeatureFinderMetabo.xml
index 907313769..1b5ca1d4a 100644
--- a/tools/openms/FeatureFinderMetabo.xml
+++ b/tools/openms/FeatureFinderMetabo.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Quantitation]-->
 <tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.</description>
+  <description>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderMetabo</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_chrom &&
@@ -52,52 +51,52 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Centroided mzML file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Centroided mzML file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <section name="common" title="Common parameters for all other subsections" help="" expanded="false">
-        <param name="noise_threshold_int" argument="-algorithm:common:noise_threshold_int" type="float" optional="true" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help=""/>
-        <param name="chrom_peak_snr" argument="-algorithm:common:chrom_peak_snr" type="float" optional="true" value="3.0" label="Minimum signal-to-noise a mass trace should have" help=""/>
-        <param name="chrom_fwhm" argument="-algorithm:common:chrom_fwhm" type="float" optional="true" value="5.0" label="Expected chromatographic peak width (in seconds)" help=""/>
+        <param name="noise_threshold_int" argument="-algorithm:common:noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help=""/>
+        <param name="chrom_peak_snr" argument="-algorithm:common:chrom_peak_snr" type="float" value="3.0" label="Minimum signal-to-noise a mass trace should have" help=""/>
+        <param name="chrom_fwhm" argument="-algorithm:common:chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)" help=""/>
       </section>
       <section name="mtd" title="Mass Trace Detection parameters" help="" expanded="false">
-        <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" optional="true" value="20.0" label="Allowed mass deviation (in ppm)" help=""/>
+        <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" value="20.0" label="Allowed mass deviation (in ppm)" help=""/>
         <param name="reestimate_mt_sd" argument="-algorithm:mtd:reestimate_mt_sd" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help=""/>
-        <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" optional="true" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace">
+        <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace">
           <option value="area" selected="true">area</option>
           <option value="median">median</option>
           <option value="max_height">max_height</option>
           <expand macro="list_string_san" name="quant_method"/>
         </param>
-        <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" optional="true" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
+        <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
           <option value="outlier" selected="true">outlier</option>
           <option value="sample_rate">sample_rate</option>
           <expand macro="list_string_san" name="trace_termination_criterion"/>
         </param>
-        <param name="trace_termination_outliers" argument="-algorithm:mtd:trace_termination_outliers" type="integer" optional="true" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help=""/>
-        <param name="min_sample_rate" argument="-algorithm:mtd:min_sample_rate" type="float" optional="true" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help=""/>
-        <param name="min_trace_length" argument="-algorithm:mtd:min_trace_length" type="float" optional="true" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help=""/>
-        <param name="max_trace_length" argument="-algorithm:mtd:max_trace_length" type="float" optional="true" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="Set to a negative value to disable maximal length check during mass trace detection"/>
+        <param name="trace_termination_outliers" argument="-algorithm:mtd:trace_termination_outliers" type="integer" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help=""/>
+        <param name="min_sample_rate" argument="-algorithm:mtd:min_sample_rate" type="float" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help=""/>
+        <param name="min_trace_length" argument="-algorithm:mtd:min_trace_length" type="float" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help=""/>
+        <param name="max_trace_length" argument="-algorithm:mtd:max_trace_length" type="float" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="Set to a negative value to disable maximal length check during mass trace detection"/>
       </section>
       <section name="epd" title="Elution Profile Detection (to separate isobaric Mass Traces by elution time)" help="" expanded="false">
         <param name="enabled" argument="-algorithm:epd:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable splitting of isobaric mass traces by chromatographic peak detection" help="Disable for direct injection"/>
-        <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" optional="true" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
+        <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
           <option value="off">off</option>
           <option value="fixed" selected="true">fixed</option>
           <option value="auto">auto</option>
           <expand macro="list_string_san" name="width_filtering"/>
         </param>
-        <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" optional="true" value="1.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
-        <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" optional="true" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
+        <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" value="1.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
+        <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
         <param name="masstrace_snr_filtering" argument="-algorithm:epd:masstrace_snr_filtering" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply post-filtering by signal-to-noise ratio after smoothing" help=""/>
       </section>
       <section name="ffm" title="FeatureFinder parameters (assembling mass traces to charged features)" help="" expanded="false">
-        <param name="local_rt_range" argument="-algorithm:ffm:local_rt_range" type="float" optional="true" value="10.0" label="RT range where to look for coeluting mass traces" help=""/>
-        <param name="local_mz_range" argument="-algorithm:ffm:local_mz_range" type="float" optional="true" value="6.5" label="MZ range where to look for isotopic mass traces" help=""/>
-        <param name="charge_lower_bound" argument="-algorithm:ffm:charge_lower_bound" type="integer" optional="true" value="1" label="Lowest charge state to conside" help=""/>
-        <param name="charge_upper_bound" argument="-algorithm:ffm:charge_upper_bound" type="integer" optional="true" value="3" label="Highest charge state to conside" help=""/>
+        <param name="local_rt_range" argument="-algorithm:ffm:local_rt_range" type="float" value="10.0" label="RT range where to look for coeluting mass traces" help=""/>
+        <param name="local_mz_range" argument="-algorithm:ffm:local_mz_range" type="float" value="6.5" label="MZ range where to look for isotopic mass traces" help=""/>
+        <param name="charge_lower_bound" argument="-algorithm:ffm:charge_lower_bound" type="integer" value="1" label="Lowest charge state to conside" help=""/>
+        <param name="charge_upper_bound" argument="-algorithm:ffm:charge_upper_bound" type="integer" value="3" label="Highest charge state to conside" help=""/>
         <param name="report_summed_ints" argument="-algorithm:ffm:report_summed_ints" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone" help=""/>
         <param name="enable_RT_filtering" argument="-algorithm:ffm:enable_RT_filtering" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Require sufficient overlap in RT while assembling mass traces" help="Disable for direct injection data"/>
-        <param name="isotope_filtering_model" argument="-algorithm:ffm:isotope_filtering_model" type="select" optional="true" label="Remove/score candidate assemblies based on isotope intensities" help="SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device">
+        <param name="isotope_filtering_model" argument="-algorithm:ffm:isotope_filtering_model" type="select" label="Remove/score candidate assemblies based on isotope intensities" help="SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device">
           <option value="metabolites (2% RMS)">metabolites (2% RMS)</option>
           <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option>
           <option value="peptides">peptides</option>
@@ -109,14 +108,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="report_convex_hulls" argument="-algorithm:ffm:report_convex_hulls" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably)" help=""/>
         <param name="remove_single_traces" argument="-algorithm:ffm:remove_single_traces" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove unassembled traces (single traces)" help=""/>
         <param name="mz_scoring_by_elements" argument="-algorithm:ffm:mz_scoring_by_elements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the m/z range of the assumed elements to detect isotope peaks" help="A expected m/z range is computed from the isotopes of the assumed elements. If enabled, this ignores 'mz_scoring_13C'"/>
-        <param name="elements" argument="-algorithm:ffm:elements" type="text" optional="true" value="CHNOPS" label="Elements assumes to be present in the sample (this influences isotope detection)" help="">
+        <param name="elements" argument="-algorithm:ffm:elements" type="text" value="CHNOPS" label="Elements assumes to be present in the sample (this influences isotope detection)" help="">
           <expand macro="list_string_san" name="elements"/>
         </param>
       </section>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -134,14 +133,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FeatureFinderMetabo_1 -->
+  <tests>
+    <!-- TOPP_FeatureFinderMetabo_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMetabo_1_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <section name="algorithm">
         <section name="common">
           <param name="noise_threshold_int" value="10.0"/>
@@ -187,6 +187,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureFinderMetabo_2 -->
     <test expect_num_outputs="2">
@@ -195,7 +198,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMetabo_2_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <section name="algorithm">
         <section name="common">
           <param name="noise_threshold_int" value="100.0"/>
@@ -241,6 +244,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureFinderMetabo_3 -->
     <test expect_num_outputs="3">
@@ -249,8 +255,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_3.tmp" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FeatureFinderMetabo_3.tmp" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_chrom" value="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <section name="common">
           <param name="noise_threshold_int" value="10.0"/>
@@ -296,6 +302,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureFinderMetabo_4 -->
     <test expect_num_outputs="3">
@@ -304,8 +313,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_chrom" value="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <section name="common">
           <param name="noise_threshold_int" value="10.0"/>
@@ -351,6 +360,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureFinderMetabo_5 -->
     <test expect_num_outputs="2">
@@ -359,7 +371,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMetabo_1_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <section name="algorithm">
         <section name="common">
           <param name="noise_threshold_int" value="10.0"/>
@@ -405,11 +417,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderMetabo.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderMetabo.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FeatureFinderMetaboIdent.xml b/tools/openms/FeatureFinderMetaboIdent.xml
index e26af9bf2..00ae0de81 100644
--- a/tools/openms/FeatureFinderMetaboIdent.xml
+++ b/tools/openms/FeatureFinderMetaboIdent.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Quantitation]-->
 <tool id="FeatureFinderMetaboIdent" name="FeatureFinderMetaboIdent" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Detects features in MS1 data based on metabolite identifications.</description>
+  <description>Detects features in MS1 data based on metabolite identifications</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderMetaboIdent</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir id &&
-ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
+cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
 mkdir out &&
 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir lib_out &&
@@ -25,12 +24,12 @@ mkdir out &&
 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir chrom_out &&
 #end if
-#if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir candidates_out &&
-#end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir trafo_out &&
 #end if
+#if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir candidates_out &&
+#end if
 
 ## Main program call
 
@@ -52,14 +51,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   -chrom_out
   'chrom_out/output.${gxy2omsext("mzml")}'
 #end if
-#if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -candidates_out
-  'candidates_out/output.${gxy2omsext("featurexml")}'
-#end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -trafo_out
   'trafo_out/output.${gxy2omsext("trafoxml")}'
 #end if
+#if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -candidates_out
+  'candidates_out/output.${gxy2omsext("txt")}'
+#end if
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
 #end if
@@ -72,12 +71,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   && mv 'chrom_out/output.${gxy2omsext("mzml")}' '$chrom_out'
 #end if
-#if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'candidates_out/output.${gxy2omsext("featurexml")}' '$candidates_out'
-#end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   && mv 'trafo_out/output.${gxy2omsext("trafoxml")}' '$trafo_out'
 #end if
+#if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'candidates_out/output.${gxy2omsext("txt")}' '$candidates_out'
+#end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
@@ -86,52 +85,52 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/>
-    <param argument="-id" type="data" format="tabular" optional="false" label="Input file: Metabolite identifications" help=" select tabular data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/>
+    <param argument="-id" type="data" format="tabular" label="Input file: Metabolite identifications" help=" select tabular data sets(s)"/>
     <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false">
-      <param name="mz_window" argument="-extract:mz_window" type="float" optional="true" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/>
-      <param name="rt_window" argument="-extract:rt_window" type="float" optional="true" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If set, this parameter takes precedence over 'extract:rt_quantile'"/>
-      <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" optional="true" min="2" value="2" label="Number of isotopes to include in each peptide assay" help=""/>
-      <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/>
+      <param name="mz_window" argument="-extract:mz_window" type="float" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/>
+      <param name="rt_window" argument="-extract:rt_window" type="float" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If set, this parameter takes precedence over 'extract:rt_quantile'"/>
+      <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" min="2" value="2" label="Number of isotopes to include in each peptide assay" help=""/>
+      <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/>
     </section>
     <section name="detect" title="Parameters for detecting features in extracted ion chromatograms" help="" expanded="false">
-      <param name="peak_width" argument="-detect:peak_width" type="float" optional="true" min="0.0" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
-      <param name="min_peak_width" argument="-detect:min_peak_width" type="float" optional="true" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
-      <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" optional="true" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/>
+      <param name="peak_width" argument="-detect:peak_width" type="float" min="0.0" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
+      <param name="min_peak_width" argument="-detect:min_peak_width" type="float" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
+      <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/>
     </section>
     <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false">
-      <param name="type" argument="-model:type" type="select" optional="true" label="Type of elution model to fit to features" help="">
+      <param name="type" argument="-model:type" type="select" label="Type of elution model to fit to features" help="">
         <option value="symmetric" selected="true">symmetric</option>
         <option value="asymmetric">asymmetric</option>
         <option value="none">none</option>
         <expand macro="list_string_san" name="type"/>
       </param>
-      <param name="add_zeros" argument="-model:add_zeros" type="float" optional="true" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/>
+      <param name="add_zeros" argument="-model:add_zeros" type="float" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/>
       <param name="unweighted_fit" argument="-model:unweighted_fit" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help=""/>
       <param name="no_imputation" argument="-model:no_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help=""/>
       <param name="each_trace" argument="-model:each_trace" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit elution model to each individual mass trace" help=""/>
       <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false">
-        <param name="min_area" argument="-model:check:min_area" type="float" optional="true" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/>
-        <param name="boundaries" argument="-model:check:boundaries" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help=""/>
-        <param name="width" argument="-model:check:width" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
-        <param name="asymmetry" argument="-model:check:asymmetry" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
+        <param name="min_area" argument="-model:check:min_area" type="float" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/>
+        <param name="boundaries" argument="-model:check:boundaries" type="float" min="0.0" max="1.0" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help=""/>
+        <param name="width" argument="-model:check:width" type="float" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
+        <param name="asymmetry" argument="-model:check:asymmetry" type="float" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
       </section>
     </section>
     <section name="EMGScoring" title="Parameters for fitting exp" help="mod. Gaussians to mass traces" expanded="false">
-      <param name="max_iteration" argument="-EMGScoring:max_iteration" type="integer" optional="true" min="1" value="100" label="Maximum number of iterations for EMG fitting" help=""/>
+      <param name="max_iteration" argument="-EMGScoring:max_iteration" type="integer" min="1" value="100" label="Maximum number of iterations for EMG fitting" help=""/>
       <param name="init_mom" argument="-EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Alternative initial parameters for fitting through method of moments" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
       <option value="lib_out_FLAG">lib_out (Output file: Assay library)</option>
       <option value="chrom_out_FLAG">chrom_out (Output file: Chromatograms)</option>
-      <option value="candidates_out_FLAG">candidates_out (Optional output file with feature candidates)</option>
       <option value="trafo_out_FLAG">trafo_out (Output file: Retention times (expected vs)</option>
+      <option value="candidates_out_FLAG">candidates_out (Optional output file: Feature candidates (before filtering and model fitting))</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
@@ -143,17 +142,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <data name="chrom_out" label="${tool.name} on ${on_string}: chrom_out" format="mzml">
       <filter>OPTIONAL_OUTPUTS is not None and "chrom_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
-    <data name="candidates_out" label="${tool.name} on ${on_string}: candidates_out" format="featurexml">
-      <filter>OPTIONAL_OUTPUTS is not None and "candidates_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
     <data name="trafo_out" label="${tool.name} on ${on_string}: trafo_out" format="trafoxml">
       <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
+    <data name="candidates_out" label="${tool.name} on ${on_string}: candidates_out" format="txt">
+      <filter>OPTIONAL_OUTPUTS is not None and "candidates_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_FeatureFinderMetaboIdent_1 -->
+  <tests>
+    <!-- TOPP_FeatureFinderMetaboIdent_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -161,7 +161,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="FeatureFinderMetaboIdent_1_input.mzML"/>
       <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/>
-      <output name="out" file="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <section name="extract">
         <param name="mz_window" value="5.0"/>
         <param name="rt_window" value="20.0"/>
@@ -196,11 +196,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Detects features in MS1 data based on metabolite identifications.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_FeatureFinderMetaboIdent.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderMetaboIdent.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FeatureFinderMultiplex.xml b/tools/openms/FeatureFinderMultiplex.xml
index 7a09910f8..d87d5de5f 100644
--- a/tools/openms/FeatureFinderMultiplex.xml
+++ b/tools/openms/FeatureFinderMultiplex.xml
@@ -1,4 +1,3 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Quantitation]-->
 <tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
 #end if
@@ -68,38 +67,38 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="LC-MS dataset in either centroid or profile mode" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="LC-MS dataset in either centroid or profile mode" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="algorithmic parameters" help="" expanded="false">
-      <param name="labels" argument="-algorithm:labels" type="text" optional="true" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="If the sample is unlabelled (i.e. you want to detect only single peptide features) please leave this parameter empty. [...] specifies the labels for a single sample. For example.  [][Lys8,Arg10]        ... SILAC. [][Lys4,Arg6][Lys8,Arg10]        ... triple-SILAC. [Dimethyl0][Dimethyl6]        ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8]        ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10]        ... ICPL">
+      <param name="labels" argument="-algorithm:labels" type="text" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="If the sample is unlabelled (i.e. you want to detect only single peptide features) please leave this parameter empty. [...] specifies the labels for a single sample. For example.  [][Lys8,Arg10]        ... SILAC. [][Lys4,Arg6][Lys8,Arg10]        ... triple-SILAC. [Dimethyl0][Dimethyl6]        ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8]        ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10]        ... ICPL">
         <expand macro="list_string_san" name="labels"/>
       </param>
-      <param name="charge" argument="-algorithm:charge" type="text" optional="true" value="1:4" label="Range of charge states in the sample" help="i.e. min charge : max charge">
+      <param name="charge" argument="-algorithm:charge" type="text" value="1:4" label="Range of charge states in the sample" help="i.e. min charge : max charge">
         <expand macro="list_string_san" name="charge"/>
       </param>
-      <param name="isotopes_per_peptide" argument="-algorithm:isotopes_per_peptide" type="text" optional="true" value="3:6" label="Range of isotopes per peptide in the sample" help="For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. ">
+      <param name="isotopes_per_peptide" argument="-algorithm:isotopes_per_peptide" type="text" value="3:6" label="Range of isotopes per peptide in the sample" help="For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. ">
         <expand macro="list_string_san" name="isotopes_per_peptide"/>
       </param>
-      <param name="rt_typical" argument="-algorithm:rt_typical" type="float" optional="true" min="0.0" value="40.0" label="Typical retention time [s] over which a characteristic peptide elutes" help="(This is not an upper bound. Peptides that elute for longer will be reported.)"/>
-      <param name="rt_band" argument="-algorithm:rt_band" type="float" optional="true" min="0.0" value="0.0" label="The algorithm searches for characteristic isotopic peak patterns, spectrum by spectrum" help="For some low-intensity peptides, an important peak might be missing in one spectrum but be present in one of the neighbouring ones. The algorithm takes a bundle of neighbouring spectra with width rt_band into account. For example with rt_band = 0, all characteristic isotopic peaks have to be present in one and the same spectrum. As rt_band increases, the sensitivity of the algorithm but also the likelihood of false detections increases"/>
-      <param name="rt_min" argument="-algorithm:rt_min" type="float" optional="true" min="0.0" value="2.0" label="Lower bound for the retention time [s]" help="(Any peptides seen for a shorter time period are not reported.)"/>
-      <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="float" optional="true" min="0.0" value="6.0" label="m/z tolerance for search of peak patterns" help=""/>
-      <param name="mz_unit" argument="-algorithm:mz_unit" type="select" optional="true" label="Unit of the 'mz_tolerance' paramete" help="">
+      <param name="rt_typical" argument="-algorithm:rt_typical" type="float" min="0.0" value="40.0" label="Typical retention time [s] over which a characteristic peptide elutes" help="(This is not an upper bound. Peptides that elute for longer will be reported.)"/>
+      <param name="rt_band" argument="-algorithm:rt_band" type="float" min="0.0" value="0.0" label="The algorithm searches for characteristic isotopic peak patterns, spectrum by spectrum" help="For some low-intensity peptides, an important peak might be missing in one spectrum but be present in one of the neighbouring ones. The algorithm takes a bundle of neighbouring spectra with width rt_band into account. For example with rt_band = 0, all characteristic isotopic peaks have to be present in one and the same spectrum. As rt_band increases, the sensitivity of the algorithm but also the likelihood of false detections increases"/>
+      <param name="rt_min" argument="-algorithm:rt_min" type="float" min="0.0" value="2.0" label="Lower bound for the retention time [s]" help="(Any peptides seen for a shorter time period are not reported.)"/>
+      <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="float" min="0.0" value="6.0" label="m/z tolerance for search of peak patterns" help=""/>
+      <param name="mz_unit" argument="-algorithm:mz_unit" type="select" label="Unit of the 'mz_tolerance' paramete" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mz_unit"/>
       </param>
-      <param name="intensity_cutoff" argument="-algorithm:intensity_cutoff" type="float" optional="true" min="0.0" value="1000.0" label="Lower bound for the intensity of isotopic peaks" help=""/>
-      <param name="peptide_similarity" argument="-algorithm:peptide_similarity" type="float" optional="true" min="-1.0" max="1.0" value="0.5" label="Two peptides in a multiplet are expected to have the same isotopic pattern" help="This parameter is a lower bound on their similarity"/>
-      <param name="averagine_similarity" argument="-algorithm:averagine_similarity" type="float" optional="true" min="-1.0" max="1.0" value="0.4" label="The isotopic pattern of a peptide should resemble the averagine model at this m/z position" help="This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model"/>
-      <param name="averagine_similarity_scaling" argument="-algorithm:averagine_similarity_scaling" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="Let x denote this scaling factor, and p the averagine similarity paramete" help="For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -&gt; p' = p and x = 1 -&gt; p' = 1. (For knock_out = true, peptide doublets and singlets are detected simultaneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)"/>
-      <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
-      <param name="spectrum_type" argument="-algorithm:spectrum_type" type="select" optional="true" label="Type of MS1 spectra in input mzML file" help="'automatic' determines the spectrum type directly from the input mzML file">
+      <param name="intensity_cutoff" argument="-algorithm:intensity_cutoff" type="float" min="0.0" value="1000.0" label="Lower bound for the intensity of isotopic peaks" help=""/>
+      <param name="peptide_similarity" argument="-algorithm:peptide_similarity" type="float" min="-1.0" max="1.0" value="0.5" label="Two peptides in a multiplet are expected to have the same isotopic pattern" help="This parameter is a lower bound on their similarity"/>
+      <param name="averagine_similarity" argument="-algorithm:averagine_similarity" type="float" min="-1.0" max="1.0" value="0.4" label="The isotopic pattern of a peptide should resemble the averagine model at this m/z position" help="This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model"/>
+      <param name="averagine_similarity_scaling" argument="-algorithm:averagine_similarity_scaling" type="float" min="0.0" max="1.0" value="0.95" label="Let x denote this scaling factor, and p the averagine similarity paramete" help="For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -&gt; p' = p and x = 1 -&gt; p' = 1. (For knock_out = true, peptide doublets and singlets are detected simultaneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)"/>
+      <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
+      <param name="spectrum_type" argument="-algorithm:spectrum_type" type="select" label="Type of MS1 spectra in input mzML file" help="'automatic' determines the spectrum type directly from the input mzML file">
         <option value="profile">profile</option>
         <option value="centroid">centroid</option>
         <option value="automatic" selected="true">automatic</option>
         <expand macro="list_string_san" name="spectrum_type"/>
       </param>
-      <param name="averagine_type" argument="-algorithm:averagine_type" type="select" optional="true" label="The type of averagine to use, currently RNA, DNA or peptide" help="">
+      <param name="averagine_type" argument="-algorithm:averagine_type" type="select" label="The type of averagine to use, currently RNA, DNA or peptide" help="">
         <option value="peptide" selected="true">peptide</option>
         <option value="RNA">RNA</option>
         <option value="DNA">DNA</option>
@@ -108,24 +107,24 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="knock_out" argument="-algorithm:knock_out" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Is it likely that knock-outs are present" help="(Supported for doublex, triplex and quadruplex experiments only.)"/>
     </section>
     <section name="labels" title="mass shifts for all possible labels" help="" expanded="false">
-      <param name="Arg6" argument="-labels:Arg6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help=""/>
-      <param name="Arg10" argument="-labels:Arg10" type="float" optional="true" min="0.0" value="10.0082686" label="Label:13C(6)15N(4)  |  C(-6) 13C(6) N(-4) 15N(4)  |  unimod #267" help=""/>
-      <param name="Lys4" argument="-labels:Lys4" type="float" optional="true" min="0.0" value="4.0251069836" label="Label:2H(4)  |  H(-4) 2H(4)  |  unimod #481" help=""/>
-      <param name="Lys6" argument="-labels:Lys6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help=""/>
-      <param name="Lys8" argument="-labels:Lys8" type="float" optional="true" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2)  |  C(-6) 13C(6) N(-2) 15N(2)  |  unimod #259" help=""/>
-      <param name="Leu3" argument="-labels:Leu3" type="float" optional="true" min="0.0" value="3.01883" label="Label:2H(3)  |  H(-3) 2H(3)  |  unimod #262" help=""/>
-      <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" optional="true" min="0.0" value="28.0313" label="Dimethyl  |  H(4) C(2)  |  unimod #36" help=""/>
-      <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" optional="true" min="0.0" value="32.056407" label="Dimethyl:2H(4)  |  2H(4) C(2)  |  unimod #199" help=""/>
-      <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" optional="true" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2)  |  2H(4) 13C(2)  |  unimod #510" help=""/>
-      <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" optional="true" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2)  |  H(-2) 2H(6) 13C(2)  |  unimod #330" help=""/>
-      <param name="ICPL0" argument="-labels:ICPL0" type="float" optional="true" min="0.0" value="105.021464" label="ICPL  |  H(3) C(6) N O  |  unimod #365" help=""/>
-      <param name="ICPL4" argument="-labels:ICPL4" type="float" optional="true" min="0.0" value="109.046571" label="ICPL:2H(4)  |  H(-1) 2H(4) C(6) N O  |  unimod #687" help=""/>
-      <param name="ICPL6" argument="-labels:ICPL6" type="float" optional="true" min="0.0" value="111.041593" label="ICPL:13C(6)  |  H(3) 13C(6) N O  |  unimod #364" help=""/>
-      <param name="ICPL10" argument="-labels:ICPL10" type="float" optional="true" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4)  |  H(-1) 2H(4) 13C(6) N O  |  unimod #866" help=""/>
+      <param name="Arg6" argument="-labels:Arg6" type="float" min="0.0" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help=""/>
+      <param name="Arg10" argument="-labels:Arg10" type="float" min="0.0" value="10.0082686" label="Label:13C(6)15N(4)  |  C(-6) 13C(6) N(-4) 15N(4)  |  unimod #267" help=""/>
+      <param name="Lys4" argument="-labels:Lys4" type="float" min="0.0" value="4.0251069836" label="Label:2H(4)  |  H(-4) 2H(4)  |  unimod #481" help=""/>
+      <param name="Lys6" argument="-labels:Lys6" type="float" min="0.0" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help=""/>
+      <param name="Lys8" argument="-labels:Lys8" type="float" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2)  |  C(-6) 13C(6) N(-2) 15N(2)  |  unimod #259" help=""/>
+      <param name="Leu3" argument="-labels:Leu3" type="float" min="0.0" value="3.01883" label="Label:2H(3)  |  H(-3) 2H(3)  |  unimod #262" help=""/>
+      <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" min="0.0" value="28.0313" label="Dimethyl  |  H(4) C(2)  |  unimod #36" help=""/>
+      <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" min="0.0" value="32.056407" label="Dimethyl:2H(4)  |  2H(4) C(2)  |  unimod #199" help=""/>
+      <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2)  |  2H(4) 13C(2)  |  unimod #510" help=""/>
+      <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2)  |  H(-2) 2H(6) 13C(2)  |  unimod #330" help=""/>
+      <param name="ICPL0" argument="-labels:ICPL0" type="float" min="0.0" value="105.021464" label="ICPL  |  H(3) C(6) N O  |  unimod #365" help=""/>
+      <param name="ICPL4" argument="-labels:ICPL4" type="float" min="0.0" value="109.046571" label="ICPL:2H(4)  |  H(-1) 2H(4) C(6) N O  |  unimod #687" help=""/>
+      <param name="ICPL6" argument="-labels:ICPL6" type="float" min="0.0" value="111.041593" label="ICPL:13C(6)  |  H(3) 13C(6) N O  |  unimod #364" help=""/>
+      <param name="ICPL10" argument="-labels:ICPL10" type="float" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4)  |  H(-1) 2H(4) 13C(6) N O  |  unimod #866" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -153,15 +152,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FeatureFinderMultiplex_1 -->
+  <tests>
+    <!-- TOPP_FeatureFinderMultiplex_1 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMultiplex_1_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_multiplets" value="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="labels" value="[Dimethyl0][Dimethyl8]"/>
         <param name="charge" value="1:4"/>
@@ -202,6 +202,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureFinderMultiplex_2 -->
     <test expect_num_outputs="3">
@@ -210,8 +213,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMultiplex_2_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_multiplets" value="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="labels" value="[][Lys8,Arg10]"/>
         <param name="charge" value="1:4"/>
@@ -252,6 +255,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureFinderMultiplex_3 -->
     <test expect_num_outputs="3">
@@ -260,8 +266,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMultiplex_3_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_multiplets" value="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="labels" value="[]"/>
         <param name="charge" value="5:15"/>
@@ -302,6 +308,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureFinderMultiplex_4 -->
     <test expect_num_outputs="3">
@@ -310,8 +319,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMultiplex_4_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_multiplets" value="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="labels" value="[]"/>
         <param name="charge" value="5:15"/>
@@ -352,6 +361,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureFinderMultiplex_5 -->
     <test expect_num_outputs="3">
@@ -360,8 +372,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMultiplex_5_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_multiplets" value="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
         <param name="charge" value="1:5"/>
@@ -402,6 +414,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureFinderMultiplex_6 -->
     <test expect_num_outputs="3">
@@ -410,8 +425,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMultiplex_6_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_multiplets" value="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
         <param name="charge" value="1:5"/>
@@ -452,6 +467,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureFinderMultiplex_7 -->
     <test expect_num_outputs="3">
@@ -460,8 +478,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMultiplex_7_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_multiplets" value="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="labels" value="[][Dimethyl4]"/>
         <param name="charge" value="1:4"/>
@@ -502,6 +520,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureFinderMultiplex_8 -->
     <test expect_num_outputs="3">
@@ -510,8 +531,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMultiplex_8_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_multiplets" value="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
         <param name="charge" value="1:7"/>
@@ -552,6 +573,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureFinderMultiplex_9 -->
     <test expect_num_outputs="3">
@@ -560,8 +584,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMultiplex_9_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_multiplets" value="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="labels" value="[0][6.03705]"/>
         <param name="charge" value="2:8"/>
@@ -602,6 +626,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureFinderMultiplex_10 -->
     <test expect_num_outputs="3">
@@ -610,8 +637,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMultiplex_10_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_multiplets" value="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
         <param name="charge" value="1:7"/>
@@ -652,6 +679,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureFinderMultiplex_11 -->
     <test expect_num_outputs="2">
@@ -660,7 +690,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMultiplex_11_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <section name="algorithm">
         <param name="labels" value="[]"/>
         <param name="charge" value="1:4"/>
@@ -701,11 +731,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Determination of peak ratios in LC-MS data
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderMultiplex.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderMultiplex.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FeatureLinkerLabeled.xml b/tools/openms/FeatureLinkerLabeled.xml
index ea0e10d82..8355d8926 100644
--- a/tools/openms/FeatureLinkerLabeled.xml
+++ b/tools/openms/FeatureLinkerLabeled.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Map Alignment]-->
+<!--Proposed Tool Section: [Feature Linking]-->
 <tool id="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Groups corresponding isotope-labeled features in a feature map.</description>
+  <description>Groups corresponding isotope-labeled features in a feature map</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureLinkerLabeled</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,21 +38,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="featurexml" optional="false" label="Input file" help=" select featurexml data sets(s)"/>
+    <param argument="-in" type="data" format="featurexml" label="Input file" help=" select featurexml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <param name="rt_estimate" argument="-algorithm:rt_estimate" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" help="Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance"/>
-      <param name="rt_pair_dist" argument="-algorithm:rt_pair_dist" type="float" optional="true" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help=""/>
-      <param name="rt_dev_low" argument="-algorithm:rt_dev_low" type="float" optional="true" min="0.0" value="15.0" label="maximum allowed deviation below optimal retention time distance" help=""/>
-      <param name="rt_dev_high" argument="-algorithm:rt_dev_high" type="float" optional="true" min="0.0" value="15.0" label="maximum allowed deviation above optimal retention time distance" help=""/>
-      <param name="mz_pair_dists" argument="-algorithm:mz_pair_dists" type="text" optional="true" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3" help="by division through charge) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="rt_pair_dist" argument="-algorithm:rt_pair_dist" type="float" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help=""/>
+      <param name="rt_dev_low" argument="-algorithm:rt_dev_low" type="float" min="0.0" value="15.0" label="maximum allowed deviation below optimal retention time distance" help=""/>
+      <param name="rt_dev_high" argument="-algorithm:rt_dev_high" type="float" min="0.0" value="15.0" label="maximum allowed deviation above optimal retention time distance" help=""/>
+      <param name="mz_pair_dists" argument="-algorithm:mz_pair_dists" type="text" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3" help="by division through charge) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_float_valsan" name="mz_pair_dists"/>
       </param>
-      <param name="mz_dev" argument="-algorithm:mz_dev" type="float" optional="true" min="0.0" value="0.05" label="maximum allowed deviation from optimal m/z distance" help=""/>
+      <param name="mz_dev" argument="-algorithm:mz_dev" type="float" min="0.0" value="0.05" label="maximum allowed deviation from optimal m/z distance" help=""/>
       <param name="mrm" argument="-algorithm:mrm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -67,14 +66,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FeatureLinkerLabeled_1 -->
+  <tests>
+    <!-- TOPP_FeatureLinkerLabeled_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/>
-      <output name="out" file="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="rt_estimate" value="false"/>
         <param name="rt_pair_dist" value="-1.0"/>
@@ -90,6 +90,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureLinkerLabeled_2 -->
     <test expect_num_outputs="2">
@@ -98,7 +101,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureLinkerLabeled_2_input.featureXML"/>
-      <output name="out" file="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="rt_estimate" value="true"/>
         <param name="rt_pair_dist" value="-121.0382"/>
@@ -114,11 +117,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Groups corresponding isotope-labeled features in a feature map.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureLinkerLabeled.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureLinkerLabeled.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FeatureLinkerUnlabeled.xml b/tools/openms/FeatureLinkerUnlabeled.xml
index 8f780f94b..11429e890 100644
--- a/tools/openms/FeatureLinkerUnlabeled.xml
+++ b/tools/openms/FeatureLinkerUnlabeled.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Map Alignment]-->
+<!--Proposed Tool Section: [Feature Linking]-->
 <tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Groups corresponding features from multiple maps.</description>
+  <description>Groups corresponding features from multiple maps</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token>
     <import>macros.xml</import>
@@ -17,14 +16,14 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir out &&
 #if $design:
   mkdir design &&
-  ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
+  cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
 #end if
 
 ## Main program call
@@ -62,38 +61,38 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="consensusxml,featurexml" multiple="true" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,featurexml" multiple="true" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="consensusxml,featurexml" multiple="false" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,featurexml" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
       </when>
     </conditional>
     <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
     <param argument="-keep_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help=""/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="second_nearest_gap" argument="-algorithm:second_nearest_gap" type="float" optional="true" min="1.0" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help=""/>
+      <param name="second_nearest_gap" argument="-algorithm:second_nearest_gap" type="float" min="1.0" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help=""/>
       <param name="use_identifications" argument="-algorithm:use_identifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" help=""/>
       <param name="ignore_charge" argument="-algorithm:ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help=""/>
       <param name="ignore_adduct" argument="-algorithm:ignore_adduct" type="boolean" truevalue="true" falsevalue="false" checked="true" label="true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts" help=""/>
       <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false">
-        <param name="max_difference" argument="-algorithm:distance_RT:max_difference" type="float" optional="true" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/>
-        <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" optional="true" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
-        <param name="weight" argument="-algorithm:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
+        <param name="max_difference" argument="-algorithm:distance_RT:max_difference" type="float" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/>
+        <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
+        <param name="weight" argument="-algorithm:distance_RT:weight" type="float" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
       </section>
       <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
-        <param name="max_difference" argument="-algorithm:distance_MZ:max_difference" type="float" optional="true" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
-        <param name="unit" argument="-algorithm:distance_MZ:unit" type="select" optional="true" label="Unit of the 'max_difference' paramete" help="">
+        <param name="max_difference" argument="-algorithm:distance_MZ:max_difference" type="float" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
+        <param name="unit" argument="-algorithm:distance_MZ:unit" type="select" label="Unit of the 'max_difference' paramete" help="">
           <option value="Da" selected="true">Da</option>
           <option value="ppm">ppm</option>
           <expand macro="list_string_san" name="unit"/>
         </param>
-        <param name="exponent" argument="-algorithm:distance_MZ:exponent" type="float" optional="true" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
-        <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
+        <param name="exponent" argument="-algorithm:distance_MZ:exponent" type="float" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
+        <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
       </section>
       <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
-        <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" optional="true" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
-        <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" optional="true" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
-        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" optional="true" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
+        <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
+        <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
+        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
           <option value="enabled">enabled</option>
           <option value="disabled" selected="true">disabled</option>
           <expand macro="list_string_san" name="log_transform"/>
@@ -102,7 +101,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -116,7 +115,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FeatureLinkerUnlabeled_1 -->
+  <tests>
+    <!-- TOPP_FeatureLinkerUnlabeled_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -125,7 +125,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeled_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeled_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="second_nearest_gap" value="2.0"/>
@@ -155,6 +155,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureLinkerUnlabeled_2 -->
     <test expect_num_outputs="2">
@@ -165,7 +168,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="FeatureLinkerUnlabeled_2_input1.featureXML,FeatureLinkerUnlabeled_2_input2.featureXML,FeatureLinkerUnlabeled_2_input3.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeled_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeled_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="second_nearest_gap" value="2.0"/>
@@ -195,6 +198,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureLinkerUnlabeled_3 -->
     <test expect_num_outputs="2">
@@ -205,7 +211,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="FeatureLinkerUnlabeled_3_input1.featureXML,FeatureLinkerUnlabeled_3_input2.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeled_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeled_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="second_nearest_gap" value="1.5"/>
@@ -235,6 +241,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureLinkerUnlabeled_4 -->
     <test expect_num_outputs="2">
@@ -245,7 +254,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeled_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeled_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="second_nearest_gap" value="2.0"/>
@@ -275,11 +284,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Groups corresponding features from multiple maps.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureLinkerUnlabeled.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureLinkerUnlabeled.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FeatureLinkerUnlabeledKD.xml b/tools/openms/FeatureLinkerUnlabeledKD.xml
index cf0f03346..f54bc5154 100644
--- a/tools/openms/FeatureLinkerUnlabeledKD.xml
+++ b/tools/openms/FeatureLinkerUnlabeledKD.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Map Alignment]-->
+<!--Proposed Tool Section: [Feature Linking]-->
 <tool id="FeatureLinkerUnlabeledKD" name="FeatureLinkerUnlabeledKD" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Groups corresponding features from multiple maps.</description>
+  <description>Groups corresponding features from multiple maps</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureLinkerUnlabeledKD</token>
     <import>macros.xml</import>
@@ -17,14 +16,14 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir out &&
 #if $design:
   mkdir design &&
-  ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
+  cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
 #end if
 
 ## Main program call
@@ -62,39 +61,39 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="consensusxml,featurexml" multiple="true" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,featurexml" multiple="true" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="consensusxml,featurexml" multiple="false" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,featurexml" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
       </when>
     </conditional>
     <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
     <param argument="-keep_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help=""/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="mz_unit" argument="-algorithm:mz_unit" type="select" optional="true" label="Unit of m/z tolerance" help="">
+      <param name="mz_unit" argument="-algorithm:mz_unit" type="select" label="Unit of m/z tolerance" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mz_unit"/>
       </param>
-      <param name="nr_partitions" argument="-algorithm:nr_partitions" type="integer" optional="true" min="1" value="100" label="Number of partitions in m/z space" help=""/>
+      <param name="nr_partitions" argument="-algorithm:nr_partitions" type="integer" min="1" value="100" label="Number of partitions in m/z space" help=""/>
       <section name="warp" title="" help="" expanded="false">
         <param name="enabled" argument="-algorithm:warp:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether or not to internally warp feature RTs using LOWESS transformation before linking (reported RTs in results will always be the original RTs)" help=""/>
-        <param name="rt_tol" argument="-algorithm:warp:rt_tol" type="float" optional="true" min="0.0" value="100.0" label="Width of RT tolerance window (sec)" help=""/>
-        <param name="mz_tol" argument="-algorithm:warp:mz_tol" type="float" optional="true" min="0.0" value="5.0" label="m/z tolerance (in ppm or Da)" help=""/>
-        <param name="max_pairwise_log_fc" argument="-algorithm:warp:max_pairwise_log_fc" type="float" optional="true" value="0.5" label="Maximum absolute log10 fold change between two compatible signals during compatibility graph construction" help="Two signals from different maps will not be connected by an edge in the compatibility graph if absolute log fold change exceeds this limit (they might still end up in the same connected component, however). Note: this does not limit fold changes in the linking stage, only during RT alignment, where we try to find high-quality alignment anchor points. Setting this to a value &lt; 0 disables the FC check"/>
-        <param name="min_rel_cc_size" argument="-algorithm:warp:min_rel_cc_size" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Only connected components containing compatible features from at least max(2, (warp_min_occur * number_of_input_maps)) input maps are considered for computing the warping function" help=""/>
-        <param name="max_nr_conflicts" argument="-algorithm:warp:max_nr_conflicts" type="integer" optional="true" min="-1" value="0" label="Allow up to this many conflicts (features from the same map) per connected component to be used for alignment (-1 means allow any number of conflicts)" help=""/>
+        <param name="rt_tol" argument="-algorithm:warp:rt_tol" type="float" min="0.0" value="100.0" label="Width of RT tolerance window (sec)" help=""/>
+        <param name="mz_tol" argument="-algorithm:warp:mz_tol" type="float" min="0.0" value="5.0" label="m/z tolerance (in ppm or Da)" help=""/>
+        <param name="max_pairwise_log_fc" argument="-algorithm:warp:max_pairwise_log_fc" type="float" value="0.5" label="Maximum absolute log10 fold change between two compatible signals during compatibility graph construction" help="Two signals from different maps will not be connected by an edge in the compatibility graph if absolute log fold change exceeds this limit (they might still end up in the same connected component, however). Note: this does not limit fold changes in the linking stage, only during RT alignment, where we try to find high-quality alignment anchor points. Setting this to a value &lt; 0 disables the FC check"/>
+        <param name="min_rel_cc_size" argument="-algorithm:warp:min_rel_cc_size" type="float" min="0.0" max="1.0" value="0.5" label="Only connected components containing compatible features from at least max(2, (warp_min_occur * number_of_input_maps)) input maps are considered for computing the warping function" help=""/>
+        <param name="max_nr_conflicts" argument="-algorithm:warp:max_nr_conflicts" type="integer" min="-1" value="0" label="Allow up to this many conflicts (features from the same map) per connected component to be used for alignment (-1 means allow any number of conflicts)" help=""/>
       </section>
       <section name="link" title="" help="" expanded="false">
-        <param name="rt_tol" argument="-algorithm:link:rt_tol" type="float" optional="true" min="0.0" value="30.0" label="Width of RT tolerance window (sec)" help=""/>
-        <param name="mz_tol" argument="-algorithm:link:mz_tol" type="float" optional="true" min="0.0" value="10.0" label="m/z tolerance (in ppm or Da)" help=""/>
-        <param name="charge_merging" argument="-algorithm:link:charge_merging" type="select" optional="true" label="whether to disallow charge mismatches (Identical), allow to link charge zero" help="(i.e., unknown charge state) with every charge state, or disregard charges (Any)">
+        <param name="rt_tol" argument="-algorithm:link:rt_tol" type="float" min="0.0" value="30.0" label="Width of RT tolerance window (sec)" help=""/>
+        <param name="mz_tol" argument="-algorithm:link:mz_tol" type="float" min="0.0" value="10.0" label="m/z tolerance (in ppm or Da)" help=""/>
+        <param name="charge_merging" argument="-algorithm:link:charge_merging" type="select" label="whether to disallow charge mismatches (Identical), allow to link charge zero" help="(i.e., unknown charge state) with every charge state, or disregard charges (Any)">
           <option value="Identical">Identical</option>
           <option value="With_charge_zero" selected="true">With_charge_zero</option>
           <option value="Any">Any</option>
           <expand macro="list_string_san" name="charge_merging"/>
         </param>
-        <param name="adduct_merging" argument="-algorithm:link:adduct_merging" type="select" optional="true" label="whether to only allow the same adduct for linking (Identical), also allow linking features with adduct-free ones, or disregard adducts (Any)" help="">
+        <param name="adduct_merging" argument="-algorithm:link:adduct_merging" type="select" label="whether to only allow the same adduct for linking (Identical), also allow linking features with adduct-free ones, or disregard adducts (Any)" help="">
           <option value="Identical">Identical</option>
           <option value="With_unknown_adducts">With_unknown_adducts</option>
           <option value="Any" selected="true">Any</option>
@@ -102,33 +101,33 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         </param>
       </section>
       <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false">
-        <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" optional="true" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
-        <param name="weight" argument="-algorithm:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
+        <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
+        <param name="weight" argument="-algorithm:distance_RT:weight" type="float" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
       </section>
       <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
-        <param name="exponent" argument="-algorithm:distance_MZ:exponent" type="float" optional="true" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
-        <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
+        <param name="exponent" argument="-algorithm:distance_MZ:exponent" type="float" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
+        <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
       </section>
       <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
-        <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" optional="true" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
-        <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" optional="true" min="0.0" value="1.0" label="Final intensity distances are weighted by this facto" help=""/>
-        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" optional="true" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
+        <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
+        <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" min="0.0" value="1.0" label="Final intensity distances are weighted by this facto" help=""/>
+        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
           <option value="enabled" selected="true">enabled</option>
           <option value="disabled">disabled</option>
           <expand macro="list_string_san" name="log_transform"/>
         </param>
       </section>
       <section name="LOWESS" title="LOWESS parameters for internal RT transformations (only relevant if 'warp:enabled' is set to 'true')" help="" expanded="false">
-        <param name="span" argument="-algorithm:LOWESS:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
-        <param name="num_iterations" argument="-algorithm:LOWESS:num_iterations" type="integer" optional="true" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
-        <param name="delta" argument="-algorithm:LOWESS:delta" type="float" optional="true" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
-        <param name="interpolation_type" argument="-algorithm:LOWESS:interpolation_type" type="select" optional="true" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
+        <param name="span" argument="-algorithm:LOWESS:span" type="float" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
+        <param name="num_iterations" argument="-algorithm:LOWESS:num_iterations" type="integer" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
+        <param name="delta" argument="-algorithm:LOWESS:delta" type="float" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
+        <param name="interpolation_type" argument="-algorithm:LOWESS:interpolation_type" type="select" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
           <option value="linear">linear</option>
           <option value="cspline" selected="true">cspline</option>
           <option value="akima">akima</option>
           <expand macro="list_string_san" name="interpolation_type"/>
         </param>
-        <param name="extrapolation_type" argument="-algorithm:LOWESS:extrapolation_type" type="select" optional="true" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
+        <param name="extrapolation_type" argument="-algorithm:LOWESS:extrapolation_type" type="select" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
           <option value="two-point-linear">two-point-linear</option>
           <option value="four-point-linear" selected="true">four-point-linear</option>
           <option value="global-linear">global-linear</option>
@@ -138,7 +137,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -152,7 +151,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FeatureLinkerUnlabeledKD_1 -->
+  <tests>
+    <!-- TOPP_FeatureLinkerUnlabeledKD_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -161,7 +161,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledKD_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledKD_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="mz_unit" value="Da"/>
@@ -207,6 +207,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureLinkerUnlabeledKD_2 -->
     <test expect_num_outputs="2">
@@ -215,9 +218,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="test" value="true"/>
       </section>
       <conditional name="in_cond">
-        <param name="in" value="FeatureLinkerUnlabeledKD_1_output.consensusXML,FeatureLinkerUnlabeledKD_1_output_2.consensusXML"/>
+        <param name="in" value="FeatureLinkerUnlabeledKD_1_output_0.consensusXML,FeatureLinkerUnlabeledKD_1_output_1.consensusXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledKD_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledKD_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="true"/>
       <section name="algorithm">
         <param name="mz_unit" value="Da"/>
@@ -263,6 +266,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureLinkerUnlabeledKD_3 -->
     <test expect_num_outputs="2">
@@ -273,7 +279,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledKD_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledKD_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="mz_unit" value="Da"/>
@@ -319,6 +325,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureLinkerUnlabeledKD_4 -->
     <test expect_num_outputs="2">
@@ -327,9 +336,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="test" value="true"/>
       </section>
       <conditional name="in_cond">
-        <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
+        <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1_0.featureXML,FeatureLinkerUnlabeledKD_dc_input2_0.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_1.featureXML,FeatureLinkerUnlabeledKD_dc_input2_1.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledKD_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledKD_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="mz_unit" value="ppm"/>
@@ -375,6 +384,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureLinkerUnlabeledKD_5 -->
     <test expect_num_outputs="2">
@@ -383,9 +395,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="test" value="true"/>
       </section>
       <conditional name="in_cond">
-        <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
+        <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1_0.featureXML,FeatureLinkerUnlabeledKD_dc_input2_0.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_1.featureXML,FeatureLinkerUnlabeledKD_dc_input2_1.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledKD_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledKD_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="mz_unit" value="ppm"/>
@@ -431,6 +443,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureLinkerUnlabeledKD_6 -->
     <test expect_num_outputs="2">
@@ -439,9 +454,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="test" value="true"/>
       </section>
       <conditional name="in_cond">
-        <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
+        <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1_0.featureXML,FeatureLinkerUnlabeledKD_dc_input2_0.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_1.featureXML,FeatureLinkerUnlabeledKD_dc_input2_1.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledKD_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledKD_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="mz_unit" value="ppm"/>
@@ -487,6 +502,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureLinkerUnlabeledKD_7 -->
     <test expect_num_outputs="2">
@@ -495,9 +513,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="test" value="true"/>
       </section>
       <conditional name="in_cond">
-        <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
+        <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1_0.featureXML,FeatureLinkerUnlabeledKD_dc_input2_0.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_1.featureXML,FeatureLinkerUnlabeledKD_dc_input2_1.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledKD_7_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledKD_7_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="mz_unit" value="ppm"/>
@@ -543,11 +561,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Groups corresponding features from multiple maps.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureLinkerUnlabeledKD.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureLinkerUnlabeledKD.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FeatureLinkerUnlabeledQT.xml b/tools/openms/FeatureLinkerUnlabeledQT.xml
index 0126de387..19ce0c7e2 100644
--- a/tools/openms/FeatureLinkerUnlabeledQT.xml
+++ b/tools/openms/FeatureLinkerUnlabeledQT.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Map Alignment]-->
+<!--Proposed Tool Section: [Feature Linking]-->
 <tool id="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Groups corresponding features from multiple maps.</description>
+  <description>Groups corresponding features from multiple maps</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureLinkerUnlabeledQT</token>
     <import>macros.xml</import>
@@ -17,14 +16,14 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir out &&
 #if $design:
   mkdir design &&
-  ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
+  cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
 #end if
 
 ## Main program call
@@ -62,41 +61,41 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="consensusxml,featurexml" multiple="true" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,featurexml" multiple="true" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="consensusxml,featurexml" multiple="false" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,featurexml" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
       </when>
     </conditional>
     <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
     <param argument="-keep_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help=""/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <param name="use_identifications" argument="-algorithm:use_identifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)" help=""/>
-      <param name="nr_partitions" argument="-algorithm:nr_partitions" type="integer" optional="true" min="1" value="100" label="How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution)" help=""/>
-      <param name="min_nr_diffs_per_bin" argument="-algorithm:min_nr_diffs_per_bin" type="integer" optional="true" min="5" value="50" label="If IDs are used: How many differences from matching IDs should be used to calculate a linking tolerance for unIDed features in an RT region" help="RT regions will be extended until that number is reached"/>
-      <param name="min_IDscore_forTolCalc" argument="-algorithm:min_IDscore_forTolCalc" type="float" optional="true" value="1.0" label="If IDs are used: What is the minimum score of an ID to assume a reliable match for tolerance calculation" help="Check your current score type!"/>
-      <param name="noID_penalty" argument="-algorithm:noID_penalty" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="If IDs are used: For the normalized distances, how high should the penalty for missing IDs be" help="0 = no bias, 1 = IDs inside the max tolerances always preferred (even if much further away)"/>
+      <param name="nr_partitions" argument="-algorithm:nr_partitions" type="integer" min="1" value="100" label="How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution)" help=""/>
+      <param name="min_nr_diffs_per_bin" argument="-algorithm:min_nr_diffs_per_bin" type="integer" min="5" value="50" label="If IDs are used: How many differences from matching IDs should be used to calculate a linking tolerance for unIDed features in an RT region" help="RT regions will be extended until that number is reached"/>
+      <param name="min_IDscore_forTolCalc" argument="-algorithm:min_IDscore_forTolCalc" type="float" value="1.0" label="If IDs are used: What is the minimum score of an ID to assume a reliable match for tolerance calculation" help="Check your current score type!"/>
+      <param name="noID_penalty" argument="-algorithm:noID_penalty" type="float" min="0.0" max="1.0" value="0.0" label="If IDs are used: For the normalized distances, how high should the penalty for missing IDs be" help="0 = no bias, 1 = IDs inside the max tolerances always preferred (even if much further away)"/>
       <param name="ignore_charge" argument="-algorithm:ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help=""/>
       <param name="ignore_adduct" argument="-algorithm:ignore_adduct" type="boolean" truevalue="true" falsevalue="false" checked="true" label="true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts" help=""/>
       <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false">
-        <param name="max_difference" argument="-algorithm:distance_RT:max_difference" type="float" optional="true" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/>
-        <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" optional="true" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
-        <param name="weight" argument="-algorithm:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
+        <param name="max_difference" argument="-algorithm:distance_RT:max_difference" type="float" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/>
+        <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
+        <param name="weight" argument="-algorithm:distance_RT:weight" type="float" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
       </section>
       <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
-        <param name="max_difference" argument="-algorithm:distance_MZ:max_difference" type="float" optional="true" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
-        <param name="unit" argument="-algorithm:distance_MZ:unit" type="select" optional="true" label="Unit of the 'max_difference' paramete" help="">
+        <param name="max_difference" argument="-algorithm:distance_MZ:max_difference" type="float" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
+        <param name="unit" argument="-algorithm:distance_MZ:unit" type="select" label="Unit of the 'max_difference' paramete" help="">
           <option value="Da" selected="true">Da</option>
           <option value="ppm">ppm</option>
           <expand macro="list_string_san" name="unit"/>
         </param>
-        <param name="exponent" argument="-algorithm:distance_MZ:exponent" type="float" optional="true" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
-        <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
+        <param name="exponent" argument="-algorithm:distance_MZ:exponent" type="float" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
+        <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
       </section>
       <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
-        <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" optional="true" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
-        <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" optional="true" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
-        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" optional="true" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
+        <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
+        <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
+        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
           <option value="enabled">enabled</option>
           <option value="disabled" selected="true">disabled</option>
           <expand macro="list_string_san" name="log_transform"/>
@@ -105,7 +104,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -119,7 +118,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FeatureLinkerUnlabeledQT_1 -->
+  <tests>
+    <!-- TOPP_FeatureLinkerUnlabeledQT_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -128,7 +128,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="use_identifications" value="false"/>
@@ -161,6 +161,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureLinkerUnlabeledQT_2 -->
     <test expect_num_outputs="2">
@@ -169,9 +172,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="test" value="true"/>
       </section>
       <conditional name="in_cond">
-        <param name="in" value="FeatureLinkerUnlabeledQT_1_output.consensusXML,FeatureLinkerUnlabeledQT_1_output_2.consensusXML"/>
+        <param name="in" value="FeatureLinkerUnlabeledQT_1_output_0.consensusXML,FeatureLinkerUnlabeledQT_1_output_1.consensusXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="true"/>
       <section name="algorithm">
         <param name="use_identifications" value="false"/>
@@ -204,6 +207,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureLinkerUnlabeledQT_3 -->
     <test expect_num_outputs="2">
@@ -214,7 +220,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="use_identifications" value="false"/>
@@ -247,6 +253,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureLinkerUnlabeledQT_4 -->
     <test expect_num_outputs="2">
@@ -257,7 +266,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="use_identifications" value="true"/>
@@ -290,6 +299,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureLinkerUnlabeledQT_5 -->
     <test expect_num_outputs="2">
@@ -300,7 +312,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="use_identifications" value="false"/>
@@ -333,6 +345,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FeatureLinkerUnlabeledQT_6 -->
     <test expect_num_outputs="2">
@@ -343,7 +358,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
       </conditional>
-      <output name="out" file="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="keep_subelements" value="false"/>
       <section name="algorithm">
         <param name="use_identifications" value="true"/>
@@ -376,11 +391,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Groups corresponding features from multiple maps.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureLinkerUnlabeledQT.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureLinkerUnlabeledQT.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FidoAdapter.xml b/tools/openms/FidoAdapter.xml
deleted file mode 100644
index 008db8972..000000000
--- a/tools/openms/FidoAdapter.xml
+++ /dev/null
@@ -1,259 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [ID Processing]-->
-<tool id="FidoAdapter" name="FidoAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Runs the protein inference engine Fido.</description>
-  <macros>
-    <token name="@EXECUTABLE@">FidoAdapter</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-mkdir out &&
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in
-'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
--out
-'out/output.${gxy2omsext("idxml")}'
-
-## Postprocessing
-&& mv 'out/output.${gxy2omsext("idxml")}' '$out'
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"fido_executable": "Fido", "fidocp_executable": "FidoChooseParameters", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
-  </configfiles>
-  <inputs>
-    <param argument="-in" type="data" format="idxml" optional="false" label="Input: identification results" help=" select idxml data sets(s)"/>
-    <param argument="-separate_runs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Process multiple protein identification runs in the input separately, don't merge them" help="Merging results in loss of descriptive information of the single protein identification runs"/>
-    <param argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Post-process Fido output with greedy resolution of shared peptides based on the protein probabilities" help="Also adds the resolved ambiguity groups to output"/>
-    <param argument="-no_cleanup" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Omit clean-up of peptide sequences (removal of non-letter characters, replacement of I with L)" help=""/>
-    <param argument="-all_PSMs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Consider all PSMs of each peptide, instead of only the best one" help=""/>
-    <param argument="-group_level" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform inference on protein group level (instead of individual protein level)" help="This will lead to higher probabilities for (bigger) protein groups"/>
-    <param argument="-log2_states" type="integer" optional="true" min="0" value="0" label="Binary logarithm of the max" help="number of connected states in a subgraph. For a value N, subgraphs that are bigger than 2^N will be split up, sacrificing accuracy for runtime. '0' uses the default (18)"/>
-    <section name="prob" title="Probability values for running Fido directly" help="i.e. without parameter estimation (in which case other settings, except 'log2_states', are ignored)" expanded="false">
-      <param name="protein" argument="-prob:protein" type="float" optional="true" min="0.0" value="0.0" label="Protein prior probability ('gamma' parameter)" help=""/>
-      <param name="peptide" argument="-prob:peptide" type="float" optional="true" min="0.0" value="0.0" label="Peptide emission probability ('alpha' parameter)" help=""/>
-      <param name="spurious" argument="-prob:spurious" type="float" optional="true" min="0.0" value="0.0" label="Spurious peptide identification probability ('beta' parameter)" help=""/>
-    </section>
-    <expand macro="adv_opts_macro">
-      <param argument="-keep_zero_group" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep the group of proteins with estimated probability of zero, which is otherwise removed (it may be very large)" help=""/>
-      <param argument="-accuracy" type="select" optional="true" label="Accuracy level of start parameters" help="There is a trade-off between accuracy and runtime. Empty uses the default ('best')">
-        <option value=""></option>
-        <option value="best">best</option>
-        <option value="relaxed">relaxed</option>
-        <option value="sloppy">sloppy</option>
-        <expand macro="list_string_san" name="accuracy"/>
-      </param>
-      <param argument="-log2_states_precalc" type="integer" optional="true" min="0" value="0" label="Like 'log2_states', but allows to set a separate limit for the precalculation" help=""/>
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><!-- TOPP_FidoAdapter_1 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy"/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="FidoAdapter_1_input.idXML"/>
-      <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <param name="separate_runs" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="false"/>
-      <param name="group_level" value="false"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.0"/>
-        <param name="peptide" value="0.0"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_FidoAdapter_2 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy"/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="FidoAdapter_1_input.idXML"/>
-      <output name="out" file="FidoAdapter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <param name="separate_runs" value="true"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="false"/>
-      <param name="group_level" value="false"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.0"/>
-        <param name="peptide" value="0.0"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_FidoAdapter_3 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy"/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="FidoAdapter_1_input.idXML"/>
-      <output name="out" file="FidoAdapter_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <param name="separate_runs" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="true"/>
-      <param name="group_level" value="true"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.0"/>
-        <param name="peptide" value="0.0"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_FidoAdapter_4 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy"/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="FidoAdapter_4_input.idXML"/>
-      <output name="out" file="FidoAdapter_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <param name="separate_runs" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="false"/>
-      <param name="group_level" value="false"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.0"/>
-        <param name="peptide" value="0.0"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_FidoAdapter_5 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy"/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="FidoAdapter_5_input.idXML"/>
-      <output name="out" file="FidoAdapter_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <param name="separate_runs" value="false"/>
-      <param name="greedy_group_resolution" value="true"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="false"/>
-      <param name="group_level" value="false"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.0"/>
-        <param name="peptide" value="0.0"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_FidoAdapter_6 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy"/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="FidoAdapter_1_input.idXML"/>
-      <output name="out" file="FidoAdapter_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <param name="separate_runs" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="false"/>
-      <param name="group_level" value="false"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.9"/>
-        <param name="peptide" value="0.01"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
-  <help><![CDATA[Runs the protein inference engine Fido.
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FidoAdapter.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/FileConverter.xml b/tools/openms/FileConverter.xml
index 80c65f817..f8211cd47 100644
--- a/tools/openms/FileConverter.xml
+++ b/tools/openms/FileConverter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [File Handling]-->
+<!--Proposed Tool Section: [File Converter]-->
 <tool id="FileConverter" name="FileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Converts between different MS file formats.</description>
+  <description>Converts between different MS file formats</description>
   <macros>
     <token name="@EXECUTABLE@">FileConverter</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,8 +38,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"ThermoRaw_executable": "ThermoRawFileParser.exe", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,sqlite,tabular,thermo.raw" optional="false" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,sqlite,tabular,thermo.raw data sets(s)"/>
-    <param argument="-out_type" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense">
+    <param argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,sqlite,tabular,thermo.raw" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,sqlite,tabular,thermo.raw data sets(s)"/>
+    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense">
       <option value="consensusXML">consensusxml</option>
       <option value="csv">csv</option>
       <option value="dta2d">dta2d</option>
@@ -51,10 +50,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="mzML">mzml</option>
       <option value="mzXML">mzxml</option>
       <option value="oms">sqlite (oms)</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
     <expand macro="adv_opts_macro">
-      <param argument="-UID_postprocessing" type="select" optional="true" label="unique ID post-processing for output data" help="'none' keeps current IDs even if invalid.. 'ensure' keeps current IDs but reassigns invalid ones.. 'reassign' assigns new unique IDs">
+      <param argument="-UID_postprocessing" type="select" label="unique ID post-processing for output data" help="'none' keeps current IDs even if invalid.. 'ensure' keeps current IDs but reassigns invalid ones.. 'reassign' assigns new unique IDs">
         <option value="none">none</option>
         <option value="ensure" selected="true">ensure</option>
         <option value="reassign">reassign</option>
@@ -65,7 +65,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param argument="-force_MaxQuant_compatibility" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to 'Thermo Scientific'" help=""/>
       <param argument="-force_TPP_compatibility" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzML output only] Make sure that TPP parsers can read the mzML and the precursor ion m/z in the file (otherwise it will be set to zero by the TPP)" help=""/>
       <param argument="-convert_to_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzML output only] Assumes that the provided spectra represent data in SRM mode or targeted MS1 mode and converts them to chromatogram data" help=""/>
-      <param argument="-change_im_format" type="select" optional="true" label="[mzML output only] How to store ion mobility scans (none: no change in format; multiple_spectra: store each IM frame as multiple scans (one per drift time value); concatenated: store whole frame as single scan with IM values in a FloatDataArray" help="">
+      <param argument="-change_im_format" type="select" label="[mzML output only] How to store ion mobility scans (none: no change in format; multiple_spectra: store each IM frame as multiple scans (one per drift time value); concatenated: store whole frame as single scan with IM values in a FloatDataArray" help="">
         <option value="none" selected="true">none</option>
         <option value="concatenated">concatenated</option>
         <option value="multiple_spectra">multiple_spectra</option>
@@ -74,11 +74,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </param>
       <param argument="-write_scan_index" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Append an index when writing mzML or mzXML files" help="Some external tools might rely on it"/>
       <param argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use numpress compression to achieve optimally small file size using linear compression for m/z domain and slof for intensity and float data arrays (attention: may cause small loss of precision; only for mzML data)" help=""/>
-      <param argument="-lossy_mass_accuracy" type="float" optional="true" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
+      <param argument="-lossy_mass_accuracy" type="float" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
       <param argument="-process_lowmemory" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML)" help="Note: this flag will prevent conversion from spectra to chromatograms"/>
       <param argument="-no_peak_picking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables vendor peak picking for raw files" help=""/>
+      <param argument="-no_zlib_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables zlib compression for raw file conversion" help="Enables compatibility with some tools that do not support compressed input files, e.g. X!Tandem"/>
+      <param argument="-include_noise" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include noise data in mzML output" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -104,7 +106,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FileConverter_1 -->
+  <tests>
+    <!-- TOPP_FileConverter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="UID_postprocessing" value="ensure"/>
@@ -119,11 +122,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_1_input.mzData"/>
-      <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileConverter_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -131,6 +136,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_2 -->
     <test expect_num_outputs="2">
@@ -147,11 +155,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_2_input.someInputDTA2D"/>
-      <output name="out" file="FileConverter_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileConverter_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -159,6 +169,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_3 -->
     <test expect_num_outputs="2">
@@ -175,11 +188,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_3_input.featureXML"/>
-      <output name="out" file="FileConverter_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileConverter_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -187,6 +202,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_4 -->
     <test expect_num_outputs="2">
@@ -203,11 +221,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_4_input.mzXML"/>
-      <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileConverter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -215,6 +235,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_5 -->
     <test expect_num_outputs="2">
@@ -231,11 +254,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_5_input.mzML"/>
-      <output name="out" file="FileConverter_5_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
+      <output name="out" value="FileConverter_5_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
       <param name="out_type" value="mzXML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -243,6 +268,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_6 -->
     <test expect_num_outputs="2">
@@ -259,11 +287,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_6_input.mzML"/>
-      <output name="out" file="FileConverter_6_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
+      <output name="out" value="FileConverter_6_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
       <param name="out_type" value="mzXML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -271,6 +301,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_7 -->
     <test expect_num_outputs="2">
@@ -287,11 +320,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_7_input.consensusXML"/>
-      <output name="out" file="FileConverter_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileConverter_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -299,6 +334,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_8 -->
     <test expect_num_outputs="2">
@@ -315,11 +353,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_8_input.mzML"/>
-      <output name="out" file="FileConverter_8_output.mzData" compare="sim_size" delta_frac="0.7" ftype="mzdata"/>
+      <output name="out" value="FileConverter_8_output.mzData" compare="sim_size" delta_frac="0.7" ftype="mzdata"/>
       <param name="out_type" value="mzData"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -327,6 +367,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_9 -->
     <test expect_num_outputs="2">
@@ -343,11 +386,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_9_input.consensusXML"/>
-      <output name="out" file="FileConverter_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileConverter_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -355,6 +400,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_10 -->
     <test expect_num_outputs="2">
@@ -371,11 +419,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
-      <output name="out" file="FileConverter_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileConverter_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -383,6 +433,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_11 -->
     <test expect_num_outputs="2">
@@ -399,11 +452,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_11_input.peplist"/>
-      <output name="out" file="FileConverter_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileConverter_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -411,6 +466,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_12 -->
     <test expect_num_outputs="2">
@@ -427,11 +485,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_12_input.peptides.tsv" ftype="tabular"/>
-      <output name="out" file="FileConverter_12_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileConverter_12_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -439,6 +499,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_13 -->
     <test expect_num_outputs="2">
@@ -455,11 +518,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_13_input.peptides.kroenik"/>
-      <output name="out" file="FileConverter_13_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileConverter_13_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -467,6 +532,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_14 -->
     <test expect_num_outputs="2">
@@ -483,11 +551,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_9_output.featureXML"/>
-      <output name="out" file="FileConverter_14_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileConverter_14_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -495,6 +565,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_15 -->
     <test expect_num_outputs="2">
@@ -511,11 +584,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
-      <output name="out" file="FileConverter_15_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileConverter_15_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -523,6 +598,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_16 -->
     <test expect_num_outputs="2">
@@ -539,11 +617,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_16_input.edta" ftype="edta"/>
-      <output name="out" file="FileConverter_16_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileConverter_16_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -551,6 +631,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_17 -->
     <test expect_num_outputs="2">
@@ -567,11 +650,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_17_input.consensusXML"/>
-      <output name="out" file="FileConverter_17.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out" value="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="out_type" value="csv"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -579,6 +664,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_18 -->
     <test expect_num_outputs="2">
@@ -595,11 +683,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_17_input.consensusXML"/>
-      <output name="out" file="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out" value="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="out_type" value="csv"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -607,6 +697,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_19 -->
     <test expect_num_outputs="2">
@@ -623,11 +716,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="true"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileConverter_19_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileConverter_19_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -635,6 +730,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_20 -->
     <test expect_num_outputs="2">
@@ -651,11 +749,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_20_input.featureXML"/>
-      <output name="out" file="FileConverter_20_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileConverter_20_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -663,6 +763,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_21 -->
     <test expect_num_outputs="2">
@@ -679,11 +782,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="true"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_4_input.mzXML"/>
-      <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileConverter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -691,6 +796,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_23 -->
     <test expect_num_outputs="2">
@@ -707,11 +815,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_23_input.mzML"/>
-      <output name="out" file="FileConverter_23_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileConverter_23_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -719,6 +829,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_24 -->
     <test expect_num_outputs="2">
@@ -735,11 +848,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="0.0001"/>
         <param name="process_lowmemory" value="true"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileConverter_24_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileConverter_24_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -747,6 +862,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_25 -->
     <test expect_num_outputs="2">
@@ -763,11 +881,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="true"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileConverter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileConverter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -775,6 +895,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_26 -->
     <test expect_num_outputs="2">
@@ -791,11 +914,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileConverter_26_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
+      <output name="out" value="FileConverter_26_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
       <param name="out_type" value="mzXML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -803,6 +928,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_26-2 -->
     <test expect_num_outputs="2">
@@ -819,11 +947,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_26_output.mzXML"/>
-      <output name="out" file="FileConverter_26-2_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
+      <output name="out" value="FileConverter_26-2_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
       <param name="out_type" value="mzXML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -831,6 +961,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_27 -->
     <test expect_num_outputs="2">
@@ -847,11 +980,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_27_input.mzML"/>
-      <output name="out" file="FileConverter_27_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileConverter_27_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -859,6 +994,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_28 -->
     <test expect_num_outputs="2">
@@ -875,11 +1013,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_28_input.mzML"/>
-      <output name="out" file="FileConverter_28_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileConverter_28_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -887,6 +1027,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_29 -->
     <test expect_num_outputs="2">
@@ -903,11 +1046,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="1e-05"/>
         <param name="process_lowmemory" value="true"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
-      <output name="out" file="FileConverter_29_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileConverter_29_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -915,6 +1060,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_29_back -->
     <test expect_num_outputs="2">
@@ -931,11 +1079,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_29_output.mzML"/>
-      <output name="out" file="FileConverter_29.back.tmp" compare="sim_size" delta_frac="0.7"/>
+      <output name="out" value="FileConverter_29.back.tmp" compare="sim_size" delta_frac="0.7"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -943,6 +1093,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_30 -->
     <test expect_num_outputs="2">
@@ -959,11 +1112,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_30_input.mzML"/>
-      <output name="out" file="FileConverter_30_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileConverter_30_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -971,6 +1126,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_31 -->
     <test expect_num_outputs="2">
@@ -987,11 +1145,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_30_output.mzML"/>
-      <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileConverter_31_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -999,6 +1159,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileConverter_32 -->
     <test expect_num_outputs="2">
@@ -1015,11 +1178,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileConverter_32_input.mzML"/>
-      <output name="out" file="FileConverter_32_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileConverter_32_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -1027,6 +1192,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_32_File_Conversion -->
     <test expect_num_outputs="2">
@@ -1043,11 +1211,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_32_output.tmp"/>
-      <output name="out" file="IDFileConverter_32_output.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
+      <output name="out" value="IDFileConverter_32_output.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
       <param name="out_type" value="mgf"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -1055,6 +1225,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_33_File_Conversion -->
     <test expect_num_outputs="2">
@@ -1071,11 +1244,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_33_output.tmp"/>
-      <output name="out" file="IDFileConverter_33_output.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
+      <output name="out" value="IDFileConverter_33_output.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
       <param name="out_type" value="mgf"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -1083,6 +1258,42 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_CometAdapter_2_prepare -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="UID_postprocessing" value="ensure"/>
+        <param name="TIC_DTA2D" value="false"/>
+        <param name="MGF_compact" value="false"/>
+        <param name="force_MaxQuant_compatibility" value="false"/>
+        <param name="force_TPP_compatibility" value="true"/>
+        <param name="convert_to_chromatograms" value="false"/>
+        <param name="change_im_format" value="none"/>
+        <param name="write_scan_index" value="true"/>
+        <param name="lossy_compression" value="false"/>
+        <param name="lossy_mass_accuracy" value="-1.0"/>
+        <param name="process_lowmemory" value="false"/>
+        <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="CometAdapter_2_in.mzML"/>
+      <output name="out" value="CometAdapter_2_prepared.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <param name="out_type" value="mzML"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_THERMORAWFILEPARSER_1 -->
     <test expect_num_outputs="2">
@@ -1099,11 +1310,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="lossy_mass_accuracy" value="-1.0"/>
         <param name="process_lowmemory" value="false"/>
         <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ginkgotoxin-ms-switching.raw"/>
-      <output name="out" file="ginkgotoxin-ms-switching_out_tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="ginkgotoxin-ms-switching_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -1111,16 +1324,52 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_SpectrastSearchAdapter_0_prepare -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="UID_postprocessing" value="ensure"/>
+        <param name="TIC_DTA2D" value="false"/>
+        <param name="MGF_compact" value="false"/>
+        <param name="force_MaxQuant_compatibility" value="false"/>
+        <param name="force_TPP_compatibility" value="true"/>
+        <param name="convert_to_chromatograms" value="false"/>
+        <param name="change_im_format" value="none"/>
+        <param name="write_scan_index" value="true"/>
+        <param name="lossy_compression" value="false"/>
+        <param name="lossy_mass_accuracy" value="-1.0"/>
+        <param name="process_lowmemory" value="false"/>
+        <param name="no_peak_picking" value="false"/>
+        <param name="no_zlib_compression" value="false"/>
+        <param name="include_noise" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="spectra_spectrast.mzXML"/>
+      <output name="out" value="SpectrastAdapter_1_hack.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <param name="out_type" value="mzML"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <test expect_num_outputs="1">
+      <param name="in" value="FileConverter_1_input.mzData"/>
+      <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
+      <param name="out_type" value="mzML"/>
     </test>
-  <test expect_num_outputs="1">
-  <param name="in" value="FileConverter_1_input.mzData"/>
-  <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-  <param name="out_type" value="mzML"/>
-</test>
-</tests>
+  </tests>
   <help><![CDATA[Converts between different MS file formats.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FileConverter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FileConverter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FileFilter.xml b/tools/openms/FileFilter.xml
index 1bcbd2ac9..21b6fa5b1 100644
--- a/tools/openms/FileFilter.xml
+++ b/tools/openms/FileFilter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [File Handling]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="FileFilter" name="FileFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description>
+  <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files</description>
   <macros>
     <token name="@EXECUTABLE@">FileFilter</token>
     <import>macros.xml</import>
@@ -15,19 +14,19 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if $spectra.blackorwhitelist.file:
   mkdir spectra.blackorwhitelist.file &&
-  ln -s '$spectra.blackorwhitelist.file' 'spectra.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $spectra.blackorwhitelist.file.element_identifier)}.$gxy2omsext($spectra.blackorwhitelist.file.ext)' &&
+  cp '$spectra.blackorwhitelist.file' 'spectra.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $spectra.blackorwhitelist.file.element_identifier)}.$gxy2omsext($spectra.blackorwhitelist.file.ext)' &&
 #end if
 #if $consensus.blackorwhitelist.file:
   mkdir consensus.blackorwhitelist.file &&
-  ln -s '$consensus.blackorwhitelist.file' 'consensus.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $consensus.blackorwhitelist.file.element_identifier)}.$gxy2omsext($consensus.blackorwhitelist.file.ext)' &&
+  cp '$consensus.blackorwhitelist.file' 'consensus.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $consensus.blackorwhitelist.file.element_identifier)}.$gxy2omsext($consensus.blackorwhitelist.file.ext)' &&
 #end if
 #if $id.blacklist:
   mkdir id.blacklist &&
-  ln -s '$id.blacklist' 'id.blacklist/${re.sub("[^\w\-_]", "_", $id.blacklist.element_identifier)}.$gxy2omsext($id.blacklist.ext)' &&
+  cp '$id.blacklist' 'id.blacklist/${re.sub("[^\w\-_]", "_", $id.blacklist.element_identifier)}.$gxy2omsext($id.blacklist.ext)' &&
 #end if
 
 ## Main program call
@@ -63,47 +62,48 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml,featurexml,mzml" optional="false" label="Input file" help=" select consensusxml,featurexml,mzml data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
+    <param argument="-in" type="data" format="consensusxml,featurexml,mzml" label="Input file" help=" select consensusxml,featurexml,mzml data sets(s)"/>
+    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
       <option value="consensusXML">consensusxml</option>
       <option value="featureXML">featurexml</option>
       <option value="mzML">mzml</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param argument="-rt" type="text" optional="true" value=":" label="Retention time range to extract" help="">
+    <param argument="-rt" type="text" value=":" label="Retention time range to extract" help="">
       <expand macro="list_string_san" name="rt"/>
     </param>
-    <param argument="-mz" type="text" optional="true" value=":" label="m/z range to extract (applies to ALL ms levels!)" help="">
+    <param argument="-mz" type="text" value=":" label="m/z range to extract (applies to ALL ms levels!)" help="">
       <expand macro="list_string_san" name="mz"/>
     </param>
-    <param argument="-int" type="text" optional="true" value=":" label="Intensity range to extract" help="">
+    <param argument="-int" type="text" value=":" label="Intensity range to extract" help="">
       <expand macro="list_string_san" name="int"/>
     </param>
     <param argument="-sort" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sorts the output according to RT and m/z" help=""/>
     <section name="peak_options" title="Peak data options" help="" expanded="false">
-      <param name="sn" argument="-peak_options:sn" type="float" optional="true" value="0.0" label="Write peaks with S/N &gt; 'sn' values only" help=""/>
+      <param name="sn" argument="-peak_options:sn" type="float" value="0.0" label="Write peaks with S/N &gt; 'sn' values only" help=""/>
       <param name="rm_pc_charge" argument="-peak_options:rm_pc_charge" type="text" optional="true" value="" label="Remove MS(2) spectra with these precursor charges" help="All spectra without precursor are kept! (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_integer_valsan" name="rm_pc_charge"/>
       </param>
-      <param name="pc_mz_range" argument="-peak_options:pc_mz_range" type="text" optional="true" value=":" label="MSn (n&gt;=2) precursor filtering according to their m/z value" help="Do not use this flag in conjunction with 'mz', unless you want to actually remove peaks in spectra (see 'mz'). RT filtering is covered by 'rt' and compatible with this flag">
+      <param name="pc_mz_range" argument="-peak_options:pc_mz_range" type="text" value=":" label="MSn (n&gt;=2) precursor filtering according to their m/z value" help="Do not use this flag in conjunction with 'mz', unless you want to actually remove peaks in spectra (see 'mz'). RT filtering is covered by 'rt' and compatible with this flag">
         <expand macro="list_string_san" name="pc_mz_range"/>
       </param>
       <param name="pc_mz_list" argument="-peak_options:pc_mz_list" type="text" optional="true" value="" label="List of m/z values" help="If a precursor window covers ANY of these values, the corresponding MS/MS spectrum will be kept (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_float_valsan" name="pc_mz_list"/>
       </param>
-      <param name="level" argument="-peak_options:level" type="text" optional="true" value="1 2 3" label="MS levels to extract" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="level" argument="-peak_options:level" type="text" value="1 2 3" label="MS levels to extract" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_integer_valsan" name="level"/>
       </param>
       <param name="sort_peaks" argument="-peak_options:sort_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sorts the peaks according to m/z" help=""/>
       <param name="no_chromatograms" argument="-peak_options:no_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No conversion to space-saving real chromatograms" help="e.g. from SRM scans"/>
       <param name="remove_chromatograms" argument="-peak_options:remove_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Removes chromatograms stored in a file" help=""/>
       <param name="remove_empty" argument="-peak_options:remove_empty" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Removes spectra and chromatograms without peaks" help=""/>
-      <param name="mz_precision" argument="-peak_options:mz_precision" type="select" optional="true" label="Store base64 encoded m/z data using 32 or 64 bit precision" help="">
+      <param name="mz_precision" argument="-peak_options:mz_precision" type="select" label="Store base64 encoded m/z data using 32 or 64 bit precision" help="">
         <option value="32">32</option>
         <option value="64" selected="true">64</option>
         <expand macro="list_string_san" name="mz_precision"/>
       </param>
-      <param name="int_precision" argument="-peak_options:int_precision" type="select" optional="true" label="Store base64 encoded intensity data using 32 or 64 bit precision" help="">
+      <param name="int_precision" argument="-peak_options:int_precision" type="select" label="Store base64 encoded intensity data using 32 or 64 bit precision" help="">
         <option value="32" selected="true">32</option>
         <option value="64">64</option>
         <expand macro="list_string_san" name="int_precision"/>
@@ -111,22 +111,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="indexed_file" argument="-peak_options:indexed_file" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to add an index to the file when writing" help=""/>
       <param name="zlib_compression" argument="-peak_options:zlib_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to store data with zlib compression (lossless compression)" help=""/>
       <section name="numpress" title="Numpress compression for peak data" help="" expanded="false">
-        <param name="masstime" argument="-peak_options:numpress:masstime" type="select" optional="true" label="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" help="">
+        <param name="masstime" argument="-peak_options:numpress:masstime" type="select" label="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" help="">
           <option value="none" selected="true">none</option>
           <option value="linear">linear</option>
           <option value="pic">pic</option>
           <option value="slof">slof</option>
           <expand macro="list_string_san" name="masstime"/>
         </param>
-        <param name="lossy_mass_accuracy" argument="-peak_options:numpress:lossy_mass_accuracy" type="float" optional="true" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
-        <param name="intensity" argument="-peak_options:numpress:intensity" type="select" optional="true" label="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" help="">
+        <param name="lossy_mass_accuracy" argument="-peak_options:numpress:lossy_mass_accuracy" type="float" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
+        <param name="intensity" argument="-peak_options:numpress:intensity" type="select" label="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" help="">
           <option value="none" selected="true">none</option>
           <option value="linear">linear</option>
           <option value="pic">pic</option>
           <option value="slof">slof</option>
           <expand macro="list_string_san" name="intensity"/>
         </param>
-        <param name="float_da" argument="-peak_options:numpress:float_da" type="select" optional="true" label="Apply MS Numpress compression algorithms for the float data arrays (recommended: slof or pic)" help="">
+        <param name="float_da" argument="-peak_options:numpress:float_da" type="select" label="Apply MS Numpress compression algorithms for the float data arrays (recommended: slof or pic)" help="">
           <option value="none" selected="true">none</option>
           <option value="linear">linear</option>
           <option value="pic">pic</option>
@@ -175,10 +175,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Bruker proprietary method">Bruker proprietary method</option>
         <expand macro="list_string_san" name="remove_activation"/>
       </param>
-      <param name="remove_collision_energy" argument="-spectra:remove_collision_energy" type="text" optional="true" value=":" label="Remove MSn scans with a collision energy in the given interval" help="">
+      <param name="remove_collision_energy" argument="-spectra:remove_collision_energy" type="text" value=":" label="Remove MSn scans with a collision energy in the given interval" help="">
         <expand macro="list_string_san" name="remove_collision_energy"/>
       </param>
-      <param name="remove_isolation_window_width" argument="-spectra:remove_isolation_window_width" type="text" optional="true" value=":" label="Remove MSn scans whose isolation window width is in the given interval" help="">
+      <param name="remove_isolation_window_width" argument="-spectra:remove_isolation_window_width" type="text" value=":" label="Remove MSn scans whose isolation window width is in the given interval" help="">
         <expand macro="list_string_san" name="remove_isolation_window_width"/>
       </param>
       <param name="select_zoom" argument="-spectra:select_zoom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Select zoom (enhanced resolution) scans" help=""/>
@@ -220,10 +220,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Bruker proprietary method">Bruker proprietary method</option>
         <expand macro="list_string_san" name="select_activation"/>
       </param>
-      <param name="select_collision_energy" argument="-spectra:select_collision_energy" type="text" optional="true" value=":" label="Select MSn scans with a collision energy in the given interval" help="">
+      <param name="select_collision_energy" argument="-spectra:select_collision_energy" type="text" value=":" label="Select MSn scans with a collision energy in the given interval" help="">
         <expand macro="list_string_san" name="select_collision_energy"/>
       </param>
-      <param name="select_isolation_window_width" argument="-spectra:select_isolation_window_width" type="text" optional="true" value=":" label="Select MSn scans whose isolation window width is in the given interval" help="">
+      <param name="select_isolation_window_width" argument="-spectra:select_isolation_window_width" type="text" value=":" label="Select MSn scans whose isolation window width is in the given interval" help="">
         <expand macro="list_string_san" name="select_isolation_window_width"/>
       </param>
       <param name="select_polarity" argument="-spectra:select_polarity" type="select" optional="true" label="Retain MSn scans with a certain scan polarity" help="">
@@ -232,22 +232,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="negative">negative</option>
         <expand macro="list_string_san" name="select_polarity"/>
       </param>
-      <param name="replace_pc_charge" argument="-spectra:replace_pc_charge" type="text" optional="true" value=":" label="Replaces in_charge with out_charge in all precursors" help="">
+      <param name="replace_pc_charge" argument="-spectra:replace_pc_charge" type="text" value=":" label="Replaces in_charge with out_charge in all precursors" help="">
         <expand macro="list_string_san" name="replace_pc_charge"/>
       </param>
       <section name="blackorwhitelist" title="Black or white listing of of MS2 spectra by spectral similarity" help="" expanded="false">
         <param name="file" argument="-spectra:blackorwhitelist:file" type="data" format="mzml" optional="true" label="Input file containing MS2 spectra that should be retained or removed from the mzML file" help="Matching tolerances are taken from 'spectra:blackorwhitelist:similarity_threshold|rt|mz' options..  select mzml data sets(s)"/>
-        <param name="similarity_threshold" argument="-spectra:blackorwhitelist:similarity_threshold" type="float" optional="true" min="-1.0" max="1.0" value="-1.0" label="Similarity threshold when matching MS2 spectra" help="(-1 = disabled)"/>
-        <param name="rt" argument="-spectra:blackorwhitelist:rt" type="float" optional="true" value="0.01" label="Retention tolerance [s] when matching precursor positions" help="(-1 = disabled)"/>
-        <param name="mz" argument="-spectra:blackorwhitelist:mz" type="float" optional="true" value="0.01" label="m/z tolerance [Th] when matching precursor positions" help="(-1 = disabled)"/>
-        <param name="use_ppm_tolerance" argument="-spectra:blackorwhitelist:use_ppm_tolerance" type="text" optional="true" value="false" label="If ppm tolerance should be used" help="Otherwise Da are used">
+        <param name="similarity_threshold" argument="-spectra:blackorwhitelist:similarity_threshold" type="float" min="-1.0" max="1.0" value="-1.0" label="Similarity threshold when matching MS2 spectra" help="(-1 = disabled)"/>
+        <param name="rt" argument="-spectra:blackorwhitelist:rt" type="float" value="0.01" label="Retention tolerance [s] when matching precursor positions" help="(-1 = disabled)"/>
+        <param name="mz" argument="-spectra:blackorwhitelist:mz" type="float" value="0.01" label="m/z tolerance [Th] when matching precursor positions" help="(-1 = disabled)"/>
+        <param name="use_ppm_tolerance" argument="-spectra:blackorwhitelist:use_ppm_tolerance" type="text" value="false" label="If ppm tolerance should be used" help="Otherwise Da are used">
           <expand macro="list_string_san" name="use_ppm_tolerance"/>
         </param>
         <param name="blacklist" argument="-spectra:blackorwhitelist:blacklist" type="boolean" truevalue="true" falsevalue="false" checked="true" label="True: remove matched MS2" help="False: retain matched MS2 spectra. Other levels are kept"/>
       </section>
     </section>
     <section name="feature" title="Feature data options" help="" expanded="false">
-      <param name="q" argument="-feature:q" type="text" optional="true" value=":" label="Overall quality range to extract [0:1]" help="">
+      <param name="q" argument="-feature:q" type="text" value=":" label="Overall quality range to extract [0:1]" help="">
         <expand macro="list_string_san" name="q"/>
       </param>
     </section>
@@ -262,22 +262,23 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="maps" argument="-consensus:blackorwhitelist:maps" type="text" optional="true" value="" label="Maps used for black/white list filtering" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
           <expand macro="list_integer_valsan" name="maps"/>
         </param>
-        <param name="rt" argument="-consensus:blackorwhitelist:rt" type="float" optional="true" min="0.0" value="60.0" label="Retention tolerance [s] for precursor to consensus feature position" help=""/>
-        <param name="mz" argument="-consensus:blackorwhitelist:mz" type="float" optional="true" min="0.0" value="0.01" label="m/z tolerance [Th] for precursor to consensus feature position" help=""/>
+        <param name="rt" argument="-consensus:blackorwhitelist:rt" type="float" min="0.0" value="60.0" label="Retention tolerance [s] for precursor to consensus feature position" help=""/>
+        <param name="mz" argument="-consensus:blackorwhitelist:mz" type="float" min="0.0" value="0.01" label="m/z tolerance [Th] for precursor to consensus feature position" help=""/>
         <param name="use_ppm_tolerance" argument="-consensus:blackorwhitelist:use_ppm_tolerance" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If ppm tolerance should be used" help="Otherwise Da are used"/>
       </section>
     </section>
     <section name="f_and_c" title="Feature &amp; Consensus data options" help="" expanded="false">
-      <param name="charge" argument="-f_and_c:charge" type="text" optional="true" value=":" label="Charge range to extract" help="">
+      <param name="charge" argument="-f_and_c:charge" type="text" value=":" label="Charge range to extract" help="">
         <expand macro="list_string_san" name="charge"/>
       </param>
-      <param name="size" argument="-f_and_c:size" type="text" optional="true" value=":" label="Size range to extract" help="">
+      <param name="size" argument="-f_and_c:size" type="text" value=":" label="Size range to extract" help="">
         <expand macro="list_string_san" name="size"/>
       </param>
       <param name="remove_meta" argument="-f_and_c:remove_meta" type="text" optional="true" value="" label="Expects a 3-tuple (=3 entries in the list)" help="i.e. &lt;name&gt; 'lt|eq|gt' &lt;value&gt;; the first is the name of meta value, followed by the comparison operator (equal, less or greater) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)! (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="remove_meta"/>
         <expand macro="list_string_san" name="remove_meta"/>
       </param>
+      <param name="remove_hull" argument="-f_and_c:remove_hull" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove hull from features" help=""/>
     </section>
     <section name="id" title="ID options" help="The Priority of the id-flags is: remove_annotated_features / remove_unannotated_features -&gt; remove_clashes -&gt; keep_best_score_id -&gt; sequences_whitelist  / accessions_whitelist" expanded="false">
       <param name="remove_clashes" argument="-id:remove_clashes" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove features with id clashes (different sequences mapped to one feature)" help=""/>
@@ -286,7 +287,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <expand macro="list_string_val" name="sequences_whitelist"/>
         <expand macro="list_string_san" name="sequences_whitelist"/>
       </param>
-      <param name="sequence_comparison_method" argument="-id:sequence_comparison_method" type="select" optional="true" label="Comparison method used to determine if a feature is whitelisted" help="">
+      <param name="sequence_comparison_method" argument="-id:sequence_comparison_method" type="select" label="Comparison method used to determine if a feature is whitelisted" help="">
         <option value="substring" selected="true">substring</option>
         <option value="exact">exact</option>
         <expand macro="list_string_san" name="sequence_comparison_method"/>
@@ -299,26 +300,26 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="remove_unannotated_features" argument="-id:remove_unannotated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove features without annotations" help=""/>
       <param name="remove_unassigned_ids" argument="-id:remove_unassigned_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove unassigned peptide identifications" help=""/>
       <param name="blacklist" argument="-id:blacklist" type="data" format="idxml" optional="true" label="Input file containing MS2 identifications whose corresponding MS2 spectra should be removed from the mzML file" help="Matching tolerances are taken from 'id:rt' and 'id:mz' options.. This tool will require all IDs to be matched to an MS2 spectrum, and quit with error otherwise. Use 'id:blacklist_imperfect' to allow for mismatches select idxml data sets(s)"/>
-      <param name="rt" argument="-id:rt" type="float" optional="true" min="0.0" value="0.1" label="Retention tolerance [s] for precursor to id position" help=""/>
-      <param name="mz" argument="-id:mz" type="float" optional="true" min="0.0" value="0.001" label="m/z tolerance [Th] for precursor to id position" help=""/>
+      <param name="rt" argument="-id:rt" type="float" min="0.0" value="0.1" label="Retention tolerance [s] for precursor to id position" help=""/>
+      <param name="mz" argument="-id:mz" type="float" min="0.0" value="0.001" label="m/z tolerance [Th] for precursor to id position" help=""/>
       <param name="blacklist_imperfect" argument="-id:blacklist_imperfect" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow for mismatching precursor positions (see 'id:blacklist')" help=""/>
     </section>
     <section name="algorithm" title="S/N algorithm section" help="" expanded="false">
       <section name="SignalToNoise" title="" help="" expanded="false">
-        <param name="max_intensity" argument="-algorithm:SignalToNoise:max_intensity" type="integer" optional="true" min="-1" value="-1" label="maximal intensity considered for histogram construction" help="By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well.  If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/>
-        <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoise:auto_max_stdev_factor" type="float" optional="true" min="0.0" max="999.0" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help=""/>
-        <param name="auto_max_percentile" argument="-algorithm:SignalToNoise:auto_max_percentile" type="integer" optional="true" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/>
-        <param name="auto_mode" argument="-algorithm:SignalToNoise:auto_mode" type="integer" optional="true" min="-1" max="1" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help=""/>
-        <param name="win_len" argument="-algorithm:SignalToNoise:win_len" type="float" optional="true" min="1.0" value="200.0" label="window length in Thomson" help=""/>
-        <param name="bin_count" argument="-algorithm:SignalToNoise:bin_count" type="integer" optional="true" min="3" value="30" label="number of bins for intensity values" help=""/>
-        <param name="min_required_elements" argument="-algorithm:SignalToNoise:min_required_elements" type="integer" optional="true" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/>
-        <param name="noise_for_empty_window" argument="-algorithm:SignalToNoise:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/>
+        <param name="max_intensity" argument="-algorithm:SignalToNoise:max_intensity" type="integer" min="-1" value="-1" label="maximal intensity considered for histogram construction" help="By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well.  If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/>
+        <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoise:auto_max_stdev_factor" type="float" min="0.0" max="999.0" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help=""/>
+        <param name="auto_max_percentile" argument="-algorithm:SignalToNoise:auto_max_percentile" type="integer" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/>
+        <param name="auto_mode" argument="-algorithm:SignalToNoise:auto_mode" type="integer" min="-1" max="1" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help=""/>
+        <param name="win_len" argument="-algorithm:SignalToNoise:win_len" type="float" min="1.0" value="200.0" label="window length in Thomson" help=""/>
+        <param name="bin_count" argument="-algorithm:SignalToNoise:bin_count" type="integer" min="3" value="30" label="number of bins for intensity values" help=""/>
+        <param name="min_required_elements" argument="-algorithm:SignalToNoise:min_required_elements" type="integer" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/>
+        <param name="noise_for_empty_window" argument="-algorithm:SignalToNoise:noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help=""/>
         <param name="write_log_messages" argument="-algorithm:SignalToNoise:write_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help=""/>
       </section>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -337,14 +338,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FileFilter_1 -->
+  <tests>
+    <!-- TOPP_FileFilter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":30"/>
       <param name="mz" value=":1000"/>
@@ -352,9 +354,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -373,16 +373,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -396,11 +391,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -409,14 +402,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -443,6 +434,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_2 -->
     <test expect_num_outputs="2">
@@ -451,7 +445,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value="30:"/>
       <param name="mz" value="1000:"/>
@@ -459,9 +453,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -480,16 +472,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -503,11 +490,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -516,14 +501,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -550,6 +533,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_3 -->
     <test expect_num_outputs="2">
@@ -558,7 +544,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -566,9 +552,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="2"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -587,16 +571,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -610,11 +589,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -623,14 +600,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -657,6 +632,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_4 -->
     <test expect_num_outputs="2">
@@ -665,7 +643,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_4_input.mzML"/>
-      <output name="out" file="FileFilter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -673,9 +651,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -694,16 +670,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="true"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -717,11 +688,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -730,14 +699,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -764,6 +731,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_5 -->
     <test expect_num_outputs="2">
@@ -772,7 +742,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_5_input.featureXML"/>
-      <output name="out" file="FileFilter_5_out.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_5_out.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value=":1000"/>
       <param name="mz" value=":480"/>
@@ -780,9 +750,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -801,16 +769,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -824,11 +787,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":0.6"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -837,14 +798,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":3"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -871,6 +830,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_6 -->
     <test expect_num_outputs="2">
@@ -879,7 +841,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_5_input.featureXML"/>
-      <output name="out" file="FileFilter_6_out.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_6_out.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value="1000:"/>
       <param name="mz" value="440:"/>
@@ -887,9 +849,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -908,16 +868,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -931,11 +886,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value="0.51:"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -944,14 +897,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value="3:"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -978,6 +929,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_7 -->
     <test expect_num_outputs="2">
@@ -986,7 +940,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_7_input.mzML"/>
-      <output name="out" file="FileFilter_7_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_7_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -994,9 +948,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1015,16 +967,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1038,11 +985,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1051,14 +996,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -1085,6 +1028,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_8 -->
     <test expect_num_outputs="2">
@@ -1093,7 +1039,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_8_input.consensusXML"/>
-      <output name="out" file="FileFilter_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileFilter_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="rt" value="600:1400"/>
       <param name="mz" value="700:2300"/>
@@ -1101,9 +1047,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1122,16 +1066,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1145,11 +1084,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1158,14 +1095,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -1192,6 +1127,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_9 -->
     <test expect_num_outputs="2">
@@ -1200,7 +1138,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_9_input.mzML"/>
-      <output name="out" file="FileFilter_9_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_9_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -1208,9 +1146,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1230,15 +1166,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
         <param name="remove_mode" value="SelectedIonMonitoring"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1252,11 +1184,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1265,14 +1195,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -1299,6 +1227,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_10 -->
     <test expect_num_outputs="2">
@@ -1307,7 +1238,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_10_input.mzML"/>
-      <output name="out" file="FileFilter_10_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_10_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -1315,9 +1246,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1336,16 +1265,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
         <param name="remove_activation" value="Collision-induced dissociation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1359,11 +1284,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1372,14 +1295,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -1406,6 +1327,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_11 -->
     <test expect_num_outputs="2">
@@ -1414,7 +1338,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_11_input.mzML"/>
-      <output name="out" file="FileFilter_11_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_11_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -1422,9 +1346,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1443,16 +1365,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
         <param name="remove_activation" value="Plasma desorption"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1466,11 +1384,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1479,14 +1395,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -1513,6 +1427,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_12 -->
     <test expect_num_outputs="2">
@@ -1521,7 +1438,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_12_input.mzML"/>
-      <output name="out" file="FileFilter_12_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_12_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -1529,9 +1446,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1550,16 +1465,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1573,11 +1483,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1586,14 +1494,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -1620,6 +1526,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_13 -->
     <test expect_num_outputs="2">
@@ -1628,7 +1537,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_13_input.consensusXML"/>
-      <output name="out" file="FileFilter_13_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_13_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -1636,9 +1545,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1657,16 +1564,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1684,7 +1586,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1693,14 +1594,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -1727,6 +1626,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_14 -->
     <test expect_num_outputs="2">
@@ -1735,7 +1637,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_14_input.consensusXML"/>
-      <output name="out" file="FileFilter_14_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileFilter_14_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -1743,9 +1645,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1764,16 +1664,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1791,7 +1686,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1800,14 +1694,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -1834,6 +1726,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_15 -->
     <test expect_num_outputs="2">
@@ -1842,7 +1737,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_15_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_15_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -1850,9 +1745,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1871,16 +1764,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -1894,11 +1782,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -1907,14 +1793,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
         <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="true"/>
@@ -1941,6 +1826,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_16 -->
     <test expect_num_outputs="2">
@@ -1949,7 +1837,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_16_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_16_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value="3000:4000"/>
       <param name="mz" value="400:600"/>
@@ -1957,9 +1845,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -1978,16 +1864,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2001,11 +1882,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2014,14 +1893,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
         <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="true"/>
@@ -2048,6 +1926,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_17 -->
     <test expect_num_outputs="2">
@@ -2056,7 +1937,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_17_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_17_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value="3000:4000"/>
       <param name="mz" value="400:600"/>
@@ -2064,9 +1945,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2085,16 +1964,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2108,11 +1982,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2121,14 +1993,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="true"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -2155,6 +2025,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_18 -->
     <test expect_num_outputs="2">
@@ -2163,7 +2036,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_18_input.consensusXML"/>
-      <output name="out" file="FileFilter_18_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileFilter_18_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -2171,9 +2044,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2192,16 +2063,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2215,11 +2081,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2228,14 +2092,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
         <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="true"/>
@@ -2262,6 +2125,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_19 -->
     <test expect_num_outputs="2">
@@ -2270,7 +2136,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_18_input.consensusXML"/>
-      <output name="out" file="FileFilter_19_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileFilter_19_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="rt" value="3000:4000"/>
       <param name="mz" value="400:600"/>
@@ -2278,9 +2144,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2299,16 +2163,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2322,11 +2181,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2335,14 +2192,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="true"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -2369,6 +2224,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_20 -->
     <test expect_num_outputs="2">
@@ -2377,7 +2235,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_20_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_20_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -2385,9 +2243,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2406,16 +2262,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2429,11 +2280,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2442,12 +2291,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
         <param name="accessions_whitelist" value="&quot;YDL217C&quot;"/>
         <param name="remove_annotated_features" value="false"/>
@@ -2476,6 +2324,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_21 -->
     <test expect_num_outputs="2">
@@ -2484,7 +2335,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_21_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_21_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -2492,9 +2343,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2513,16 +2362,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2536,11 +2380,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2549,14 +2391,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="true"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="true"/>
         <param name="remove_unassigned_ids" value="true"/>
@@ -2583,6 +2423,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_22 -->
     <test expect_num_outputs="2">
@@ -2591,7 +2434,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_22_input.consensusXML"/>
-      <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileFilter_22_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -2599,9 +2442,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2620,16 +2461,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2643,11 +2479,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2657,13 +2491,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
         <param name="remove_meta" value="&quot;distinct_charges&quot; &quot;gt&quot; &quot;1,2&quot;"/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -2690,6 +2523,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_23 -->
     <test expect_num_outputs="2">
@@ -2698,7 +2534,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_22_input.consensusXML"/>
-      <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileFilter_22_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -2706,9 +2542,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2727,16 +2561,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2750,11 +2579,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2764,13 +2591,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
         <param name="remove_meta" value="&quot;distinct_charges_size&quot; &quot;gt&quot; &quot;2&quot;"/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -2797,6 +2623,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_24 -->
     <test expect_num_outputs="2">
@@ -2805,7 +2634,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_22_input.consensusXML"/>
-      <output name="out" file="FileFilter_24_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileFilter_24_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -2813,9 +2642,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2834,16 +2661,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2857,11 +2679,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2871,13 +2691,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
         <param name="remove_meta" value="&quot;DOESNOTEXIST&quot; &quot;lt&quot; &quot;whatever&quot;"/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -2904,6 +2723,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_25 -->
     <test expect_num_outputs="2">
@@ -2912,7 +2734,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_25_input.mzML.gz"/>
-      <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -2920,9 +2742,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -2941,16 +2761,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -2964,11 +2779,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -2977,14 +2790,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3012,6 +2823,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_26 -->
     <test expect_num_outputs="2">
@@ -3020,7 +2834,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_25_input.mzML.gz"/>
-      <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3028,9 +2842,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3049,16 +2861,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3072,11 +2879,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3085,14 +2890,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3120,6 +2923,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_28 -->
     <test expect_num_outputs="2">
@@ -3128,7 +2934,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_28_input.mzML.gz"/>
-      <output name="out" file="FileFilter_28_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_28_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3136,9 +2942,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value="832:836"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="2"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3157,16 +2961,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3180,11 +2979,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3193,14 +2990,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3227,6 +3022,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_29 -->
     <test expect_num_outputs="2">
@@ -3235,7 +3033,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_28_input.mzML.gz"/>
-      <output name="out" file="FileFilter_29_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_29_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3243,9 +3041,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value="832:836"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3264,16 +3060,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3287,11 +3078,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3300,14 +3089,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3334,6 +3121,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_30 -->
     <test expect_num_outputs="2">
@@ -3342,7 +3132,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_28_input.mzML.gz"/>
-      <output name="out" file="FileFilter_30_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_30_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3350,9 +3140,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value="832:836"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3371,16 +3159,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3394,11 +3177,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3407,14 +3188,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3441,6 +3220,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_31 -->
     <test expect_num_outputs="2">
@@ -3449,7 +3231,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_31_34_input.mzML"/>
-      <output name="out" file="FileFilter_31_remove_collision_energy.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_31_remove_collision_energy.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3457,9 +3239,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3478,16 +3258,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":2"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3501,11 +3276,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3514,14 +3287,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3548,6 +3319,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_32 -->
     <test expect_num_outputs="2">
@@ -3556,7 +3330,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_31_34_input.mzML"/>
-      <output name="out" file="FileFilter_32_select_collision_energy.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_32_select_collision_energy.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3564,9 +3338,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3585,16 +3357,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":2"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3608,11 +3375,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3621,14 +3386,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3655,6 +3418,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_33 -->
     <test expect_num_outputs="2">
@@ -3663,7 +3429,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_31_34_input.mzML"/>
-      <output name="out" file="FileFilter_33_remove_isolation_window.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_33_remove_isolation_window.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3671,9 +3437,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3692,16 +3456,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":35"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3715,11 +3474,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3728,14 +3485,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3762,6 +3517,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_34 -->
     <test expect_num_outputs="2">
@@ -3770,7 +3528,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_31_34_input.mzML"/>
-      <output name="out" file="FileFilter_34_select_isolation_window.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_34_select_isolation_window.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3778,9 +3536,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3799,16 +3555,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":35"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3822,11 +3573,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3835,14 +3584,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3869,6 +3616,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_35 -->
     <test expect_num_outputs="2">
@@ -3877,7 +3627,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_35_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_35_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3885,9 +3635,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -3906,16 +3654,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -3929,11 +3672,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -3942,14 +3683,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -3976,6 +3715,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_36 -->
     <test expect_num_outputs="2">
@@ -3984,7 +3726,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_36_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_36_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -3992,9 +3734,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4013,16 +3753,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -4036,11 +3771,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4049,14 +3782,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4083,6 +3814,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_37 -->
     <test expect_num_outputs="2">
@@ -4091,7 +3825,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_37_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_37_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4099,9 +3833,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4120,16 +3852,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -4143,11 +3870,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4156,14 +3881,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4190,6 +3913,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_38 -->
     <test expect_num_outputs="2">
@@ -4198,7 +3924,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_38_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_38_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4206,9 +3932,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4227,16 +3951,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -4250,11 +3969,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4263,14 +3980,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4297,6 +4012,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_40 -->
     <test expect_num_outputs="2">
@@ -4305,7 +4023,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_40_input.mzML"/>
-      <output name="out" file="FileFilter_40_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_40_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4313,9 +4031,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4334,13 +4050,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
         <param name="select_polarity" value="positive"/>
@@ -4357,11 +4069,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4370,14 +4080,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4404,6 +4112,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_41 -->
     <test expect_num_outputs="2">
@@ -4412,7 +4123,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_40_input.mzML"/>
-      <output name="out" file="FileFilter_41_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_41_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4420,9 +4131,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4441,13 +4150,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
         <param name="select_polarity" value="negative"/>
@@ -4464,11 +4169,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4477,14 +4180,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4511,6 +4212,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_42 -->
     <test expect_num_outputs="2">
@@ -4519,7 +4223,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_40_input.mzML"/>
-      <output name="out" file="FileFilter_42_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_42_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4527,9 +4231,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4548,16 +4250,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -4571,11 +4268,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4584,14 +4279,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4618,6 +4311,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_43 -->
     <test expect_num_outputs="2">
@@ -4626,7 +4322,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_43_input.mzML"/>
-      <output name="out" file="FileFilter_43.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_43_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4634,9 +4330,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4655,16 +4349,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -4678,11 +4367,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4691,14 +4378,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4725,6 +4410,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_43_read_again -->
     <test expect_num_outputs="2">
@@ -4732,8 +4420,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
-      <param name="in" value="FileFilter_43.tmp.mzML"/>
-      <output name="out" file="FileFilter_43.dummy.tmp" compare="sim_size" delta_frac="0.7"/>
+      <param name="in" value="FileFilter_43_output.mzML"/>
+      <output name="out" value="FileFilter_43.dummy.tmp" compare="sim_size" delta_frac="0.7"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4741,9 +4429,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4762,16 +4448,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -4785,11 +4466,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4798,14 +4477,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4832,6 +4509,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_44 -->
     <test expect_num_outputs="2">
@@ -4840,7 +4520,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_44_input.mzML"/>
-      <output name="out" file="FileFilter_44_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_44_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4848,9 +4528,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4869,16 +4547,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -4892,11 +4565,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -4905,14 +4576,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -4939,6 +4608,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_45 -->
     <test expect_num_outputs="2">
@@ -4947,7 +4619,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_45_input.featureXML"/>
-      <output name="out" file="FileFilter_45_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_45_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -4955,9 +4627,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -4976,16 +4646,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -4999,11 +4664,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -5012,14 +4675,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
         <param name="sequences_whitelist" value="&quot;YSFS&quot; &quot;STLIPPPSK(Label:13C(6)15N(2))&quot;"/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -5046,6 +4708,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_46 -->
     <test expect_num_outputs="2">
@@ -5054,7 +4719,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_46_input.featureXML"/>
-      <output name="out" file="FileFilter_46_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileFilter_46_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -5062,9 +4727,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -5083,16 +4746,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -5106,11 +4764,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -5119,14 +4775,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
         <param name="sequences_whitelist" value="&quot;YSFS&quot; &quot;STLIPPPSK(Label:13C(6)15N(2))&quot;"/>
         <param name="sequence_comparison_method" value="exact"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -5153,6 +4808,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_47 -->
     <test expect_num_outputs="2">
@@ -5161,7 +4819,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_47_input.mzML"/>
-      <output name="out" file="FileFilter_47_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_47_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -5169,9 +4827,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -5190,16 +4846,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="file" value="FileFilter_47_input_select.mzML"/>
@@ -5214,11 +4865,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -5227,14 +4876,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -5261,6 +4908,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_48 -->
     <test expect_num_outputs="2">
@@ -5269,7 +4919,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_47_input.mzML"/>
-      <output name="out" file="FileFilter_48_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_48_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -5277,9 +4927,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -5298,16 +4946,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="file" value="FileFilter_47_input_select.mzML"/>
@@ -5322,11 +4965,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -5335,14 +4976,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -5369,6 +5008,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileFilter_49 -->
     <test expect_num_outputs="2">
@@ -5377,7 +5019,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileFilter_49_input.mzML"/>
-      <output name="out" file="FileFilter_49_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileFilter_49_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="rt" value=":"/>
       <param name="mz" value=":"/>
@@ -5385,9 +5027,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="sort" value="false"/>
       <section name="peak_options">
         <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
         <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
         <param name="level" value="1 2 3"/>
         <param name="sort_peaks" value="false"/>
         <param name="no_chromatograms" value="false"/>
@@ -5406,16 +5046,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="spectra">
         <param name="remove_zoom" value="false"/>
-        <param name="remove_mode"/>
-        <param name="remove_activation"/>
         <param name="remove_collision_energy" value=":"/>
         <param name="remove_isolation_window_width" value=":"/>
         <param name="select_zoom" value="false"/>
-        <param name="select_mode"/>
-        <param name="select_activation"/>
         <param name="select_collision_energy" value=":"/>
         <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity"/>
         <param name="replace_pc_charge" value=":"/>
         <section name="blackorwhitelist">
           <param name="similarity_threshold" value="-1.0"/>
@@ -5429,11 +5064,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="q" value=":"/>
       </section>
       <section name="consensus">
-        <param name="map" value=""/>
         <param name="map_and" value="false"/>
         <section name="blackorwhitelist">
           <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
           <param name="rt" value="60.0"/>
           <param name="mz" value="0.01"/>
           <param name="use_ppm_tolerance" value="false"/>
@@ -5442,14 +5075,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="f_and_c">
         <param name="charge" value=":"/>
         <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
+        <param name="remove_hull" value="false"/>
       </section>
       <section name="id">
         <param name="remove_clashes" value="false"/>
         <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
         <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
         <param name="remove_annotated_features" value="false"/>
         <param name="remove_unannotated_features" value="false"/>
         <param name="remove_unassigned_ids" value="false"/>
@@ -5476,11 +5107,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Extracts or manipulates portions of data from peak, feature or consensus-feature files.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FileFilter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FileFilter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FileInfo.xml b/tools/openms/FileInfo.xml
index 7afa4b1a2..d742977dc 100644
--- a/tools/openms/FileInfo.xml
+++ b/tools/openms/FileInfo.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [File Handling]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="FileInfo" name="FileInfo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Shows basic information about the file, such as data ranges and file type.</description>
+  <description>Shows basic information about the file, such as data ranges and file type</description>
   <macros>
     <token name="@EXECUTABLE@">FileInfo</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_tsv &&
@@ -52,7 +51,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,sqmass,trafoxml" optional="false" label="input file" help=" select consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,sqmass,trafoxml data sets(s)"/>
+    <param argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,sqmass,trafoxml" label="input file" help=" select consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,sqmass,trafoxml data sets(s)"/>
     <param argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/>
     <param argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/>
     <param argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a five-number statistics of intensities, qualities, and widths" help=""/>
@@ -62,7 +61,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-i" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -80,14 +79,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FileInfo_1 -->
+  <tests>
+    <!-- TOPP_FileInfo_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileInfo_1_input.dta" ftype="dta"/>
-      <output name="out" file="FileInfo_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="FileInfo_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="m" value="false"/>
       <param name="p" value="false"/>
       <param name="s" value="false"/>
@@ -101,6 +101,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileInfo_2 -->
     <test expect_num_outputs="2">
@@ -109,7 +112,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileInfo_2_input.dta2d" ftype="dta2d"/>
-      <output name="out" file="FileInfo_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="FileInfo_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="m" value="false"/>
       <param name="p" value="false"/>
       <param name="s" value="false"/>
@@ -123,6 +126,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileInfo_3 -->
     <test expect_num_outputs="2">
@@ -131,7 +137,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileInfo_3_input.featureXML"/>
-      <output name="out" file="FileInfo_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="FileInfo_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="m" value="true"/>
       <param name="p" value="true"/>
       <param name="s" value="true"/>
@@ -145,6 +151,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileInfo_4 -->
     <test expect_num_outputs="2">
@@ -153,7 +162,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileInfo_4_input.mzXML"/>
-      <output name="out" file="FileInfo_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="FileInfo_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="m" value="true"/>
       <param name="p" value="false"/>
       <param name="s" value="false"/>
@@ -167,6 +176,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileInfo_5 -->
     <test expect_num_outputs="2">
@@ -175,7 +187,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileInfo_5_input.mzDat"/>
-      <output name="out" file="FileInfo_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="FileInfo_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="m" value="true"/>
       <param name="p" value="false"/>
       <param name="s" value="true"/>
@@ -189,6 +201,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileInfo_6 -->
     <test expect_num_outputs="2">
@@ -197,7 +212,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileInfo_6_input.mzData"/>
-      <output name="out" file="FileInfo_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="FileInfo_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="m" value="false"/>
       <param name="p" value="false"/>
       <param name="s" value="true"/>
@@ -211,6 +226,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileInfo_7 -->
     <test expect_num_outputs="2">
@@ -219,7 +237,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileInfo_7_input.consensusXML"/>
-      <output name="out" file="FileInfo_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="FileInfo_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="m" value="true"/>
       <param name="p" value="true"/>
       <param name="s" value="true"/>
@@ -233,6 +251,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileInfo_9 -->
     <test expect_num_outputs="2">
@@ -241,7 +262,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileInfo_9_input.mzML"/>
-      <output name="out" file="FileInfo_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="FileInfo_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="m" value="true"/>
       <param name="p" value="true"/>
       <param name="s" value="true"/>
@@ -255,6 +276,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileInfo_10 -->
     <test expect_num_outputs="2">
@@ -263,7 +287,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileInfo_10_input.idXML"/>
-      <output name="out" file="FileInfo_10_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="FileInfo_10_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="m" value="false"/>
       <param name="p" value="false"/>
       <param name="s" value="false"/>
@@ -277,6 +301,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileInfo_12 -->
     <test expect_num_outputs="2">
@@ -298,6 +325,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileInfo_13 -->
     <test expect_num_outputs="2">
@@ -319,6 +349,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileInfo_14 -->
     <test expect_num_outputs="2">
@@ -327,7 +360,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileInfo_14_input.mzid"/>
-      <output name="out" file="FileInfo_14_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="FileInfo_14_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="m" value="false"/>
       <param name="p" value="false"/>
       <param name="s" value="false"/>
@@ -341,6 +374,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileInfo_15 -->
     <test expect_num_outputs="2">
@@ -349,7 +385,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileInfo_15_input.mzid"/>
-      <output name="out" file="FileInfo_15_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="FileInfo_15_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="m" value="false"/>
       <param name="p" value="false"/>
       <param name="s" value="false"/>
@@ -363,6 +399,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileInfo_16 -->
     <test expect_num_outputs="2">
@@ -371,7 +410,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileInfo_16_input.trafoXML"/>
-      <output name="out" file="FileInfo_16_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="FileInfo_16_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="m" value="false"/>
       <param name="p" value="false"/>
       <param name="s" value="false"/>
@@ -385,6 +424,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileInfo_17 -->
     <test expect_num_outputs="2">
@@ -393,7 +435,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileInfo_17_input.fasta"/>
-      <output name="out" file="FileInfo_17_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="FileInfo_17_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="m" value="false"/>
       <param name="p" value="false"/>
       <param name="s" value="false"/>
@@ -407,6 +449,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileInfo_18 -->
     <test expect_num_outputs="2">
@@ -415,7 +460,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FileInfo_18_input.fasta"/>
-      <output name="out" file="FileInfo_18_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="FileInfo_18_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="m" value="false"/>
       <param name="p" value="false"/>
       <param name="s" value="false"/>
@@ -429,11 +474,39 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_FileInfo_19 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="FAIMS_test_data.mzML"/>
+      <output name="out" value="FileInfo_19_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <param name="m" value="false"/>
+      <param name="p" value="false"/>
+      <param name="s" value="false"/>
+      <param name="d" value="true"/>
+      <param name="c" value="false"/>
+      <param name="v" value="false"/>
+      <param name="i" value="false"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Shows basic information about the file, such as data ranges and file type.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FileInfo.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FileInfo.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FileMerger.xml b/tools/openms/FileMerger.xml
index b5387eecd..19afa0063 100644
--- a/tools/openms/FileMerger.xml
+++ b/tools/openms/FileMerger.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [File Handling]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="FileMerger" name="FileMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Merges several MS files into one file.</description>
+  <description>Merges several MS files into one file</description>
   <macros>
     <token name="@EXECUTABLE@">FileMerger</token>
     <import>macros.xml</import>
@@ -17,9 +16,9 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir out &&
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
@@ -68,13 +67,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml" multiple="true" optional="false" label="Input files separated by blank" help=" select consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml" multiple="true" label="Input files separated by blank" help=" select consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml" multiple="false" optional="false" label="Input files separated by blank" help=" select consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml" label="Input files separated by blank" help=" select consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml data sets(s)"/>
       </when>
     </conditional>
-    <param name="out_type" type="select" optional="false" label="File type of output out (Output file)">
+    <param name="out_type" type="select" label="File type of output out (Output file)">
       <option value="mzML">mzml</option>
       <option value="featureXML">featurexml</option>
       <option value="consensusXML">consensusxml</option>
@@ -82,13 +81,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <option value="fasta">fasta</option>
     </param>
     <param argument="-annotate_file_origin" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)" help=""/>
-    <param argument="-append_method" type="select" optional="true" label="(ConsensusXML-only) Append quantitative information about features row-wise or column-wise" help="- 'append_rows' is usually used when the inputs come from the same MS run (e.g. caused by manual splitting or multiple algorithms on the same file). - 'append_cols' when you want to combine consensusXMLs from e.g. different fractions to be summarized in ProteinQuantifier or jointly exported with MzTabExporter">
+    <param argument="-append_method" type="select" label="(ConsensusXML-only) Append quantitative information about features row-wise or column-wise" help="- 'append_rows' is usually used when the inputs come from the same MS run (e.g. caused by manual splitting or multiple algorithms on the same file). - 'append_cols' when you want to combine consensusXMLs from e.g. different fractions to be summarized in ProteinQuantifier or jointly exported with MzTabExporter">
       <option value="append_rows" selected="true">append_rows</option>
       <option value="append_cols">append_cols</option>
       <expand macro="list_string_san" name="append_method"/>
     </param>
     <section name="rt_concat" title="Options for concatenating files in the retention time (RT) dimension" help="The RT ranges of inputs are adjusted so they don't overlap in the merged file (traML input not supported)" expanded="false">
-      <param name="gap" argument="-rt_concat:gap" type="float" optional="true" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="RT concatenation is enabled if a value &gt; 0 is set"/>
+      <param name="gap" argument="-rt_concat:gap" type="float" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="RT concatenation is enabled if a value &gt; 0 is set"/>
     </section>
     <section name="raw" title="Options for raw data input/output (primarily for DTA files)" help="" expanded="false">
       <param name="rt_auto" argument="-raw:rt_auto" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assign retention times automatically (integers starting at 1)" help=""/>
@@ -96,11 +95,11 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <expand macro="list_float_valsan" name="rt_custom"/>
       </param>
       <param name="rt_filename" argument="-raw:rt_filename" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to guess the retention time of a file based on the filename" help="This option is useful for merging DTA files, where filenames should contain the string 'rt' directly followed by a floating point number, e.g. 'my_spectrum_rt2795.15.dta'"/>
-      <param name="ms_level" argument="-raw:ms_level" type="integer" optional="true" value="0" label="If 1 or higher, this number is assigned to spectra as the MS level" help="This option is useful for DTA files which do not contain MS level information"/>
+      <param name="ms_level" argument="-raw:ms_level" type="integer" value="0" label="If 1 or higher, this number is assigned to spectra as the MS level" help="This option is useful for DTA files which do not contain MS level information"/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -126,7 +125,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FileMerger_2 -->
+  <tests>
+    <!-- TOPP_FileMerger_2 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -136,7 +136,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="FileMerger_2_input1.dta,FileMerger_2_input2.dta" ftype="dta"/>
       </conditional>
       <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileMerger_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -154,6 +154,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileMerger_3 -->
     <test expect_num_outputs="2">
@@ -165,7 +168,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="FileMerger_3_input1.dta,FileMerger_3_input2.dta" ftype="dta"/>
       </conditional>
       <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileMerger_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -173,7 +176,6 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </section>
       <section name="raw">
         <param name="rt_auto" value="true"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="false"/>
         <param name="ms_level" value="0"/>
       </section>
@@ -183,6 +185,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileMerger_4 -->
     <test expect_num_outputs="2">
@@ -194,7 +199,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="FileMerger_4_input1.dta2d,FileMerger_4_input2.dta2d" ftype="dta2d"/>
       </conditional>
       <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileMerger_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -202,7 +207,6 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </section>
       <section name="raw">
         <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="false"/>
         <param name="ms_level" value="0"/>
       </section>
@@ -212,6 +216,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileMerger_5 -->
     <test expect_num_outputs="2">
@@ -223,7 +230,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="FileMerger_5_input_rt1023.331.dta,FileMerger_5_input_rt2044.334.dta,FileMerger_5_input_rt889.32.dta" ftype="dta"/>
       </conditional>
       <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileMerger_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -231,7 +238,6 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </section>
       <section name="raw">
         <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="true"/>
         <param name="ms_level" value="2"/>
       </section>
@@ -241,6 +247,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileMerger_6 -->
     <test expect_num_outputs="2">
@@ -252,7 +261,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="FileMerger_6_input1.mzML,FileMerger_6_input2.mzML"/>
       </conditional>
       <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_6_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileMerger_6_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -260,7 +269,6 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </section>
       <section name="raw">
         <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="false"/>
         <param name="ms_level" value="0"/>
       </section>
@@ -270,6 +278,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileMerger_7 -->
     <test expect_num_outputs="2">
@@ -281,7 +292,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="FileMerger_7_input1.featureXML,FileMerger_7_input2.featureXML"/>
       </conditional>
       <param name="out_type" value="featureXML"/>
-      <output name="out" file="FileMerger_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileMerger_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -289,7 +300,6 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </section>
       <section name="raw">
         <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="false"/>
         <param name="ms_level" value="0"/>
       </section>
@@ -299,6 +309,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileMerger_8 -->
     <test expect_num_outputs="2">
@@ -310,7 +323,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/>
       </conditional>
       <param name="out_type" value="consensusXML"/>
-      <output name="out" file="FileMerger_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileMerger_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -318,7 +331,6 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </section>
       <section name="raw">
         <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="false"/>
         <param name="ms_level" value="0"/>
       </section>
@@ -328,6 +340,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileMerger_9 -->
     <test expect_num_outputs="2">
@@ -339,7 +354,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="FileMerger_9_input1.traML,FileMerger_9_input2.traML"/>
       </conditional>
       <param name="out_type" value="traML"/>
-      <output name="out" file="FileMerger_9_output.traML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="FileMerger_9_output.traML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -347,7 +362,6 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </section>
       <section name="raw">
         <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="false"/>
         <param name="ms_level" value="0"/>
       </section>
@@ -357,6 +371,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileMerger_10 -->
     <test expect_num_outputs="3">
@@ -365,10 +382,10 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="test" value="true"/>
       </section>
       <conditional name="in_cond">
-        <param name="in" value="FileMerger_6_input2.mzML,FileMerger_6_input2_2.mzML"/>
+        <param name="in" value="FileMerger_6_input2_0.mzML,FileMerger_6_input2_1.mzML"/>
       </conditional>
       <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_10_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileMerger_10_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -377,7 +394,6 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <output_collection name="rt_concat_trafo_out" count="2"/>
       <section name="raw">
         <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="false"/>
         <param name="ms_level" value="0"/>
       </section>
@@ -387,6 +403,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_FileMerger_11 -->
     <test expect_num_outputs="2">
@@ -398,7 +417,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/>
       </conditional>
       <param name="out_type" value="consensusXML"/>
-      <output name="out" file="FileMerger_11_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileMerger_11_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_cols"/>
       <section name="rt_concat">
@@ -406,7 +425,6 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </section>
       <section name="raw">
         <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="false"/>
         <param name="ms_level" value="0"/>
       </section>
@@ -416,11 +434,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Merges several MS files into one file.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FileMerger.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FileMerger.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/FuzzyDiff.xml b/tools/openms/FuzzyDiff.xml
index 90ae46e57..80ab4c28b 100644
--- a/tools/openms/FuzzyDiff.xml
+++ b/tools/openms/FuzzyDiff.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [[for Developers]]-->
 <tool id="FuzzyDiff" name="FuzzyDiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Compares two files, tolerating numeric differences.</description>
+  <description>Compares two files, tolerating numeric differences</description>
   <macros>
     <token name="@EXECUTABLE@">FuzzyDiff</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in1 &&
-ln -s '$in1' 'in1/${re.sub("[^\w\-_]", "_", $in1.element_identifier)}.$gxy2omsext($in1.ext)' &&
+cp '$in1' 'in1/${re.sub("[^\w\-_]", "_", $in1.element_identifier)}.$gxy2omsext($in1.ext)' &&
 mkdir in2 &&
-ln -s '$in2' 'in2/${re.sub("[^\w\-_]", "_", $in2.element_identifier)}.$gxy2omsext($in2.ext)' &&
+cp '$in2' 'in2/${re.sub("[^\w\-_]", "_", $in2.element_identifier)}.$gxy2omsext($in2.ext)' &&
 
 ## Main program call
 
@@ -40,15 +39,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in1" type="data" format="txt" optional="false" label="first input file" help=" select txt data sets(s)"/>
-    <param argument="-in2" type="data" format="txt" optional="false" label="second input file" help=" select txt data sets(s)"/>
-    <param argument="-ratio" type="float" optional="true" min="1.0" value="1.0" label="acceptable relative erro" help="Only one of 'ratio' or 'absdiff' has to be satisfied.  Use &quot;absdiff&quot; to deal with cases like &quot;zero vs. epsilon&quot;"/>
-    <param argument="-absdiff" type="float" optional="true" min="0.0" value="0.0" label="acceptable absolute difference" help="Only one of 'ratio' or 'absdiff' has to be satisfied. "/>
-    <param argument="-verbose" type="integer" optional="true" min="0" max="3" value="2" label="set verbose level:" help="0 = very quiet mode (absolutely no output). 1 = quiet mode (no output unless differences detected). 2 = default (include summary at end). 3 = continue after errors. "/>
-    <param argument="-tab_width" type="integer" optional="true" min="1" value="8" label="tabulator width, used for calculation of column numbers" help=""/>
-    <param argument="-first_column" type="integer" optional="true" min="0" value="1" label="number of first column, used for calculation of column numbers" help=""/>
+    <param argument="-in1" type="data" format="txt" label="first input file" help=" select txt data sets(s)"/>
+    <param argument="-in2" type="data" format="txt" label="second input file" help=" select txt data sets(s)"/>
+    <param argument="-ratio" type="float" min="1.0" value="1.0" label="acceptable relative erro" help="Only one of 'ratio' or 'absdiff' has to be satisfied.  Use &quot;absdiff&quot; to deal with cases like &quot;zero vs. epsilon&quot;"/>
+    <param argument="-absdiff" type="float" min="0.0" value="0.0" label="acceptable absolute difference" help="Only one of 'ratio' or 'absdiff' has to be satisfied. "/>
+    <param argument="-verbose" type="integer" min="0" max="3" value="2" label="set verbose level:" help="0 = very quiet mode (absolutely no output). 1 = quiet mode (no output unless differences detected). 2 = default (include summary at end). 3 = continue after errors. "/>
+    <param argument="-tab_width" type="integer" min="1" value="8" label="tabulator width, used for calculation of column numbers" help=""/>
+    <param argument="-first_column" type="integer" min="0" value="1" label="number of first column, used for calculation of column numbers" help=""/>
     <expand macro="adv_opts_macro">
-      <param argument="-whitelist" type="text" optional="true" value="&lt;?xml-stylesheet" label="Lines containing one of these strings are skipped" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param argument="-whitelist" type="text" value="&lt;?xml-stylesheet" label="Lines containing one of these strings are skipped" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="whitelist"/>
         <expand macro="list_string_san" name="whitelist"/>
       </param>
@@ -57,7 +56,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <expand macro="list_string_san" name="matched_whitelist"/>
       </param>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -73,11 +72,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_FuzzyDiff_3 -->
+  <tests>
+    <!-- TOPP_FuzzyDiff_3 -->
     <test expect_num_outputs="1">
       <section name="adv_opts">
         <param name="whitelist" value="&quot;&lt;?xml-stylesheet&quot;"/>
-        <param name="matched_whitelist" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
@@ -94,11 +93,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Compares two files, tolerating numeric differences.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_FuzzyDiff.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FuzzyDiff.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/GNPSExport.xml b/tools/openms/GNPSExport.xml
index a317c01bf..0e0ff93b7 100644
--- a/tools/openms/GNPSExport.xml
+++ b/tools/openms/GNPSExport.xml
@@ -1,9 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [File Handling]-->
+<!--Proposed Tool Section: [File Converter]-->
 <tool id="GNPSExport" name="GNPSExport" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Tool to export representative consensus MS/MS scan per consensusElement into a .MGF file format.
-See the documentation on https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-openms</description>
+  <description>Tool to export representative consensus MS/MS scan per consensusElement into a .MGF file format</description>
   <macros>
     <token name="@EXECUTABLE@">GNPSExport</token>
     <import>macros.xml</import>
@@ -16,15 +14,22 @@ See the documentation on https://ccms-ucsd.github.io/GNPSDocumentation/featureba
 
 ## Preprocessing
 mkdir in_cm &&
-ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
+cp '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
 mkdir in_mzml_cond.in_mzml &&
 #if $in_mzml_cond.in_mzml_select == "no"
 mkdir ${' '.join(["'in_mzml_cond.in_mzml/%s'" % (i) for i, f in enumerate($in_mzml_cond.in_mzml) if f])} && 
-${' '.join(["ln -s '%s' 'in_mzml_cond.in_mzml/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_mzml_cond.in_mzml) if f])}
+${' '.join(["cp '%s' 'in_mzml_cond.in_mzml/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_mzml_cond.in_mzml) if f])}
 #else
-ln -s '$in_mzml_cond.in_mzml' 'in_mzml_cond.in_mzml/${re.sub("[^\w\-_]", "_", $in_mzml_cond.in_mzml.element_identifier)}.$gxy2omsext($in_mzml_cond.in_mzml.ext)' &&
+cp '$in_mzml_cond.in_mzml' 'in_mzml_cond.in_mzml/${re.sub("[^\w\-_]", "_", $in_mzml_cond.in_mzml.element_identifier)}.$gxy2omsext($in_mzml_cond.in_mzml.ext)' &&
 #end if
 mkdir out &&
+mkdir out_quantification &&
+#if "out_pairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_pairs &&
+#end if
+#if "out_meta_values_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_meta_values &&
+#end if
 
 ## Main program call
 
@@ -42,9 +47,29 @@ ${' '.join(["'in_mzml_cond.in_mzml/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.elem
 #end if
 -out
 'out/output.${gxy2omsext("mgf")}'
+-out_quantification
+'out_quantification/output.${gxy2omsext("txt")}'
+#if "out_pairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_pairs
+  'out_pairs/output.${gxy2omsext("csv")}'
+#end if
+#if "out_meta_values_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_meta_values
+  'out_meta_values/output.${gxy2omsext("tabular")}'
+#end if
+#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
+  | tee '$stdout'
+#end if
 
 ## Postprocessing
 && mv 'out/output.${gxy2omsext("mgf")}' '$out'
+&& mv 'out_quantification/output.${gxy2omsext("txt")}' '$out_quantification'
+#if "out_pairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_pairs/output.${gxy2omsext("csv")}' '$out_pairs'
+#end if
+#if "out_meta_values_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_meta_values/output.${gxy2omsext("tabular")}' '$out_meta_values'
+#end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
@@ -53,47 +78,57 @@ ${' '.join(["'in_mzml_cond.in_mzml/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.elem
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in_cm" type="data" format="consensusxml" optional="false" label="Input consensusXML file containing only consensusElements with &quot;peptide&quot; annotations" help=" select consensusxml data sets(s)"/>
+    <param argument="-in_cm" type="data" format="consensusxml" label="Input consensusXML file containing only consensusElements with &quot;peptide&quot; annotations" help=" select consensusxml data sets(s)"/>
     <conditional name="in_mzml_cond">
       <param name="in_mzml_select" type="select" label="Run tool in batch mode for -in_mzml">
         <option value="no">No: process all datasets jointly</option>
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in_mzml" type="data" format="mzml" multiple="true" optional="false" label="Original mzml files containing the ms2 spectra (aka peptide annotation)" help="Must be in order that the consensusXML file maps the original mzML files select mzml data sets(s)"/>
+        <param argument="-in_mzml" type="data" format="mzml" multiple="true" label="Original mzml files containing the ms2 spectra (aka peptide annotation)" help="Must be in order that the consensusXML file maps the original mzML files select mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in_mzml" type="data" format="mzml" multiple="false" optional="false" label="Original mzml files containing the ms2 spectra (aka peptide annotation)" help="Must be in order that the consensusXML file maps the original mzML files select mzml data sets(s)"/>
+        <param argument="-in_mzml" type="data" format="mzml" label="Original mzml files containing the ms2 spectra (aka peptide annotation)" help="Must be in order that the consensusXML file maps the original mzML files select mzml data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-output_type" type="select" optional="true" label="specificity of mgf output information" help="">
+    <param argument="-output_type" type="select" label="specificity of mgf output information" help="">
       <option value="merged_spectra">merged_spectra</option>
       <option value="most_intense" selected="true">most_intense</option>
       <expand macro="list_string_san" name="output_type"/>
     </param>
-    <param argument="-peptide_cutoff" type="integer" optional="true" min="-1" value="5" label="Number of most intense peptides to consider per consensus element; '-1' to consider all identifications" help=""/>
-    <param argument="-ms2_bin_size" type="float" optional="true" min="0.0" value="0.019999999552965" label="Bin size (Da) for fragment ions when merging ms2 scans" help=""/>
+    <param argument="-peptide_cutoff" type="integer" min="-1" value="5" label="Number of most intense peptides to consider per consensus element; '-1' to consider all identifications" help=""/>
+    <param argument="-ms2_bin_size" type="float" min="0.0" value="0.019999999552965" label="Bin size (Da) for fragment ions when merging ms2 scans" help=""/>
     <section name="merged_spectra" title="Options for exporting mgf file with merged spectra per consensusElement" help="" expanded="false">
-      <param name="cos_similarity" argument="-merged_spectra:cos_similarity" type="float" optional="true" min="0.0" value="0.9" label="Cosine similarity threshold for merged_spectra output" help=""/>
+      <param name="cos_similarity" argument="-merged_spectra:cos_similarity" type="float" min="0.0" value="0.9" label="Cosine similarity threshold for merged_spectra output" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="out_pairs_FLAG">out_pairs (Output supplementary pairs table for IIMN)</option>
+      <option value="out_meta_values_FLAG">out_meta_values (Output meta value file)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
   <outputs>
     <data name="out" label="${tool.name} on ${on_string}: out" format="mgf"/>
+    <data name="out_quantification" label="${tool.name} on ${on_string}: out_quantification" format="txt"/>
+    <data name="out_pairs" label="${tool.name} on ${on_string}: out_pairs" format="csv">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_pairs_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="out_meta_values" label="${tool.name} on ${on_string}: out_meta_values" format="tabular">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_meta_values_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_GNPSExport_1 -->
-    <test expect_num_outputs="2">
+  <tests>
+    <!-- TOPP_GNPSExport_1 -->
+    <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -102,7 +137,8 @@ ${' '.join(["'in_mzml_cond.in_mzml/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.elem
       <conditional name="in_mzml_cond">
         <param name="in_mzml" value="GNPSExport_mzml1.mzML,GNPSExport_mzml2.mzML"/>
       </conditional>
-      <output name="out" file="GNPSExport_1_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
+      <output name="out" value="GNPSExport_1_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
+      <output name="out_quantification" value="GNPSExport_1_out_quant.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="output_type" value="most_intense"/>
       <param name="peptide_cutoff" value="10"/>
       <param name="ms2_bin_size" value="2.0"/>
@@ -115,9 +151,12 @@ ${' '.join(["'in_mzml_cond.in_mzml/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.elem
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_GNPSExport_2 -->
-    <test expect_num_outputs="2">
+    <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -126,7 +165,8 @@ ${' '.join(["'in_mzml_cond.in_mzml/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.elem
       <conditional name="in_mzml_cond">
         <param name="in_mzml" value="GNPSExport_mzml1.mzML,GNPSExport_mzml2.mzML"/>
       </conditional>
-      <output name="out" file="GNPSExport_2_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
+      <output name="out" value="GNPSExport_2_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
+      <output name="out_quantification" value="GNPSExport_2_out_quant.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="output_type" value="merged_spectra"/>
       <param name="peptide_cutoff" value="10"/>
       <param name="ms2_bin_size" value="2.0"/>
@@ -139,9 +179,12 @@ ${' '.join(["'in_mzml_cond.in_mzml/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.elem
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_GNPSExport_3 -->
-    <test expect_num_outputs="2">
+    <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -150,7 +193,8 @@ ${' '.join(["'in_mzml_cond.in_mzml/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.elem
       <conditional name="in_mzml_cond">
         <param name="in_mzml" value="GNPSExport_mzml1.mzML,GNPSExport_mzml2.mzML"/>
       </conditional>
-      <output name="out" file="GNPSExport_3_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
+      <output name="out" value="GNPSExport_3_out.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
+      <output name="out_quantification" value="GNPSExport_3_out_quant.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="output_type" value="most_intense"/>
       <param name="peptide_cutoff" value="10"/>
       <param name="ms2_bin_size" value="0.02"/>
@@ -163,12 +207,45 @@ ${' '.join(["'in_mzml_cond.in_mzml/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.elem
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_GNPSExport_4 -->
+    <test expect_num_outputs="5">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in_cm" value="GNPSExport_cons2.consensusXML"/>
+      <conditional name="in_mzml_cond">
+        <param name="in_mzml" value="GNPSExport_mzml1.mzML,GNPSExport_mzml2.mzML"/>
+      </conditional>
+      <output name="out" value="GNPSExport_4_out.tmp" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
+      <output name="out_quantification" value="GNPSExport_4_out_quant.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out_pairs" value="GNPSExport_4_out_pairs.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out_meta_values" value="GNPSExport_4_out_meta_values.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <param name="output_type" value="most_intense"/>
+      <param name="peptide_cutoff" value="5"/>
+      <param name="ms2_bin_size" value="0.019999999552965"/>
+      <section name="merged_spectra">
+        <param name="cos_similarity" value="0.9"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_pairs_FLAG,out_meta_values_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Tool to export representative consensus MS/MS scan per consensusElement into a .MGF file format.
 See the documentation on https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-openms
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_GNPSExport.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_GNPSExport.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/HighResPrecursorMassCorrector.xml b/tools/openms/HighResPrecursorMassCorrector.xml
index 3790e12e6..a3a05ebdd 100644
--- a/tools/openms/HighResPrecursorMassCorrector.xml
+++ b/tools/openms/HighResPrecursorMassCorrector.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Mass Correction and Calibration]-->
 <tool id="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Corrects the precursor mass and charge determined by the instrument software.</description>
+  <description>Corrects the precursor mass and charge determined by the instrument software</description>
   <macros>
     <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</token>
     <import>macros.xml</import>
@@ -15,14 +14,14 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_csv &&
 #end if
 #if $feature.in:
   mkdir feature.in &&
-  ln -s '$feature.in' 'feature.in/${re.sub("[^\w\-_]", "_", $feature.in.element_identifier)}.$gxy2omsext($feature.in.ext)' &&
+  cp '$feature.in' 'feature.in/${re.sub("[^\w\-_]", "_", $feature.in.element_identifier)}.$gxy2omsext($feature.in.ext)' &&
 #end if
 
 ## Main program call
@@ -60,32 +59,32 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file (centroided data)" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Input file (centroided data)" help=" select mzml data sets(s)"/>
     <section name="feature" title="Use features for precursor mass correction" help="" expanded="false">
       <param name="in" argument="-feature:in" type="data" format="featurexml" optional="true" label="Features used to correct precursor masses" help=" select featurexml data sets(s)"/>
-      <param name="mz_tolerance" argument="-feature:mz_tolerance" type="float" optional="true" value="5.0" label="The precursor mass tolerance" help="Used to determine matching to feature mass traces"/>
-      <param name="mz_tolerance_unit" argument="-feature:mz_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
+      <param name="mz_tolerance" argument="-feature:mz_tolerance" type="float" value="5.0" label="The precursor mass tolerance" help="Used to determine matching to feature mass traces"/>
+      <param name="mz_tolerance_unit" argument="-feature:mz_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mz_tolerance_unit"/>
       </param>
-      <param name="rt_tolerance" argument="-feature:rt_tolerance" type="float" optional="true" value="0.0" label="Additional retention time tolerance added to feature boundaries" help=""/>
-      <param name="max_trace" argument="-feature:max_trace" type="integer" optional="true" value="2" label="Maximum isotopic trace considered in matching a precursor to a feature" help=""/>
+      <param name="rt_tolerance" argument="-feature:rt_tolerance" type="float" value="0.0" label="Additional retention time tolerance added to feature boundaries" help=""/>
+      <param name="max_trace" argument="-feature:max_trace" type="integer" value="2" label="Maximum isotopic trace considered in matching a precursor to a feature" help=""/>
       <param name="believe_charge" argument="-feature:believe_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assume precursor charge to be correct" help=""/>
       <param name="keep_original" argument="-feature:keep_original" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Make a copy of the precursor and MS2 (true) or discard the original (false)" help=""/>
       <param name="assign_all_matching" argument="-feature:assign_all_matching" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Correct a precursor using all matching features (true) or only the nearest (false)" help="Only evaluated if copies are created (feature:keep_original)"/>
     </section>
     <section name="nearest_peak" title="Use nearest centroided MS1 peak for precursor mass correction" help="" expanded="false">
-      <param name="mz_tolerance" argument="-nearest_peak:mz_tolerance" type="float" optional="true" value="0.0" label="The precursor mass tolerance to find the closest MS1 peak" help="(Disable method by setting value to 0.0)"/>
-      <param name="mz_tolerance_unit" argument="-nearest_peak:mz_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
+      <param name="mz_tolerance" argument="-nearest_peak:mz_tolerance" type="float" value="0.0" label="The precursor mass tolerance to find the closest MS1 peak" help="(Disable method by setting value to 0.0)"/>
+      <param name="mz_tolerance_unit" argument="-nearest_peak:mz_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mz_tolerance_unit"/>
       </param>
     </section>
     <section name="highest_intensity_peak" title="Use centroided MS1 peak with the highest intensity in a certrain mass range - for precursor mass correction" help="" expanded="false">
-      <param name="mz_tolerance" argument="-highest_intensity_peak:mz_tolerance" type="float" optional="true" value="0.0" label="The precursor mass tolerance to find the highest intensity MS1 peak" help="Suggested value 1/max. expected charge. (Disable method by setting value to 0.0)"/>
-      <param name="mz_tolerance_unit" argument="-highest_intensity_peak:mz_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
+      <param name="mz_tolerance" argument="-highest_intensity_peak:mz_tolerance" type="float" value="0.0" label="The precursor mass tolerance to find the highest intensity MS1 peak" help="Suggested value 1/max. expected charge. (Disable method by setting value to 0.0)"/>
+      <param name="mz_tolerance_unit" argument="-highest_intensity_peak:mz_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mz_tolerance_unit"/>
@@ -93,7 +92,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -111,14 +110,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_HighResPrecursorMassCorrector_1 -->
+  <tests>
+    <!-- TOPP_HighResPrecursorMassCorrector_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="feature">
         <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.featureXML"/>
         <param name="mz_tolerance" value="5.0"/>
@@ -143,39 +143,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
-    </test>
-    <!-- TOPP_HighResPrecursorMassCorrector_2 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_1035_1178_4_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
-      <section name="feature">
-        <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.featureXML"/>
-        <param name="mz_tolerance" value="10.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-        <param name="rt_tolerance" value="0.0"/>
-        <param name="max_trace" value="4"/>
-        <param name="believe_charge" value="false"/>
-        <param name="keep_original" value="false"/>
-        <param name="assign_all_matching" value="false"/>
-      </section>
-      <section name="nearest_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="highest_intensity_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_HighResPrecursorMassCorrector_3 -->
     <test expect_num_outputs="2">
@@ -184,7 +154,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="feature">
         <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.featureXML"/>
         <param name="mz_tolerance" value="5.0"/>
@@ -209,6 +179,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_HighResPrecursorMassCorrector_4 -->
     <test expect_num_outputs="2">
@@ -217,7 +190,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="feature">
         <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.featureXML"/>
         <param name="mz_tolerance" value="5.0"/>
@@ -242,6 +215,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_HighResPrecursorMassCorrector_5 -->
     <test expect_num_outputs="2">
@@ -250,7 +226,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="feature">
         <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.featureXML"/>
         <param name="mz_tolerance" value="5.0"/>
@@ -275,6 +251,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_HighResPrecursorMassCorrector_6 -->
     <test expect_num_outputs="2">
@@ -283,7 +262,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="HighResPrecursorMassCorrector_6.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="feature">
         <param name="mz_tolerance" value="5.0"/>
         <param name="mz_tolerance_unit" value="ppm"/>
@@ -307,11 +286,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Corrects the precursor mass and charge determined by the instrument software.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_HighResPrecursorMassCorrector.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_HighResPrecursorMassCorrector.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/IDConflictResolver.xml b/tools/openms/IDConflictResolver.xml
index 373575e09..4781b30db 100644
--- a/tools/openms/IDConflictResolver.xml
+++ b/tools/openms/IDConflictResolver.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [ID Processing]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="IDConflictResolver" name="IDConflictResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Resolves ambiguous annotations of features with peptide identifications</description>
   <macros>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,15 +38,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="Input file (data annotated with identifications)" help=" select consensusxml,featurexml data sets(s)"/>
-    <param argument="-resolve_between_features" type="select" optional="true" label="A map may contain multiple features with both identical (possibly modified" help="i.e. not stripped) sequence and charge state. The feature with the 'highest intensity' is very likely the most reliable one. When switched on, the filter removes the sequence annotation from the lower intensity features, thereby resolving the multiplicity. Only the most reliable features for each (possibly modified i.e. not stripped) sequence maintain annotated with this peptide sequence">
+    <param argument="-in" type="data" format="consensusxml,featurexml" label="Input file (data annotated with identifications)" help=" select consensusxml,featurexml data sets(s)"/>
+    <param argument="-resolve_between_features" type="select" label="A map may contain multiple features with both identical (possibly modified" help="i.e. not stripped) sequence and charge state. The feature with the 'highest intensity' is very likely the most reliable one. When switched on, the filter removes the sequence annotation from the lower intensity features, thereby resolving the multiplicity. Only the most reliable features for each (possibly modified i.e. not stripped) sequence maintain annotated with this peptide sequence">
       <option value="off" selected="true">off</option>
       <option value="highest_intensity">highest_intensity</option>
       <expand macro="list_string_san" name="resolve_between_features"/>
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -61,14 +60,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_IDConflictResolver_1 -->
+  <tests>
+    <!-- TOPP_IDConflictResolver_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDConflictResolver_1_input.featureXML"/>
-      <output name="out" file="IDConflictResolver_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="IDConflictResolver_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="resolve_between_features" value="off"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -76,6 +76,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDConflictResolver_2 -->
     <test expect_num_outputs="2">
@@ -84,7 +87,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDConflictResolver_2_input.consensusXML"/>
-      <output name="out" file="IDConflictResolver_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="IDConflictResolver_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="resolve_between_features" value="off"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -92,6 +95,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDConflictResolver_3 -->
     <test expect_num_outputs="2">
@@ -100,7 +106,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDConflictResolver_3_input.consensusXML"/>
-      <output name="out" file="IDConflictResolver_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="IDConflictResolver_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="resolve_between_features" value="off"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -108,6 +114,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDConflictResolver_4 -->
     <test expect_num_outputs="2">
@@ -116,7 +125,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDConflictResolver_4_input.featureXML"/>
-      <output name="out" file="IDConflictResolver_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="IDConflictResolver_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="resolve_between_features" value="highest_intensity"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -124,11 +133,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Resolves ambiguous annotations of features with peptide identifications
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDConflictResolver.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDConflictResolver.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/IDExtractor.xml b/tools/openms/IDExtractor.xml
index 7efe28e47..a43fb5cab 100644
--- a/tools/openms/IDExtractor.xml
+++ b/tools/openms/IDExtractor.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="IDExtractor" name="IDExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Extracts 'n' peptides randomly or best 'n' from idXML files.</description>
+  <description>Extracts 'n' peptides randomly or best 'n' from idXML files</description>
   <macros>
     <token name="@EXECUTABLE@">IDExtractor</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,13 +38,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/>
-    <param argument="-number_of_peptides" type="integer" optional="true" min="1" value="10" label="Number of randomly chosen peptides" help=""/>
-    <param argument="-number_of_rand_invokations" type="integer" optional="true" min="0" value="0" label="Number of rand invocations before random draw (basically a seed)" help=""/>
+    <param argument="-in" type="data" format="idxml" label="input file" help=" select idxml data sets(s)"/>
+    <param argument="-number_of_peptides" type="integer" min="1" value="10" label="Number of randomly chosen peptides" help=""/>
+    <param argument="-number_of_rand_invokations" type="integer" min="0" value="0" label="Number of rand invocations before random draw (basically a seed)" help=""/>
     <param argument="-best_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set the best n peptides are chosen" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -59,17 +58,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!--  -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
-    <param name="best_hits" value="true"/>
-    <param name="number_of_peptides" value="1"/>
-    <output name="out" value="IDExtractor.idXML" compare="sim_size"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!--  -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
+      <param name="best_hits" value="true"/>
+      <param name="number_of_peptides" value="1"/>
+      <output name="out" value="IDExtractor.idXML" compare="sim_size"/>
+    </test>
+  </tests>
   <help><![CDATA[Extracts 'n' peptides randomly or best 'n' from idXML files.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_IDExtractor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDExtractor.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/IDFileConverter.xml b/tools/openms/IDFileConverter.xml
index 21d6f1754..e34aa898e 100644
--- a/tools/openms/IDFileConverter.xml
+++ b/tools/openms/IDFileConverter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [ID Processing]-->
+<!--Proposed Tool Section: [File Converter]-->
 <tool id="IDFileConverter" name="IDFileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Converts identification engine file formats.</description>
+  <description>Converts identification engine file formats</description>
   <macros>
     <token name="@EXECUTABLE@">IDFileConverter</token>
     <import>macros.xml</import>
@@ -15,11 +14,11 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if $mz_file:
   mkdir mz_file &&
-  ln -s '$mz_file' 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)' &&
+  cp '$mz_file' 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)' &&
 #end if
 
 ## Main program call
@@ -47,8 +46,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="fasta,idxml,mascotxml,mzid,pepxml,protxml,psms,sqlite,tabular,xquest.xml" optional="false" label="Input file or directory containing the data to convert" help="This may be:. - a single file in OpenMS database format (.oms),. - a single file in a multi-purpose XML format (.idXML, .mzid, .pepXML, .protXML),. - a single file in a search engine-specific format (Mascot: .mascotXML, OMSSA: .omssaXML, X! Tandem: .xml, Percolator: .psms, xQuest: .xquest.xml),. - a single file in fasta format (can only be used to generate a theoretical mzML),. - a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits),. - for Sequest results, a directory containing .out files..  select fasta,idxml,mascotxml,mzid,pepxml,protxml,psms,sqlite,tabular,xquest.xml data sets(s)"/>
-    <param argument="-out_type" type="select" optional="false" label="Output file type (default: determined from file extension)" help="">
+    <param argument="-in" type="data" format="fasta,idxml,mascotxml,mzid,pepxml,protxml,psms,sqlite,tabular,xquest.xml" label="Input file or directory containing the data to convert" help="This may be:. - a single file in OpenMS database format (.oms),. - a single file in a multi-purpose XML format (.idXML, .mzid, .pepXML, .protXML),. - a single file in a search engine-specific format (Mascot: .mascotXML, OMSSA: .omssaXML, X! Tandem: .xml, Percolator: .psms, xQuest: .xquest.xml),. - a single file in fasta format (can only be used to generate a theoretical mzML),. - a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits),. - for Sequest results, a directory containing .out files..  select fasta,idxml,mascotxml,mzid,pepxml,protxml,psms,sqlite,tabular,xquest.xml data sets(s)"/>
+    <param argument="-out_type" type="select" label="Output file type (default: determined from file extension)" help="">
       <option value="fasta">fasta</option>
       <option value="idXML">idxml</option>
       <option value="mzML">mzml</option>
@@ -56,6 +55,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="oms">sqlite (oms)</option>
       <option value="pepXML">pepxml</option>
       <option value="xquest.xml">xquest.xml</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
     <param argument="-mz_file" type="data" format="mzdata,mzml,mzxml" optional="true" label="[pepXML, Sequest, Mascot, X" help="Tandem, mzid, Percolator only] Retention times and native spectrum ids (spectrum_references) will be looked up in this file select mzdata,mzml,mzxml data sets(s)"/>
@@ -63,21 +63,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <expand macro="list_string_san" name="mz_name"/>
     </param>
     <param argument="-peptideprophet_analyzed" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result" help="By default a 'raw' pepXML is produced that contains only search engine results"/>
-    <param argument="-score_type" type="select" optional="true" label="[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit" help="">
+    <param argument="-score_type" type="select" label="[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit" help="">
       <option value="qvalue" selected="true">qvalue</option>
       <option value="PEP">PEP</option>
       <option value="score">score</option>
       <expand macro="list_string_san" name="score_type"/>
     </param>
     <section name="fasta_to_mzml" title="[FASTA input + MzML output only] Parameters used to adjust simulation of the theoretical spectra" help="" expanded="false">
-      <param name="isotope_model" argument="-fasta_to_mzml:isotope_model" type="select" optional="true" label="Model to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks" help="Note that adding isotopic peaks is very slow">
+      <param name="isotope_model" argument="-fasta_to_mzml:isotope_model" type="select" label="Model to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks" help="Note that adding isotopic peaks is very slow">
         <option value="none" selected="true">none</option>
         <option value="coarse">coarse</option>
         <option value="fine">fine</option>
         <expand macro="list_string_san" name="isotope_model"/>
       </param>
-      <param name="max_isotope" argument="-fasta_to_mzml:max_isotope" type="integer" optional="true" value="2" label="Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'" help=""/>
-      <param name="max_isotope_probability" argument="-fasta_to_mzml:max_isotope_probability" type="float" optional="true" value="0.05" label="Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'" help=""/>
+      <param name="max_isotope" argument="-fasta_to_mzml:max_isotope" type="integer" value="2" label="Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'" help=""/>
+      <param name="max_isotope_probability" argument="-fasta_to_mzml:max_isotope_probability" type="float" value="0.05" label="Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'" help=""/>
       <param name="add_metainfo" argument="-fasta_to_mzml:add_metainfo" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help=""/>
       <param name="add_losses" argument="-fasta_to_mzml:add_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help=""/>
       <param name="sort_by_position" argument="-fasta_to_mzml:sort_by_position" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Sort output by position" help=""/>
@@ -91,56 +91,56 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="add_c_ions" argument="-fasta_to_mzml:add_c_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of c-ions to the spectrum" help=""/>
       <param name="add_x_ions" argument="-fasta_to_mzml:add_x_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of  x-ions to the spectrum" help=""/>
       <param name="add_z_ions" argument="-fasta_to_mzml:add_z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of z-ions to the spectrum" help=""/>
-      <param name="y_intensity" argument="-fasta_to_mzml:y_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the y-ions" help=""/>
-      <param name="b_intensity" argument="-fasta_to_mzml:b_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the b-ions" help=""/>
-      <param name="a_intensity" argument="-fasta_to_mzml:a_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the a-ions" help=""/>
-      <param name="c_intensity" argument="-fasta_to_mzml:c_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the c-ions" help=""/>
-      <param name="x_intensity" argument="-fasta_to_mzml:x_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the x-ions" help=""/>
-      <param name="z_intensity" argument="-fasta_to_mzml:z_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the z-ions" help=""/>
-      <param name="relative_loss_intensity" argument="-fasta_to_mzml:relative_loss_intensity" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help=""/>
-      <param name="precursor_intensity" argument="-fasta_to_mzml:precursor_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the precursor peak" help=""/>
-      <param name="precursor_H2O_intensity" argument="-fasta_to_mzml:precursor_H2O_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the H2O loss peak of the precurso" help=""/>
-      <param name="precursor_NH3_intensity" argument="-fasta_to_mzml:precursor_NH3_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the NH3 loss peak of the precurso" help=""/>
-      <param name="enzyme" argument="-fasta_to_mzml:enzyme" type="select" optional="true" label="Enzym used to digest the fasta proteins" help="">
+      <param name="y_intensity" argument="-fasta_to_mzml:y_intensity" type="float" min="0.0" value="1.0" label="Intensity of the y-ions" help=""/>
+      <param name="b_intensity" argument="-fasta_to_mzml:b_intensity" type="float" min="0.0" value="1.0" label="Intensity of the b-ions" help=""/>
+      <param name="a_intensity" argument="-fasta_to_mzml:a_intensity" type="float" min="0.0" value="1.0" label="Intensity of the a-ions" help=""/>
+      <param name="c_intensity" argument="-fasta_to_mzml:c_intensity" type="float" min="0.0" value="1.0" label="Intensity of the c-ions" help=""/>
+      <param name="x_intensity" argument="-fasta_to_mzml:x_intensity" type="float" min="0.0" value="1.0" label="Intensity of the x-ions" help=""/>
+      <param name="z_intensity" argument="-fasta_to_mzml:z_intensity" type="float" min="0.0" value="1.0" label="Intensity of the z-ions" help=""/>
+      <param name="relative_loss_intensity" argument="-fasta_to_mzml:relative_loss_intensity" type="float" min="0.0" max="1.0" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help=""/>
+      <param name="precursor_intensity" argument="-fasta_to_mzml:precursor_intensity" type="float" min="0.0" value="1.0" label="Intensity of the precursor peak" help=""/>
+      <param name="precursor_H2O_intensity" argument="-fasta_to_mzml:precursor_H2O_intensity" type="float" min="0.0" value="1.0" label="Intensity of the H2O loss peak of the precurso" help=""/>
+      <param name="precursor_NH3_intensity" argument="-fasta_to_mzml:precursor_NH3_intensity" type="float" min="0.0" value="1.0" label="Intensity of the NH3 loss peak of the precurso" help=""/>
+      <param name="enzyme" argument="-fasta_to_mzml:enzyme" type="select" label="Enzym used to digest the fasta proteins" help="">
         <option value="Trypsin" selected="true">Trypsin</option>
-        <option value="Chymotrypsin">Chymotrypsin</option>
-        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
-        <option value="CNBr">CNBr</option>
-        <option value="Formic_acid">Formic_acid</option>
-        <option value="leukocyte elastase">leukocyte elastase</option>
-        <option value="proline endopeptidase">proline endopeptidase</option>
-        <option value="Arg-C/P">Arg-C/P</option>
-        <option value="Asp-N">Asp-N</option>
-        <option value="Asp-N/B">Asp-N/B</option>
-        <option value="Asp-N_ambic">Asp-N_ambic</option>
+        <option value="Arg-C">Arg-C</option>
+        <option value="no cleavage">no cleavage</option>
+        <option value="unspecific cleavage">unspecific cleavage</option>
+        <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
+        <option value="Glu-C+P">Glu-C+P</option>
+        <option value="PepsinA + P">PepsinA + P</option>
+        <option value="cyanogen-bromide">cyanogen-bromide</option>
+        <option value="Clostripain/P">Clostripain/P</option>
+        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
         <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
         <option value="Alpha-lytic protease">Alpha-lytic protease</option>
         <option value="2-iodobenzoate">2-iodobenzoate</option>
         <option value="iodosobenzoate">iodosobenzoate</option>
-        <option value="cyanogen-bromide">cyanogen-bromide</option>
-        <option value="Clostripain/P">Clostripain/P</option>
-        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
-        <option value="no cleavage">no cleavage</option>
-        <option value="unspecific cleavage">unspecific cleavage</option>
+        <option value="staphylococcal protease/D">staphylococcal protease/D</option>
+        <option value="Trypsin/P">Trypsin/P</option>
+        <option value="V8-DE">V8-DE</option>
+        <option value="Arg-C/P">Arg-C/P</option>
+        <option value="Asp-N">Asp-N</option>
+        <option value="Asp-N/B">Asp-N/B</option>
+        <option value="Asp-N_ambic">Asp-N_ambic</option>
+        <option value="Chymotrypsin">Chymotrypsin</option>
+        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+        <option value="CNBr">CNBr</option>
+        <option value="Formic_acid">Formic_acid</option>
         <option value="Lys-C">Lys-C</option>
         <option value="Lys-N">Lys-N</option>
         <option value="Lys-C/P">Lys-C/P</option>
         <option value="PepsinA">PepsinA</option>
         <option value="TrypChymo">TrypChymo</option>
-        <option value="Trypsin/P">Trypsin/P</option>
-        <option value="V8-DE">V8-DE</option>
         <option value="V8-E">V8-E</option>
-        <option value="staphylococcal protease/D">staphylococcal protease/D</option>
-        <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
-        <option value="Glu-C+P">Glu-C+P</option>
-        <option value="PepsinA + P">PepsinA + P</option>
-        <option value="Arg-C">Arg-C</option>
+        <option value="leukocyte elastase">leukocyte elastase</option>
+        <option value="proline endopeptidase">proline endopeptidase</option>
         <expand macro="list_string_san" name="enzyme"/>
       </param>
-      <param name="missed_cleavages" argument="-fasta_to_mzml:missed_cleavages" type="integer" optional="true" value="0" label="Number of allowed missed cleavages while digesting the fasta proteins" help=""/>
-      <param name="min_charge" argument="-fasta_to_mzml:min_charge" type="integer" optional="true" value="1" label="Minimum charge" help=""/>
-      <param name="max_charge" argument="-fasta_to_mzml:max_charge" type="integer" optional="true" value="1" label="Maximum charge" help=""/>
-      <param name="precursor_charge" argument="-fasta_to_mzml:precursor_charge" type="integer" optional="true" value="0" label="Manually set precursor charge" help="(default: 0, meaning max_charge + 1 will be used as precursor charge)"/>
+      <param name="missed_cleavages" argument="-fasta_to_mzml:missed_cleavages" type="integer" value="0" label="Number of allowed missed cleavages while digesting the fasta proteins" help=""/>
+      <param name="min_charge" argument="-fasta_to_mzml:min_charge" type="integer" value="1" label="Minimum charge" help=""/>
+      <param name="max_charge" argument="-fasta_to_mzml:max_charge" type="integer" value="1" label="Maximum charge" help=""/>
+      <param name="precursor_charge" argument="-fasta_to_mzml:precursor_charge" type="integer" value="0" label="Manually set precursor charge" help="(default: 0, meaning max_charge + 1 will be used as precursor charge)"/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-ignore_proteins_per_peptide" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[Sequest only] Workaround to deal with .out files that contain" help="e.g. &quot;+1&quot; in references column,. but do not list extra references in subsequent lines (try -debug 3 or 4)"/>
@@ -149,11 +149,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </param>
       <param argument="-no_spectra_data_override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[+mz_file only] Avoid overriding 'spectra_data' in protein identifications if 'mz_file' is given and 'spectrum_reference's are added/updated" help="Use only if you are sure it is absolutely the same 'mz_file' as used for identification"/>
       <param argument="-no_spectra_references_override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[+mz_file only] Avoid overriding 'spectrum_reference' in peptide identifications if 'mz_file' is given and a 'spectrum_reference' is already present" help=""/>
-      <param argument="-add_ionmatch_annotation" type="float" optional="true" value="0.0" label="[+mz_file only] Annotate the identifications with ion matches from spectra in 'mz_file' using the given tolerance (in Da)" help="This will take quite some time"/>
+      <param argument="-add_ionmatch_annotation" type="float" value="0.0" label="[+mz_file only] Annotate the identifications with ion matches from spectra in 'mz_file' using the given tolerance (in Da)" help="This will take quite some time"/>
       <param argument="-concatenate_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[FASTA output only] Will concatenate the top peptide hits to one peptide sequence, rather than write a new peptide for each hit" help=""/>
-      <param argument="-number_of_hits" type="integer" optional="true" value="1" label="[FASTA output only] Controls how many peptide hits will be exported" help="A value of 0 or less exports all hits"/>
+      <param argument="-number_of_hits" type="integer" value="1" label="[FASTA output only] Controls how many peptide hits will be exported" help="A value of 0 or less exports all hits"/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -176,7 +176,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_IDFileConverter_1 -->
+  <tests>
+    <!-- TOPP_IDFileConverter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="ignore_proteins_per_peptide" value="false"/>
@@ -190,7 +191,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
-      <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
       <param name="mz_name" value=""/>
@@ -235,6 +236,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_2 -->
     <test expect_num_outputs="2">
@@ -250,7 +254,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PepXMLFile_test.pepxml"/>
-      <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_file" value="PepXMLFile_test.mzML"/>
       <param name="mz_name" value="PepXMLFile_test"/>
@@ -295,6 +299,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_3 -->
     <test expect_num_outputs="2">
@@ -310,7 +317,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_3_input.protXML"/>
-      <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -354,6 +361,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_5 -->
     <test expect_num_outputs="2">
@@ -369,7 +379,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
-      <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
       <param name="mz_name" value=""/>
@@ -414,6 +424,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_6 -->
     <test expect_num_outputs="2">
@@ -429,7 +442,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_6_input1.pepXML"/>
-      <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
       <param name="mz_name" value="F025589.dat.mzML"/>
@@ -474,6 +487,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_7 -->
     <test expect_num_outputs="2">
@@ -489,7 +505,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_7_input1.xml"/>
-      <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -533,6 +549,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_8 -->
     <test expect_num_outputs="2">
@@ -548,7 +567,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_8_input.mzid"/>
-      <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -592,6 +611,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_9 -->
     <test expect_num_outputs="2">
@@ -607,7 +629,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_9_input.idXML"/>
-      <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
+      <output name="out" value="IDFileConverter_9_output.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
       <param name="out_type" value="mzid"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -651,6 +673,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_10 -->
     <test expect_num_outputs="2">
@@ -666,7 +691,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_10_input.pepXML"/>
-      <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_10_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -710,6 +735,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_11 -->
     <test expect_num_outputs="2">
@@ -725,7 +753,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/>
-      <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_11_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -769,6 +797,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_12 -->
     <test expect_num_outputs="2">
@@ -784,7 +815,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_12_input.psms"/>
-      <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_12_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -828,6 +859,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_13 -->
     <test expect_num_outputs="2">
@@ -843,7 +877,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_12_input.psms"/>
-      <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -887,6 +921,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_14 -->
     <test expect_num_outputs="2">
@@ -902,7 +939,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_12_input.psms"/>
-      <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_14_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -946,6 +983,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_15 -->
     <test expect_num_outputs="2">
@@ -961,7 +1001,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
-      <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_15_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_file" value="spectra.mzML"/>
       <param name="mz_name" value=""/>
@@ -1006,6 +1046,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_16 -->
     <test expect_num_outputs="2">
@@ -1021,7 +1064,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_16_input.pepXML"/>
-      <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_16_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -1065,6 +1108,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_17 -->
     <test expect_num_outputs="2">
@@ -1080,7 +1126,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_17_input.idXML"/>
-      <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
+      <output name="out" value="IDFileConverter_17_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
       <param name="out_type" value="pepXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -1124,6 +1170,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_18 -->
     <test expect_num_outputs="2">
@@ -1139,7 +1188,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_18_input.idXML"/>
-      <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
+      <output name="out" value="IDFileConverter_18_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
       <param name="out_type" value="pepXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -1183,6 +1232,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_19 -->
     <test expect_num_outputs="2">
@@ -1198,7 +1250,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_19_input.idXML"/>
-      <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
+      <output name="out" value="IDFileConverter_19_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
       <param name="out_type" value="pepXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -1242,6 +1294,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_20 -->
     <test expect_num_outputs="2">
@@ -1257,7 +1312,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_20_input.idXML"/>
-      <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
+      <output name="out" value="IDFileConverter_20_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
       <param name="out_type" value="pepXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -1301,6 +1356,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_21 -->
     <test expect_num_outputs="2">
@@ -1316,7 +1374,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_21_input.idXML"/>
-      <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_21_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_file" value="IDMapper_4_input.mzML"/>
       <param name="mz_name" value=""/>
@@ -1361,6 +1419,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_22 -->
     <test expect_num_outputs="2">
@@ -1376,7 +1437,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
-      <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_22_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_file" value="spectra.mzML"/>
       <param name="mz_name" value=""/>
@@ -1421,6 +1482,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_23 -->
     <test expect_num_outputs="2">
@@ -1436,7 +1500,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_23_input.mzid"/>
-      <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_23_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -1480,6 +1544,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_24 -->
     <test expect_num_outputs="2">
@@ -1495,7 +1562,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_24_input.pep.xml"/>
-      <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_24_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -1539,6 +1606,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_25 -->
     <test expect_num_outputs="2">
@@ -1554,7 +1624,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_25_input.idXML"/>
-      <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
+      <output name="out" value="IDFileConverter_25_output.pep.xml" compare="sim_size" delta_frac="0.7" ftype="pepxml"/>
       <param name="out_type" value="pepXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -1598,6 +1668,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_26 -->
     <test expect_num_outputs="2">
@@ -1613,7 +1686,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_26_input.mzid"/>
-      <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_26_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -1657,6 +1730,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_27 -->
     <test expect_num_outputs="2">
@@ -1672,7 +1748,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_27_input.idXML"/>
-      <output name="out" file="IDFileConverter_27_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
+      <output name="out" value="IDFileConverter_27_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
       <param name="out_type" value="fasta"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -1716,6 +1792,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_28 -->
     <test expect_num_outputs="2">
@@ -1731,7 +1810,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_27_input.idXML"/>
-      <output name="out" file="IDFileConverter_28_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
+      <output name="out" value="IDFileConverter_28_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
       <param name="out_type" value="fasta"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -1775,6 +1854,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_29 -->
     <test expect_num_outputs="2">
@@ -1790,7 +1872,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_27_input.idXML"/>
-      <output name="out" file="IDFileConverter_29_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
+      <output name="out" value="IDFileConverter_29_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
       <param name="out_type" value="fasta"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -1834,6 +1916,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_30 -->
     <test expect_num_outputs="2">
@@ -1849,7 +1934,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_27_input.idXML"/>
-      <output name="out" file="IDFileConverter_30_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
+      <output name="out" value="IDFileConverter_30_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
       <param name="out_type" value="fasta"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -1893,6 +1978,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_31 -->
     <test expect_num_outputs="2">
@@ -1908,7 +1996,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_31_input.mzid"/>
-      <output name="out" file="IDFileConverter_31_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_31_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -1952,6 +2040,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_32 -->
     <test expect_num_outputs="2">
@@ -1967,7 +2058,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_32_input.FASTA"/>
-      <output name="out" file="IDFileConverter_32_output.tmp" compare="sim_size" delta_frac="0.7"/>
+      <output name="out" value="IDFileConverter_32_output.tmp" compare="sim_size" delta_frac="0.7"/>
       <param name="out_type" value="mzML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -2011,6 +2102,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_33 -->
     <test expect_num_outputs="2">
@@ -2026,7 +2120,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_32_input.FASTA"/>
-      <output name="out" file="IDFileConverter_33_output.tmp" compare="sim_size" delta_frac="0.7"/>
+      <output name="out" value="IDFileConverter_33_output.tmp" compare="sim_size" delta_frac="0.7"/>
       <param name="out_type" value="mzML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -2070,6 +2164,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_34_1 -->
     <test expect_num_outputs="2">
@@ -2085,7 +2182,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_34_input.idXML"/>
-      <output name="out" file="IDFileConverter_34_output1.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
+      <output name="out" value="IDFileConverter_34_output1.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
       <param name="out_type" value="oms"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -2129,6 +2226,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFileConverter_34_2 -->
     <test expect_num_outputs="2">
@@ -2144,7 +2244,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_34_output1.oms"/>
-      <output name="out" file="IDFileConverter_34_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFileConverter_34_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="mz_name" value=""/>
       <param name="peptideprophet_analyzed" value="false"/>
@@ -2188,11 +2288,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Converts identification engine file formats.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDFileConverter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDFileConverter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/IDFilter.xml b/tools/openms/IDFilter.xml
index 771bc43ef..312b25589 100644
--- a/tools/openms/IDFilter.xml
+++ b/tools/openms/IDFilter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [ID Processing]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="IDFilter" name="IDFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Filters results from protein or peptide identification engines based on different criteria.</description>
+  <description>Filters results from protein or peptide identification engines based on different criteria</description>
   <macros>
     <token name="@EXECUTABLE@">IDFilter</token>
     <import>macros.xml</import>
@@ -15,27 +14,27 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if $whitelist.proteins:
   mkdir whitelist.proteins &&
-  ln -s '$whitelist.proteins' 'whitelist.proteins/${re.sub("[^\w\-_]", "_", $whitelist.proteins.element_identifier)}.$gxy2omsext($whitelist.proteins.ext)' &&
+  cp '$whitelist.proteins' 'whitelist.proteins/${re.sub("[^\w\-_]", "_", $whitelist.proteins.element_identifier)}.$gxy2omsext($whitelist.proteins.ext)' &&
 #end if
 #if $whitelist.peptides:
   mkdir whitelist.peptides &&
-  ln -s '$whitelist.peptides' 'whitelist.peptides/${re.sub("[^\w\-_]", "_", $whitelist.peptides.element_identifier)}.$gxy2omsext($whitelist.peptides.ext)' &&
+  cp '$whitelist.peptides' 'whitelist.peptides/${re.sub("[^\w\-_]", "_", $whitelist.peptides.element_identifier)}.$gxy2omsext($whitelist.peptides.ext)' &&
 #end if
 #if $blacklist.proteins:
   mkdir blacklist.proteins &&
-  ln -s '$blacklist.proteins' 'blacklist.proteins/${re.sub("[^\w\-_]", "_", $blacklist.proteins.element_identifier)}.$gxy2omsext($blacklist.proteins.ext)' &&
+  cp '$blacklist.proteins' 'blacklist.proteins/${re.sub("[^\w\-_]", "_", $blacklist.proteins.element_identifier)}.$gxy2omsext($blacklist.proteins.ext)' &&
 #end if
 #if $blacklist.peptides:
   mkdir blacklist.peptides &&
-  ln -s '$blacklist.peptides' 'blacklist.peptides/${re.sub("[^\w\-_]", "_", $blacklist.peptides.element_identifier)}.$gxy2omsext($blacklist.peptides.ext)' &&
+  cp '$blacklist.peptides' 'blacklist.peptides/${re.sub("[^\w\-_]", "_", $blacklist.peptides.element_identifier)}.$gxy2omsext($blacklist.peptides.ext)' &&
 #end if
 #if $in_silico_digestion.fasta:
   mkdir in_silico_digestion.fasta &&
-  ln -s '$in_silico_digestion.fasta' 'in_silico_digestion.fasta/${re.sub("[^\w\-_]", "_", $in_silico_digestion.fasta.element_identifier)}.$gxy2omsext($in_silico_digestion.fasta.ext)' &&
+  cp '$in_silico_digestion.fasta' 'in_silico_digestion.fasta/${re.sub("[^\w\-_]", "_", $in_silico_digestion.fasta.element_identifier)}.$gxy2omsext($in_silico_digestion.fasta.ext)' &&
 #end if
 
 ## Main program call
@@ -79,30 +78,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml,idxml" optional="false" label="input file" help=" select consensusxml,idxml data sets(s)"/>
+    <param argument="-in" type="data" format="consensusxml,idxml" label="input file" help=" select consensusxml,idxml data sets(s)"/>
     <param argument="-var_mods" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep only peptide hits with variable modifications (as defined in the 'SearchParameters' section of the input file)" help=""/>
     <param argument="-remove_shared_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only peptides matching exactly one protein are kept" help="Remember that isoforms count as different proteins!"/>
     <param argument="-keep_unreferenced_protein_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Proteins not referenced by a peptide are retained in the IDs" help=""/>
     <param argument="-remove_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove proteins according to the information in the user parameters" help="Usually used in combination with 'delete_unreferenced_peptide_hits'"/>
     <param argument="-delete_unreferenced_peptide_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Peptides not referenced by any protein are deleted in the IDs" help="Usually used in combination with 'score:prot' or 'thresh:prot'"/>
     <section name="precursor" title="Filtering by precursor attributes (RT, m/z, charge, length)" help="" expanded="false">
-      <param name="rt" argument="-precursor:rt" type="text" optional="true" value=":" label="Retention time range to extract" help="">
+      <param name="rt" argument="-precursor:rt" type="text" value=":" label="Retention time range to extract" help="">
         <expand macro="list_string_san" name="rt"/>
       </param>
-      <param name="mz" argument="-precursor:mz" type="text" optional="true" value=":" label="Mass-to-charge range to extract" help="">
+      <param name="mz" argument="-precursor:mz" type="text" value=":" label="Mass-to-charge range to extract" help="">
         <expand macro="list_string_san" name="mz"/>
       </param>
-      <param name="length" argument="-precursor:length" type="text" optional="true" value=":" label="Keep only peptide hits with a sequence length in this range" help="">
+      <param name="length" argument="-precursor:length" type="text" value=":" label="Keep only peptide hits with a sequence length in this range" help="">
         <expand macro="list_string_san" name="length"/>
       </param>
-      <param name="charge" argument="-precursor:charge" type="text" optional="true" value=":" label="Keep only peptide hits with charge states in this range" help="">
+      <param name="charge" argument="-precursor:charge" type="text" value=":" label="Keep only peptide hits with charge states in this range" help="">
         <expand macro="list_string_san" name="charge"/>
       </param>
     </section>
     <section name="score" title="Filtering by peptide/protein score" help="" expanded="false">
-      <param name="pep" argument="-score:pep" type="float" optional="true" value="0.0" label="The score which should be reached by a peptide hit to be kept" help=""/>
-      <param name="prot" argument="-score:prot" type="float" optional="true" value="0.0" label="The score which should be reached by a protein hit to be kept" help="All proteins are filtered based on their singleton scores irrespective of grouping. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides"/>
-      <param name="protgroup" argument="-score:protgroup" type="float" optional="true" value="0.0" label="The score which should be reached by a protein group to be kept" help="Performs group level score filtering (including groups of single proteins). Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides"/>
+      <param name="pep" argument="-score:pep" type="float" value="0.0" label="The score which should be reached by a peptide hit to be kept" help=""/>
+      <param name="prot" argument="-score:prot" type="float" value="0.0" label="The score which should be reached by a protein hit to be kept" help="All proteins are filtered based on their singleton scores irrespective of grouping. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides"/>
+      <param name="protgroup" argument="-score:protgroup" type="float" value="0.0" label="The score which should be reached by a protein group to be kept" help="Performs group level score filtering (including groups of single proteins). Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides"/>
     </section>
     <section name="whitelist" title="Filtering by whitelisting (only peptides/proteins from a given set can pass)" help="" expanded="false">
       <param name="proteins" argument="-whitelist:proteins" type="data" format="fasta" optional="true" label="Filename of a FASTA file containing protein sequences" help="All peptides that are not referencing a protein in this file are removed.. All proteins whose accessions are not present in this file are removed select fasta data sets(s)"/>
@@ -112,7 +111,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </param>
       <param name="peptides" argument="-whitelist:peptides" type="data" format="idxml" optional="true" label="Only peptides with the same sequence and modification assignment as any peptide in this file are kept" help="Use with 'whitelist:ignore_modifications' to only compare by sequence..  select idxml data sets(s)"/>
       <param name="ignore_modifications" argument="-whitelist:ignore_modifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compare whitelisted peptides by sequence only" help=""/>
-      <param name="modifications" argument="-whitelist:modifications" multiple="true" type="select" optional="true" label="Keep only peptides with sequences that contain (any of) the selected modification(s)" help="">
+      <param name="modifications" argument="-whitelist:modifications" type="select" multiple="true" optional="true" label="Keep only peptides with sequences that contain (any of) the selected modification(s)" help="">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
         <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -122,6 +121,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="2-succinyl (C)">2-succinyl (C)</option>
         <option value="2HPG (R)">2HPG (R)</option>
         <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+        <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+        <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+        <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+        <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
         <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
         <option value="3sulfo (N-term)">3sulfo (N-term)</option>
         <option value="4-ONE (C)">4-ONE (C)</option>
@@ -211,6 +214,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
         <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
         <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+        <option value="Andro-H2O (C)">Andro-H2O (C)</option>
         <option value="Archaeol (C)">Archaeol (C)</option>
         <option value="Arg (N-term)">Arg (N-term)</option>
         <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -314,6 +318,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
         <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
         <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+        <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
         <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
         <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
         <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -346,7 +351,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="BITC (N-term)">BITC (N-term)</option>
         <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
         <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-        <option value="Bodipy (C)">Bodipy (C)</option>
         <option value="Brij35 (N-term)">Brij35 (N-term)</option>
         <option value="Brij58 (N-term)">Brij58 (N-term)</option>
         <option value="Bromo (F)">Bromo (F)</option>
@@ -778,9 +782,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Dehydrated (T)">Dehydrated (T)</option>
         <option value="Dehydrated (Y)">Dehydrated (Y)</option>
         <option value="Dehydro (C)">Dehydro (C)</option>
+        <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
         <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-        <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
         <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
         <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -790,7 +794,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
         <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
         <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-        <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
         <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
         <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -802,6 +805,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
         <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
         <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+        <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
         <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
         <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -1374,7 +1378,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Ethanolyl (C)">Ethanolyl (C)</option>
         <option value="Ethanolyl (K)">Ethanolyl (K)</option>
         <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-        <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
         <option value="Ethyl (C-term)">Ethyl (C-term)</option>
         <option value="Ethyl (D)">Ethyl (D)</option>
         <option value="Ethyl (E)">Ethyl (E)</option>
@@ -1468,6 +1471,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
         <option value="Glu (E)">Glu (E)</option>
         <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+        <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
         <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
         <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
         <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -1482,7 +1486,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
         <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
         <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
         <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -1506,6 +1509,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gly (K)">Gly (K)</option>
         <option value="Gly (S)">Gly (S)</option>
         <option value="Gly (T)">Gly (T)</option>
+        <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
         <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
         <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
         <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -1896,6 +1900,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
         <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
         <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+        <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
         <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
         <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
         <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -1907,6 +1912,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
         <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
         <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+        <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+        <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+        <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
         <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
         <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
         <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -1962,6 +1970,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
         <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
         <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+        <option value="His+O(2) (H)">His+O(2) (H)</option>
         <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
         <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
         <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -2099,11 +2108,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+        <option value="Kdo (S)">Kdo (S)</option>
+        <option value="Kdo (T)">Kdo (T)</option>
         <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
         <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
         <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
         <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
         <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+        <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
         <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
         <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
         <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -2188,13 +2200,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
         <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
         <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+        <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
         <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
         <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
         <option value="Lipoyl (K)">Lipoyl (K)</option>
         <option value="LRGG (K)">LRGG (K)</option>
         <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
         <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+        <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
         <option value="Lys (N-term)">Lys (N-term)</option>
+        <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
         <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
         <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
         <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -2229,6 +2244,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Malonyl (C)">Malonyl (C)</option>
         <option value="Malonyl (K)">Malonyl (K)</option>
         <option value="Malonyl (S)">Malonyl (S)</option>
+        <option value="MBS+peptide (C)">MBS+peptide (C)</option>
         <option value="MDCC (C)">MDCC (C)</option>
         <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
         <option value="Menadione (C)">Menadione (C)</option>
@@ -2240,6 +2256,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="MesitylOxide (H)">MesitylOxide (H)</option>
         <option value="MesitylOxide (K)">MesitylOxide (K)</option>
         <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+        <option value="Met+O(2) (H)">Met+O(2) (H)</option>
         <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
         <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
         <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -2423,7 +2440,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
         <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
         <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-        <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
         <option value="NP40 (N-term)">NP40 (N-term)</option>
         <option value="NQIGG (K)">NQIGG (K)</option>
         <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -2511,6 +2527,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
         <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
         <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+        <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+        <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+        <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+        <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
         <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
         <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
         <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -2525,6 +2545,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phospho (Y)">Phospho (Y)</option>
         <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
         <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+        <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
         <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
         <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
         <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -2556,6 +2577,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
         <option value="Piperidine (K)">Piperidine (K)</option>
         <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+        <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
         <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
         <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
         <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -2633,18 +2655,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="QTGG (K)">QTGG (K)</option>
         <option value="Quinone (W)">Quinone (W)</option>
         <option value="Quinone (Y)">Quinone (Y)</option>
+        <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+        <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+        <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+        <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+        <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+        <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+        <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+        <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+        <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+        <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+        <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+        <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+        <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+        <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+        <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+        <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+        <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+        <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+        <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+        <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
         <option value="Retinylidene (K)">Retinylidene (K)</option>
         <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
         <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
         <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-        <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-        <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-        <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-        <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-        <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-        <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-        <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-        <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
         <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
         <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
         <option value="Saligenin (H)">Saligenin (H)</option>
@@ -2672,6 +2706,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="shTMT (K)">shTMT (K)</option>
         <option value="shTMT (N-term)">shTMT (N-term)</option>
         <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+        <option value="shTMTpro (K)">shTMTpro (K)</option>
+        <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+        <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
         <option value="SMA (K)">SMA (K)</option>
         <option value="SMA (N-term)">SMA (N-term)</option>
         <option value="spermidine (Q)">spermidine (Q)</option>
@@ -2847,7 +2884,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
         <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
         <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-        <option value="Ub-amide (C)">Ub-amide (C)</option>
         <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
         <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
         <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -3051,7 +3087,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </param>
       <param name="peptides" argument="-blacklist:peptides" type="data" format="idxml" optional="true" label="Peptides with the same sequence and modification assignment as any peptide in this file are filtered out" help="Use with 'blacklist:ignore_modifications' to only compare by sequence..  select idxml data sets(s)"/>
       <param name="ignore_modifications" argument="-blacklist:ignore_modifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compare blacklisted peptides by sequence only" help=""/>
-      <param name="modifications" argument="-blacklist:modifications" multiple="true" type="select" optional="true" label="Remove all peptides with sequences that contain (any of) the selected modification(s)" help="">
+      <param name="modifications" argument="-blacklist:modifications" type="select" multiple="true" optional="true" label="Remove all peptides with sequences that contain (any of) the selected modification(s)" help="">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
         <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -3061,6 +3097,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="2-succinyl (C)">2-succinyl (C)</option>
         <option value="2HPG (R)">2HPG (R)</option>
         <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+        <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+        <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+        <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+        <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
         <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
         <option value="3sulfo (N-term)">3sulfo (N-term)</option>
         <option value="4-ONE (C)">4-ONE (C)</option>
@@ -3150,6 +3190,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
         <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
         <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+        <option value="Andro-H2O (C)">Andro-H2O (C)</option>
         <option value="Archaeol (C)">Archaeol (C)</option>
         <option value="Arg (N-term)">Arg (N-term)</option>
         <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -3253,6 +3294,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
         <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
         <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+        <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
         <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
         <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
         <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -3285,7 +3327,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="BITC (N-term)">BITC (N-term)</option>
         <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
         <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-        <option value="Bodipy (C)">Bodipy (C)</option>
         <option value="Brij35 (N-term)">Brij35 (N-term)</option>
         <option value="Brij58 (N-term)">Brij58 (N-term)</option>
         <option value="Bromo (F)">Bromo (F)</option>
@@ -3717,9 +3758,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Dehydrated (T)">Dehydrated (T)</option>
         <option value="Dehydrated (Y)">Dehydrated (Y)</option>
         <option value="Dehydro (C)">Dehydro (C)</option>
+        <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
         <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-        <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
         <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
         <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -3729,7 +3770,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
         <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
         <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-        <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
         <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
         <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -3741,6 +3781,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
         <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
         <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+        <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
         <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
         <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -4313,7 +4354,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Ethanolyl (C)">Ethanolyl (C)</option>
         <option value="Ethanolyl (K)">Ethanolyl (K)</option>
         <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-        <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
         <option value="Ethyl (C-term)">Ethyl (C-term)</option>
         <option value="Ethyl (D)">Ethyl (D)</option>
         <option value="Ethyl (E)">Ethyl (E)</option>
@@ -4407,6 +4447,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
         <option value="Glu (E)">Glu (E)</option>
         <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+        <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
         <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
         <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
         <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -4421,7 +4462,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
         <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
         <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
         <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -4445,6 +4485,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gly (K)">Gly (K)</option>
         <option value="Gly (S)">Gly (S)</option>
         <option value="Gly (T)">Gly (T)</option>
+        <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
         <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
         <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
         <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -4835,6 +4876,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
         <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
         <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+        <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
         <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
         <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
         <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -4846,6 +4888,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
         <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
         <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+        <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+        <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+        <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
         <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
         <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
         <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -4901,6 +4946,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
         <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
         <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+        <option value="His+O(2) (H)">His+O(2) (H)</option>
         <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
         <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
         <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -5038,11 +5084,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+        <option value="Kdo (S)">Kdo (S)</option>
+        <option value="Kdo (T)">Kdo (T)</option>
         <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
         <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
         <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
         <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
         <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+        <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
         <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
         <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
         <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -5127,13 +5176,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
         <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
         <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+        <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
         <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
         <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
         <option value="Lipoyl (K)">Lipoyl (K)</option>
         <option value="LRGG (K)">LRGG (K)</option>
         <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
         <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+        <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
         <option value="Lys (N-term)">Lys (N-term)</option>
+        <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
         <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
         <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
         <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -5168,6 +5220,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Malonyl (C)">Malonyl (C)</option>
         <option value="Malonyl (K)">Malonyl (K)</option>
         <option value="Malonyl (S)">Malonyl (S)</option>
+        <option value="MBS+peptide (C)">MBS+peptide (C)</option>
         <option value="MDCC (C)">MDCC (C)</option>
         <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
         <option value="Menadione (C)">Menadione (C)</option>
@@ -5179,6 +5232,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="MesitylOxide (H)">MesitylOxide (H)</option>
         <option value="MesitylOxide (K)">MesitylOxide (K)</option>
         <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+        <option value="Met+O(2) (H)">Met+O(2) (H)</option>
         <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
         <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
         <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -5362,7 +5416,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
         <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
         <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-        <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
         <option value="NP40 (N-term)">NP40 (N-term)</option>
         <option value="NQIGG (K)">NQIGG (K)</option>
         <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -5450,6 +5503,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
         <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
         <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+        <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+        <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+        <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+        <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
         <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
         <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
         <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -5464,6 +5521,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phospho (Y)">Phospho (Y)</option>
         <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
         <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+        <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
         <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
         <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
         <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -5495,6 +5553,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
         <option value="Piperidine (K)">Piperidine (K)</option>
         <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+        <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
         <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
         <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
         <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -5572,18 +5631,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="QTGG (K)">QTGG (K)</option>
         <option value="Quinone (W)">Quinone (W)</option>
         <option value="Quinone (Y)">Quinone (Y)</option>
+        <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+        <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+        <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+        <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+        <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+        <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+        <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+        <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+        <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+        <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+        <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+        <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+        <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+        <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+        <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+        <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+        <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+        <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+        <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+        <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
         <option value="Retinylidene (K)">Retinylidene (K)</option>
         <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
         <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
         <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-        <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-        <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-        <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-        <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-        <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-        <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-        <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-        <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
         <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
         <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
         <option value="Saligenin (H)">Saligenin (H)</option>
@@ -5611,6 +5682,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="shTMT (K)">shTMT (K)</option>
         <option value="shTMT (N-term)">shTMT (N-term)</option>
         <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+        <option value="shTMTpro (K)">shTMTpro (K)</option>
+        <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+        <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
         <option value="SMA (K)">SMA (K)</option>
         <option value="SMA (N-term)">SMA (N-term)</option>
         <option value="spermidine (Q)">spermidine (Q)</option>
@@ -5786,7 +5860,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
         <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
         <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-        <option value="Ub-amide (C)">Ub-amide (C)</option>
         <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
         <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
         <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -5987,110 +6060,118 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <section name="in_silico_digestion" title="This filter option removes peptide hits which are not in the list of in silico peptides generated by the rules specified below" help="" expanded="false">
       <param name="fasta" argument="-in_silico_digestion:fasta" type="data" format="fasta" optional="true" label="fasta protein sequence database" help=" select fasta data sets(s)"/>
-      <param name="enzyme" argument="-in_silico_digestion:enzyme" type="select" optional="true" label="enzyme used for the digestion of the sample" help="">
-        <option value="Trypsin" selected="true">Trypsin</option>
-        <option value="cyanogen-bromide">cyanogen-bromide</option>
-        <option value="Clostripain/P">Clostripain/P</option>
-        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
-        <option value="no cleavage">no cleavage</option>
-        <option value="unspecific cleavage">unspecific cleavage</option>
-        <option value="Arg-C/P">Arg-C/P</option>
-        <option value="Formic_acid">Formic_acid</option>
+      <param name="enzyme" argument="-in_silico_digestion:enzyme" type="select" label="enzyme used for the digestion of the sample" help="">
         <option value="Lys-C">Lys-C</option>
         <option value="Lys-N">Lys-N</option>
-        <option value="leukocyte elastase">leukocyte elastase</option>
-        <option value="proline endopeptidase">proline endopeptidase</option>
-        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
         <option value="Lys-C/P">Lys-C/P</option>
         <option value="PepsinA">PepsinA</option>
         <option value="TrypChymo">TrypChymo</option>
         <option value="Trypsin/P">Trypsin/P</option>
         <option value="V8-DE">V8-DE</option>
         <option value="V8-E">V8-E</option>
-        <option value="Asp-N_ambic">Asp-N_ambic</option>
+        <option value="leukocyte elastase">leukocyte elastase</option>
         <option value="Chymotrypsin">Chymotrypsin</option>
+        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+        <option value="CNBr">CNBr</option>
+        <option value="Formic_acid">Formic_acid</option>
+        <option value="Arg-C">Arg-C</option>
+        <option value="Arg-C/P">Arg-C/P</option>
+        <option value="Asp-N">Asp-N</option>
+        <option value="Asp-N/B">Asp-N/B</option>
+        <option value="Asp-N_ambic">Asp-N_ambic</option>
+        <option value="Trypsin" selected="true">Trypsin</option>
+        <option value="proline endopeptidase">proline endopeptidase</option>
+        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
         <option value="2-iodobenzoate">2-iodobenzoate</option>
         <option value="iodosobenzoate">iodosobenzoate</option>
         <option value="staphylococcal protease/D">staphylococcal protease/D</option>
         <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
         <option value="Glu-C+P">Glu-C+P</option>
         <option value="PepsinA + P">PepsinA + P</option>
-        <option value="Arg-C">Arg-C</option>
-        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
-        <option value="CNBr">CNBr</option>
-        <option value="Asp-N">Asp-N</option>
-        <option value="Asp-N/B">Asp-N/B</option>
+        <option value="cyanogen-bromide">cyanogen-bromide</option>
+        <option value="Clostripain/P">Clostripain/P</option>
+        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+        <option value="no cleavage">no cleavage</option>
+        <option value="unspecific cleavage">unspecific cleavage</option>
         <expand macro="list_string_san" name="enzyme"/>
       </param>
-      <param name="specificity" argument="-in_silico_digestion:specificity" type="select" optional="true" label="Specificity of the filte" help="">
+      <param name="specificity" argument="-in_silico_digestion:specificity" type="select" label="Specificity of the filte" help="">
         <option value="none">none</option>
         <option value="semi">semi</option>
         <option value="full" selected="true">full</option>
         <expand macro="list_string_san" name="specificity"/>
       </param>
-      <param name="missed_cleavages" argument="-in_silico_digestion:missed_cleavages" type="integer" optional="true" min="-1" value="-1" label="range of allowed missed cleavages in the peptide sequences" help="By default missed cleavages are ignored"/>
+      <param name="missed_cleavages" argument="-in_silico_digestion:missed_cleavages" type="integer" min="-1" value="-1" label="range of allowed missed cleavages in the peptide sequences" help="By default missed cleavages are ignored"/>
       <param name="methionine_cleavage" argument="-in_silico_digestion:methionine_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow methionine cleavage at the N-terminus of the protein" help=""/>
     </section>
     <section name="missed_cleavages" title="This filter option removes peptide hits which do not confirm with the allowed missed cleavages specified below" help="" expanded="false">
-      <param name="number_of_missed_cleavages" argument="-missed_cleavages:number_of_missed_cleavages" type="text" optional="true" value=":" label="range of allowed missed cleavages in the peptide sequences" help="For example: 0:1 -&gt; peptides with two or more missed cleavages will be removed,. 0:0 -&gt; peptides with any missed cleavages will be removed">
+      <param name="number_of_missed_cleavages" argument="-missed_cleavages:number_of_missed_cleavages" type="text" value=":" label="range of allowed missed cleavages in the peptide sequences" help="For example: 0:1 -&gt; peptides with two or more missed cleavages will be removed,. 0:0 -&gt; peptides with any missed cleavages will be removed">
         <expand macro="list_string_san" name="number_of_missed_cleavages"/>
       </param>
-      <param name="enzyme" argument="-missed_cleavages:enzyme" type="select" optional="true" label="enzyme used for the digestion of the sample" help="">
-        <option value="Trypsin" selected="true">Trypsin</option>
-        <option value="cyanogen-bromide">cyanogen-bromide</option>
-        <option value="Clostripain/P">Clostripain/P</option>
-        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
-        <option value="no cleavage">no cleavage</option>
-        <option value="unspecific cleavage">unspecific cleavage</option>
-        <option value="Arg-C/P">Arg-C/P</option>
-        <option value="Formic_acid">Formic_acid</option>
+      <param name="enzyme" argument="-missed_cleavages:enzyme" type="select" label="enzyme used for the digestion of the sample" help="">
         <option value="Lys-C">Lys-C</option>
         <option value="Lys-N">Lys-N</option>
-        <option value="leukocyte elastase">leukocyte elastase</option>
-        <option value="proline endopeptidase">proline endopeptidase</option>
-        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
         <option value="Lys-C/P">Lys-C/P</option>
         <option value="PepsinA">PepsinA</option>
         <option value="TrypChymo">TrypChymo</option>
         <option value="Trypsin/P">Trypsin/P</option>
         <option value="V8-DE">V8-DE</option>
         <option value="V8-E">V8-E</option>
-        <option value="Asp-N_ambic">Asp-N_ambic</option>
+        <option value="leukocyte elastase">leukocyte elastase</option>
         <option value="Chymotrypsin">Chymotrypsin</option>
+        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+        <option value="CNBr">CNBr</option>
+        <option value="Formic_acid">Formic_acid</option>
+        <option value="Arg-C">Arg-C</option>
+        <option value="Arg-C/P">Arg-C/P</option>
+        <option value="Asp-N">Asp-N</option>
+        <option value="Asp-N/B">Asp-N/B</option>
+        <option value="Asp-N_ambic">Asp-N_ambic</option>
+        <option value="Trypsin" selected="true">Trypsin</option>
+        <option value="proline endopeptidase">proline endopeptidase</option>
+        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
         <option value="2-iodobenzoate">2-iodobenzoate</option>
         <option value="iodosobenzoate">iodosobenzoate</option>
         <option value="staphylococcal protease/D">staphylococcal protease/D</option>
         <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
         <option value="Glu-C+P">Glu-C+P</option>
         <option value="PepsinA + P">PepsinA + P</option>
-        <option value="Arg-C">Arg-C</option>
-        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
-        <option value="CNBr">CNBr</option>
-        <option value="Asp-N">Asp-N</option>
-        <option value="Asp-N/B">Asp-N/B</option>
+        <option value="cyanogen-bromide">cyanogen-bromide</option>
+        <option value="Clostripain/P">Clostripain/P</option>
+        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+        <option value="no cleavage">no cleavage</option>
+        <option value="unspecific cleavage">unspecific cleavage</option>
         <expand macro="list_string_san" name="enzyme"/>
       </param>
     </section>
     <section name="rt" title="Filtering by RT predicted by 'RTPredict'" help="" expanded="false">
-      <param name="p_value" argument="-rt:p_value" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Retention time filtering by the p-value predicted by RTPredict" help=""/>
-      <param name="p_value_1st_dim" argument="-rt:p_value_1st_dim" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Retention time filtering by the p-value predicted by RTPredict for first dimension" help=""/>
+      <param name="p_value" argument="-rt:p_value" type="float" min="0.0" max="1.0" value="0.0" label="Retention time filtering by the p-value predicted by RTPredict" help=""/>
+      <param name="p_value_1st_dim" argument="-rt:p_value_1st_dim" type="float" min="0.0" max="1.0" value="0.0" label="Retention time filtering by the p-value predicted by RTPredict for first dimension" help=""/>
     </section>
     <section name="mz" title="Filtering by mass erro" help="" expanded="false">
-      <param name="error" argument="-mz:error" type="float" optional="true" value="-1.0" label="Filtering by deviation to theoretical mass (disabled for negative values)" help=""/>
-      <param name="unit" argument="-mz:unit" type="select" optional="true" label="Absolute or relative erro" help="">
+      <param name="error" argument="-mz:error" type="float" value="-1.0" label="Filtering by deviation to theoretical mass (disabled for negative values)" help=""/>
+      <param name="unit" argument="-mz:unit" type="select" label="Absolute or relative erro" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="unit"/>
       </param>
     </section>
     <section name="best" title="Filtering best hits per spectrum (for peptides) or from proteins" help="" expanded="false">
-      <param name="n_spectra" argument="-best:n_spectra" type="integer" optional="true" min="0" value="0" label="Keep only the 'n' best spectra" help="(i.e., PeptideIdentifications) (for n &gt; 0). A spectrum is considered better if it has a higher scoring peptide hit than the other spectrum"/>
-      <param name="n_peptide_hits" argument="-best:n_peptide_hits" type="integer" optional="true" min="0" value="0" label="Keep only the 'n' highest scoring peptide hits per spectrum (for n &gt; 0)" help=""/>
-      <param name="n_protein_hits" argument="-best:n_protein_hits" type="integer" optional="true" min="0" value="0" label="Keep only the 'n' highest scoring protein hits (for n &gt; 0)" help=""/>
+      <param name="n_spectra" argument="-best:n_spectra" type="integer" min="0" value="0" label="Keep only the 'n' best spectra" help="(i.e., PeptideIdentifications) (for n &gt; 0). A spectrum is considered better if it has a higher scoring peptide hit than the other spectrum"/>
+      <param name="n_peptide_hits" argument="-best:n_peptide_hits" type="integer" min="0" value="0" label="Keep only the 'n' highest scoring peptide hits per spectrum (for n &gt; 0)" help=""/>
+      <param name="spectrum_per_peptide" argument="-best:spectrum_per_peptide" type="select" label="Keep one spectrum per peptide" help="Value determines if same sequence but different charges or modifications are treated as separate peptides or the same peptide. (default: false = filter disabled)">
+        <option value="false" selected="true">false</option>
+        <option value="sequence">sequence</option>
+        <option value="sequence+charge">sequence+charge</option>
+        <option value="sequence+modification">sequence+modification</option>
+        <option value="sequence+charge+modification">sequence+charge+modification</option>
+        <expand macro="list_string_san" name="spectrum_per_peptide"/>
+      </param>
+      <param name="n_protein_hits" argument="-best:n_protein_hits" type="integer" min="0" value="0" label="Keep only the 'n' highest scoring protein hits (for n &gt; 0)" help=""/>
       <param name="strict" argument="-best:strict" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep only the highest scoring peptide hit" help="Similar to n_peptide_hits=1, but if there are ties between two or more highest scoring hits, none are kept"/>
-      <param name="n_to_m_peptide_hits" argument="-best:n_to_m_peptide_hits" type="text" optional="true" value=":" label="Peptide hit rank range to extracts" help="">
+      <param name="n_to_m_peptide_hits" argument="-best:n_to_m_peptide_hits" type="text" value=":" label="Peptide hit rank range to extracts" help="">
         <expand macro="list_string_san" name="n_to_m_peptide_hits"/>
       </param>
     </section>
@@ -6101,7 +6182,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <expand macro="list_string_san" name="remove_peptide_hits_by_metavalue"/>
       </param>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -6115,16 +6196,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_IDFilter_1 -->
+  <tests>
+    <!-- TOPP_IDFilter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_1_input.idXML"/>
-      <output name="out" file="IDFilter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -6143,14 +6224,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="whitelist">
         <param name="proteins" value="IDFilter_1_input.fas"/>
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -6174,6 +6251,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -6184,17 +6262,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_3 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_3_input.idXML"/>
-      <output name="out" file="IDFilter_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -6212,15 +6292,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="peptides" value="IDFilter_3_2_input.idXML"/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -6244,6 +6320,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -6254,17 +6331,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_4 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_4_input.idXML"/>
-      <output name="out" file="IDFilter_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -6282,14 +6361,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -6313,6 +6388,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -6323,17 +6399,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_5 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_5_input.idXML"/>
-      <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -6351,14 +6429,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -6382,6 +6456,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -6392,17 +6467,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_5a -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_5_input.idXML"/>
-      <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -6420,14 +6497,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -6451,6 +6524,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -6461,17 +6535,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_5b -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_5_input.idXML"/>
-      <output name="out" file="IDFilter_5b_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_5b_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -6489,14 +6565,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -6520,6 +6592,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -6530,17 +6603,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_5c -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_5_input.idXML"/>
-      <output name="out" file="IDFilter_5c_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_5c_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -6558,14 +6633,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -6589,6 +6660,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -6599,17 +6671,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_6 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_6_input.idXML"/>
-      <output name="out" file="IDFilter_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -6627,14 +6701,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -6658,6 +6728,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="2"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="10"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -6668,17 +6739,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_7 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="true"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_7_input.idXML"/>
-      <output name="out" file="IDFilter_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -6696,14 +6769,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -6727,6 +6796,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -6737,17 +6807,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_8 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_8_input.idXML"/>
-      <output name="out" file="IDFilter_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -6765,14 +6837,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -6796,6 +6864,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -6806,17 +6875,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_9 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_9_input.idXML"/>
-      <output name="out" file="IDFilter_9_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_9_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -6834,14 +6905,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -6865,6 +6932,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -6875,17 +6943,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_10 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_10_input.idXML"/>
-      <output name="out" file="IDFilter_10_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_10_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -6903,14 +6973,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -6934,6 +7000,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -6944,17 +7011,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_11 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_11_input.idXML"/>
-      <output name="out" file="IDFilter_11_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_11_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -6972,14 +7041,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -7003,6 +7068,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -7013,17 +7079,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_12 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_12_input.idXML"/>
-      <output name="out" file="IDFilter_12_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_12_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -7041,14 +7109,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -7073,6 +7137,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -7083,17 +7148,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_13 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_13_input.idXML"/>
-      <output name="out" file="IDFilter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -7111,14 +7178,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -7143,6 +7206,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -7153,17 +7217,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_14 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_14_input.idXML"/>
-      <output name="out" file="IDFilter_14_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_14_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -7181,14 +7247,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -7213,6 +7275,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -7223,17 +7286,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_15 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_15_input.idXML"/>
-      <output name="out" file="IDFilter_15_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_15_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -7251,14 +7316,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -7283,6 +7344,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -7293,17 +7355,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_16 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_16_input.idXML"/>
-      <output name="out" file="IDFilter_16_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_16_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -7321,14 +7385,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -7353,6 +7413,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -7363,17 +7424,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_17 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
-      <output name="out" file="IDFilter_17_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_17_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -7391,14 +7454,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -7422,6 +7481,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -7432,17 +7492,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_18 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
-      <output name="out" file="IDFilter_18_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_18_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -7460,14 +7522,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -7491,6 +7549,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -7501,17 +7560,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_19 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
-      <output name="out" file="IDFilter_19_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_19_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -7529,14 +7590,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -7560,6 +7617,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -7570,17 +7628,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_20 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
-      <output name="out" file="IDFilter_20_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_20_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -7598,14 +7658,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -7629,6 +7685,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -7639,6 +7696,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_21 -->
     <test expect_num_outputs="2">
@@ -7649,7 +7709,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_16_input.idXML"/>
-      <output name="out" file="IDFilter_21_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_21_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -7667,14 +7727,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -7698,6 +7754,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -7708,6 +7765,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_22 -->
     <test expect_num_outputs="2">
@@ -7718,7 +7778,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFilter_16_input.idXML"/>
-      <output name="out" file="IDFilter_22_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDFilter_22_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -7736,14 +7796,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -7767,6 +7823,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -7777,17 +7834,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_23 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDMapper_2_output.consensusXML"/>
-      <output name="out" file="IDFilter_23_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="IDFilter_23_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -7807,12 +7866,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="whitelist">
         <param name="protein_accessions" value="&quot;Q9HP81&quot;"/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -7836,6 +7892,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -7846,17 +7903,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDFilter_24 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="Epifany_3_out.consensusXML"/>
-      <output name="out" file="IDFilter_24_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="IDFilter_24_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="var_mods" value="false"/>
       <param name="remove_shared_peptides" value="false"/>
       <param name="keep_unreferenced_protein_hits" value="false"/>
@@ -7874,14 +7933,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="protgroup" value="0.99"/>
       </section>
       <section name="whitelist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
       </section>
       <section name="blacklist">
-        <param name="protein_accessions" value=""/>
         <param name="ignore_modifications" value="false"/>
-        <param name="modifications"/>
         <param name="RegEx" value=""/>
       </section>
       <section name="in_silico_digestion">
@@ -7905,6 +7960,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <section name="best">
         <param name="n_spectra" value="0"/>
         <param name="n_peptide_hits" value="0"/>
+        <param name="spectrum_per_peptide" value="false"/>
         <param name="n_protein_hits" value="0"/>
         <param name="strict" value="false"/>
         <param name="n_to_m_peptide_hits" value=":"/>
@@ -7915,11 +7971,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Filters results from protein or peptide identification engines based on different criteria.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDFilter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDFilter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/IDMapper.xml b/tools/openms/IDMapper.xml
index 6f75f0ac1..4266acfa2 100644
--- a/tools/openms/IDMapper.xml
+++ b/tools/openms/IDMapper.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [ID Processing]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="IDMapper" name="IDMapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Assigns protein/peptide identifications to features or consensus features.</description>
+  <description>Assigns protein/peptide identifications to features or consensus features</description>
   <macros>
     <token name="@EXECUTABLE@">IDMapper</token>
     <import>macros.xml</import>
@@ -15,13 +14,13 @@
 
 ## Preprocessing
 mkdir id &&
-ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
+cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if $spectra._in:
   mkdir spectra.in &&
-  ln -s '$spectra._in' 'spectra.in/${re.sub("[^\w\-_]", "_", $spectra._in.element_identifier)}.$gxy2omsext($spectra._in.ext)' &&
+  cp '$spectra._in' 'spectra.in/${re.sub("[^\w\-_]", "_", $spectra._in.element_identifier)}.$gxy2omsext($spectra._in.ext)' &&
 #end if
 
 ## Main program call
@@ -51,16 +50,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-id" type="data" format="idxml,mzid" optional="false" label="Protein/peptide identifications file" help=" select idxml,mzid data sets(s)"/>
-    <param argument="-in" type="data" format="consensusxml,featurexml,mzq" optional="false" label="Feature map/consensus map file" help=" select consensusxml,featurexml,mzq data sets(s)"/>
-    <param argument="-rt_tolerance" type="float" optional="true" min="0.0" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
-    <param argument="-mz_tolerance" type="float" optional="true" min="0.0" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
-    <param argument="-mz_measure" type="select" optional="true" label="Unit of 'mz_tolerance'" help="">
+    <param argument="-id" type="data" format="idxml,mzid" label="Protein/peptide identifications file" help=" select idxml,mzid data sets(s)"/>
+    <param argument="-in" type="data" format="consensusxml,featurexml,mzq" label="Feature map/consensus map file" help=" select consensusxml,featurexml,mzq data sets(s)"/>
+    <param argument="-rt_tolerance" type="float" min="0.0" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
+    <param argument="-mz_tolerance" type="float" min="0.0" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
+    <param argument="-mz_measure" type="select" label="Unit of 'mz_tolerance'" help="">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
       <expand macro="list_string_san" name="mz_measure"/>
     </param>
-    <param argument="-mz_reference" type="select" optional="true" label="Source of m/z values for peptide identifications" help="If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',. masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.. ('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)">
+    <param argument="-mz_reference" type="select" label="Source of m/z values for peptide identifications" help="If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',. masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.. ('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)">
       <option value="precursor">precursor</option>
       <option value="peptide" selected="true">peptide</option>
       <expand macro="list_string_san" name="mz_reference"/>
@@ -79,7 +78,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <expand macro="adv_opts_macro">
       <param argument="-ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -93,7 +92,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_IDMapper_1 -->
+  <tests>
+    <!-- TOPP_IDMapper_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="ignore_charge" value="true"/>
@@ -102,7 +102,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="id" value="IDMapper_1_input.idXML"/>
       <param name="in" value="IDMapper_1_input.featureXML"/>
-      <output name="out" file="IDMapper_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="IDMapper_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="rt_tolerance" value="5.0"/>
       <param name="mz_tolerance" value="1.0"/>
       <param name="mz_measure" value="Da"/>
@@ -122,6 +122,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDMapper_2 -->
     <test expect_num_outputs="2">
@@ -132,7 +135,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="id" value="IDMapper_2_input.idXML"/>
       <param name="in" value="IDMapper_2_input.consensusXML"/>
-      <output name="out" file="IDMapper_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="IDMapper_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="rt_tolerance" value="5.0"/>
       <param name="mz_tolerance" value="1.0"/>
       <param name="mz_measure" value="Da"/>
@@ -152,6 +155,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDMapper_3 -->
     <test expect_num_outputs="2">
@@ -162,7 +168,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="id" value="IDMapper_3_input.idXML"/>
       <param name="in" value="IDMapper_3_input.featureXML"/>
-      <output name="out" file="IDMapper_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="IDMapper_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="rt_tolerance" value="4.0"/>
       <param name="mz_tolerance" value="3.0"/>
       <param name="mz_measure" value="ppm"/>
@@ -182,75 +188,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
-    </test>
-    <!-- TOPP_IDMapper_4 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="ignore_charge" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="id" value="IDMapper_4_input.idXML"/>
-      <param name="in" value="IDMapper_4_input.featureXML"/>
-      <output name="out" file="IDMapper_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <param name="rt_tolerance" value="10.0"/>
-      <param name="mz_tolerance" value="20.0"/>
-      <param name="mz_measure" value="ppm"/>
-      <param name="mz_reference" value="peptide"/>
-      <section name="feature">
-        <param name="use_centroid_rt" value="false"/>
-        <param name="use_centroid_mz" value="true"/>
-      </section>
-      <section name="consensus">
-        <param name="use_subelements" value="false"/>
-        <param name="annotate_ids_with_subelements" value="false"/>
-      </section>
-      <section name="spectra">
-        <param name="_in" value="IDMapper_4_input.mzML"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_IDMapper_5 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="ignore_charge" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="id" value="IDMapper_5_input.idXML"/>
-      <param name="in" value="IDMapper_5_input.featureXML"/>
-      <output name="out" file="IDMapper_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <param name="rt_tolerance" value="20.0"/>
-      <param name="mz_tolerance" value="10.0"/>
-      <param name="mz_measure" value="ppm"/>
-      <param name="mz_reference" value="peptide"/>
-      <section name="feature">
-        <param name="use_centroid_rt" value="false"/>
-        <param name="use_centroid_mz" value="false"/>
-      </section>
-      <section name="consensus">
-        <param name="use_subelements" value="false"/>
-        <param name="annotate_ids_with_subelements" value="false"/>
-      </section>
-      <section name="spectra">
-        <param name="_in" value="IDMapper_5_input.mzML"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Assigns protein/peptide identifications to features or consensus features.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDMapper.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDMapper.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/IDMassAccuracy.xml b/tools/openms/IDMassAccuracy.xml
index 577394e25..2fbbf72ab 100644
--- a/tools/openms/IDMassAccuracy.xml
+++ b/tools/openms/IDMassAccuracy.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="IDMassAccuracy" name="IDMassAccuracy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description>
+  <description>Calculates a distribution of the mass error from given mass spectra and IDs</description>
   <macros>
     <token name="@EXECUTABLE@">IDMassAccuracy</token>
     <import>macros.xml</import>
@@ -17,16 +16,16 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir id_in_cond.id_in &&
 #if $id_in_cond.id_in_select == "no"
 mkdir ${' '.join(["'id_in_cond.id_in/%s'" % (i) for i, f in enumerate($id_in_cond.id_in) if f])} && 
-${' '.join(["ln -s '%s' 'id_in_cond.id_in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])}
+${' '.join(["cp '%s' 'id_in_cond.id_in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])}
 #else
-ln -s '$id_in_cond.id_in' 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)' &&
+cp '$id_in_cond.id_in' 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)' &&
 #end if
 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_precursor &&
@@ -106,10 +105,10 @@ ${' '.join(["'id_in_cond.id_in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" multiple="true" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
       </when>
     </conditional>
     <conditional name="id_in_cond">
@@ -118,19 +117,19 @@ ${' '.join(["'id_in_cond.id_in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-id_in" type="data" format="idxml" multiple="true" optional="false" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
+        <param argument="-id_in" type="data" format="idxml" multiple="true" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-id_in" type="data" format="idxml" multiple="false" optional="false" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
+        <param argument="-id_in" type="data" format="idxml" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
       </when>
     </conditional>
     <param argument="-precursor_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help=""/>
     <param argument="-fragment_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help=""/>
-    <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help=""/>
+    <param argument="-fragment_mass_tolerance" type="float" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help=""/>
     <expand macro="adv_opts_macro">
-      <param argument="-number_of_bins" type="integer" optional="true" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help=""/>
+      <param argument="-number_of_bins" type="integer" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -162,7 +161,8 @@ ${' '.join(["'id_in_cond.id_in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_IDMassAccuracy_1 -->
+  <tests>
+    <!-- TOPP_IDMassAccuracy_1 -->
     <test expect_num_outputs="5">
       <section name="adv_opts">
         <param name="number_of_bins" value="10"/>
@@ -175,24 +175,27 @@ ${' '.join(["'id_in_cond.id_in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
       <conditional name="id_in_cond">
         <param name="id_in" value="MSGFPlusAdapter_1_out.idXML"/>
       </conditional>
-      <output name="out_precursor" file="IDMassAccuracy_1_out_precursor.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out_precursor" value="IDMassAccuracy_1_out_precursor.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="precursor_error_ppm" value="false"/>
-      <output name="out_fragment" file="IDMassAccuracy_1_out_fragment.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out_fragment" value="IDMassAccuracy_1_out_fragment.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="fragment_error_ppm" value="false"/>
       <param name="fragment_mass_tolerance" value="0.5"/>
-      <output name="out_precursor_fit" file="IDMassAccuracy_1_out_precursor_fit.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
-      <output name="out_fragment_fit" file="IDMassAccuracy_1_out_fragment_fit.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out_precursor_fit" value="IDMassAccuracy_1_out_precursor_fit.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out_fragment_fit" value="IDMassAccuracy_1_out_fragment_fit.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_precursor_FLAG,out_fragment_FLAG,out_precursor_fit_FLAG,out_fragment_fit_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Calculates a distribution of the mass error from given mass spectra and IDs.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_IDMassAccuracy.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDMassAccuracy.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/IDMerger.xml b/tools/openms/IDMerger.xml
index b6c1271ea..8b9ad50f2 100644
--- a/tools/openms/IDMerger.xml
+++ b/tools/openms/IDMerger.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [File Handling]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="IDMerger" name="IDMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Merges several protein/peptide identification files into one file.</description>
+  <description>Merges several protein/peptide identification files into one file</description>
   <macros>
     <token name="@EXECUTABLE@">IDMerger</token>
     <import>macros.xml</import>
@@ -17,14 +16,14 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir out &&
 #if $add_to:
   mkdir add_to &&
-  ln -s '$add_to' 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)' &&
+  cp '$add_to' 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)' &&
 #end if
 
 ## Main program call
@@ -62,15 +61,16 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="idxml,sqlite" multiple="true" optional="false" label="Input files separated by blanks (all must have the same type)" help=" select idxml,sqlite data sets(s)"/>
+        <param argument="-in" type="data" format="idxml,sqlite" multiple="true" label="Input files separated by blanks (all must have the same type)" help=" select idxml,sqlite data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="idxml,sqlite" multiple="false" optional="false" label="Input files separated by blanks (all must have the same type)" help=" select idxml,sqlite data sets(s)"/>
+        <param argument="-in" type="data" format="idxml,sqlite" label="Input files separated by blanks (all must have the same type)" help=" select idxml,sqlite data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type (default: determined from file extension)" help="">
+    <param argument="-out_type" type="select" label="Output file type (default: determined from file extension)" help="">
       <option value="idXML">idxml</option>
       <option value="oms">sqlite (oms)</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
     <param argument="-add_to" type="data" format="idxml" optional="true" label="Optional input file" help="IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum) select idxml data sets(s)"/>
@@ -79,7 +79,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
     <param argument="-merge_proteins_add_PSMs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge all identified proteins by accession into one protein identification run but keep all the PSMs with updated links to potential new protein ID#s" help="Not compatible with 'add_to'"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -97,7 +97,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_IDMerger_1 -->
+  <tests>
+    <!-- TOPP_IDMerger_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -106,7 +107,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input2.idXML"/>
       </conditional>
-      <output name="out" file="IDMerger_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDMerger_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="annotate_file_origin" value="true"/>
       <param name="pepxml_protxml" value="false"/>
@@ -117,6 +118,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDMerger_2 -->
     <test expect_num_outputs="2">
@@ -127,7 +131,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="IDMerger_2_input1.idXML,IDMerger_2_input2.idXML"/>
       </conditional>
-      <output name="out" file="IDMerger_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDMerger_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="pepxml_protxml" value="true"/>
@@ -138,6 +142,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDMerger_3 -->
     <test expect_num_outputs="2">
@@ -146,9 +153,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="test" value="true"/>
       </section>
       <conditional name="in_cond">
-        <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input1_2.idXML"/>
+        <param name="in" value="IDMerger_1_input1_0.idXML,IDMerger_1_input1_1.idXML"/>
       </conditional>
-      <output name="out" file="IDMerger_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDMerger_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="pepxml_protxml" value="false"/>
@@ -159,6 +166,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDMerger_4 -->
     <test expect_num_outputs="2">
@@ -167,9 +177,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="test" value="true"/>
       </section>
       <conditional name="in_cond">
-        <param name="in" value="degenerated_empty.idXML,degenerated_empty_2.idXML"/>
+        <param name="in" value="degenerated_empty_0.idXML,degenerated_empty_1.idXML"/>
       </conditional>
-      <output name="out" file="IDMerger_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDMerger_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="pepxml_protxml" value="false"/>
@@ -180,6 +190,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDMerger_5 -->
     <test expect_num_outputs="2">
@@ -190,7 +203,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="IDMerger_2_input1.idXML"/>
       </conditional>
-      <output name="out" file="IDMerger_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDMerger_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="add_to" value="IDMerger_5_input1.idXML"/>
       <param name="annotate_file_origin" value="false"/>
@@ -202,6 +215,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDMerger_6 -->
     <test expect_num_outputs="2">
@@ -212,7 +228,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="IDMerger_6_input1.oms,IDMerger_6_input2.oms"/>
       </conditional>
-      <output name="out" file="IDMerger_6_output1.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
+      <output name="out" value="IDMerger_6_output1.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
       <param name="out_type" value="oms"/>
       <param name="annotate_file_origin" value="true"/>
       <param name="pepxml_protxml" value="false"/>
@@ -223,6 +239,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDRipper_3_prep -->
     <test expect_num_outputs="2">
@@ -233,7 +252,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="IDRipper_3_input1.idXML,IDRipper_3_input2.idXML"/>
       </conditional>
-      <output name="out" file="IDRipper_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDRipper_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="annotate_file_origin" value="true"/>
       <param name="pepxml_protxml" value="false"/>
@@ -244,11 +263,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Merges several protein/peptide identification files into one file.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDMerger.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDMerger.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/IDPosteriorErrorProbability.xml b/tools/openms/IDPosteriorErrorProbability.xml
index 1b2035ccd..16fcc2fca 100644
--- a/tools/openms/IDPosteriorErrorProbability.xml
+++ b/tools/openms/IDPosteriorErrorProbability.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [ID Processing]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</description>
+  <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model</description>
   <macros>
     <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if "out_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_plot &&
@@ -52,21 +51,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/>
+    <param argument="-in" type="data" format="idxml" label="input file" help=" select idxml data sets(s)"/>
     <param argument="-split_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The search engine scores are split by charge if this flag is set" help="Thus, for each charge state a new model will be computed"/>
     <param argument="-top_hits_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set only the top hits of every PeptideIdentification will be used" help=""/>
     <param argument="-ignore_bad_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set errors will be written but ignored" help="Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through"/>
     <param argument="-prob_correct" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set scores will be calculated as '1 - ErrorProbabilities' and can be interpreted as probabilities for correct identifications" help=""/>
     <section name="fit_algorithm" title="Algorithm parameter subsection" help="" expanded="false">
-      <param name="number_of_bins" argument="-fit_algorithm:number_of_bins" type="integer" optional="true" value="100" label="Number of bins used for visualization" help="Only needed if each iteration step of the EM-Algorithm will be visualized"/>
-      <param name="incorrectly_assigned" argument="-fit_algorithm:incorrectly_assigned" type="select" optional="true" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" help="For 'Gauss', the Gauss distribution is used">
+      <param name="number_of_bins" argument="-fit_algorithm:number_of_bins" type="integer" value="100" label="Number of bins used for visualization" help="Only needed if each iteration step of the EM-Algorithm will be visualized"/>
+      <param name="incorrectly_assigned" argument="-fit_algorithm:incorrectly_assigned" type="select" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" help="For 'Gauss', the Gauss distribution is used">
         <option value="Gumbel" selected="true">Gumbel</option>
         <option value="Gauss">Gauss</option>
         <expand macro="list_string_san" name="incorrectly_assigned"/>
       </param>
-      <param name="max_nr_iterations" argument="-fit_algorithm:max_nr_iterations" type="integer" optional="true" value="1000" label="Bounds the number of iterations for the EM algorithm when convergence is slow" help=""/>
-      <param name="neg_log_delta" argument="-fit_algorithm:neg_log_delta" type="integer" optional="true" value="6" label="The negative logarithm of the convergence threshold for the likelihood increase" help=""/>
-      <param name="outlier_handling" argument="-fit_algorithm:outlier_handling" type="select" optional="true" label="What to do with outliers:" help="- ignore_iqr_outliers: ignore outliers outside of 3*IQR from Q1/Q3 for fitting. - set_iqr_to_closest_valid: set IQR-based outliers to the last valid value for fitting. - ignore_extreme_percentiles: ignore everything outside 99th and 1st percentile (also removes equal values like potential censored max values in XTandem). - none: do nothing">
+      <param name="max_nr_iterations" argument="-fit_algorithm:max_nr_iterations" type="integer" value="1000" label="Bounds the number of iterations for the EM algorithm when convergence is slow" help=""/>
+      <param name="neg_log_delta" argument="-fit_algorithm:neg_log_delta" type="integer" value="6" label="The negative logarithm of the convergence threshold for the likelihood increase" help=""/>
+      <param name="outlier_handling" argument="-fit_algorithm:outlier_handling" type="select" label="What to do with outliers:" help="- ignore_iqr_outliers: ignore outliers outside of 3*IQR from Q1/Q3 for fitting. - set_iqr_to_closest_valid: set IQR-based outliers to the last valid value for fitting. - ignore_extreme_percentiles: ignore everything outside 99th and 1st percentile (also removes equal values like potential censored max values in XTandem). - none: do nothing">
         <option value="ignore_iqr_outliers" selected="true">ignore_iqr_outliers</option>
         <option value="set_iqr_to_closest_valid">set_iqr_to_closest_valid</option>
         <option value="ignore_extreme_percentiles">ignore_extreme_percentiles</option>
@@ -75,9 +74,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </param>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-fdr_for_targets_smaller" type="float" optional="true" value="0.05" label="Only used, when top_hits_only set" help="Additionally, target/decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run"/>
+      <param argument="-fdr_for_targets_smaller" type="float" value="0.05" label="Only used, when top_hits_only set" help="Additionally, target/decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run"/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -95,7 +94,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_IDPosteriorErrorProbability_1 -->
+  <tests>
+    <!-- TOPP_IDPosteriorErrorProbability_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="fdr_for_targets_smaller" value="0.05"/>
@@ -103,7 +103,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDPosteriorErrorProbability_Mascot_input.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_Mascot_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDPosteriorErrorProbability_Mascot_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="split_charge" value="false"/>
       <param name="top_hits_only" value="false"/>
       <param name="ignore_bad_data" value="false"/>
@@ -121,6 +121,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDPosteriorErrorProbability_2 -->
     <test expect_num_outputs="2">
@@ -130,7 +133,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDPosteriorErrorProbability_XTandem_input.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_XTandem_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDPosteriorErrorProbability_XTandem_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="split_charge" value="false"/>
       <param name="top_hits_only" value="false"/>
       <param name="ignore_bad_data" value="false"/>
@@ -148,6 +151,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDPosteriorErrorProbability_3 -->
     <test expect_num_outputs="2">
@@ -157,7 +163,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_OMSSA_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDPosteriorErrorProbability_OMSSA_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="split_charge" value="false"/>
       <param name="top_hits_only" value="false"/>
       <param name="ignore_bad_data" value="false"/>
@@ -175,6 +181,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDPosteriorErrorProbability_4 -->
     <test expect_num_outputs="2">
@@ -184,7 +193,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDPosteriorErrorProbability_OMSSA_input2.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_OMSSA_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDPosteriorErrorProbability_OMSSA_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="split_charge" value="true"/>
       <param name="top_hits_only" value="false"/>
       <param name="ignore_bad_data" value="false"/>
@@ -202,6 +211,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDPosteriorErrorProbability_5 -->
     <test expect_num_outputs="2">
@@ -211,7 +223,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDPosteriorErrorProbability_XTandem_input2.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_XTandem_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDPosteriorErrorProbability_XTandem_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="split_charge" value="true"/>
       <param name="top_hits_only" value="false"/>
       <param name="ignore_bad_data" value="false"/>
@@ -229,6 +241,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDPosteriorErrorProbability_6 -->
     <test expect_num_outputs="2">
@@ -238,7 +253,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDPosteriorErrorProbability_Mascot_input2.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_Mascot_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDPosteriorErrorProbability_Mascot_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="split_charge" value="true"/>
       <param name="top_hits_only" value="false"/>
       <param name="ignore_bad_data" value="false"/>
@@ -256,6 +271,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDPosteriorErrorProbability_7 -->
     <test expect_num_outputs="2">
@@ -265,7 +283,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDPosteriorErrorProbability_bad_data.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_bad_data_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDPosteriorErrorProbability_bad_data_output.tmp" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="split_charge" value="false"/>
       <param name="top_hits_only" value="false"/>
       <param name="ignore_bad_data" value="true"/>
@@ -283,6 +301,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDPosteriorErrorProbability_8 -->
     <test expect_num_outputs="2">
@@ -292,7 +313,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_prob_correct_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDPosteriorErrorProbability_prob_correct_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="split_charge" value="false"/>
       <param name="top_hits_only" value="false"/>
       <param name="ignore_bad_data" value="false"/>
@@ -310,11 +331,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDPosteriorErrorProbability.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDPosteriorErrorProbability.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/IDRTCalibration.xml b/tools/openms/IDRTCalibration.xml
index cfca8e784..6fd1a91d3 100644
--- a/tools/openms/IDRTCalibration.xml
+++ b/tools/openms/IDRTCalibration.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [ID Processing]-->
+<!--Proposed Tool Section: [Mass Correction and Calibration]-->
 <tool id="IDRTCalibration" name="IDRTCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Can be used to calibrate RTs of peptide hits linearly to standards.</description>
+  <description>Can be used to calibrate RTs of peptide hits linearly to standards</description>
   <macros>
     <token name="@EXECUTABLE@">IDRTCalibration</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,14 +38,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/>
-    <param argument="-calibrant_1_reference" type="float" optional="true" value="0.1" label="The RT of the first calibrant in the reference file" help=""/>
-    <param argument="-calibrant_2_reference" type="float" optional="true" value="0.9" label="The RT of the second calibrant in the reference file" help=""/>
-    <param argument="-calibrant_1_input" type="float" optional="true" value="-1.0" label="The RT of the first calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/>
-    <param argument="-calibrant_2_input" type="float" optional="true" value="-1.0" label="The RT of the second calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/>
+    <param argument="-in" type="data" format="idxml" label="input file" help=" select idxml data sets(s)"/>
+    <param argument="-calibrant_1_reference" type="float" value="0.1" label="The RT of the first calibrant in the reference file" help=""/>
+    <param argument="-calibrant_2_reference" type="float" value="0.9" label="The RT of the second calibrant in the reference file" help=""/>
+    <param argument="-calibrant_1_input" type="float" value="-1.0" label="The RT of the first calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/>
+    <param argument="-calibrant_2_input" type="float" value="-1.0" label="The RT of the second calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -60,14 +59,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_IDRTCalibration_1 -->
+  <tests>
+    <!-- TOPP_IDRTCalibration_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDRTCalibration_1_input.idXML"/>
-      <output name="out" file="IDRTCalibration_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDRTCalibration_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="calibrant_1_reference" value="0.1"/>
       <param name="calibrant_2_reference" value="0.9"/>
       <param name="calibrant_1_input" value="10.0"/>
@@ -78,6 +78,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IDRTCalibration_2 -->
     <test expect_num_outputs="2">
@@ -86,7 +89,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="degenerated_empty.idXML"/>
-      <output name="out" file="IDRTCalibration_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDRTCalibration_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="calibrant_1_reference" value="0.1"/>
       <param name="calibrant_2_reference" value="0.9"/>
       <param name="calibrant_1_input" value="10.0"/>
@@ -97,11 +100,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Can be used to calibrate RTs of peptide hits linearly to standards.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDRTCalibration.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDRTCalibration.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/IDRipper.xml b/tools/openms/IDRipper.xml
index 5c3803267..973aff849 100644
--- a/tools/openms/IDRipper.xml
+++ b/tools/openms/IDRipper.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [File Handling]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="IDRipper" name="IDRipper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Split protein/peptide identification file into several files according to identification run and annotated file origin.</description>
+  <description>Split protein/peptide identification file into several files according to identification run and annotated file origin</description>
   <macros>
     <token name="@EXECUTABLE@">IDRipper</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -38,12 +37,12 @@ out/
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="idxml" optional="false" label="Input file, in which the protein/peptide identifications must be tagged with 'file_origin'" help=" select idxml data sets(s)"/>
+    <param argument="-in" type="data" format="idxml" label="Input file, in which the protein/peptide identifications must be tagged with 'file_origin'" help=" select idxml data sets(s)"/>
     <param argument="-numeric_filenames" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not infer output filenames from spectra_data or file_origin but use the input filename with numeric suffixes" help=""/>
     <param argument="-split_ident_runs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Split different identification runs into separate files" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -59,11 +58,12 @@ out/
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_IDRipper_1 -->
+  <tests>
+    <!-- TOPP_IDRipper_1 -->
     <!-- TOPP_IDRipper_2 -->
     <!-- TOPP_IDRipper_2a -->
     <!-- TOPP_IDRipper_3 -->
-  <test expect_num_outputs="2">
+    <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="test" value="true"/>
       </section>
@@ -80,7 +80,8 @@ out/
           <is_valid_xml/>
         </assert_contents>
       </output>
-    </test><test expect_num_outputs="2">
+    </test>
+    <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="test" value="true"/>
       </section>
@@ -98,7 +99,8 @@ out/
           <is_valid_xml/>
         </assert_contents>
       </output>
-    </test><test expect_num_outputs="2">
+    </test>
+    <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="test" value="true"/>
       </section>
@@ -115,7 +117,8 @@ out/
           <is_valid_xml/>
         </assert_contents>
       </output>
-    </test><test expect_num_outputs="2">
+    </test>
+    <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="test" value="true"/>
       </section>
@@ -133,10 +136,10 @@ out/
         </assert_contents>
       </output>
     </test>
-</tests>
+  </tests>
   <help><![CDATA[Split protein/peptide identification file into several files according to identification run and annotated file origin.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDRipper.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDRipper.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/IDScoreSwitcher.xml b/tools/openms/IDScoreSwitcher.xml
index bee07766d..8e615ae63 100644
--- a/tools/openms/IDScoreSwitcher.xml
+++ b/tools/openms/IDScoreSwitcher.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="IDScoreSwitcher" name="IDScoreSwitcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Switches between different scores of peptide or protein hits in identification data</description>
   <macros>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,8 +38,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/>
-    <param argument="-proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply to protein scores instead of PSM scores" help=""/>
+    <param argument="-in" type="data" format="idxml" label="Input file" help=" select idxml data sets(s)"/>
     <param argument="-new_score" type="text" optional="true" value="" label="Name of the meta value to use as the new score" help="">
       <expand macro="list_string_san" name="new_score"/>
     </param>
@@ -55,9 +53,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-old_score" type="text" optional="true" value="" label="Name to use for the meta value storing the old score (default: old score type)" help="">
       <expand macro="list_string_san" name="old_score"/>
     </param>
+    <param argument="-proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply to protein scores instead of PSM scores" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -71,50 +70,57 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_IDScoreSwitcher_1 -->
+  <tests>
+    <!-- TOPP_IDScoreSwitcher_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDFileConverter_12_output.idXML"/>
-      <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <param name="proteins" value="false"/>
+      <output name="out" value="IDFileConverter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="new_score" value="Percolator_PEP"/>
       <param name="new_score_orientation" value="lower_better"/>
       <param name="new_score_type" value="Posterior Error Probability"/>
       <param name="old_score" value="Percolator_qvalue"/>
+      <param name="proteins" value="false"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_IDScoreSwitcher_2 -->
+    <!-- TOPP_IDScoreSwitcher_2 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDScoreSwitcher_2_input.idXML"/>
-      <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <param name="proteins" value="true"/>
+      <output name="out" value="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="new_score" value="Posterior Probability_score"/>
       <param name="new_score_orientation" value="higher_better"/>
       <param name="new_score_type" value="Posterior Probability"/>
       <param name="old_score" value=""/>
+      <param name="proteins" value="true"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Switches between different scores of peptide or protein hits in identification data
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_IDScoreSwitcher.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDScoreSwitcher.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/IDSplitter.xml b/tools/openms/IDSplitter.xml
index 7d37657fe..ac90092d5 100644
--- a/tools/openms/IDSplitter.xml
+++ b/tools/openms/IDSplitter.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="IDSplitter" name="IDSplitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Splits protein/peptide identifications off of annotated data files</description>
   <macros>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
 #end if
@@ -58,10 +57,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml,featurexml,mzml" optional="false" label="Input file (data annotated with identifications)" help=" select consensusxml,featurexml,mzml data sets(s)"/>
+    <param argument="-in" type="data" format="consensusxml,featurexml,mzml" label="Input file (data annotated with identifications)" help=" select consensusxml,featurexml,mzml data sets(s)"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -85,26 +84,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_IDSplitter_1 -->
+  <tests>
+    <!-- TOPP_IDSplitter_1 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDMapper_1_output.featureXML"/>
-      <output name="out" file="IDSplitter_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="id_out" file="IDSplitter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDSplitter_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="id_out" value="IDSplitter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,id_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Splits protein/peptide identifications off of annotated data files
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_IDSplitter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDSplitter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/InternalCalibration.xml b/tools/openms/InternalCalibration.xml
index a3f1bf3b4..7d92d6318 100644
--- a/tools/openms/InternalCalibration.xml
+++ b/tools/openms/InternalCalibration.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Mass Correction and Calibration]-->
 <tool id="InternalCalibration" name="InternalCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies an internal mass recalibration.</description>
+  <description>Applies an internal mass recalibration</description>
   <macros>
     <token name="@EXECUTABLE@">InternalCalibration</token>
     <import>macros.xml</import>
@@ -15,15 +14,15 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if $cal.id_in:
   mkdir cal.id_in &&
-  ln -s '$cal.id_in' 'cal.id_in/${re.sub("[^\w\-_]", "_", $cal.id_in.element_identifier)}.$gxy2omsext($cal.id_in.ext)' &&
+  cp '$cal.id_in' 'cal.id_in/${re.sub("[^\w\-_]", "_", $cal.id_in.element_identifier)}.$gxy2omsext($cal.id_in.ext)' &&
 #end if
 #if $cal.lock_in:
   mkdir cal.lock_in &&
-  ln -s '$cal.lock_in' 'cal.lock_in/${re.sub("[^\w\-_]", "_", $cal.lock_in.element_identifier)}.$gxy2omsext($cal.lock_in.ext)' &&
+  cp '$cal.lock_in' 'cal.lock_in/${re.sub("[^\w\-_]", "_", $cal.lock_in.element_identifier)}.$gxy2omsext($cal.lock_in.ext)' &&
 #end if
 #if "lock_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir cal_lock_out &&
@@ -118,18 +117,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"rscript_executable": "Rscript", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input peak file" help=" select mzml data sets(s)"/>
-    <param argument="-ppm_match_tolerance" type="float" optional="true" value="25.0" label="Finding calibrants in raw data uses this tolerance (for lock masses and ID's)" help=""/>
-    <param argument="-ms_level" type="text" optional="true" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Does not affect calibrant collection (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-in" type="data" format="mzml" label="Input peak file" help=" select mzml data sets(s)"/>
+    <param argument="-ppm_match_tolerance" type="float" value="25.0" label="Finding calibrants in raw data uses this tolerance (for lock masses and ID's)" help=""/>
+    <param argument="-ms_level" type="text" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Does not affect calibrant collection (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_integer_valsan" name="ms_level"/>
     </param>
-    <param argument="-RT_chunking" type="float" optional="true" value="300.0" label="RT window (one-sided" help="i.e. left-&gt;center, or center-&gt;right) around an MS scan in which calibrants are collected to build a model. Set to -1 to use ALL calibrants for all scans, i.e. a global model"/>
+    <param argument="-RT_chunking" type="float" value="300.0" label="RT window (one-sided" help="i.e. left-&gt;center, or center-&gt;right) around an MS scan in which calibrants are collected to build a model. Set to -1 to use ALL calibrants for all scans, i.e. a global model"/>
     <section name="cal" title="Chose one of two optional input files ('id_in' or 'lock_in') to define the calibration masses/function" help="" expanded="false">
       <param name="id_in" argument="-cal:id_in" type="data" format="featurexml,idxml" optional="true" label="Identifications or features whose peptide ID's serve as calibration masses" help=" select featurexml,idxml data sets(s)"/>
       <param name="lock_in" argument="-cal:lock_in" type="data" format="csv" optional="true" label="Input file containing reference m/z values (text file with each line as: m/z ms-level charge) which occur in all scans" help=" select csv data sets(s)"/>
       <param name="lock_require_mono" argument="-cal:lock_require_mono" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require all lock masses to be monoisotopic" help="i.e. not the iso1, iso2 etc ('charge' column is used to determine the spacing). Peaks which are not mono-isotopic are not used"/>
       <param name="lock_require_iso" argument="-cal:lock_require_iso" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require all lock masses to have at least the +1 isotope" help="Peaks without isotope pattern are not used"/>
-      <param name="model_type" argument="-cal:model_type" type="select" optional="true" label="Type of function to be fitted to the calibration points" help="">
+      <param name="model_type" argument="-cal:model_type" type="select" label="Type of function to be fitted to the calibration points" help="">
         <option value="linear">linear</option>
         <option value="linear_weighted" selected="true">linear_weighted</option>
         <option value="quadratic">quadratic</option>
@@ -139,17 +138,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <section name="RANSAC" title="Robust outlier removal using RANSAC" help="" expanded="false">
       <param name="enabled" argument="-RANSAC:enabled" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply RANSAC to calibration points to remove outliers before fitting a model" help=""/>
-      <param name="threshold" argument="-RANSAC:threshold" type="float" optional="true" value="10.0" label="Threshold for accepting inliers (instrument precision (not accuracy!) as ppm^2 distance)" help=""/>
-      <param name="pc_inliers" argument="-RANSAC:pc_inliers" type="integer" optional="true" min="1" max="99" value="30" label="Minimum percentage (of available data) of inliers (&lt;threshold away from model) to accept the model" help=""/>
-      <param name="iter" argument="-RANSAC:iter" type="integer" optional="true" value="70" label="Maximal # iterations" help=""/>
+      <param name="threshold" argument="-RANSAC:threshold" type="float" value="10.0" label="Threshold for accepting inliers (instrument precision (not accuracy!) as ppm^2 distance)" help=""/>
+      <param name="pc_inliers" argument="-RANSAC:pc_inliers" type="integer" min="1" max="99" value="30" label="Minimum percentage (of available data) of inliers (&lt;threshold away from model) to accept the model" help=""/>
+      <param name="iter" argument="-RANSAC:iter" type="integer" value="70" label="Maximal # iterations" help=""/>
     </section>
     <section name="goodness" title="Thresholds for accepting calibration success" help="" expanded="false">
-      <param name="median" argument="-goodness:median" type="float" optional="true" value="4.0" label="The median ppm error of calibrated masses must be smaller than this threshold" help=""/>
-      <param name="MAD" argument="-goodness:MAD" type="float" optional="true" value="2.0" label="The median absolute deviation of the ppm error of calibrated masses must be smaller than this threshold" help=""/>
+      <param name="median" argument="-goodness:median" type="float" value="4.0" label="The median ppm error of calibrated masses must be smaller than this threshold" help=""/>
+      <param name="MAD" argument="-goodness:MAD" type="float" value="2.0" label="The median absolute deviation of the ppm error of calibrated masses must be smaller than this threshold" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -187,14 +186,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_InternalCalibration_1 -->
+  <tests>
+    <!-- TOPP_InternalCalibration_1 -->
     <test expect_num_outputs="4">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="InternalCalibration_1_BSA1.mzML"/>
-      <output name="out" file="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="ppm_match_tolerance" value="25.0"/>
       <param name="ms_level" value="1"/>
       <param name="RT_chunking" value="-1.0"/>
@@ -215,14 +215,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="MAD" value="2.0"/>
       </section>
       <section name="quality_control"/>
-      <output name="quality_control_models" file="InternalCalibration_1_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="quality_control_residuals" file="InternalCalibration_1_residuals.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="quality_control_models" value="InternalCalibration_1_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="quality_control_residuals" value="InternalCalibration_1_residuals.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_InternalCalibration_2 -->
     <test expect_num_outputs="4">
@@ -231,7 +234,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="InternalCalibration_2_lockmass.mzML.gz"/>
-      <output name="out" file="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="ppm_match_tolerance" value="25.0"/>
       <param name="ms_level" value="1 2 3"/>
       <param name="RT_chunking" value="60.0"/>
@@ -252,19 +255,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="MAD" value="2.0"/>
       </section>
       <section name="quality_control"/>
-      <output name="quality_control_models" file="InternalCalibration_2_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="quality_control_residuals" file="InternalCalibration_2_residuals.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="quality_control_models" value="InternalCalibration_2_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="quality_control_residuals" value="InternalCalibration_2_residuals.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Applies an internal mass recalibration.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_InternalCalibration.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_InternalCalibration.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/IsobaricAnalyzer.xml b/tools/openms/IsobaricAnalyzer.xml
index fb3d1c36d..93d252df0 100644
--- a/tools/openms/IsobaricAnalyzer.xml
+++ b/tools/openms/IsobaricAnalyzer.xml
@@ -1,4 +1,3 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Quantitation]-->
 <tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,18 +38,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-type" type="select" optional="true" label="Isobaric Quantitation method used in the experiment" help="">
+    <param argument="-type" type="select" label="Isobaric Quantitation method used in the experiment" help="">
       <option value="itraq4plex" selected="true">itraq4plex</option>
       <option value="itraq8plex">itraq8plex</option>
       <option value="tmt10plex">tmt10plex</option>
       <option value="tmt11plex">tmt11plex</option>
       <option value="tmt16plex">tmt16plex</option>
+      <option value="tmt18plex">tmt18plex</option>
       <option value="tmt6plex">tmt6plex</option>
       <expand macro="list_string_san" name="type"/>
     </param>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input raw/picked data file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input raw/picked data file" help=" select mzml data sets(s)"/>
     <section name="extraction" title="Parameters for the channel extraction" help="" expanded="false">
-      <param name="select_activation" argument="-extraction:select_activation" type="select" optional="true" label="Operate only on MSn scans where any of its precursors features a certain activation method" help="Setting to &quot;auto&quot; uses HCD and HCID spectra. Set to empty string if you want to disable filtering">
+      <param name="select_activation" argument="-extraction:select_activation" type="select" label="Operate only on MSn scans where any of its precursors features a certain activation method" help="Setting to &quot;auto&quot; uses HCD and HCID spectra. Set to empty string if you want to disable filtering">
         <option value="auto" selected="true">auto</option>
         <option value="Collision-induced dissociation">Collision-induced dissociation</option>
         <option value="Post-source decay">Post-source decay</option>
@@ -68,16 +68,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="trap-type collision-induced dissociation">trap-type collision-induced dissociation</option>
         <option value="beam-type collision-induced dissociation">beam-type collision-induced dissociation</option>
         <option value="in-source collision-induced dissociation">in-source collision-induced dissociation</option>
-        <option value=""></option>
+        <option value="any">any</option>
         <expand macro="list_string_san" name="select_activation"/>
       </param>
-      <param name="reporter_mass_shift" argument="-extraction:reporter_mass_shift" type="float" optional="true" min="0.0001" max="0.5" value="0.002" label="Allowed shift (left to right) in Th from the expected position" help=""/>
-      <param name="min_precursor_intensity" argument="-extraction:min_precursor_intensity" type="float" optional="true" min="0.0" value="1.0" label="Minimum intensity of the precursor to be extracted" help="MS/MS scans having a precursor with a lower intensity will not be considered for quantitation"/>
+      <param name="reporter_mass_shift" argument="-extraction:reporter_mass_shift" type="float" min="0.0001" max="0.5" value="0.002" label="Allowed shift (left to right) in Th from the expected position" help=""/>
+      <param name="min_precursor_intensity" argument="-extraction:min_precursor_intensity" type="float" min="0.0" value="1.0" label="Minimum intensity of the precursor to be extracted" help="MS/MS scans having a precursor with a lower intensity will not be considered for quantitation"/>
       <param name="keep_unannotated_precursor" argument="-extraction:keep_unannotated_precursor" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not" help=""/>
-      <param name="min_reporter_intensity" argument="-extraction:min_reporter_intensity" type="float" optional="true" min="0.0" value="0.0" label="Minimum intensity of the individual reporter ions to be extracted" help=""/>
+      <param name="min_reporter_intensity" argument="-extraction:min_reporter_intensity" type="float" min="0.0" value="0.0" label="Minimum intensity of the individual reporter ions to be extracted" help=""/>
       <param name="discard_low_intensity_quantifications" argument="-extraction:discard_low_intensity_quantifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove all reporter intensities if a single reporter is below the threshold given in 'min_reporter_intensity'" help=""/>
-      <param name="min_precursor_purity" argument="-extraction:min_precursor_purity" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precurso" help=""/>
-      <param name="precursor_isotope_deviation" argument="-extraction:precursor_isotope_deviation" type="float" optional="true" min="0.0" value="10.0" label="Maximum allowed deviation (in ppm) between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precurso" help=""/>
+      <param name="min_precursor_purity" argument="-extraction:min_precursor_purity" type="float" min="0.0" max="1.0" value="0.0" label="Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precurso" help=""/>
+      <param name="precursor_isotope_deviation" argument="-extraction:precursor_isotope_deviation" type="float" min="0.0" value="10.0" label="Maximum allowed deviation (in ppm) between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precurso" help=""/>
       <param name="purity_interpolation" argument="-extraction:purity_interpolation" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If set to true the algorithm will try to compute the purity as a time weighted linear combination of the precursor scan and the following scan" help="If set to false, only the precursor scan will be used"/>
     </section>
     <section name="itraq4plex" title="Algorithm parameters for iTRAQ 4-plex" help="" expanded="false">
@@ -93,8 +93,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="channel_117_description" argument="-itraq4plex:channel_117_description" type="text" optional="true" value="" label="Description for the content of the 117 channel" help="">
         <expand macro="list_string_san" name="channel_117_description"/>
       </param>
-      <param name="reference_channel" argument="-itraq4plex:reference_channel" type="integer" optional="true" min="114" max="117" value="114" label="Number of the reference channel (114-117)" help=""/>
-      <param name="correction_matrix" argument="-itraq4plex:correction_matrix" type="text" optional="true" value="0.0/1.0/5.9/0.2 0.0/2.0/5.6/0.1 0.0/3.0/4.5/0.1 0.1/4.0/3.5/0.1" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="reference_channel" argument="-itraq4plex:reference_channel" type="integer" min="114" max="117" value="114" label="Number of the reference channel (114-117)" help=""/>
+      <param name="correction_matrix" argument="-itraq4plex:correction_matrix" type="text" value="0.0/1.0/5.9/0.2 0.0/2.0/5.6/0.1 0.0/3.0/4.5/0.1 0.1/4.0/3.5/0.1" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="correction_matrix"/>
         <expand macro="list_string_san" name="correction_matrix"/>
       </param>
@@ -124,8 +124,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="channel_121_description" argument="-itraq8plex:channel_121_description" type="text" optional="true" value="" label="Description for the content of the 121 channel" help="">
         <expand macro="list_string_san" name="channel_121_description"/>
       </param>
-      <param name="reference_channel" argument="-itraq8plex:reference_channel" type="integer" optional="true" min="113" max="121" value="113" label="Number of the reference channel (113-121)" help="Please note that 120 is not valid"/>
-      <param name="correction_matrix" argument="-itraq8plex:correction_matrix" type="text" optional="true" value="0.00/0.00/6.89/0.22 0.00/0.94/5.90/0.16 0.00/1.88/4.90/0.10 0.00/2.82/3.90/0.07 0.06/3.77/2.99/0.00 0.09/4.71/1.88/0.00 0.14/5.66/0.87/0.00 0.27/7.44/0.18/0.00" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="reference_channel" argument="-itraq8plex:reference_channel" type="integer" min="113" max="121" value="113" label="Number of the reference channel (113-121)" help="Please note that 120 is not valid"/>
+      <param name="correction_matrix" argument="-itraq8plex:correction_matrix" type="text" value="0.00/0.00/6.89/0.22 0.00/0.94/5.90/0.16 0.00/1.88/4.90/0.10 0.00/2.82/3.90/0.07 0.06/3.77/2.99/0.00 0.09/4.71/1.88/0.00 0.14/5.66/0.87/0.00 0.27/7.44/0.18/0.00" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="correction_matrix"/>
         <expand macro="list_string_san" name="correction_matrix"/>
       </param>
@@ -165,7 +165,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="channel_131_description" argument="-tmt10plex:channel_131_description" type="text" optional="true" value="" label="Description for the content of the 131 channel" help="">
         <expand macro="list_string_san" name="channel_131_description"/>
       </param>
-      <param name="reference_channel" argument="-tmt10plex:reference_channel" type="select" optional="true" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131)" help="">
+      <param name="reference_channel" argument="-tmt10plex:reference_channel" type="select" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131)" help="">
         <option value="126" selected="true">126</option>
         <option value="127N">127N</option>
         <option value="127C">127C</option>
@@ -178,7 +178,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="131">131</option>
         <expand macro="list_string_san" name="reference_channel"/>
       </param>
-      <param name="correction_matrix" argument="-tmt10plex:correction_matrix" type="text" optional="true" value="0.0/0.0/5.09/0.0 0.0/0.25/5.27/0.0 0.0/0.37/5.36/0.15 0.0/0.65/4.17/0.1 0.08/0.49/3.06/0.0 0.01/0.71/3.07/0.0 0.0/1.32/2.62/0.0 0.02/1.28/2.75/2.53 0.03/2.08/2.23/0.0 0.08/1.99/1.65/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="correction_matrix" argument="-tmt10plex:correction_matrix" type="text" value="0.0/0.0/5.09/0.0 0.0/0.25/5.27/0.0 0.0/0.37/5.36/0.15 0.0/0.65/4.17/0.1 0.08/0.49/3.06/0.0 0.01/0.71/3.07/0.0 0.0/1.32/2.62/0.0 0.02/1.28/2.75/2.53 0.03/2.08/2.23/0.0 0.08/1.99/1.65/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="correction_matrix"/>
         <expand macro="list_string_san" name="correction_matrix"/>
       </param>
@@ -217,7 +217,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="channel_131C_description" argument="-tmt11plex:channel_131C_description" type="text" optional="true" value="" label="Description for the content of the 131C channel" help="">
         <expand macro="list_string_san" name="channel_131C_description"/>
       </param>
-      <param name="reference_channel" argument="-tmt11plex:reference_channel" type="select" optional="true" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C)" help="">
+      <param name="reference_channel" argument="-tmt11plex:reference_channel" type="select" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C)" help="">
         <option value="126" selected="true">126</option>
         <option value="127N">127N</option>
         <option value="127C">127C</option>
@@ -231,7 +231,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="131C">131C</option>
         <expand macro="list_string_san" name="reference_channel"/>
       </param>
-      <param name="correction_matrix" argument="-tmt11plex:correction_matrix" type="text" optional="true" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="correction_matrix" argument="-tmt11plex:correction_matrix" type="text" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="correction_matrix"/>
         <expand macro="list_string_san" name="correction_matrix"/>
       </param>
@@ -285,7 +285,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="channel_134N_description" argument="-tmt16plex:channel_134N_description" type="text" optional="true" value="" label="Description for the content of the 134N channel" help="">
         <expand macro="list_string_san" name="channel_134N_description"/>
       </param>
-      <param name="reference_channel" argument="-tmt16plex:reference_channel" type="select" optional="true" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C)" help="">
+      <param name="reference_channel" argument="-tmt16plex:reference_channel" type="select" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C, 132N, 132C, 133N, 133C, 134N)" help="">
         <option value="126" selected="true">126</option>
         <option value="127N">127N</option>
         <option value="127C">127C</option>
@@ -304,7 +304,88 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="134N">134N</option>
         <expand macro="list_string_san" name="reference_channel"/>
       </param>
-      <param name="correction_matrix" argument="-tmt16plex:correction_matrix" type="text" optional="true" value="0.0/0.0/8.02/0.0 0.0/0.68/7.46/0.0 0.0/0.71/6.94/0.0 0.0/1.88/6.67/0.0 0.0/1.34/5.59/0.0 0.0/2.41/5.48/0.0 0.0/2.34/5.19/0.0 0.0/3.53/4.57/0.0 0.0/2.67/4.16/0.0 0.0/3.92/3.73/0.0 0.0/3.69/3.14/0.0 0.0/3.22/2.76/0.0 0.0/4.11/2.0/0.0 0.0/3.85/1.58/0.0 0.0/4.63/1.18/0.0 0.0/5.22/0.86/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="correction_matrix" argument="-tmt16plex:correction_matrix" type="text" value="&quot;NA/NA / NA/NA / 0.31/9.09 / 0.02/0.32&quot; &quot;NA/NA / NA/0.78 / NA/9.41 / NA/0.33&quot; &quot;NA/NA / 0.93/NA / 0.35/8.63 / 0.01/0.27&quot; &quot;NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26&quot; &quot;0.00/NA / 1.47/NA / 0.34/6.91 / 0.00/0.15&quot; &quot;0.00/0.00 / 1.46/1.28 / NA/6.86 / NA/0.15&quot; &quot;0.13/NA / 2.59/NA / 0.32/6.07 / 0.1/0.09&quot; &quot;0.13/0.00 / 2.41/0.27 / NA/5.58 / NA/0.10&quot; &quot;0.04/NA / 3.10/NA / 0.42/4.82 / 0.02/0.06&quot; &quot;0.03/0.00 / 2.78/0.63 / NA/4.57 / NA/0.12&quot; &quot;0.08/NA / 3.90/NA / 0.47/3.57 / 0.00/0.04&quot; &quot;0.15/0.01 / 3.58/0.72 / NA/1.80 / NA/0.00&quot; &quot;0.11/NA / 4.55/NA / 0.43/1.86 / 0.00/0.00&quot; &quot;0.07/0.01 / 3.14/0.73 / NA/3.40 / NA/0.03&quot; &quot;0.22/NA / 4.96/NA / 0.34/1.03 / 0.00/NA&quot; &quot;0.30/0.03 / 5.49/0.62 / NA/1.14 / NA/NA&quot;" label="Correction matrix for isotope distributions in percent from the Thermo data sheet (see documentation); Please provide 16 entries (rows), separated by comma, where each entry contains 8 values in the following format: &lt;-2C13&gt;/&lt;-N15-C13&gt;/&lt;-C13&gt;/&lt;-N15&gt;/&lt;+N15&gt;/&lt;+C13&gt;/&lt;+N15+C13&gt;/&lt;+2C13" help="e.g. one row may look like this: 'NA/0.00  /  0.82/0.65  /  NA/8.13  /  NA/0.26'. You may use whitespaces at your leisure to ease reading (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+        <expand macro="list_string_val" name="correction_matrix"/>
+        <expand macro="list_string_san" name="correction_matrix"/>
+      </param>
+    </section>
+    <section name="tmt18plex" title="Algorithm parameters for TMT 18-plex" help="" expanded="false">
+      <param name="channel_126_description" argument="-tmt18plex:channel_126_description" type="text" optional="true" value="" label="Description for the content of the 126 channel" help="">
+        <expand macro="list_string_san" name="channel_126_description"/>
+      </param>
+      <param name="channel_127N_description" argument="-tmt18plex:channel_127N_description" type="text" optional="true" value="" label="Description for the content of the 127N channel" help="">
+        <expand macro="list_string_san" name="channel_127N_description"/>
+      </param>
+      <param name="channel_127C_description" argument="-tmt18plex:channel_127C_description" type="text" optional="true" value="" label="Description for the content of the 127C channel" help="">
+        <expand macro="list_string_san" name="channel_127C_description"/>
+      </param>
+      <param name="channel_128N_description" argument="-tmt18plex:channel_128N_description" type="text" optional="true" value="" label="Description for the content of the 128N channel" help="">
+        <expand macro="list_string_san" name="channel_128N_description"/>
+      </param>
+      <param name="channel_128C_description" argument="-tmt18plex:channel_128C_description" type="text" optional="true" value="" label="Description for the content of the 128C channel" help="">
+        <expand macro="list_string_san" name="channel_128C_description"/>
+      </param>
+      <param name="channel_129N_description" argument="-tmt18plex:channel_129N_description" type="text" optional="true" value="" label="Description for the content of the 129N channel" help="">
+        <expand macro="list_string_san" name="channel_129N_description"/>
+      </param>
+      <param name="channel_129C_description" argument="-tmt18plex:channel_129C_description" type="text" optional="true" value="" label="Description for the content of the 129C channel" help="">
+        <expand macro="list_string_san" name="channel_129C_description"/>
+      </param>
+      <param name="channel_130N_description" argument="-tmt18plex:channel_130N_description" type="text" optional="true" value="" label="Description for the content of the 130N channel" help="">
+        <expand macro="list_string_san" name="channel_130N_description"/>
+      </param>
+      <param name="channel_130C_description" argument="-tmt18plex:channel_130C_description" type="text" optional="true" value="" label="Description for the content of the 130C channel" help="">
+        <expand macro="list_string_san" name="channel_130C_description"/>
+      </param>
+      <param name="channel_131N_description" argument="-tmt18plex:channel_131N_description" type="text" optional="true" value="" label="Description for the content of the 131N channel" help="">
+        <expand macro="list_string_san" name="channel_131N_description"/>
+      </param>
+      <param name="channel_131C_description" argument="-tmt18plex:channel_131C_description" type="text" optional="true" value="" label="Description for the content of the 131C channel" help="">
+        <expand macro="list_string_san" name="channel_131C_description"/>
+      </param>
+      <param name="channel_132N_description" argument="-tmt18plex:channel_132N_description" type="text" optional="true" value="" label="Description for the content of the 132N channel" help="">
+        <expand macro="list_string_san" name="channel_132N_description"/>
+      </param>
+      <param name="channel_132C_description" argument="-tmt18plex:channel_132C_description" type="text" optional="true" value="" label="Description for the content of the 132C channel" help="">
+        <expand macro="list_string_san" name="channel_132C_description"/>
+      </param>
+      <param name="channel_133N_description" argument="-tmt18plex:channel_133N_description" type="text" optional="true" value="" label="Description for the content of the 133N channel" help="">
+        <expand macro="list_string_san" name="channel_133N_description"/>
+      </param>
+      <param name="channel_133C_description" argument="-tmt18plex:channel_133C_description" type="text" optional="true" value="" label="Description for the content of the 133C channel" help="">
+        <expand macro="list_string_san" name="channel_133C_description"/>
+      </param>
+      <param name="channel_134N_description" argument="-tmt18plex:channel_134N_description" type="text" optional="true" value="" label="Description for the content of the 134N channel" help="">
+        <expand macro="list_string_san" name="channel_134N_description"/>
+      </param>
+      <param name="channel_134C_description" argument="-tmt18plex:channel_134C_description" type="text" optional="true" value="" label="Description for the content of the 134C channel" help="">
+        <expand macro="list_string_san" name="channel_134C_description"/>
+      </param>
+      <param name="channel_135N_description" argument="-tmt18plex:channel_135N_description" type="text" optional="true" value="" label="Description for the content of the 135N channel" help="">
+        <expand macro="list_string_san" name="channel_135N_description"/>
+      </param>
+      <param name="reference_channel" argument="-tmt18plex:reference_channel" type="select" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C, 132N, 132C, 133N, 133C, 134N, 134C, 135N)" help="">
+        <option value="126" selected="true">126</option>
+        <option value="127N">127N</option>
+        <option value="127C">127C</option>
+        <option value="128N">128N</option>
+        <option value="128C">128C</option>
+        <option value="129N">129N</option>
+        <option value="129C">129C</option>
+        <option value="130N">130N</option>
+        <option value="130C">130C</option>
+        <option value="131N">131N</option>
+        <option value="131C">131C</option>
+        <option value="132N">132N</option>
+        <option value="132C">132C</option>
+        <option value="133N">133N</option>
+        <option value="133C">133C</option>
+        <option value="134N">134N</option>
+        <option value="134C">134C</option>
+        <option value="135N">135N</option>
+        <expand macro="list_string_san" name="reference_channel"/>
+      </param>
+      <param name="correction_matrix" argument="-tmt18plex:correction_matrix" type="text" value="&quot;NA/NA     /NA/NA     /0.31/9.09  /0.02/0.32&quot; &quot;NA/NA     /NA/0.78   /NA/9.41    /NA/0.33&quot; &quot;NA/NA     /0.93/NA   /0.35/8.63  /0.01/0.27&quot; &quot;NA/0.00   /0.82/0.65 /NA/8.13    /NA/0.26&quot; &quot;0.00/NA   /1.47/NA   /0.34/6.91  /0.00/0.15&quot; &quot;0.00/0.00 /1.46/1.28 /NA/6.86    /NA/0.15&quot; &quot;0.13/NA   /2.59/NA   /0.32/6.07  /0.1/0.09&quot; &quot;0.13/0.00 /2.41/0.27 /NA/5.58    /NA/0.10&quot; &quot;0.04/NA   /3.10/NA   /0.42/4.82  /0.02/0.06&quot; &quot;0.03/0.00 /2.78/0.63 /NA/4.57    /NA/0.12&quot; &quot;0.08/NA   /3.90/NA   /0.47/3.57  /0.00/0.04&quot; &quot;0.15/0.01 /3.58/0.72 /NA/1.80    /NA/0.00&quot; &quot;0.11/NA   /4.55/NA   /0.43/1.86  /0.00/0.00&quot; &quot;0.07/0.01 /3.14/0.73 /NA/3.40    /NA/0.03&quot; &quot;0.22/NA   /4.96/NA   /0.34/1.03  /0.00/NA&quot; &quot;0.30/0.03 /5.49/0.62 /NA/1.14    /NA/NA&quot; &quot;0.14/NA   /5.81/NA   /0.31/NA    /NA/NA&quot; &quot;0.19/0.02 /5.42/0.36 /NA/NA      /NA/NA&quot;" label="Correction matrix for isotope distributions in percent from the Thermo data sheet (see documentation); Please provide 18 entries (rows), separated by comma, where each entry contains 8 values in the following format: &lt;-2C13&gt;/&lt;-N15-C13&gt;/&lt;-C13&gt;/&lt;-N15&gt;/&lt;+N15&gt;/&lt;+C13&gt;/&lt;+N15+C13&gt;/&lt;+2C13" help="e.g. one row may look like this: 'NA/0.00  /  0.82/0.65  /  NA/8.13  /  NA/0.26'. You may use whitespaces at your leisure to ease reading (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="correction_matrix"/>
         <expand macro="list_string_san" name="correction_matrix"/>
       </param>
@@ -328,15 +409,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="channel_131_description" argument="-tmt6plex:channel_131_description" type="text" optional="true" value="" label="Description for the content of the 131 channel" help="">
         <expand macro="list_string_san" name="channel_131_description"/>
       </param>
-      <param name="reference_channel" argument="-tmt6plex:reference_channel" type="integer" optional="true" min="126" max="131" value="126" label="Number of the reference channel (126-131)" help=""/>
-      <param name="correction_matrix" argument="-tmt6plex:correction_matrix" type="text" optional="true" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="reference_channel" argument="-tmt6plex:reference_channel" type="integer" min="126" max="131" value="126" label="Number of the reference channel (126-131)" help=""/>
+      <param name="correction_matrix" argument="-tmt6plex:correction_matrix" type="text" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="correction_matrix"/>
         <expand macro="list_string_san" name="correction_matrix"/>
       </param>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -350,7 +431,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_IsobaricAnalyzer_1 -->
+  <tests>
+    <!-- TOPP_IsobaricAnalyzer_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -358,9 +440,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="type" value="itraq4plex"/>
       <param name="in" value="IsobaricAnalyzer_input_1.mzML"/>
-      <output name="out" file="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="extraction">
-        <param name="select_activation"/>
+        <param name="select_activation" value="any"/>
         <param name="reporter_mass_shift" value="0.1"/>
         <param name="min_precursor_intensity" value="1.0"/>
         <param name="keep_unannotated_precursor" value="true"/>
@@ -441,7 +523,29 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="channel_133C_description" value=""/>
         <param name="channel_134N_description" value=""/>
         <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
+        <param name="correction_matrix" value="&quot;NA/NA / NA/NA / 0.31/9.09 / 0.02/0.32&quot; &quot;NA/NA / NA/0.78 / NA/9.41 / NA/0.33&quot; &quot;NA/NA / 0.93/NA / 0.35/8.63 / 0.01/0.27&quot; &quot;NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26&quot; &quot;0.00/NA / 1.47/NA / 0.34/6.91 / 0.00/0.15&quot; &quot;0.00/0.00 / 1.46/1.28 / NA/6.86 / NA/0.15&quot; &quot;0.13/NA / 2.59/NA / 0.32/6.07 / 0.1/0.09&quot; &quot;0.13/0.00 / 2.41/0.27 / NA/5.58 / NA/0.10&quot; &quot;0.04/NA / 3.10/NA / 0.42/4.82 / 0.02/0.06&quot; &quot;0.03/0.00 / 2.78/0.63 / NA/4.57 / NA/0.12&quot; &quot;0.08/NA / 3.90/NA / 0.47/3.57 / 0.00/0.04&quot; &quot;0.15/0.01 / 3.58/0.72 / NA/1.80 / NA/0.00&quot; &quot;0.11/NA / 4.55/NA / 0.43/1.86 / 0.00/0.00&quot; &quot;0.07/0.01 / 3.14/0.73 / NA/3.40 / NA/0.03&quot; &quot;0.22/NA / 4.96/NA / 0.34/1.03 / 0.00/NA&quot; &quot;0.30/0.03 / 5.49/0.62 / NA/1.14 / NA/NA&quot;"/>
+      </section>
+      <section name="tmt18plex">
+        <param name="channel_126_description" value=""/>
+        <param name="channel_127N_description" value=""/>
+        <param name="channel_127C_description" value=""/>
+        <param name="channel_128N_description" value=""/>
+        <param name="channel_128C_description" value=""/>
+        <param name="channel_129N_description" value=""/>
+        <param name="channel_129C_description" value=""/>
+        <param name="channel_130N_description" value=""/>
+        <param name="channel_130C_description" value=""/>
+        <param name="channel_131N_description" value=""/>
+        <param name="channel_131C_description" value=""/>
+        <param name="channel_132N_description" value=""/>
+        <param name="channel_132C_description" value=""/>
+        <param name="channel_133N_description" value=""/>
+        <param name="channel_133C_description" value=""/>
+        <param name="channel_134N_description" value=""/>
+        <param name="channel_134C_description" value=""/>
+        <param name="channel_135N_description" value=""/>
+        <param name="reference_channel" value="126"/>
+        <param name="correction_matrix" value="&quot;NA/NA     /NA/NA     /0.31/9.09  /0.02/0.32&quot; &quot;NA/NA     /NA/0.78   /NA/9.41    /NA/0.33&quot; &quot;NA/NA     /0.93/NA   /0.35/8.63  /0.01/0.27&quot; &quot;NA/0.00   /0.82/0.65 /NA/8.13    /NA/0.26&quot; &quot;0.00/NA   /1.47/NA   /0.34/6.91  /0.00/0.15&quot; &quot;0.00/0.00 /1.46/1.28 /NA/6.86    /NA/0.15&quot; &quot;0.13/NA   /2.59/NA   /0.32/6.07  /0.1/0.09&quot; &quot;0.13/0.00 /2.41/0.27 /NA/5.58    /NA/0.10&quot; &quot;0.04/NA   /3.10/NA   /0.42/4.82  /0.02/0.06&quot; &quot;0.03/0.00 /2.78/0.63 /NA/4.57    /NA/0.12&quot; &quot;0.08/NA   /3.90/NA   /0.47/3.57  /0.00/0.04&quot; &quot;0.15/0.01 /3.58/0.72 /NA/1.80    /NA/0.00&quot; &quot;0.11/NA   /4.55/NA   /0.43/1.86  /0.00/0.00&quot; &quot;0.07/0.01 /3.14/0.73 /NA/3.40    /NA/0.03&quot; &quot;0.22/NA   /4.96/NA   /0.34/1.03  /0.00/NA&quot; &quot;0.30/0.03 /5.49/0.62 /NA/1.14    /NA/NA&quot; &quot;0.14/NA   /5.81/NA   /0.31/NA    /NA/NA&quot; &quot;0.19/0.02 /5.42/0.36 /NA/NA      /NA/NA&quot;"/>
       </section>
       <section name="tmt6plex">
         <param name="channel_126_description" value=""/>
@@ -459,6 +563,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IsobaricAnalyzer_TMTTenPlexMethod_1 -->
     <test expect_num_outputs="2">
@@ -468,7 +575,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="type" value="itraq4plex"/>
       <param name="in" value="TMTTenPlexMethod_test.mzML"/>
-      <output name="out" file="TMTTenPlexMethod_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="TMTTenPlexMethod_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="extraction">
         <param name="select_activation" value="auto"/>
         <param name="reporter_mass_shift" value="0.002"/>
@@ -551,7 +658,29 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="channel_133C_description" value=""/>
         <param name="channel_134N_description" value=""/>
         <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
+        <param name="correction_matrix" value="&quot;NA/NA / NA/NA / 0.31/9.09 / 0.02/0.32&quot; &quot;NA/NA / NA/0.78 / NA/9.41 / NA/0.33&quot; &quot;NA/NA / 0.93/NA / 0.35/8.63 / 0.01/0.27&quot; &quot;NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26&quot; &quot;0.00/NA / 1.47/NA / 0.34/6.91 / 0.00/0.15&quot; &quot;0.00/0.00 / 1.46/1.28 / NA/6.86 / NA/0.15&quot; &quot;0.13/NA / 2.59/NA / 0.32/6.07 / 0.1/0.09&quot; &quot;0.13/0.00 / 2.41/0.27 / NA/5.58 / NA/0.10&quot; &quot;0.04/NA / 3.10/NA / 0.42/4.82 / 0.02/0.06&quot; &quot;0.03/0.00 / 2.78/0.63 / NA/4.57 / NA/0.12&quot; &quot;0.08/NA / 3.90/NA / 0.47/3.57 / 0.00/0.04&quot; &quot;0.15/0.01 / 3.58/0.72 / NA/1.80 / NA/0.00&quot; &quot;0.11/NA / 4.55/NA / 0.43/1.86 / 0.00/0.00&quot; &quot;0.07/0.01 / 3.14/0.73 / NA/3.40 / NA/0.03&quot; &quot;0.22/NA / 4.96/NA / 0.34/1.03 / 0.00/NA&quot; &quot;0.30/0.03 / 5.49/0.62 / NA/1.14 / NA/NA&quot;"/>
+      </section>
+      <section name="tmt18plex">
+        <param name="channel_126_description" value=""/>
+        <param name="channel_127N_description" value=""/>
+        <param name="channel_127C_description" value=""/>
+        <param name="channel_128N_description" value=""/>
+        <param name="channel_128C_description" value=""/>
+        <param name="channel_129N_description" value=""/>
+        <param name="channel_129C_description" value=""/>
+        <param name="channel_130N_description" value=""/>
+        <param name="channel_130C_description" value=""/>
+        <param name="channel_131N_description" value=""/>
+        <param name="channel_131C_description" value=""/>
+        <param name="channel_132N_description" value=""/>
+        <param name="channel_132C_description" value=""/>
+        <param name="channel_133N_description" value=""/>
+        <param name="channel_133C_description" value=""/>
+        <param name="channel_134N_description" value=""/>
+        <param name="channel_134C_description" value=""/>
+        <param name="channel_135N_description" value=""/>
+        <param name="reference_channel" value="126"/>
+        <param name="correction_matrix" value="&quot;NA/NA     /NA/NA     /0.31/9.09  /0.02/0.32&quot; &quot;NA/NA     /NA/0.78   /NA/9.41    /NA/0.33&quot; &quot;NA/NA     /0.93/NA   /0.35/8.63  /0.01/0.27&quot; &quot;NA/0.00   /0.82/0.65 /NA/8.13    /NA/0.26&quot; &quot;0.00/NA   /1.47/NA   /0.34/6.91  /0.00/0.15&quot; &quot;0.00/0.00 /1.46/1.28 /NA/6.86    /NA/0.15&quot; &quot;0.13/NA   /2.59/NA   /0.32/6.07  /0.1/0.09&quot; &quot;0.13/0.00 /2.41/0.27 /NA/5.58    /NA/0.10&quot; &quot;0.04/NA   /3.10/NA   /0.42/4.82  /0.02/0.06&quot; &quot;0.03/0.00 /2.78/0.63 /NA/4.57    /NA/0.12&quot; &quot;0.08/NA   /3.90/NA   /0.47/3.57  /0.00/0.04&quot; &quot;0.15/0.01 /3.58/0.72 /NA/1.80    /NA/0.00&quot; &quot;0.11/NA   /4.55/NA   /0.43/1.86  /0.00/0.00&quot; &quot;0.07/0.01 /3.14/0.73 /NA/3.40    /NA/0.03&quot; &quot;0.22/NA   /4.96/NA   /0.34/1.03  /0.00/NA&quot; &quot;0.30/0.03 /5.49/0.62 /NA/1.14    /NA/NA&quot; &quot;0.14/NA   /5.81/NA   /0.31/NA    /NA/NA&quot; &quot;0.19/0.02 /5.42/0.36 /NA/NA      /NA/NA&quot;"/>
       </section>
       <section name="tmt6plex">
         <param name="channel_126_description" value=""/>
@@ -569,6 +698,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IsobaricAnalyzer_TMTElevenPlexMethod_1 -->
     <test expect_num_outputs="2">
@@ -578,7 +710,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="type" value="itraq4plex"/>
       <param name="in" value="TMTTenPlexMethod_test.mzML"/>
-      <output name="out" file="TMTElevenPlexMethod_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="TMTElevenPlexMethod_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="extraction">
         <param name="select_activation" value="auto"/>
         <param name="reporter_mass_shift" value="0.002"/>
@@ -661,7 +793,29 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="channel_133C_description" value=""/>
         <param name="channel_134N_description" value=""/>
         <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
+        <param name="correction_matrix" value="&quot;NA/NA / NA/NA / 0.31/9.09 / 0.02/0.32&quot; &quot;NA/NA / NA/0.78 / NA/9.41 / NA/0.33&quot; &quot;NA/NA / 0.93/NA / 0.35/8.63 / 0.01/0.27&quot; &quot;NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26&quot; &quot;0.00/NA / 1.47/NA / 0.34/6.91 / 0.00/0.15&quot; &quot;0.00/0.00 / 1.46/1.28 / NA/6.86 / NA/0.15&quot; &quot;0.13/NA / 2.59/NA / 0.32/6.07 / 0.1/0.09&quot; &quot;0.13/0.00 / 2.41/0.27 / NA/5.58 / NA/0.10&quot; &quot;0.04/NA / 3.10/NA / 0.42/4.82 / 0.02/0.06&quot; &quot;0.03/0.00 / 2.78/0.63 / NA/4.57 / NA/0.12&quot; &quot;0.08/NA / 3.90/NA / 0.47/3.57 / 0.00/0.04&quot; &quot;0.15/0.01 / 3.58/0.72 / NA/1.80 / NA/0.00&quot; &quot;0.11/NA / 4.55/NA / 0.43/1.86 / 0.00/0.00&quot; &quot;0.07/0.01 / 3.14/0.73 / NA/3.40 / NA/0.03&quot; &quot;0.22/NA / 4.96/NA / 0.34/1.03 / 0.00/NA&quot; &quot;0.30/0.03 / 5.49/0.62 / NA/1.14 / NA/NA&quot;"/>
+      </section>
+      <section name="tmt18plex">
+        <param name="channel_126_description" value=""/>
+        <param name="channel_127N_description" value=""/>
+        <param name="channel_127C_description" value=""/>
+        <param name="channel_128N_description" value=""/>
+        <param name="channel_128C_description" value=""/>
+        <param name="channel_129N_description" value=""/>
+        <param name="channel_129C_description" value=""/>
+        <param name="channel_130N_description" value=""/>
+        <param name="channel_130C_description" value=""/>
+        <param name="channel_131N_description" value=""/>
+        <param name="channel_131C_description" value=""/>
+        <param name="channel_132N_description" value=""/>
+        <param name="channel_132C_description" value=""/>
+        <param name="channel_133N_description" value=""/>
+        <param name="channel_133C_description" value=""/>
+        <param name="channel_134N_description" value=""/>
+        <param name="channel_134C_description" value=""/>
+        <param name="channel_135N_description" value=""/>
+        <param name="reference_channel" value="126"/>
+        <param name="correction_matrix" value="&quot;NA/NA     /NA/NA     /0.31/9.09  /0.02/0.32&quot; &quot;NA/NA     /NA/0.78   /NA/9.41    /NA/0.33&quot; &quot;NA/NA     /0.93/NA   /0.35/8.63  /0.01/0.27&quot; &quot;NA/0.00   /0.82/0.65 /NA/8.13    /NA/0.26&quot; &quot;0.00/NA   /1.47/NA   /0.34/6.91  /0.00/0.15&quot; &quot;0.00/0.00 /1.46/1.28 /NA/6.86    /NA/0.15&quot; &quot;0.13/NA   /2.59/NA   /0.32/6.07  /0.1/0.09&quot; &quot;0.13/0.00 /2.41/0.27 /NA/5.58    /NA/0.10&quot; &quot;0.04/NA   /3.10/NA   /0.42/4.82  /0.02/0.06&quot; &quot;0.03/0.00 /2.78/0.63 /NA/4.57    /NA/0.12&quot; &quot;0.08/NA   /3.90/NA   /0.47/3.57  /0.00/0.04&quot; &quot;0.15/0.01 /3.58/0.72 /NA/1.80    /NA/0.00&quot; &quot;0.11/NA   /4.55/NA   /0.43/1.86  /0.00/0.00&quot; &quot;0.07/0.01 /3.14/0.73 /NA/3.40    /NA/0.03&quot; &quot;0.22/NA   /4.96/NA   /0.34/1.03  /0.00/NA&quot; &quot;0.30/0.03 /5.49/0.62 /NA/1.14    /NA/NA&quot; &quot;0.14/NA   /5.81/NA   /0.31/NA    /NA/NA&quot; &quot;0.19/0.02 /5.42/0.36 /NA/NA      /NA/NA&quot;"/>
       </section>
       <section name="tmt6plex">
         <param name="channel_126_description" value=""/>
@@ -679,6 +833,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_IsobaricAnalyzer_MS3TMT10Plex_1 -->
     <test expect_num_outputs="2">
@@ -688,7 +845,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="type" value="tmt10plex"/>
       <param name="in" value="MS3_nonHierarchical.mzML"/>
-      <output name="out" file="MS3TMT10Plex_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="MS3TMT10Plex_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="extraction">
         <param name="select_activation" value="Collision-induced dissociation"/>
         <param name="reporter_mass_shift" value="0.002"/>
@@ -771,7 +928,29 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="channel_133C_description" value=""/>
         <param name="channel_134N_description" value=""/>
         <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
+        <param name="correction_matrix" value="&quot;NA/NA / NA/NA / 0.31/9.09 / 0.02/0.32&quot; &quot;NA/NA / NA/0.78 / NA/9.41 / NA/0.33&quot; &quot;NA/NA / 0.93/NA / 0.35/8.63 / 0.01/0.27&quot; &quot;NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26&quot; &quot;0.00/NA / 1.47/NA / 0.34/6.91 / 0.00/0.15&quot; &quot;0.00/0.00 / 1.46/1.28 / NA/6.86 / NA/0.15&quot; &quot;0.13/NA / 2.59/NA / 0.32/6.07 / 0.1/0.09&quot; &quot;0.13/0.00 / 2.41/0.27 / NA/5.58 / NA/0.10&quot; &quot;0.04/NA / 3.10/NA / 0.42/4.82 / 0.02/0.06&quot; &quot;0.03/0.00 / 2.78/0.63 / NA/4.57 / NA/0.12&quot; &quot;0.08/NA / 3.90/NA / 0.47/3.57 / 0.00/0.04&quot; &quot;0.15/0.01 / 3.58/0.72 / NA/1.80 / NA/0.00&quot; &quot;0.11/NA / 4.55/NA / 0.43/1.86 / 0.00/0.00&quot; &quot;0.07/0.01 / 3.14/0.73 / NA/3.40 / NA/0.03&quot; &quot;0.22/NA / 4.96/NA / 0.34/1.03 / 0.00/NA&quot; &quot;0.30/0.03 / 5.49/0.62 / NA/1.14 / NA/NA&quot;"/>
+      </section>
+      <section name="tmt18plex">
+        <param name="channel_126_description" value=""/>
+        <param name="channel_127N_description" value=""/>
+        <param name="channel_127C_description" value=""/>
+        <param name="channel_128N_description" value=""/>
+        <param name="channel_128C_description" value=""/>
+        <param name="channel_129N_description" value=""/>
+        <param name="channel_129C_description" value=""/>
+        <param name="channel_130N_description" value=""/>
+        <param name="channel_130C_description" value=""/>
+        <param name="channel_131N_description" value=""/>
+        <param name="channel_131C_description" value=""/>
+        <param name="channel_132N_description" value=""/>
+        <param name="channel_132C_description" value=""/>
+        <param name="channel_133N_description" value=""/>
+        <param name="channel_133C_description" value=""/>
+        <param name="channel_134N_description" value=""/>
+        <param name="channel_134C_description" value=""/>
+        <param name="channel_135N_description" value=""/>
+        <param name="reference_channel" value="126"/>
+        <param name="correction_matrix" value="&quot;NA/NA     /NA/NA     /0.31/9.09  /0.02/0.32&quot; &quot;NA/NA     /NA/0.78   /NA/9.41    /NA/0.33&quot; &quot;NA/NA     /0.93/NA   /0.35/8.63  /0.01/0.27&quot; &quot;NA/0.00   /0.82/0.65 /NA/8.13    /NA/0.26&quot; &quot;0.00/NA   /1.47/NA   /0.34/6.91  /0.00/0.15&quot; &quot;0.00/0.00 /1.46/1.28 /NA/6.86    /NA/0.15&quot; &quot;0.13/NA   /2.59/NA   /0.32/6.07  /0.1/0.09&quot; &quot;0.13/0.00 /2.41/0.27 /NA/5.58    /NA/0.10&quot; &quot;0.04/NA   /3.10/NA   /0.42/4.82  /0.02/0.06&quot; &quot;0.03/0.00 /2.78/0.63 /NA/4.57    /NA/0.12&quot; &quot;0.08/NA   /3.90/NA   /0.47/3.57  /0.00/0.04&quot; &quot;0.15/0.01 /3.58/0.72 /NA/1.80    /NA/0.00&quot; &quot;0.11/NA   /4.55/NA   /0.43/1.86  /0.00/0.00&quot; &quot;0.07/0.01 /3.14/0.73 /NA/3.40    /NA/0.03&quot; &quot;0.22/NA   /4.96/NA   /0.34/1.03  /0.00/NA&quot; &quot;0.30/0.03 /5.49/0.62 /NA/1.14    /NA/NA&quot; &quot;0.14/NA   /5.81/NA   /0.31/NA    /NA/NA&quot; &quot;0.19/0.02 /5.42/0.36 /NA/NA      /NA/NA&quot;"/>
       </section>
       <section name="tmt6plex">
         <param name="channel_126_description" value=""/>
@@ -789,11 +968,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Calculates isobaric quantitative values for peptides
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IsobaricAnalyzer.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IsobaricAnalyzer.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/JSONExporter.xml b/tools/openms/JSONExporter.xml
new file mode 100644
index 000000000..7a0d35ad1
--- /dev/null
+++ b/tools/openms/JSONExporter.xml
@@ -0,0 +1,101 @@
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
+<!--Proposed Tool Section: [[for Developers]]-->
+<tool id="JSONExporter" name="JSONExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+  <description>Exports .oms (SQLite) files in JSON format</description>
+  <macros>
+    <token name="@EXECUTABLE@">JSONExporter</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
+
+## Preprocessing
+mkdir in &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir out &&
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-out
+'out/output.${gxy2omsext("json")}'
+
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("json")}' '$out'
+#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
+  && mv '@EXECUTABLE@.ctd' '$ctd_out'
+#end if]]></command>
+  <configfiles>
+    <inputs name="args_json" data_style="paths"/>
+    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
+  <inputs>
+    <param argument="-in" type="data" format="sqlite" label="Input file" help=" select sqlite data sets(s)"/>
+    <expand macro="adv_opts_macro">
+      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
+        <expand macro="list_string_san" name="test"/>
+      </param>
+    </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="json"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+  </outputs>
+  <tests>
+    <!-- TOPP_JSONExporter_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="JSONExporter_protein.oms"/>
+      <output name="out" value="JSONExporter_1_output.json" compare="sim_size" delta_frac="0.7" ftype="json"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_JSONExporter_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="JSONExporter_RNA.oms"/>
+      <output name="out" value="JSONExporter_2_output.json" compare="sim_size" delta_frac="0.7" ftype="json"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+  </tests>
+  <help><![CDATA[Exports .oms (SQLite) files in JSON format
+
+
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_JSONExporter.html]]></help>
+  <expand macro="references"/>
+</tool>
diff --git a/tools/openms/LabeledEval.xml b/tools/openms/LabeledEval.xml
deleted file mode 100644
index d40ae00b1..000000000
--- a/tools/openms/LabeledEval.xml
+++ /dev/null
@@ -1,77 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
-<tool id="LabeledEval" name="LabeledEval" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description> Evaluation tool for isotope-labeled quantitation experiments.</description>
-  <macros>
-    <token name="@EXECUTABLE@">LabeledEval</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-mkdir truth &&
-ln -s '$truth' 'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)' &&
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in
-'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
--truth
-'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)'
-| tee '$stdout'
-
-## Postprocessing
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
-  </configfiles>
-  <inputs>
-    <param argument="-in" type="data" format="featurexml" optional="false" label="Feature result file" help=" select featurexml data sets(s)"/>
-    <param argument="-truth" type="data" format="consensusxml" optional="false" label="Expected result file" help=" select consensusxml data sets(s)"/>
-    <param argument="-rt_tol" type="float" optional="true" value="20.0" label="Maximum allowed retention time deviation" help=""/>
-    <param argument="-mz_tol" type="float" optional="true" value="0.25" label="Maximum allowed m/z deviation (divided by charge)" help=""/>
-    <expand macro="adv_opts_macro">
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
-      <filter>OPTIONAL_OUTPUTS is None</filter>
-    </data>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><test expect_num_outputs="1"><!-- comparing an arbitarty featureXML that has a corresponding consensusXML -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/>
-    <param name="truth" value="FeatureLinkerLabeled_1_output.consensusXML"/>
-    <output name="stdout" value="LabeledEval.txt" compare="sim_size"/>
-  </test>
-</tests>
-  <help><![CDATA[ Evaluation tool for isotope-labeled quantitation experiments.
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_LabeledEval.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/LuciphorAdapter.xml b/tools/openms/LuciphorAdapter.xml
index 0bbcf9d5f..919fa4f38 100644
--- a/tools/openms/LuciphorAdapter.xml
+++ b/tools/openms/LuciphorAdapter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [ID Processing]-->
+<!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
 <tool id="LuciphorAdapter" name="LuciphorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Modification site localisation using LuciPHOr2.</description>
+  <description>Modification site localisation using LuciPHOr2</description>
   <macros>
     <token name="@EXECUTABLE@">LuciphorAdapter</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir id &&
-ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
+cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -43,21 +42,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(dirname \$(realpath \$(which luciphor2)))/luciphor2.jar", "num_threads": "\${GALAXY_SLOTS:-1}", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input spectrum file" help=" select mzml data sets(s)"/>
-    <param argument="-id" type="data" format="idxml" optional="false" label="Protein/peptide identifications file" help=" select idxml data sets(s)"/>
-    <param argument="-fragment_method" type="select" optional="true" label="Fragmentation method" help="">
+    <param argument="-in" type="data" format="mzml" label="Input spectrum file" help=" select mzml data sets(s)"/>
+    <param argument="-id" type="data" format="idxml" label="Protein/peptide identifications file" help=" select idxml data sets(s)"/>
+    <param argument="-fragment_method" type="select" label="Fragmentation method" help="">
       <option value="CID" selected="true">CID</option>
       <option value="HCD">HCD</option>
       <expand macro="list_string_san" name="fragment_method"/>
     </param>
-    <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Tolerance of the peaks in the fragment spectrum" help=""/>
-    <param argument="-fragment_error_units" type="select" optional="true" label="Unit of fragment mass tolerance" help="">
+    <param argument="-fragment_mass_tolerance" type="float" value="0.5" label="Tolerance of the peaks in the fragment spectrum" help=""/>
+    <param argument="-fragment_error_units" type="select" label="Unit of fragment mass tolerance" help="">
       <option value="Da" selected="true">Da</option>
       <option value="ppm">ppm</option>
       <expand macro="list_string_san" name="fragment_error_units"/>
     </param>
-    <param argument="-min_mz" type="float" optional="true" value="150.0" label="Do not consider peaks below this value for matching fragment ions" help=""/>
-    <param argument="-target_modifications" multiple="true" type="select" optional="true" label="List the amino acids to be searched for and their mass modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
+    <param argument="-min_mz" type="float" value="150.0" label="Do not consider peaks below this value for matching fragment ions" help=""/>
+    <param argument="-target_modifications" type="select" multiple="true" optional="false" label="List the amino acids to be searched for and their mass modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
       <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
       <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
       <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -67,6 +66,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="2-succinyl (C)">2-succinyl (C)</option>
       <option value="2HPG (R)">2HPG (R)</option>
       <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+      <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+      <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+      <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+      <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
       <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
       <option value="3sulfo (N-term)">3sulfo (N-term)</option>
       <option value="4-ONE (C)">4-ONE (C)</option>
@@ -156,6 +159,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
       <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
       <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+      <option value="Andro-H2O (C)">Andro-H2O (C)</option>
       <option value="Archaeol (C)">Archaeol (C)</option>
       <option value="Arg (N-term)">Arg (N-term)</option>
       <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -259,6 +263,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
       <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
       <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+      <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
       <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
       <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
       <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -291,7 +296,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="BITC (N-term)">BITC (N-term)</option>
       <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
       <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-      <option value="Bodipy (C)">Bodipy (C)</option>
       <option value="Brij35 (N-term)">Brij35 (N-term)</option>
       <option value="Brij58 (N-term)">Brij58 (N-term)</option>
       <option value="Bromo (F)">Bromo (F)</option>
@@ -723,9 +727,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Dehydrated (T)">Dehydrated (T)</option>
       <option value="Dehydrated (Y)">Dehydrated (Y)</option>
       <option value="Dehydro (C)">Dehydro (C)</option>
+      <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
       <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-      <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
       <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
       <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -735,7 +739,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
       <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
       <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-      <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
       <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
       <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -747,6 +750,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
       <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
       <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+      <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
       <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
       <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -1319,7 +1323,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Ethanolyl (C)">Ethanolyl (C)</option>
       <option value="Ethanolyl (K)">Ethanolyl (K)</option>
       <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-      <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
       <option value="Ethyl (C-term)">Ethyl (C-term)</option>
       <option value="Ethyl (D)">Ethyl (D)</option>
       <option value="Ethyl (E)">Ethyl (E)</option>
@@ -1413,6 +1416,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
       <option value="Glu (E)">Glu (E)</option>
       <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+      <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
       <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
       <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
       <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -1427,7 +1431,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
       <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
       <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
       <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -1451,6 +1454,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gly (K)">Gly (K)</option>
       <option value="Gly (S)">Gly (S)</option>
       <option value="Gly (T)">Gly (T)</option>
+      <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
       <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
       <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
       <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -1841,6 +1845,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
       <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
       <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+      <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
       <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
       <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
       <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -1852,6 +1857,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
       <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
       <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+      <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+      <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+      <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
       <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
       <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
       <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -1907,6 +1915,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
       <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
       <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+      <option value="His+O(2) (H)">His+O(2) (H)</option>
       <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
       <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
       <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -2044,11 +2053,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+      <option value="Kdo (S)">Kdo (S)</option>
+      <option value="Kdo (T)">Kdo (T)</option>
       <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
       <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
       <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
       <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
       <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+      <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
       <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
       <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
       <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -2133,13 +2145,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
       <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
       <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+      <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
       <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
       <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
       <option value="Lipoyl (K)">Lipoyl (K)</option>
       <option value="LRGG (K)">LRGG (K)</option>
       <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
       <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+      <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
       <option value="Lys (N-term)">Lys (N-term)</option>
+      <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
       <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
       <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
       <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -2174,6 +2189,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Malonyl (C)">Malonyl (C)</option>
       <option value="Malonyl (K)">Malonyl (K)</option>
       <option value="Malonyl (S)">Malonyl (S)</option>
+      <option value="MBS+peptide (C)">MBS+peptide (C)</option>
       <option value="MDCC (C)">MDCC (C)</option>
       <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
       <option value="Menadione (C)">Menadione (C)</option>
@@ -2185,6 +2201,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="MesitylOxide (H)">MesitylOxide (H)</option>
       <option value="MesitylOxide (K)">MesitylOxide (K)</option>
       <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+      <option value="Met+O(2) (H)">Met+O(2) (H)</option>
       <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
       <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
       <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -2368,7 +2385,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
       <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
       <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-      <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
       <option value="NP40 (N-term)">NP40 (N-term)</option>
       <option value="NQIGG (K)">NQIGG (K)</option>
       <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -2456,6 +2472,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
       <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
       <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+      <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+      <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+      <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+      <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
       <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
       <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
       <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -2470,6 +2490,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phospho (Y)" selected="true">Phospho (Y)</option>
       <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
       <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+      <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
       <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
       <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
       <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -2501,6 +2522,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
       <option value="Piperidine (K)">Piperidine (K)</option>
       <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+      <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
       <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
       <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
       <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -2578,18 +2600,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="QTGG (K)">QTGG (K)</option>
       <option value="Quinone (W)">Quinone (W)</option>
       <option value="Quinone (Y)">Quinone (Y)</option>
+      <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+      <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+      <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+      <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+      <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+      <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+      <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+      <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+      <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+      <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+      <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+      <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+      <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+      <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+      <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+      <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+      <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+      <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+      <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+      <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
       <option value="Retinylidene (K)">Retinylidene (K)</option>
       <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
       <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
       <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-      <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-      <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-      <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-      <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-      <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-      <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-      <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-      <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
       <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
       <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
       <option value="Saligenin (H)">Saligenin (H)</option>
@@ -2617,6 +2651,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="shTMT (K)">shTMT (K)</option>
       <option value="shTMT (N-term)">shTMT (N-term)</option>
       <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+      <option value="shTMTpro (K)">shTMTpro (K)</option>
+      <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+      <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
       <option value="SMA (K)">SMA (K)</option>
       <option value="SMA (N-term)">SMA (N-term)</option>
       <option value="spermidine (Q)">spermidine (Q)</option>
@@ -2792,7 +2829,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
       <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
       <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-      <option value="Ub-amide (C)">Ub-amide (C)</option>
       <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
       <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
       <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -2987,30 +3023,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="ZQG (K)">ZQG (K)</option>
       <expand macro="list_string_san" name="target_modifications"/>
     </param>
-    <param argument="-neutral_losses" type="text" optional="true" value="&quot;sty -H3PO4 -97.97690&quot;" label="List the types of neutral losses that you want to conside" help="The residue field is case sensitive. For example: lower case 'sty' implies that the neutral loss can only occur if the specified modification is present. Syntax: NL = &lt;RESDIUES&gt; -&lt;NEUTRAL_LOSS_MOLECULAR_FORMULA&gt; &lt;MASS_LOST&gt; (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-neutral_losses" type="text" value="&quot;sty -H3PO4 -97.97690&quot;" label="List the types of neutral losses that you want to conside" help="The residue field is case sensitive. For example: lower case 'sty' implies that the neutral loss can only occur if the specified modification is present. Syntax: NL = &lt;RESDIUES&gt; -&lt;NEUTRAL_LOSS_MOLECULAR_FORMULA&gt; &lt;MASS_LOST&gt; (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="neutral_losses"/>
       <expand macro="list_string_san" name="neutral_losses"/>
     </param>
-    <param argument="-decoy_mass" type="float" optional="true" min="1.0" value="79.966331" label="How much to add to an amino acid to make it a decoy" help=""/>
-    <param argument="-decoy_neutral_losses" type="text" optional="true" value="&quot;X -H3PO4 -97.97690&quot;" label="For handling the neutral loss from a decoy sequence" help="The syntax for this is identical to that of the normal neutral losses given above except that the residue is always 'X'. Syntax: DECOY_NL = X -&lt;NEUTRAL_LOSS_MOLECULAR_FORMULA&gt; &lt;MASS_LOST&gt; (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-decoy_mass" type="float" min="1.0" value="79.966331" label="How much to add to an amino acid to make it a decoy" help=""/>
+    <param argument="-decoy_neutral_losses" type="text" value="&quot;X -H3PO4 -97.97690&quot;" label="For handling the neutral loss from a decoy sequence" help="The syntax for this is identical to that of the normal neutral losses given above except that the residue is always 'X'. Syntax: DECOY_NL = X -&lt;NEUTRAL_LOSS_MOLECULAR_FORMULA&gt; &lt;MASS_LOST&gt; (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="decoy_neutral_losses"/>
       <expand macro="list_string_san" name="decoy_neutral_losses"/>
     </param>
-    <param argument="-max_charge_state" type="integer" optional="true" min="1" value="5" label="Do not consider PSMs with a charge state above this value" help=""/>
-    <param argument="-max_peptide_length" type="integer" optional="true" min="1" value="40" label="Restrict scoring to peptides with a length shorter than this value" help=""/>
-    <param argument="-max_num_perm" type="integer" optional="true" min="1" value="16384" label="Maximum number of permutations a sequence can have" help=""/>
-    <param argument="-modeling_score_threshold" type="float" optional="true" min="0.0" value="0.95" label="Minimum score a PSM needs to be considered for modeling" help=""/>
-    <param argument="-scoring_threshold" type="float" optional="true" min="0.0" value="0.0" label="PSMs below this value will be discarded" help=""/>
-    <param argument="-min_num_psms_model" type="integer" optional="true" min="1" value="50" label="The minimum number of PSMs you need for any charge state in order to build a model for it" help=""/>
-    <param argument="-run_mode" type="select" optional="true" label="Determines how Luciphor will run: 0 = calculate FLR then rerun scoring without decoys (two iterations), 1 = Report Decoys: calculate FLR but don't rescore PSMs, all decoy hits will be reported" help="">
+    <param argument="-max_charge_state" type="integer" min="1" value="5" label="Do not consider PSMs with a charge state above this value" help=""/>
+    <param argument="-max_peptide_length" type="integer" min="1" value="40" label="Restrict scoring to peptides with a length shorter than this value" help=""/>
+    <param argument="-max_num_perm" type="integer" min="1" value="16384" label="Maximum number of permutations a sequence can have" help=""/>
+    <param argument="-modeling_score_threshold" type="float" min="0.0" value="0.95" label="Minimum score a PSM needs to be considered for modeling" help=""/>
+    <param argument="-scoring_threshold" type="float" min="0.0" value="0.0" label="PSMs below this value will be discarded" help=""/>
+    <param argument="-min_num_psms_model" type="integer" min="1" value="50" label="The minimum number of PSMs you need for any charge state in order to build a model for it" help=""/>
+    <param argument="-run_mode" type="select" label="Determines how Luciphor will run: 0 = calculate FLR then rerun scoring without decoys (two iterations), 1 = Report Decoys: calculate FLR but don't rescore PSMs, all decoy hits will be reported" help="">
       <option value="0" selected="true">0</option>
       <option value="1">1</option>
       <expand macro="list_string_san" name="run_mode"/>
     </param>
-    <param argument="-rt_tolerance" type="float" optional="true" min="0.0" value="0.01" label="Set the retention time tolerance (for the mapping of identifications to spectra in case multiple search engines were used)" help=""/>
+    <param argument="-rt_tolerance" type="float" min="0.0" value="0.01" label="Set the retention time tolerance (for the mapping of identifications to spectra in case multiple search engines were used)" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -3024,7 +3060,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_LuciphorAdapter_1 -->
+  <tests>
+    <!-- TOPP_LuciphorAdapter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -3032,7 +3069,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="LuciphorAdapter_1_input.mzML"/>
       <param name="id" value="LuciphorAdapter_1_input.idXML"/>
-      <output name="out" file="LuciphorAdapter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="LuciphorAdapter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="fragment_method" value="CID"/>
       <param name="fragment_mass_tolerance" value="0.5"/>
       <param name="fragment_error_units" value="Da"/>
@@ -3055,11 +3092,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Modification site localisation using LuciPHOr2.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_LuciphorAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_LuciphorAdapter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MRMMapper.xml b/tools/openms/MRMMapper.xml
index eece07759..f5f1d0a4e 100644
--- a/tools/openms/MRMMapper.xml
+++ b/tools/openms/MRMMapper.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="MRMMapper" name="MRMMapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description>
   <macros>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir tr &&
-ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
+cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -43,17 +42,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file containing chromatograms (converted mzXML file)" help=" select mzml data sets(s)"/>
-    <param argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Input file containing chromatograms (converted mzXML file)" help=" select mzml data sets(s)"/>
+    <param argument="-tr" type="data" format="traml" label="transition file" help=" select traml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="precursor_tolerance" argument="-algorithm:precursor_tolerance" type="float" optional="true" value="0.1" label="Precursor tolerance when mapping (in Th)" help=""/>
-      <param name="product_tolerance" argument="-algorithm:product_tolerance" type="float" optional="true" value="0.1" label="Product tolerance when mapping (in Th)" help=""/>
+      <param name="precursor_tolerance" argument="-algorithm:precursor_tolerance" type="float" value="0.1" label="Precursor tolerance when mapping (in Th)" help=""/>
+      <param name="product_tolerance" argument="-algorithm:product_tolerance" type="float" value="0.1" label="Product tolerance when mapping (in Th)" help=""/>
       <param name="map_multiple_assays" argument="-algorithm:map_multiple_assays" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow to map multiple assays to chromatograms and duplicate these chromatograms in the output" help=""/>
       <param name="error_on_unmapped" argument="-algorithm:error_on_unmapped" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat remaining, unmapped chromatograms as an erro" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -67,7 +66,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MRMMapper_test_1 -->
+  <tests>
+    <!-- TOPP_MRMMapper_test_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -75,7 +75,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="MRMMapping_input.chrom.mzML"/>
       <param name="tr" value="MRMMapping_input.TraML"/>
-      <output name="out" file="MRMMapping_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="MRMMapping_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="precursor_tolerance" value="0.3"/>
         <param name="product_tolerance" value="0.3"/>
@@ -88,6 +88,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MRMMapper_test_2 -->
     <test expect_num_outputs="2">
@@ -97,7 +100,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="MRMMapping_input.chrom.mzML"/>
       <param name="tr" value="MRMMapping_input_2.TraML"/>
-      <output name="out" file="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="precursor_tolerance" value="0.01"/>
         <param name="product_tolerance" value="0.01"/>
@@ -110,11 +113,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MRMMapper.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MRMMapper.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MRMPairFinder.xml b/tools/openms/MRMPairFinder.xml
index b0e02de0c..f42e179bb 100644
--- a/tools/openms/MRMPairFinder.xml
+++ b/tools/openms/MRMPairFinder.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="MRMPairFinder" name="MRMPairFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Util which can be used to evaluate labeled pair ratios on MRM features.</description>
+  <description>Util which can be used to evaluate labeled pair ratios on MRM features</description>
   <macros>
     <token name="@EXECUTABLE@">MRMPairFinder</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir pair_in &&
-ln -s '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' &&
+cp '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' &&
 mkdir out &&
 #if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir feature_out &&
@@ -56,14 +55,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="featurexml" optional="false" label="Input featureXML file containing the features of the MRM experiment spectra" help=" select featurexml data sets(s)"/>
-    <param argument="-pair_in" type="data" format="csv" optional="false" label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" help=" select csv data sets(s)"/>
+    <param argument="-in" type="data" format="featurexml" label="Input featureXML file containing the features of the MRM experiment spectra" help=" select featurexml data sets(s)"/>
+    <param argument="-pair_in" type="data" format="csv" label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" help=" select csv data sets(s)"/>
     <expand macro="adv_opts_macro">
-      <param argument="-mass_tolerance" type="float" optional="true" min="0.0" value="0.01" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help=""/>
-      <param argument="-RT_tolerance" type="float" optional="true" min="0.0" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help=""/>
-      <param argument="-RT_pair_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have" help=""/>
+      <param argument="-mass_tolerance" type="float" min="0.0" value="0.01" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help=""/>
+      <param argument="-RT_tolerance" type="float" min="0.0" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help=""/>
+      <param argument="-RT_pair_tolerance" type="float" min="0.0" value="5.0" label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -81,11 +80,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TODO no idea about a useful input for pair_in -->
-</tests>
+  <tests>
+    <!-- TODO no idea about a useful input for pair_in -->
+  </tests>
   <help><![CDATA[Util which can be used to evaluate labeled pair ratios on MRM features.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MRMPairFinder.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MRMPairFinder.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MRMTransitionGroupPicker.xml b/tools/openms/MRMTransitionGroupPicker.xml
index 5632b2ff4..17e1546b6 100644
--- a/tools/openms/MRMTransitionGroupPicker.xml
+++ b/tools/openms/MRMTransitionGroupPicker.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Picks peaks in SRM/MRM chromatograms.</description>
+  <description>Picks peaks in SRM/MRM chromatograms</description>
   <macros>
     <token name="@EXECUTABLE@">MRMTransitionGroupPicker</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir tr &&
-ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
+cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -43,18 +42,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
-    <param argument="-tr" type="data" format="csv,traml" optional="false" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Input file" help=" select mzml data sets(s)"/>
+    <param argument="-tr" type="data" format="csv,traml" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="stop_after_feature" argument="-algorithm:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
-      <param name="stop_after_intensity_ratio" argument="-algorithm:stop_after_intensity_ratio" type="float" optional="true" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
-      <param name="min_peak_width" argument="-algorithm:min_peak_width" type="float" optional="true" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
-      <param name="peak_integration" argument="-algorithm:peak_integration" type="select" optional="true" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
+      <param name="stop_after_feature" argument="-algorithm:stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
+      <param name="stop_after_intensity_ratio" argument="-algorithm:stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
+      <param name="min_peak_width" argument="-algorithm:min_peak_width" type="float" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
+      <param name="peak_integration" argument="-algorithm:peak_integration" type="select" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
         <option value="original" selected="true">original</option>
         <option value="smoothed">smoothed</option>
         <expand macro="list_string_san" name="peak_integration"/>
       </param>
-      <param name="background_subtraction" argument="-algorithm:background_subtraction" type="select" optional="true" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
+      <param name="background_subtraction" argument="-algorithm:background_subtraction" type="select" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
         <option value="none" selected="true">none</option>
         <option value="original">original</option>
         <option value="exact">exact</option>
@@ -63,29 +62,29 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="recalculate_peaks" argument="-algorithm:recalculate_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="Tries to use the consensus (median) peak border if the variation within the picked peaks is too large"/>
       <param name="use_precursors" argument="-algorithm:use_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)" help=""/>
       <param name="use_consensus" argument="-algorithm:use_consensus" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)" help=""/>
-      <param name="recalculate_peaks_max_z" argument="-algorithm:recalculate_peaks_max_z" type="float" optional="true" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
-      <param name="minimal_quality" argument="-algorithm:minimal_quality" type="float" optional="true" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
-      <param name="resample_boundary" argument="-algorithm:resample_boundary" type="float" optional="true" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
+      <param name="recalculate_peaks_max_z" argument="-algorithm:recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
+      <param name="minimal_quality" argument="-algorithm:minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
+      <param name="resample_boundary" argument="-algorithm:resample_boundary" type="float" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
       <param name="compute_peak_quality" argument="-algorithm:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
       <param name="compute_peak_shape_metrics" argument="-algorithm:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/>
       <param name="compute_total_mi" argument="-algorithm:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/>
-      <param name="boundary_selection_method" argument="-algorithm:boundary_selection_method" type="select" optional="true" label="Method to use when selecting the best boundaries for peaks" help="">
+      <param name="boundary_selection_method" argument="-algorithm:boundary_selection_method" type="select" label="Method to use when selecting the best boundaries for peaks" help="">
         <option value="largest" selected="true">largest</option>
         <option value="widest">widest</option>
         <expand macro="list_string_san" name="boundary_selection_method"/>
       </param>
       <section name="PeakPickerMRM" title="" help="" expanded="false">
-        <param name="sgolay_frame_length" argument="-algorithm:PeakPickerMRM:sgolay_frame_length" type="integer" optional="true" value="15" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
-        <param name="sgolay_polynomial_order" argument="-algorithm:PeakPickerMRM:sgolay_polynomial_order" type="integer" optional="true" value="3" label="Order of the polynomial that is fitted" help=""/>
-        <param name="gauss_width" argument="-algorithm:PeakPickerMRM:gauss_width" type="float" optional="true" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/>
+        <param name="sgolay_frame_length" argument="-algorithm:PeakPickerMRM:sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
+        <param name="sgolay_polynomial_order" argument="-algorithm:PeakPickerMRM:sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help=""/>
+        <param name="gauss_width" argument="-algorithm:PeakPickerMRM:gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/>
         <param name="use_gauss" argument="-algorithm:PeakPickerMRM:use_gauss" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help=""/>
-        <param name="peak_width" argument="-algorithm:PeakPickerMRM:peak_width" type="float" optional="true" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
-        <param name="signal_to_noise" argument="-algorithm:PeakPickerMRM:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
-        <param name="sn_win_len" argument="-algorithm:PeakPickerMRM:sn_win_len" type="float" optional="true" value="1000.0" label="Signal to noise window length" help=""/>
-        <param name="sn_bin_count" argument="-algorithm:PeakPickerMRM:sn_bin_count" type="integer" optional="true" value="30" label="Signal to noise bin count" help=""/>
+        <param name="peak_width" argument="-algorithm:PeakPickerMRM:peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
+        <param name="signal_to_noise" argument="-algorithm:PeakPickerMRM:signal_to_noise" type="float" min="0.0" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
+        <param name="sn_win_len" argument="-algorithm:PeakPickerMRM:sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help=""/>
+        <param name="sn_bin_count" argument="-algorithm:PeakPickerMRM:sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help=""/>
         <param name="write_sn_log_messages" argument="-algorithm:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/>
         <param name="remove_overlapping_peaks" argument="-algorithm:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to remove overlapping peaks during peak picking" help=""/>
-        <param name="method" argument="-algorithm:PeakPickerMRM:method" type="select" optional="true" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
+        <param name="method" argument="-algorithm:PeakPickerMRM:method" type="select" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
           <option value="legacy">legacy</option>
           <option value="corrected" selected="true">corrected</option>
           <option value="crawdad">crawdad</option>
@@ -93,13 +92,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         </param>
       </section>
       <section name="PeakIntegrator" title="" help="" expanded="false">
-        <param name="integration_type" argument="-algorithm:PeakIntegrator:integration_type" type="select" optional="true" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
+        <param name="integration_type" argument="-algorithm:PeakIntegrator:integration_type" type="select" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
           <option value="intensity_sum" selected="true">intensity_sum</option>
           <option value="simpson">simpson</option>
           <option value="trapezoid">trapezoid</option>
           <expand macro="list_string_san" name="integration_type"/>
         </param>
-        <param name="baseline_type" argument="-algorithm:PeakIntegrator:baseline_type" type="select" optional="true" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
+        <param name="baseline_type" argument="-algorithm:PeakIntegrator:baseline_type" type="select" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
           <option value="base_to_base" selected="true">base_to_base</option>
           <option value="vertical_division">vertical_division</option>
           <option value="vertical_division_min">vertical_division_min</option>
@@ -111,7 +110,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -125,7 +124,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_MRMTransitionGroupPicker_test_1 -->
+  <tests>
+    <!-- TOPP_MRMTransitionGroupPicker_test_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -133,7 +133,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/>
       <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/>
-      <output name="out" file="MRMTransitionGroupPicker_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="MRMTransitionGroupPicker_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <section name="algorithm">
         <param name="stop_after_feature" value="-1"/>
         <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -175,8 +175,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_MRMTransitionGroupPicker_test_2 -->
+    <!-- TOPP_MRMTransitionGroupPicker_test_2 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -184,7 +187,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/>
       <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/>
-      <output name="out" file="MRMTransitionGroupPicker_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="MRMTransitionGroupPicker_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <section name="algorithm">
         <param name="stop_after_feature" value="-1"/>
         <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -226,11 +229,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Picks peaks in SRM/MRM chromatograms.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MRMTransitionGroupPicker.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MRMTransitionGroupPicker.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MSFraggerAdapter.xml b/tools/openms/MSFraggerAdapter.xml
index 007018ca5..29c8713b7 100644
--- a/tools/openms/MSFraggerAdapter.xml
+++ b/tools/openms/MSFraggerAdapter.xml
@@ -1,22 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: []-->
 <tool id="MSFraggerAdapter" name="MSFraggerAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Peptide Identification with MSFragger.
-Important note:
-The Regents of the University of Michigan (“Michigan”) grants us permission to redistribute    
-the MS Fragger application developed by Michigan within the OpenMS Pipeline and make available 
-for use on related service offerings supported by the University of Tubingen and the Center for
-Integrative Bioinformatics.                                                                    
-Per the license agreement the use of the pipeline and associated materials is for academic     
-research, non-commercial or educational purposes. Any commercial use inquiries                 
-must be directed to the University of Michigan Technology Transfer Office at                   
-techtransfer@umich.edu. All right title and interest in MS Fragger shall remain with the       
-University of Michigan.
-
-For details, please see the supplied license file or                                           
-https://raw.githubusercontent.com/OpenMS/THIRDPARTY/master/All/MSFragger/License.txt           
-</description>
+  <description>Peptide Identification with MSFragger</description>
   <macros>
     <token name="@EXECUTABLE@">MSFraggerAdapter</token>
     <import>macros.xml</import>
@@ -29,13 +14,13 @@ https://raw.githubusercontent.com/OpenMS/THIRDPARTY/master/All/MSFragger/License
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if "opt_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir opt_out &&
 #end if
 mkdir database &&
-ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
 
 ## Main program call
 
@@ -70,36 +55,37 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"java_executable": "java", "executable": "/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-license" display="radio" type="select" optional="false" label="Set to yes, if you have read and agreed to the MSFragger license terms" help="">
+    <param argument="-license" type="select" label="Set to yes, if you have read and agreed to the MSFragger license terms" help="">
       <option value="yes">yes</option>
       <option value="no">no</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="license"/>
     </param>
-    <param argument="-java_heapmemory" type="integer" optional="true" value="3500" label="Maximum Java heap size (in MB)" help=""/>
-    <param argument="-in" type="data" format="mzml,mzxml" optional="false" label="Input File with specta for MSFragge" help=" select mzml,mzxml data sets(s)"/>
-    <param argument="-database" type="data" format="fasta" optional="false" label="Protein FASTA database file path" help=" select fasta data sets(s)"/>
+    <param argument="-java_heapmemory" type="integer" value="3500" label="Maximum Java heap size (in MB)" help=""/>
+    <param argument="-in" type="data" format="mzml,mzxml" label="Input File with specta for MSFragge" help=" select mzml,mzxml data sets(s)"/>
+    <param argument="-database" type="data" format="fasta" label="Protein FASTA database file path" help=" select fasta data sets(s)"/>
     <param argument="-reindex" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Recalculate peptide to protein association using OpenMS" help="Annotates target-decoy information"/>
     <section name="tolerance" title="Search Tolerances" help="" expanded="false">
-      <param name="precursor_mass_tolerance_lower" argument="-tolerance:precursor_mass_tolerance_lower" type="float" optional="true" min="0.0" value="20.0" label="Lower precursor mass tolerance" help=""/>
-      <param name="precursor_mass_tolerance_upper" argument="-tolerance:precursor_mass_tolerance_upper" type="float" optional="true" min="0.0" value="20.0" label="Upper precursor mass tolerance" help=""/>
-      <param name="precursor_mass_unit" argument="-tolerance:precursor_mass_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
+      <param name="precursor_mass_tolerance_lower" argument="-tolerance:precursor_mass_tolerance_lower" type="float" min="0.0" value="20.0" label="Lower precursor mass tolerance" help=""/>
+      <param name="precursor_mass_tolerance_upper" argument="-tolerance:precursor_mass_tolerance_upper" type="float" min="0.0" value="20.0" label="Upper precursor mass tolerance" help=""/>
+      <param name="precursor_mass_unit" argument="-tolerance:precursor_mass_unit" type="select" label="Unit of precursor mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="precursor_mass_unit"/>
       </param>
-      <param name="precursor_true_tolerance" argument="-tolerance:precursor_true_tolerance" type="float" optional="true" min="0.0" value="0.0" label="True precursor mass tolerance (window is +/- this value)" help="Used for tie breaker of results (in spectrally ambiguous cases) and zero bin boosting in open searches (0 disables these features). This option is STRONGLY recommended for open searches"/>
-      <param name="precursor_true_unit" argument="-tolerance:precursor_true_unit" type="select" optional="true" label="Unit of precursor true tolerance" help="">
+      <param name="precursor_true_tolerance" argument="-tolerance:precursor_true_tolerance" type="float" min="0.0" value="0.0" label="True precursor mass tolerance (window is +/- this value)" help="Used for tie breaker of results (in spectrally ambiguous cases) and zero bin boosting in open searches (0 disables these features). This option is STRONGLY recommended for open searches"/>
+      <param name="precursor_true_unit" argument="-tolerance:precursor_true_unit" type="select" label="Unit of precursor true tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="precursor_true_unit"/>
       </param>
-      <param name="fragment_mass_tolerance" argument="-tolerance:fragment_mass_tolerance" type="float" optional="true" min="0.0" value="20.0" label="Fragment mass tolerance (window is +/- this value)" help=""/>
-      <param name="fragment_mass_unit" argument="-tolerance:fragment_mass_unit" type="select" optional="true" label="Unit of fragment mass tolerance" help="">
+      <param name="fragment_mass_tolerance" argument="-tolerance:fragment_mass_tolerance" type="float" min="0.0" value="20.0" label="Fragment mass tolerance (window is +/- this value)" help=""/>
+      <param name="fragment_mass_unit" argument="-tolerance:fragment_mass_unit" type="select" label="Unit of fragment mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="fragment_mass_unit"/>
       </param>
-      <param name="isotope_error" argument="-tolerance:isotope_error" type="select" optional="true" label="Isotope correction for MS/MS events triggered on isotopic peaks" help="Should be set to 0 (disabled) for open search or 0/1/2 for correction of narrow window searches. Shifts the precursor mass window to multiples of this value multiplied by the mass of C13-C12">
+      <param name="isotope_error" argument="-tolerance:isotope_error" type="select" label="Isotope correction for MS/MS events triggered on isotopic peaks" help="Should be set to 0 (disabled) for open search or 0/1/2 for correction of narrow window searches. Shifts the precursor mass window to multiples of this value multiplied by the mass of C13-C12">
         <option value="0" selected="true">0</option>
         <option value="1">1</option>
         <option value="2">2</option>
@@ -108,25 +94,23 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </param>
     </section>
     <section name="digest" title="In-Silico Digestion Parameters" help="" expanded="false">
-      <param name="search_enzyme_name" argument="-digest:search_enzyme_name" type="select" optional="true" label="Name of the enzyme to be written to the pepXML file" help="">
-        <option value="proline endopeptidase">proline endopeptidase</option>
-        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+      <param name="search_enzyme_name" argument="-digest:search_enzyme_name" type="select" label="Name of the enzyme to be written to the pepXML file" help="">
         <option value="no cleavage">no cleavage</option>
         <option value="unspecific cleavage">unspecific cleavage</option>
-        <option value="Arg-C">Arg-C</option>
         <option value="Arg-C/P">Arg-C/P</option>
         <option value="Asp-N">Asp-N</option>
-        <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
+        <option value="Asp-N/B">Asp-N/B</option>
+        <option value="Asp-N_ambic">Asp-N_ambic</option>
+        <option value="Chymotrypsin">Chymotrypsin</option>
+        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+        <option value="Trypsin" selected="true">Trypsin</option>
+        <option value="Arg-C">Arg-C</option>
         <option value="Glu-C+P">Glu-C+P</option>
         <option value="PepsinA + P">PepsinA + P</option>
         <option value="cyanogen-bromide">cyanogen-bromide</option>
         <option value="Clostripain/P">Clostripain/P</option>
-        <option value="V8-E">V8-E</option>
-        <option value="leukocyte elastase">leukocyte elastase</option>
-        <option value="Asp-N/B">Asp-N/B</option>
-        <option value="Asp-N_ambic">Asp-N_ambic</option>
-        <option value="Chymotrypsin">Chymotrypsin</option>
+        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
         <option value="Chymotrypsin/P">Chymotrypsin/P</option>
         <option value="CNBr">CNBr</option>
         <option value="Formic_acid">Formic_acid</option>
@@ -137,26 +121,28 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="TrypChymo">TrypChymo</option>
         <option value="Trypsin/P">Trypsin/P</option>
         <option value="V8-DE">V8-DE</option>
-        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+        <option value="V8-E">V8-E</option>
+        <option value="leukocyte elastase">leukocyte elastase</option>
+        <option value="proline endopeptidase">proline endopeptidase</option>
         <option value="2-iodobenzoate">2-iodobenzoate</option>
         <option value="iodosobenzoate">iodosobenzoate</option>
         <option value="staphylococcal protease/D">staphylococcal protease/D</option>
-        <option value="Trypsin" selected="true">Trypsin</option>
+        <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
         <expand macro="list_string_san" name="search_enzyme_name"/>
       </param>
-      <param name="search_enzyme_cutafter" argument="-digest:search_enzyme_cutafter" type="text" optional="true" value="KR" label="Residues after which the enzyme cuts (specified as a string of amino acids)" help="">
+      <param name="search_enzyme_cutafter" argument="-digest:search_enzyme_cutafter" type="text" value="KR" label="Residues after which the enzyme cuts (specified as a string of amino acids)" help="">
         <expand macro="list_string_san" name="search_enzyme_cutafter"/>
       </param>
-      <param name="search_enzyme_nocutbefore" argument="-digest:search_enzyme_nocutbefore" type="text" optional="true" value="P" label="Residues that the enzyme will not cut before" help="">
+      <param name="search_enzyme_nocutbefore" argument="-digest:search_enzyme_nocutbefore" type="text" value="P" label="Residues that the enzyme will not cut before" help="">
         <expand macro="list_string_san" name="search_enzyme_nocutbefore"/>
       </param>
-      <param name="num_enzyme_termini" argument="-digest:num_enzyme_termini" type="select" optional="true" label="Number of enzyme termini (non-enzymatic (0), semi (1), fully (2)" help="">
+      <param name="num_enzyme_termini" argument="-digest:num_enzyme_termini" type="select" label="Number of enzyme termini (non-enzymatic (0), semi (1), fully (2)" help="">
         <option value="non-enzymatic">non-enzymatic</option>
         <option value="semi">semi</option>
         <option value="fully" selected="true">fully</option>
         <expand macro="list_string_san" name="num_enzyme_termini"/>
       </param>
-      <param name="allowed_missed_cleavage" argument="-digest:allowed_missed_cleavage" type="select" optional="true" label="Allowed number of missed cleavages" help="">
+      <param name="allowed_missed_cleavage" argument="-digest:allowed_missed_cleavage" type="select" label="Allowed number of missed cleavages" help="">
         <option value="0">0</option>
         <option value="1">1</option>
         <option value="2" selected="true">2</option>
@@ -165,10 +151,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="5">5</option>
         <expand macro="list_string_san" name="allowed_missed_cleavage"/>
       </param>
-      <param name="min_length" argument="-digest:min_length" type="integer" optional="true" min="0" value="7" label="Minimum length of peptides to be generated during in-silico digestion" help=""/>
-      <param name="max_length" argument="-digest:max_length" type="integer" optional="true" min="0" value="64" label="Maximum length of peptides to be generated during in-silico digestion" help=""/>
-      <param name="mass_range_min" argument="-digest:mass_range_min" type="float" optional="true" min="0.0" value="500.0" label="Min mass of peptides to be generated (Da)" help=""/>
-      <param name="mass_range_max" argument="-digest:mass_range_max" type="float" optional="true" min="0.0" value="5000.0" label="Max mass of peptides to be generated (Da)" help=""/>
+      <param name="min_length" argument="-digest:min_length" type="integer" min="0" value="7" label="Minimum length of peptides to be generated during in-silico digestion" help=""/>
+      <param name="max_length" argument="-digest:max_length" type="integer" min="0" value="64" label="Maximum length of peptides to be generated during in-silico digestion" help=""/>
+      <param name="mass_range_min" argument="-digest:mass_range_min" type="float" min="0.0" value="500.0" label="Min mass of peptides to be generated (Da)" help=""/>
+      <param name="mass_range_max" argument="-digest:mass_range_max" type="float" min="0.0" value="5000.0" label="Max mass of peptides to be generated (Da)" help=""/>
     </section>
     <section name="varmod" title="Variable Modification Parameters" help="" expanded="false">
       <param name="clip_nterm_m" argument="-varmod:clip_nterm_m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Specifies the trimming of a protein N-terminal methionine as a variable modification" help=""/>
@@ -185,7 +171,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </param>
       <param name="enable_common" argument="-varmod:enable_common" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable common variable modifications (15.9949 M and 42.0106 [^)" help=""/>
       <param name="not_allow_multiple_variable_mods_on_residue" argument="-varmod:not_allow_multiple_variable_mods_on_residue" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not allow any one amino acid to be modified by multiple variable modifications" help=""/>
-      <param name="max_variable_mods_per_peptide" argument="-varmod:max_variable_mods_per_peptide" type="select" optional="true" label="Maximum total number of variable modifications per peptide" help="">
+      <param name="max_variable_mods_per_peptide" argument="-varmod:max_variable_mods_per_peptide" type="select" label="Maximum total number of variable modifications per peptide" help="">
         <option value="0">0</option>
         <option value="1">1</option>
         <option value="2" selected="true">2</option>
@@ -194,15 +180,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="5">5</option>
         <expand macro="list_string_san" name="max_variable_mods_per_peptide"/>
       </param>
-      <param name="max_variable_mods_combinations" argument="-varmod:max_variable_mods_combinations" type="integer" optional="true" min="0" max="65534" value="5000" label="Maximum allowed number of modified variably modified peptides from each peptide sequence, (maximum of 65534)" help="If a greater number than the maximum is generated, only the unmodified peptide is considered"/>
+      <param name="max_variable_mods_combinations" argument="-varmod:max_variable_mods_combinations" type="integer" min="0" max="65534" value="5000" label="Maximum allowed number of modified variably modified peptides from each peptide sequence, (maximum of 65534)" help="If a greater number than the maximum is generated, only the unmodified peptide is considered"/>
     </section>
     <section name="spectrum" title="Spectrum Processing Parameters" help="" expanded="false">
-      <param name="minimum_peaks" argument="-spectrum:minimum_peaks" type="integer" optional="true" min="0" value="10" label="Minimum number of peaks in experimental spectrum for matching" help=""/>
-      <param name="use_topn_peaks" argument="-spectrum:use_topn_peaks" type="integer" optional="true" min="0" value="50" label="Pre-process experimental spectrum to only use top N peaks" help=""/>
-      <param name="minimum_ratio" argument="-spectrum:minimum_ratio" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Filters out all peaks in experimental spectrum less intense than this multiple of the base peak intensity" help=""/>
-      <param name="clear_mz_range_min" argument="-spectrum:clear_mz_range_min" type="float" optional="true" min="0.0" value="0.0" label="Removes peaks in this m/z range prior to matching (minimum value)" help="Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)"/>
-      <param name="clear_mz_range_max" argument="-spectrum:clear_mz_range_max" type="float" optional="true" min="0.0" value="0.0" label="Removes peaks in this m/z range prior to matching (maximum value)" help="Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)"/>
-      <param name="max_fragment_charge" argument="-spectrum:max_fragment_charge" type="select" optional="true" label="Maximum charge state for theoretical fragments to match" help="">
+      <param name="minimum_peaks" argument="-spectrum:minimum_peaks" type="integer" min="0" value="10" label="Minimum number of peaks in experimental spectrum for matching" help=""/>
+      <param name="use_topn_peaks" argument="-spectrum:use_topn_peaks" type="integer" min="0" value="50" label="Pre-process experimental spectrum to only use top N peaks" help=""/>
+      <param name="minimum_ratio" argument="-spectrum:minimum_ratio" type="float" min="0.0" max="1.0" value="0.0" label="Filters out all peaks in experimental spectrum less intense than this multiple of the base peak intensity" help=""/>
+      <param name="clear_mz_range_min" argument="-spectrum:clear_mz_range_min" type="float" min="0.0" value="0.0" label="Removes peaks in this m/z range prior to matching (minimum value)" help="Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)"/>
+      <param name="clear_mz_range_max" argument="-spectrum:clear_mz_range_max" type="float" min="0.0" value="0.0" label="Removes peaks in this m/z range prior to matching (maximum value)" help="Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)"/>
+      <param name="max_fragment_charge" argument="-spectrum:max_fragment_charge" type="select" label="Maximum charge state for theoretical fragments to match" help="">
         <option value="1">1</option>
         <option value="2" selected="true">2</option>
         <option value="3">3</option>
@@ -210,45 +196,45 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <expand macro="list_string_san" name="max_fragment_charge"/>
       </param>
       <param name="override_charge" argument="-spectrum:override_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Ignores precursor charge and uses charge state specified in precursor_charge range (parameters: spectrum:precursor_charge_min and spectrum:precursor_charge_max)" help=""/>
-      <param name="precursor_charge_min" argument="-spectrum:precursor_charge_min" type="integer" optional="true" min="0" value="1" label="Min charge of precursor charge range to conside" help="If specified, also spectrum:override_charge must be set)"/>
-      <param name="precursor_charge_max" argument="-spectrum:precursor_charge_max" type="integer" optional="true" min="0" value="4" label="Max charge of precursor charge range to conside" help="If specified, also spectrum:override_charge must be set)"/>
+      <param name="precursor_charge_min" argument="-spectrum:precursor_charge_min" type="integer" min="0" value="1" label="Min charge of precursor charge range to conside" help="If specified, also spectrum:override_charge must be set)"/>
+      <param name="precursor_charge_max" argument="-spectrum:precursor_charge_max" type="integer" min="0" value="4" label="Max charge of precursor charge range to conside" help="If specified, also spectrum:override_charge must be set)"/>
     </section>
     <section name="search" title="Open Search Features" help="" expanded="false">
-      <param name="track_zero_topn" argument="-search:track_zero_topn" type="integer" optional="true" min="0" value="0" label="Track top N unmodified peptide results separately from main results internally for boosting features" help="Should be set to a number greater than search:output_report_topN if zero bin boosting is desired"/>
-      <param name="zero_bin_accept_expect" argument="-search:zero_bin_accept_expect" type="float" optional="true" min="0.0" value="0.0" label="Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value" help=""/>
-      <param name="zero_bin_mult_expect" argument="-search:zero_bin_mult_expect" type="float" optional="true" min="0.0" value="1.0" label="Multiplies expect value of PSMs in the zero-bin during results ordering (set to less than 1 for boosting)" help=""/>
-      <param name="add_topn_complementary" argument="-search:add_topn_complementary" type="integer" optional="true" min="0" value="0" label="Inserts complementary ions corresponding to the top N most intense fragments in each experimental spectrum" help="Useful for recovery of modified peptides near C-terminus in open search. 0 disables this option"/>
-      <param name="min_fragments_modeling" argument="-search:min_fragments_modeling" type="integer" optional="true" min="0" value="3" label="Minimum number of matched peaks in PSM for inclusion in statistical modeling" help=""/>
-      <param name="min_matched_fragments" argument="-search:min_matched_fragments" type="integer" optional="true" min="0" value="4" label="Minimum number of matched peaks for PSM to be reported" help="MSFragger recommends a minimum of 4 for narrow window searching and 6 for open searches"/>
-      <param name="output_report_topn" argument="-search:output_report_topn" type="integer" optional="true" min="0" value="1" label="Reports top N PSMs per input spectrum" help=""/>
-      <param name="output_max_expect" argument="-search:output_max_expect" type="float" optional="true" min="0.0" value="50.0" label="Suppresses reporting of PSM if top hit has expectation greater than this threshold" help=""/>
-      <param name="localize_delta_mass" argument="-search:localize_delta_mass" type="integer" optional="true" min="0" value="0" label="Include fragment ions mass-shifted by unknown modifications (recommended for open and mass offset searches) (0 for OFF, 1 for ON)" help=""/>
+      <param name="track_zero_topn" argument="-search:track_zero_topn" type="integer" min="0" value="0" label="Track top N unmodified peptide results separately from main results internally for boosting features" help="Should be set to a number greater than search:output_report_topN if zero bin boosting is desired"/>
+      <param name="zero_bin_accept_expect" argument="-search:zero_bin_accept_expect" type="float" min="0.0" value="0.0" label="Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value" help=""/>
+      <param name="zero_bin_mult_expect" argument="-search:zero_bin_mult_expect" type="float" min="0.0" value="1.0" label="Multiplies expect value of PSMs in the zero-bin during results ordering (set to less than 1 for boosting)" help=""/>
+      <param name="add_topn_complementary" argument="-search:add_topn_complementary" type="integer" min="0" value="0" label="Inserts complementary ions corresponding to the top N most intense fragments in each experimental spectrum" help="Useful for recovery of modified peptides near C-terminus in open search. 0 disables this option"/>
+      <param name="min_fragments_modeling" argument="-search:min_fragments_modeling" type="integer" min="0" value="3" label="Minimum number of matched peaks in PSM for inclusion in statistical modeling" help=""/>
+      <param name="min_matched_fragments" argument="-search:min_matched_fragments" type="integer" min="0" value="4" label="Minimum number of matched peaks for PSM to be reported" help="MSFragger recommends a minimum of 4 for narrow window searching and 6 for open searches"/>
+      <param name="output_report_topn" argument="-search:output_report_topn" type="integer" min="0" value="1" label="Reports top N PSMs per input spectrum" help=""/>
+      <param name="output_max_expect" argument="-search:output_max_expect" type="float" min="0.0" value="50.0" label="Suppresses reporting of PSM if top hit has expectation greater than this threshold" help=""/>
+      <param name="localize_delta_mass" argument="-search:localize_delta_mass" type="integer" min="0" value="0" label="Include fragment ions mass-shifted by unknown modifications (recommended for open and mass offset searches) (0 for OFF, 1 for ON)" help=""/>
     </section>
     <section name="statmod" title="Static Modification Parameters" help="" expanded="false">
-      <param name="add_cterm_peptide" argument="-statmod:add_cterm_peptide" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to C-terminal of peptide" help=""/>
-      <param name="add_nterm_peptide" argument="-statmod:add_nterm_peptide" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to N-terminal of peptide" help=""/>
-      <param name="add_cterm_protein" argument="-statmod:add_cterm_protein" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to C-terminal of protein" help=""/>
-      <param name="add_nterm_protein" argument="-statmod:add_nterm_protein" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to N-terminal of protein" help=""/>
-      <param name="add_G_glycine" argument="-statmod:add_G_glycine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to glycine" help=""/>
-      <param name="add_A_alanine" argument="-statmod:add_A_alanine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to alanine" help=""/>
-      <param name="add_S_serine" argument="-statmod:add_S_serine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to serine" help=""/>
-      <param name="add_P_proline" argument="-statmod:add_P_proline" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to proline" help=""/>
-      <param name="add_V_valine" argument="-statmod:add_V_valine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to valine" help=""/>
-      <param name="add_T_threonine" argument="-statmod:add_T_threonine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to threonine" help=""/>
-      <param name="add_C_cysteine" argument="-statmod:add_C_cysteine" type="float" optional="true" min="0.0" value="57.021464" label="Statically add mass to cysteine" help=""/>
-      <param name="add_L_leucine" argument="-statmod:add_L_leucine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to leucine" help=""/>
-      <param name="add_I_isoleucine" argument="-statmod:add_I_isoleucine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to isoleucine" help=""/>
-      <param name="add_N_asparagine" argument="-statmod:add_N_asparagine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to asparagine" help=""/>
-      <param name="add_D_aspartic_acid" argument="-statmod:add_D_aspartic_acid" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to aspartic_acid" help=""/>
-      <param name="add_Q_glutamine" argument="-statmod:add_Q_glutamine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to glutamine" help=""/>
-      <param name="add_K_lysine" argument="-statmod:add_K_lysine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to lysine" help=""/>
-      <param name="add_E_glutamic_acid" argument="-statmod:add_E_glutamic_acid" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to glutamic_acid" help=""/>
-      <param name="add_M_methionine" argument="-statmod:add_M_methionine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to methionine" help=""/>
-      <param name="add_H_histidine" argument="-statmod:add_H_histidine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to histidine" help=""/>
-      <param name="add_F_phenylalanine" argument="-statmod:add_F_phenylalanine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to phenylalanine" help=""/>
-      <param name="add_R_arginine" argument="-statmod:add_R_arginine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to arginine" help=""/>
-      <param name="add_Y_tyrosine" argument="-statmod:add_Y_tyrosine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to tyrosine" help=""/>
-      <param name="add_W_tryptophan" argument="-statmod:add_W_tryptophan" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to tryptophan" help=""/>
+      <param name="add_cterm_peptide" argument="-statmod:add_cterm_peptide" type="float" min="0.0" value="0.0" label="Statically add mass in Da to C-terminal of peptide" help=""/>
+      <param name="add_nterm_peptide" argument="-statmod:add_nterm_peptide" type="float" min="0.0" value="0.0" label="Statically add mass in Da to N-terminal of peptide" help=""/>
+      <param name="add_cterm_protein" argument="-statmod:add_cterm_protein" type="float" min="0.0" value="0.0" label="Statically add mass in Da to C-terminal of protein" help=""/>
+      <param name="add_nterm_protein" argument="-statmod:add_nterm_protein" type="float" min="0.0" value="0.0" label="Statically add mass in Da to N-terminal of protein" help=""/>
+      <param name="add_G_glycine" argument="-statmod:add_G_glycine" type="float" min="0.0" value="0.0" label="Statically add mass to glycine" help=""/>
+      <param name="add_A_alanine" argument="-statmod:add_A_alanine" type="float" min="0.0" value="0.0" label="Statically add mass to alanine" help=""/>
+      <param name="add_S_serine" argument="-statmod:add_S_serine" type="float" min="0.0" value="0.0" label="Statically add mass to serine" help=""/>
+      <param name="add_P_proline" argument="-statmod:add_P_proline" type="float" min="0.0" value="0.0" label="Statically add mass to proline" help=""/>
+      <param name="add_V_valine" argument="-statmod:add_V_valine" type="float" min="0.0" value="0.0" label="Statically add mass to valine" help=""/>
+      <param name="add_T_threonine" argument="-statmod:add_T_threonine" type="float" min="0.0" value="0.0" label="Statically add mass to threonine" help=""/>
+      <param name="add_C_cysteine" argument="-statmod:add_C_cysteine" type="float" min="0.0" value="57.021464" label="Statically add mass to cysteine" help=""/>
+      <param name="add_L_leucine" argument="-statmod:add_L_leucine" type="float" min="0.0" value="0.0" label="Statically add mass to leucine" help=""/>
+      <param name="add_I_isoleucine" argument="-statmod:add_I_isoleucine" type="float" min="0.0" value="0.0" label="Statically add mass to isoleucine" help=""/>
+      <param name="add_N_asparagine" argument="-statmod:add_N_asparagine" type="float" min="0.0" value="0.0" label="Statically add mass to asparagine" help=""/>
+      <param name="add_D_aspartic_acid" argument="-statmod:add_D_aspartic_acid" type="float" min="0.0" value="0.0" label="Statically add mass to aspartic_acid" help=""/>
+      <param name="add_Q_glutamine" argument="-statmod:add_Q_glutamine" type="float" min="0.0" value="0.0" label="Statically add mass to glutamine" help=""/>
+      <param name="add_K_lysine" argument="-statmod:add_K_lysine" type="float" min="0.0" value="0.0" label="Statically add mass to lysine" help=""/>
+      <param name="add_E_glutamic_acid" argument="-statmod:add_E_glutamic_acid" type="float" min="0.0" value="0.0" label="Statically add mass to glutamic_acid" help=""/>
+      <param name="add_M_methionine" argument="-statmod:add_M_methionine" type="float" min="0.0" value="0.0" label="Statically add mass to methionine" help=""/>
+      <param name="add_H_histidine" argument="-statmod:add_H_histidine" type="float" min="0.0" value="0.0" label="Statically add mass to histidine" help=""/>
+      <param name="add_F_phenylalanine" argument="-statmod:add_F_phenylalanine" type="float" min="0.0" value="0.0" label="Statically add mass to phenylalanine" help=""/>
+      <param name="add_R_arginine" argument="-statmod:add_R_arginine" type="float" min="0.0" value="0.0" label="Statically add mass to arginine" help=""/>
+      <param name="add_Y_tyrosine" argument="-statmod:add_Y_tyrosine" type="float" min="0.0" value="0.0" label="Statically add mass to tyrosine" help=""/>
+      <param name="add_W_tryptophan" argument="-statmod:add_W_tryptophan" type="float" min="0.0" value="0.0" label="Statically add mass to tryptophan" help=""/>
       <param name="unimod" argument="-statmod:unimod" type="text" optional="true" value="" label="Fixed modifications in unimod syntax if specific mass is unknown" help="e.g. Carbamidomethylation (C). When multiple different masses are given for one aminoacid this parameter (unimod) will have priority (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="unimod"/>
         <expand macro="list_string_san" name="unimod"/>
@@ -258,12 +244,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
         <expand macro="list_string_san" name="decoy_string"/>
       </param>
-      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="true" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
+      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
         <option value="prefix" selected="true">prefix</option>
         <option value="suffix">suffix</option>
         <expand macro="list_string_san" name="decoy_string_position"/>
       </param>
-      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="true" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
+      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
         <option value="error">error</option>
         <option value="warn" selected="true">warn</option>
         <option value="silent">silent</option>
@@ -272,54 +258,55 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
       <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
       <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
-      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="true" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
+      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
         <option value="error" selected="true">error</option>
         <option value="warn">warn</option>
         <option value="remove">remove</option>
         <expand macro="list_string_san" name="unmatched_action"/>
       </param>
-      <param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
-      <param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
+      <param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
+      <param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
       <param name="IL_equivalent" argument="-PeptideIndexing:IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/>
+      <param name="allow_nterm_protein_cleavage" argument="-PeptideIndexing:allow_nterm_protein_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Allow the protein N-terminus amino acid to clip" help=""/>
       <section name="enzyme" title="" help="" expanded="false">
-        <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" optional="true" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
+        <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
           <option value="auto" selected="true">auto</option>
+          <option value="TrypChymo">TrypChymo</option>
+          <option value="Trypsin/P">Trypsin/P</option>
+          <option value="V8-DE">V8-DE</option>
+          <option value="V8-E">V8-E</option>
+          <option value="Arg-C">Arg-C</option>
+          <option value="Arg-C/P">Arg-C/P</option>
+          <option value="Asp-N">Asp-N</option>
           <option value="Asp-N/B">Asp-N/B</option>
           <option value="Asp-N_ambic">Asp-N_ambic</option>
           <option value="Chymotrypsin">Chymotrypsin</option>
           <option value="Chymotrypsin/P">Chymotrypsin/P</option>
           <option value="CNBr">CNBr</option>
           <option value="Formic_acid">Formic_acid</option>
-          <option value="Trypsin">Trypsin</option>
-          <option value="Lys-C">Lys-C</option>
-          <option value="Lys-N">Lys-N</option>
-          <option value="unspecific cleavage">unspecific cleavage</option>
-          <option value="V8-DE">V8-DE</option>
-          <option value="V8-E">V8-E</option>
-          <option value="leukocyte elastase">leukocyte elastase</option>
-          <option value="proline endopeptidase">proline endopeptidase</option>
-          <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-          <option value="Alpha-lytic protease">Alpha-lytic protease</option>
-          <option value="2-iodobenzoate">2-iodobenzoate</option>
-          <option value="iodosobenzoate">iodosobenzoate</option>
-          <option value="staphylococcal protease/D">staphylococcal protease/D</option>
-          <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
           <option value="Glu-C+P">Glu-C+P</option>
           <option value="PepsinA + P">PepsinA + P</option>
           <option value="cyanogen-bromide">cyanogen-bromide</option>
           <option value="Clostripain/P">Clostripain/P</option>
           <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
           <option value="no cleavage">no cleavage</option>
-          <option value="Arg-C/P">Arg-C/P</option>
-          <option value="Asp-N">Asp-N</option>
+          <option value="Lys-C">Lys-C</option>
+          <option value="Lys-N">Lys-N</option>
           <option value="Lys-C/P">Lys-C/P</option>
           <option value="PepsinA">PepsinA</option>
-          <option value="TrypChymo">TrypChymo</option>
-          <option value="Trypsin/P">Trypsin/P</option>
-          <option value="Arg-C">Arg-C</option>
+          <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+          <option value="2-iodobenzoate">2-iodobenzoate</option>
+          <option value="iodosobenzoate">iodosobenzoate</option>
+          <option value="staphylococcal protease/D">staphylococcal protease/D</option>
+          <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
+          <option value="unspecific cleavage">unspecific cleavage</option>
+          <option value="leukocyte elastase">leukocyte elastase</option>
+          <option value="proline endopeptidase">proline endopeptidase</option>
+          <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+          <option value="Trypsin">Trypsin</option>
           <expand macro="list_string_san" name="name"/>
         </param>
-        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="true" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
+        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
           <option value="auto" selected="true">auto</option>
           <option value="full">full</option>
           <option value="semi">semi</option>
@@ -330,7 +317,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -348,12 +335,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MSFraggerAdapter_7 -->
+  <tests>
+    <!-- TOPP_MSFraggerAdapter_7 -->
     <!-- TOPP_MSFraggerAdapter_8 -->
   </tests>
   <help><![CDATA[Peptide Identification with MSFragger.
 Important note:
-The Regents of the University of Michigan (“Michigan”) grants us permission to redistribute    
+The Regents of the University of Michigan ("Michigan") grants us permission to redistribute    
 the MS Fragger application developed by Michigan within the OpenMS Pipeline and make available 
 for use on related service offerings supported by the University of Tubingen and the Center for
 Integrative Bioinformatics.                                                                    
@@ -368,6 +356,6 @@ https://raw.githubusercontent.com/OpenMS/THIRDPARTY/master/All/MSFragger/License
 
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MSFraggerAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MSFraggerAdapter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MSGFPlusAdapter.xml b/tools/openms/MSGFPlusAdapter.xml
index c2d121c91..df450a0ff 100644
--- a/tools/openms/MSGFPlusAdapter.xml
+++ b/tools/openms/MSGFPlusAdapter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
 <tool id="MSGFPlusAdapter" name="MSGFPlusAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>MS/MS database search using MS-GF+.</description>
+  <description>MS/MS database search using MS-GF+</description>
   <macros>
     <token name="@EXECUTABLE@">MSGFPlusAdapter</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
 #end if
@@ -23,10 +22,10 @@ ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($
   mkdir mzid_out &&
 #end if
 mkdir database &&
-ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
 #if $conf:
   mkdir conf &&
-  ln -s '$conf' 'conf/${re.sub("[^\w\-_]", "_", $conf.element_identifier)}.$gxy2omsext($conf.ext)' &&
+  cp '$conf' 'conf/${re.sub("[^\w\-_]", "_", $conf.element_identifier)}.$gxy2omsext($conf.ext)' &&
 #end if
 
 ## Main program call
@@ -70,32 +69,32 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(msgf_plus -get_jar_path)", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mgf,ms2,mzml,mzxml" optional="false" label="Input file (MS-GF+ parameter '-s')" help=" select mgf,ms2,mzml,mzxml data sets(s)"/>
-    <param argument="-database" type="data" format="fasta" optional="false" label="Protein sequence database (FASTA file; MS-GF+ parameter '-d')" help="Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir' select fasta data sets(s)"/>
-    <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" help=""/>
-    <param argument="-precursor_error_units" type="select" optional="true" label="Unit of precursor mass tolerance (MS-GF+ parameter '-t')" help="">
+    <param argument="-in" type="data" format="mgf,ms2,mzml,mzxml" label="Input file (MS-GF+ parameter '-s')" help=" select mgf,ms2,mzml,mzxml data sets(s)"/>
+    <param argument="-database" type="data" format="fasta" label="Protein sequence database (FASTA file; MS-GF+ parameter '-d')" help="Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir' select fasta data sets(s)"/>
+    <param argument="-precursor_mass_tolerance" type="float" value="10.0" label="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" help=""/>
+    <param argument="-precursor_error_units" type="select" label="Unit of precursor mass tolerance (MS-GF+ parameter '-t')" help="">
       <option value="Da">Da</option>
       <option value="ppm" selected="true">ppm</option>
       <expand macro="list_string_san" name="precursor_error_units"/>
     </param>
-    <param argument="-isotope_error_range" type="text" optional="true" value="0,1" label="Range of allowed isotope peak errors (MS-GF+ parameter '-ti')" help="Takes into account the error introduced by choosing a non-monoisotopic peak for fragmentation. Combined with 'precursor_mass_tolerance'/'precursor_error_units', this determines the actual precursor mass tolerance. E.g. for experimental mass 'exp' and calculated mass 'calc', '-precursor_mass_tolerance 20 -precursor_error_units ppm -isotope_error_range -1,2' tests '|exp - calc - n * 1.00335 Da| &lt; 20 ppm' for n = -1, 0, 1, 2">
+    <param argument="-isotope_error_range" type="text" value="0,1" label="Range of allowed isotope peak errors (MS-GF+ parameter '-ti')" help="Takes into account the error introduced by choosing a non-monoisotopic peak for fragmentation. Combined with 'precursor_mass_tolerance'/'precursor_error_units', this determines the actual precursor mass tolerance. E.g. for experimental mass 'exp' and calculated mass 'calc', '-precursor_mass_tolerance 20 -precursor_error_units ppm -isotope_error_range -1,2' tests '|exp - calc - n * 1.00335 Da| &lt; 20 ppm' for n = -1, 0, 1, 2">
       <expand macro="list_string_san" name="isotope_error_range"/>
     </param>
-    <param argument="-fragment_method" type="select" optional="true" label="Fragmentation method ('from_spectrum' relies on spectrum meta data and uses CID as fallback option; MS-GF+ parameter '-m')" help="">
+    <param argument="-fragment_method" type="select" label="Fragmentation method ('from_spectrum' relies on spectrum meta data and uses CID as fallback option; MS-GF+ parameter '-m')" help="">
       <option value="from_spectrum" selected="true">from_spectrum</option>
       <option value="CID">CID</option>
       <option value="ETD">ETD</option>
       <option value="HCD">HCD</option>
       <expand macro="list_string_san" name="fragment_method"/>
     </param>
-    <param argument="-instrument" type="select" optional="true" label="Instrument that generated the data ('low_res'/'high_res' refer to LCQ and LTQ instruments; MS-GF+ parameter '-inst')" help="">
+    <param argument="-instrument" type="select" label="Instrument that generated the data ('low_res'/'high_res' refer to LCQ and LTQ instruments; MS-GF+ parameter '-inst')" help="">
       <option value="low_res" selected="true">low_res</option>
       <option value="high_res">high_res</option>
       <option value="TOF">TOF</option>
       <option value="Q_Exactive">Q_Exactive</option>
       <expand macro="list_string_san" name="instrument"/>
     </param>
-    <param argument="-enzyme" type="select" optional="true" label="Enzyme used for digestion, or type of cleavage" help="Note: MS-GF+ does not support blocking rules. (MS-GF+ parameter '-e')">
+    <param argument="-enzyme" type="select" label="Enzyme used for digestion, or type of cleavage" help="Note: MS-GF+ does not support blocking rules. (MS-GF+ parameter '-e')">
       <option value="Alpha-lytic protease">Alpha-lytic protease</option>
       <option value="Arg-C/P">Arg-C/P</option>
       <option value="Asp-N/B">Asp-N/B</option>
@@ -108,7 +107,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="unspecific cleavage">unspecific cleavage</option>
       <expand macro="list_string_san" name="enzyme"/>
     </param>
-    <param argument="-protocol" type="select" optional="true" label="Labeling or enrichment protocol used, if any (MS-GF+ parameter '-p')" help="">
+    <param argument="-protocol" type="select" label="Labeling or enrichment protocol used, if any (MS-GF+ parameter '-p')" help="">
       <option value="automatic" selected="true">automatic</option>
       <option value="phospho">phospho</option>
       <option value="iTRAQ">iTRAQ</option>
@@ -117,22 +116,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="none">none</option>
       <expand macro="list_string_san" name="protocol"/>
     </param>
-    <param argument="-tryptic" type="select" optional="true" label="Level of cleavage specificity required (MS-GF+ parameter '-ntt')" help="">
+    <param argument="-tryptic" type="select" label="Level of cleavage specificity required (MS-GF+ parameter '-ntt')" help="">
       <option value="non">non</option>
       <option value="semi">semi</option>
       <option value="fully" selected="true">fully</option>
       <expand macro="list_string_san" name="tryptic"/>
     </param>
-    <param argument="-min_precursor_charge" type="integer" optional="true" min="1" value="2" label="Minimum precursor ion charge (only used for spectra without charge information; MS-GF+ parameter '-minCharge')" help=""/>
-    <param argument="-max_precursor_charge" type="integer" optional="true" min="1" value="3" label="Maximum precursor ion charge (only used for spectra without charge information; MS-GF+ parameter '-maxCharge')" help=""/>
-    <param argument="-min_peptide_length" type="integer" optional="true" min="1" value="6" label="Minimum peptide length to consider (MS-GF+ parameter '-minLength')" help=""/>
-    <param argument="-max_peptide_length" type="integer" optional="true" min="1" value="40" label="Maximum peptide length to consider (MS-GF+ parameter '-maxLength')" help=""/>
-    <param argument="-matches_per_spec" type="integer" optional="true" min="1" value="1" label="Number of matches per spectrum to be reported (MS-GF+ parameter '-n')" help=""/>
+    <param argument="-min_precursor_charge" type="integer" min="1" value="2" label="Minimum precursor ion charge (only used for spectra without charge information; MS-GF+ parameter '-minCharge')" help=""/>
+    <param argument="-max_precursor_charge" type="integer" min="1" value="3" label="Maximum precursor ion charge (only used for spectra without charge information; MS-GF+ parameter '-maxCharge')" help=""/>
+    <param argument="-min_peptide_length" type="integer" min="1" value="6" label="Minimum peptide length to consider (MS-GF+ parameter '-minLength')" help=""/>
+    <param argument="-max_peptide_length" type="integer" min="1" value="40" label="Maximum peptide length to consider (MS-GF+ parameter '-maxLength')" help=""/>
+    <param argument="-matches_per_spec" type="integer" min="1" value="1" label="Number of matches per spectrum to be reported (MS-GF+ parameter '-n')" help=""/>
     <param argument="-add_features" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output additional features (MS-GF+ parameter '-addFeatures')" help="This is required by Percolator and hence by default enabled"/>
-    <param argument="-max_mods" type="integer" optional="true" min="0" value="2" label="Maximum number of modifications per peptide" help="If this value is large, the search may take very long"/>
-    <param argument="-max_missed_cleavages" type="integer" optional="true" min="-1" value="-1" label="Maximum number of missed cleavages allowed for a peptide to be considered for scoring" help="(default: -1 meaning unlimited)"/>
-    <param argument="-tasks" type="integer" optional="true" value="0" label="(Override the number of tasks to use on the threads; Default: (internally calculated based on inputs))" help="More tasks than threads will reduce the memory requirements of the search, but will be slower (how much depends on the inputs)..    1 &lt;= tasks &lt;= numThreads: will create one task per thread, which is the original behavior..    tasks = 0: use default calculation - minimum of: (threads*3) and (numSpectra/250)..    tasks &lt; 0: multiply number of threads by abs(tasks) to determine number of tasks (i.e., -2 means &quot;2 * numThreads&quot; tasks)..    One task per thread will use the most memory, but will usually finish the fastest..    2-3 tasks per thread will use comparably less memory, but may cause the search to take 1.5 to 2 times as long"/>
-    <param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
+    <param argument="-max_mods" type="integer" min="0" value="2" label="Maximum number of modifications per peptide" help="If this value is large, the search may take very long"/>
+    <param argument="-max_missed_cleavages" type="integer" min="-1" value="-1" label="Maximum number of missed cleavages allowed for a peptide to be considered for scoring" help="(default: -1 meaning unlimited)"/>
+    <param argument="-tasks" type="integer" value="0" label="(Override the number of tasks to use on the threads; Default: (internally calculated based on inputs))" help="More tasks than threads will reduce the memory requirements of the search, but will be slower (how much depends on the inputs)..    1 &lt;= tasks &lt;= numThreads: will create one task per thread, which is the original behavior..    tasks = 0: use default calculation - minimum of: (threads*3) and (numSpectra/250)..    tasks &lt; 0: multiply number of threads by abs(tasks) to determine number of tasks (i.e., -2 means &quot;2 * numThreads&quot; tasks)..    One task per thread will use the most memory, but will usually finish the fastest..    2-3 tasks per thread will use comparably less memory, but may cause the search to take 1.5 to 2 times as long"/>
+    <param argument="-fixed_modifications" type="select" multiple="true" optional="false" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
       <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
       <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
       <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -142,6 +141,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="2-succinyl (C)">2-succinyl (C)</option>
       <option value="2HPG (R)">2HPG (R)</option>
       <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+      <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+      <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+      <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+      <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
       <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
       <option value="3sulfo (N-term)">3sulfo (N-term)</option>
       <option value="4-ONE (C)">4-ONE (C)</option>
@@ -231,6 +234,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
       <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
       <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+      <option value="Andro-H2O (C)">Andro-H2O (C)</option>
       <option value="Archaeol (C)">Archaeol (C)</option>
       <option value="Arg (N-term)">Arg (N-term)</option>
       <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -334,6 +338,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
       <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
       <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+      <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
       <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
       <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
       <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -366,7 +371,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="BITC (N-term)">BITC (N-term)</option>
       <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
       <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-      <option value="Bodipy (C)">Bodipy (C)</option>
       <option value="Brij35 (N-term)">Brij35 (N-term)</option>
       <option value="Brij58 (N-term)">Brij58 (N-term)</option>
       <option value="Bromo (F)">Bromo (F)</option>
@@ -798,9 +802,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Dehydrated (T)">Dehydrated (T)</option>
       <option value="Dehydrated (Y)">Dehydrated (Y)</option>
       <option value="Dehydro (C)">Dehydro (C)</option>
+      <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
       <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-      <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
       <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
       <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -810,7 +814,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
       <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
       <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-      <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
       <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
       <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -822,6 +825,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
       <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
       <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+      <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
       <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
       <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -1394,7 +1398,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Ethanolyl (C)">Ethanolyl (C)</option>
       <option value="Ethanolyl (K)">Ethanolyl (K)</option>
       <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-      <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
       <option value="Ethyl (C-term)">Ethyl (C-term)</option>
       <option value="Ethyl (D)">Ethyl (D)</option>
       <option value="Ethyl (E)">Ethyl (E)</option>
@@ -1488,6 +1491,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
       <option value="Glu (E)">Glu (E)</option>
       <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+      <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
       <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
       <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
       <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -1502,7 +1506,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
       <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
       <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
       <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -1526,6 +1529,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gly (K)">Gly (K)</option>
       <option value="Gly (S)">Gly (S)</option>
       <option value="Gly (T)">Gly (T)</option>
+      <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
       <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
       <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
       <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -1916,6 +1920,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
       <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
       <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+      <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
       <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
       <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
       <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -1927,6 +1932,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
       <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
       <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+      <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+      <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+      <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
       <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
       <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
       <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -1982,6 +1990,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
       <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
       <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+      <option value="His+O(2) (H)">His+O(2) (H)</option>
       <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
       <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
       <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -2119,11 +2128,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+      <option value="Kdo (S)">Kdo (S)</option>
+      <option value="Kdo (T)">Kdo (T)</option>
       <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
       <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
       <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
       <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
       <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+      <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
       <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
       <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
       <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -2208,13 +2220,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
       <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
       <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+      <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
       <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
       <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
       <option value="Lipoyl (K)">Lipoyl (K)</option>
       <option value="LRGG (K)">LRGG (K)</option>
       <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
       <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+      <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
       <option value="Lys (N-term)">Lys (N-term)</option>
+      <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
       <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
       <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
       <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -2249,6 +2264,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Malonyl (C)">Malonyl (C)</option>
       <option value="Malonyl (K)">Malonyl (K)</option>
       <option value="Malonyl (S)">Malonyl (S)</option>
+      <option value="MBS+peptide (C)">MBS+peptide (C)</option>
       <option value="MDCC (C)">MDCC (C)</option>
       <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
       <option value="Menadione (C)">Menadione (C)</option>
@@ -2260,6 +2276,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="MesitylOxide (H)">MesitylOxide (H)</option>
       <option value="MesitylOxide (K)">MesitylOxide (K)</option>
       <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+      <option value="Met+O(2) (H)">Met+O(2) (H)</option>
       <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
       <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
       <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -2443,7 +2460,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
       <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
       <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-      <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
       <option value="NP40 (N-term)">NP40 (N-term)</option>
       <option value="NQIGG (K)">NQIGG (K)</option>
       <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -2531,6 +2547,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
       <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
       <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+      <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+      <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+      <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+      <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
       <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
       <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
       <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -2545,6 +2565,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phospho (Y)">Phospho (Y)</option>
       <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
       <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+      <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
       <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
       <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
       <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -2576,6 +2597,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
       <option value="Piperidine (K)">Piperidine (K)</option>
       <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+      <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
       <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
       <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
       <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -2653,18 +2675,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="QTGG (K)">QTGG (K)</option>
       <option value="Quinone (W)">Quinone (W)</option>
       <option value="Quinone (Y)">Quinone (Y)</option>
+      <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+      <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+      <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+      <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+      <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+      <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+      <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+      <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+      <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+      <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+      <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+      <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+      <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+      <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+      <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+      <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+      <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+      <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+      <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+      <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
       <option value="Retinylidene (K)">Retinylidene (K)</option>
       <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
       <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
       <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-      <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-      <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-      <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-      <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-      <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-      <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-      <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-      <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
       <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
       <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
       <option value="Saligenin (H)">Saligenin (H)</option>
@@ -2692,6 +2726,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="shTMT (K)">shTMT (K)</option>
       <option value="shTMT (N-term)">shTMT (N-term)</option>
       <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+      <option value="shTMTpro (K)">shTMTpro (K)</option>
+      <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+      <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
       <option value="SMA (K)">SMA (K)</option>
       <option value="SMA (N-term)">SMA (N-term)</option>
       <option value="spermidine (Q)">spermidine (Q)</option>
@@ -2867,7 +2904,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
       <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
       <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-      <option value="Ub-amide (C)">Ub-amide (C)</option>
       <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
       <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
       <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -3062,7 +3098,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="ZQG (K)">ZQG (K)</option>
       <expand macro="list_string_san" name="fixed_modifications"/>
     </param>
-    <param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
+    <param argument="-variable_modifications" type="select" multiple="true" optional="false" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
       <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
       <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
       <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -3072,6 +3108,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="2-succinyl (C)">2-succinyl (C)</option>
       <option value="2HPG (R)">2HPG (R)</option>
       <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+      <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+      <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+      <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+      <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
       <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
       <option value="3sulfo (N-term)">3sulfo (N-term)</option>
       <option value="4-ONE (C)">4-ONE (C)</option>
@@ -3161,6 +3201,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
       <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
       <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+      <option value="Andro-H2O (C)">Andro-H2O (C)</option>
       <option value="Archaeol (C)">Archaeol (C)</option>
       <option value="Arg (N-term)">Arg (N-term)</option>
       <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -3264,6 +3305,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
       <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
       <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+      <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
       <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
       <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
       <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -3296,7 +3338,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="BITC (N-term)">BITC (N-term)</option>
       <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
       <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-      <option value="Bodipy (C)">Bodipy (C)</option>
       <option value="Brij35 (N-term)">Brij35 (N-term)</option>
       <option value="Brij58 (N-term)">Brij58 (N-term)</option>
       <option value="Bromo (F)">Bromo (F)</option>
@@ -3728,9 +3769,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Dehydrated (T)">Dehydrated (T)</option>
       <option value="Dehydrated (Y)">Dehydrated (Y)</option>
       <option value="Dehydro (C)">Dehydro (C)</option>
+      <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
       <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-      <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
       <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
       <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -3740,7 +3781,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
       <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
       <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-      <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
       <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
       <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -3752,6 +3792,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
       <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
       <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+      <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
       <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
       <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -4324,7 +4365,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Ethanolyl (C)">Ethanolyl (C)</option>
       <option value="Ethanolyl (K)">Ethanolyl (K)</option>
       <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-      <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
       <option value="Ethyl (C-term)">Ethyl (C-term)</option>
       <option value="Ethyl (D)">Ethyl (D)</option>
       <option value="Ethyl (E)">Ethyl (E)</option>
@@ -4418,6 +4458,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
       <option value="Glu (E)">Glu (E)</option>
       <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+      <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
       <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
       <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
       <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -4432,7 +4473,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
       <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
       <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
       <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -4456,6 +4496,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gly (K)">Gly (K)</option>
       <option value="Gly (S)">Gly (S)</option>
       <option value="Gly (T)">Gly (T)</option>
+      <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
       <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
       <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
       <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -4846,6 +4887,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
       <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
       <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+      <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
       <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
       <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
       <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -4857,6 +4899,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
       <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
       <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+      <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+      <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+      <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
       <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
       <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
       <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -4912,6 +4957,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
       <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
       <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+      <option value="His+O(2) (H)">His+O(2) (H)</option>
       <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
       <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
       <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -5049,11 +5095,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+      <option value="Kdo (S)">Kdo (S)</option>
+      <option value="Kdo (T)">Kdo (T)</option>
       <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
       <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
       <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
       <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
       <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+      <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
       <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
       <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
       <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -5138,13 +5187,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
       <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
       <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+      <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
       <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
       <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
       <option value="Lipoyl (K)">Lipoyl (K)</option>
       <option value="LRGG (K)">LRGG (K)</option>
       <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
       <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+      <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
       <option value="Lys (N-term)">Lys (N-term)</option>
+      <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
       <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
       <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
       <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -5179,6 +5231,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Malonyl (C)">Malonyl (C)</option>
       <option value="Malonyl (K)">Malonyl (K)</option>
       <option value="Malonyl (S)">Malonyl (S)</option>
+      <option value="MBS+peptide (C)">MBS+peptide (C)</option>
       <option value="MDCC (C)">MDCC (C)</option>
       <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
       <option value="Menadione (C)">Menadione (C)</option>
@@ -5190,6 +5243,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="MesitylOxide (H)">MesitylOxide (H)</option>
       <option value="MesitylOxide (K)">MesitylOxide (K)</option>
       <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+      <option value="Met+O(2) (H)">Met+O(2) (H)</option>
       <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
       <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
       <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -5373,7 +5427,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
       <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
       <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-      <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
       <option value="NP40 (N-term)">NP40 (N-term)</option>
       <option value="NQIGG (K)">NQIGG (K)</option>
       <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -5461,6 +5514,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
       <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
       <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+      <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+      <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+      <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+      <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
       <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
       <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
       <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -5475,6 +5532,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phospho (Y)">Phospho (Y)</option>
       <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
       <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+      <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
       <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
       <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
       <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -5506,6 +5564,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
       <option value="Piperidine (K)">Piperidine (K)</option>
       <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+      <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
       <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
       <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
       <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -5583,18 +5642,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="QTGG (K)">QTGG (K)</option>
       <option value="Quinone (W)">Quinone (W)</option>
       <option value="Quinone (Y)">Quinone (Y)</option>
+      <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+      <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+      <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+      <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+      <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+      <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+      <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+      <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+      <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+      <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+      <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+      <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+      <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+      <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+      <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+      <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+      <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+      <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+      <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+      <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
       <option value="Retinylidene (K)">Retinylidene (K)</option>
       <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
       <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
       <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-      <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-      <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-      <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-      <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-      <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-      <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-      <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-      <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
       <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
       <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
       <option value="Saligenin (H)">Saligenin (H)</option>
@@ -5622,6 +5693,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="shTMT (K)">shTMT (K)</option>
       <option value="shTMT (N-term)">shTMT (N-term)</option>
       <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+      <option value="shTMTpro (K)">shTMTpro (K)</option>
+      <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+      <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
       <option value="SMA (K)">SMA (K)</option>
       <option value="SMA (N-term)">SMA (N-term)</option>
       <option value="spermidine (Q)">spermidine (Q)</option>
@@ -5797,7 +5871,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
       <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
       <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-      <option value="Ub-amide (C)">Ub-amide (C)</option>
       <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
       <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
       <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -5998,12 +6071,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
         <expand macro="list_string_san" name="decoy_string"/>
       </param>
-      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="true" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
+      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
         <option value="prefix" selected="true">prefix</option>
         <option value="suffix">suffix</option>
         <expand macro="list_string_san" name="decoy_string_position"/>
       </param>
-      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="true" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
+      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
         <option value="error">error</option>
         <option value="warn" selected="true">warn</option>
         <option value="silent">silent</option>
@@ -6012,54 +6085,55 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
       <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
       <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
-      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="true" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
+      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
         <option value="error" selected="true">error</option>
         <option value="warn">warn</option>
         <option value="remove">remove</option>
         <expand macro="list_string_san" name="unmatched_action"/>
       </param>
-      <param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
-      <param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
+      <param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
+      <param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
       <param name="IL_equivalent" argument="-PeptideIndexing:IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/>
+      <param name="allow_nterm_protein_cleavage" argument="-PeptideIndexing:allow_nterm_protein_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Allow the protein N-terminus amino acid to clip" help=""/>
       <section name="enzyme" title="" help="" expanded="false">
-        <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" optional="true" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
+        <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
           <option value="auto" selected="true">auto</option>
           <option value="Trypsin">Trypsin</option>
-          <option value="CNBr">CNBr</option>
           <option value="Formic_acid">Formic_acid</option>
-          <option value="PepsinA">PepsinA</option>
-          <option value="TrypChymo">TrypChymo</option>
-          <option value="Trypsin/P">Trypsin/P</option>
-          <option value="V8-DE">V8-DE</option>
-          <option value="V8-E">V8-E</option>
-          <option value="leukocyte elastase">leukocyte elastase</option>
-          <option value="proline endopeptidase">proline endopeptidase</option>
-          <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+          <option value="Lys-C">Lys-C</option>
+          <option value="Lys-N">Lys-N</option>
+          <option value="Glu-C+P">Glu-C+P</option>
+          <option value="PepsinA + P">PepsinA + P</option>
           <option value="cyanogen-bromide">cyanogen-bromide</option>
           <option value="Clostripain/P">Clostripain/P</option>
           <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
           <option value="no cleavage">no cleavage</option>
           <option value="unspecific cleavage">unspecific cleavage</option>
-          <option value="Alpha-lytic protease">Alpha-lytic protease</option>
-          <option value="2-iodobenzoate">2-iodobenzoate</option>
-          <option value="iodosobenzoate">iodosobenzoate</option>
-          <option value="staphylococcal protease/D">staphylococcal protease/D</option>
-          <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
-          <option value="Glu-C+P">Glu-C+P</option>
-          <option value="PepsinA + P">PepsinA + P</option>
-          <option value="Lys-C">Lys-C</option>
-          <option value="Lys-N">Lys-N</option>
           <option value="Lys-C/P">Lys-C/P</option>
-          <option value="Arg-C/P">Arg-C/P</option>
+          <option value="PepsinA">PepsinA</option>
+          <option value="TrypChymo">TrypChymo</option>
+          <option value="Trypsin/P">Trypsin/P</option>
+          <option value="Chymotrypsin">Chymotrypsin</option>
+          <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+          <option value="CNBr">CNBr</option>
           <option value="Arg-C">Arg-C</option>
+          <option value="Arg-C/P">Arg-C/P</option>
           <option value="Asp-N">Asp-N</option>
           <option value="Asp-N/B">Asp-N/B</option>
           <option value="Asp-N_ambic">Asp-N_ambic</option>
-          <option value="Chymotrypsin">Chymotrypsin</option>
-          <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+          <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+          <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+          <option value="2-iodobenzoate">2-iodobenzoate</option>
+          <option value="iodosobenzoate">iodosobenzoate</option>
+          <option value="staphylococcal protease/D">staphylococcal protease/D</option>
+          <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
+          <option value="V8-DE">V8-DE</option>
+          <option value="V8-E">V8-E</option>
+          <option value="leukocyte elastase">leukocyte elastase</option>
+          <option value="proline endopeptidase">proline endopeptidase</option>
           <expand macro="list_string_san" name="name"/>
         </param>
-        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="true" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
+        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
           <option value="auto" selected="true">auto</option>
           <option value="full">full</option>
           <option value="semi">semi</option>
@@ -6069,10 +6143,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-add_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda')" help="This allows the calculation of FDRs, but should only be used if the database does not already contain decoys"/>
       <param argument="-legacy_conversion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the indirect conversion of MS-GF+ results to idXML via export to TSV" help="Try this only if the default conversion takes too long or uses too much memory"/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -6096,17 +6169,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MSGFPlusAdapter_1 -->
+  <tests>
+    <!-- TOPP_MSGFPlusAdapter_1 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
-        <param name="add_decoys" value="false"/>
         <param name="legacy_conversion" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="spectra.mzML"/>
-      <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
+      <output name="out" value="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="mzid_out" value="MSGFPlusAdapter_1_out.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
       <param name="database" value="proteins.fasta"/>
       <param name="precursor_mass_tolerance" value="10.0"/>
       <param name="precursor_error_units" value="ppm"/>
@@ -6125,7 +6198,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="max_mods" value="2"/>
       <param name="max_missed_cleavages" value="-1"/>
       <param name="tasks" value="0"/>
-      <param name="fixed_modifications"/>
       <param name="variable_modifications" value="Oxidation (M)"/>
       <param name="reindex" value="true"/>
       <section name="PeptideIndexing">
@@ -6139,6 +6211,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="aaa_max" value="3"/>
         <param name="mismatches_max" value="0"/>
         <param name="IL_equivalent" value="false"/>
+        <param name="allow_nterm_protein_cleavage" value="true"/>
         <section name="enzyme">
           <param name="name" value="auto"/>
           <param name="specificity" value="auto"/>
@@ -6150,11 +6223,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[MS/MS database search using MS-GF+.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MSGFPlusAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MSGFPlusAdapter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MSSimulator.xml b/tools/openms/MSSimulator.xml
deleted file mode 100644
index 47b53b15a..000000000
--- a/tools/openms/MSSimulator.xml
+++ /dev/null
@@ -1,591 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
-<tool id="MSSimulator" name="MSSimulator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>A highly configurable simulator for mass spectrometry experiments.</description>
-  <macros>
-    <token name="@EXECUTABLE@">MSSimulator</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in_cond.in &&
-#if $in_cond.in_select == "no"
-mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
-#else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
-#end if
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out &&
-#end if
-#if "out_pm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out_pm &&
-#end if
-#if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out_fm &&
-#end if
-#if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out_cm &&
-#end if
-#if "out_lcm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out_lcm &&
-#end if
-#if "out_cntm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out_cntm &&
-#end if
-#if "out_id_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out_id &&
-#end if
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in
-#if $in_cond.in_select == "no"
-${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
-#else
-'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
-#end if
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out
-  'out/output.${gxy2omsext("mzml")}'
-#end if
-#if "out_pm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out_pm
-  'out_pm/output.${gxy2omsext("mzml")}'
-#end if
-#if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out_fm
-  'out_fm/output.${gxy2omsext("featurexml")}'
-#end if
-#if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out_cm
-  'out_cm/output.${gxy2omsext("consensusxml")}'
-#end if
-#if "out_lcm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out_lcm
-  'out_lcm/output.${gxy2omsext("consensusxml")}'
-#end if
-#if "out_cntm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out_cntm
-  'out_cntm/output.${gxy2omsext("featurexml")}'
-#end if
-#if "out_id_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out_id
-  'out_id/output.${gxy2omsext("idxml")}'
-#end if
-#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
-  | tee '$stdout'
-#end if
-
-## Postprocessing
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out/output.${gxy2omsext("mzml")}' '$out'
-#end if
-#if "out_pm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out_pm/output.${gxy2omsext("mzml")}' '$out_pm'
-#end if
-#if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out_fm/output.${gxy2omsext("featurexml")}' '$out_fm'
-#end if
-#if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
-#end if
-#if "out_lcm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out_lcm/output.${gxy2omsext("consensusxml")}' '$out_lcm'
-#end if
-#if "out_cntm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out_cntm/output.${gxy2omsext("featurexml")}' '$out_cntm'
-#end if
-#if "out_id_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out_id/output.${gxy2omsext("idxml")}' '$out_id'
-#end if
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "algorithm": {"MSSim": {"RT": {"HPLC": {"model_file": "SIMULATION/RTPredict.model"}}, "Detectability": {"dt_model_file": "SIMULATION/DTPredict.model"}}}}]]></configfile>
-  </configfiles>
-  <inputs>
-    <conditional name="in_cond">
-      <param name="in_select" type="select" label="Run tool in batch mode for -in">
-        <option value="no">No: process all datasets jointly</option>
-        <option value="yes">Yes: process each dataset in an independent job</option>
-      </param>
-      <when value="no">
-        <param argument="-in" type="data" format="fasta" multiple="true" optional="false" label="Input protein sequences" help=" select fasta data sets(s)"/>
-      </when>
-      <when value="yes">
-        <param argument="-in" type="data" format="fasta" multiple="false" optional="false" label="Input protein sequences" help=" select fasta data sets(s)"/>
-      </when>
-    </conditional>
-    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <section name="MSSim" title="" help="" expanded="false">
-        <section name="Digestion" title="" help="" expanded="false">
-          <param name="enzyme" argument="-algorithm:MSSim:Digestion:enzyme" type="select" optional="true" label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" help="">
-            <option value="Asp-N/B">Asp-N/B</option>
-            <option value="Asp-N_ambic">Asp-N_ambic</option>
-            <option value="Chymotrypsin">Chymotrypsin</option>
-            <option value="2-iodobenzoate">2-iodobenzoate</option>
-            <option value="iodosobenzoate">iodosobenzoate</option>
-            <option value="Arg-C">Arg-C</option>
-            <option value="Chymotrypsin/P">Chymotrypsin/P</option>
-            <option value="CNBr">CNBr</option>
-            <option value="Formic_acid">Formic_acid</option>
-            <option value="Arg-C/P">Arg-C/P</option>
-            <option value="Asp-N">Asp-N</option>
-            <option value="cyanogen-bromide">cyanogen-bromide</option>
-            <option value="Clostripain/P">Clostripain/P</option>
-            <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
-            <option value="no cleavage">no cleavage</option>
-            <option value="unspecific cleavage">unspecific cleavage</option>
-            <option value="Lys-C">Lys-C</option>
-            <option value="Lys-N">Lys-N</option>
-            <option value="Lys-C/P">Lys-C/P</option>
-            <option value="PepsinA">PepsinA</option>
-            <option value="TrypChymo">TrypChymo</option>
-            <option value="Trypsin/P">Trypsin/P</option>
-            <option value="V8-DE">V8-DE</option>
-            <option value="V8-E">V8-E</option>
-            <option value="leukocyte elastase">leukocyte elastase</option>
-            <option value="proline endopeptidase">proline endopeptidase</option>
-            <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-            <option value="Alpha-lytic protease">Alpha-lytic protease</option>
-            <option value="staphylococcal protease/D">staphylococcal protease/D</option>
-            <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
-            <option value="Glu-C+P">Glu-C+P</option>
-            <option value="PepsinA + P">PepsinA + P</option>
-            <option value="Trypsin" selected="true">Trypsin</option>
-            <expand macro="list_string_san" name="enzyme"/>
-          </param>
-          <param name="model" argument="-algorithm:MSSim:Digestion:model" type="select" optional="true" label="The cleavage model to use for digestion" help="'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)">
-            <option value="trained">trained</option>
-            <option value="naive" selected="true">naive</option>
-            <expand macro="list_string_san" name="model"/>
-          </param>
-          <param name="min_peptide_length" argument="-algorithm:MSSim:Digestion:min_peptide_length" type="integer" optional="true" min="1" value="3" label="Minimum peptide length after digestion (shorter ones will be discarded)" help=""/>
-          <section name="model_trained" title="" help="" expanded="false">
-            <param name="threshold" argument="-algorithm:MSSim:Digestion:model_trained:threshold" type="float" optional="true" min="-2.0" max="4.0" value="0.5" label="Model threshold for calling a cleavage" help="Higher values increase the number of cleavages. -2 will give no cleavages, +4 almost full cleavage"/>
-          </section>
-          <section name="model_naive" title="" help="" expanded="false">
-            <param name="missed_cleavages" argument="-algorithm:MSSim:Digestion:model_naive:missed_cleavages" type="integer" optional="true" min="0" value="1" label="Maximum number of missed cleavages considered" help="All possible resulting peptides will be created"/>
-          </section>
-        </section>
-        <section name="RT" title="" help="" expanded="false">
-          <param name="rt_column" argument="-algorithm:MSSim:RT:rt_column" type="select" optional="true" label="Modelling of an RT or CE column" help="">
-            <option value="none">none</option>
-            <option value="HPLC" selected="true">HPLC</option>
-            <option value="CE">CE</option>
-            <expand macro="list_string_san" name="rt_column"/>
-          </param>
-          <param name="auto_scale" argument="-algorithm:MSSim:RT:auto_scale" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Scale predicted RT's/MT's to given 'total_gradient_time'" help="If 'true', for CE this means that 'CE:lenght_d', 'CE:length_total', 'CE:voltage' have no influence"/>
-          <param name="total_gradient_time" argument="-algorithm:MSSim:RT:total_gradient_time" type="float" optional="true" min="1e-05" value="2500.0" label="The duration [s] of the gradient" help=""/>
-          <param name="sampling_rate" argument="-algorithm:MSSim:RT:sampling_rate" type="float" optional="true" min="0.01" max="60.0" value="2.0" label="Time interval [s] between consecutive scans" help=""/>
-          <section name="scan_window" title="" help="" expanded="false">
-            <param name="min" argument="-algorithm:MSSim:RT:scan_window:min" type="float" optional="true" min="0.0" value="500.0" label="Start of RT Scan Window [s]" help=""/>
-            <param name="max" argument="-algorithm:MSSim:RT:scan_window:max" type="float" optional="true" min="1.0" value="1500.0" label="End of RT Scan Window [s]" help=""/>
-          </section>
-          <section name="variation" title="Random component that simulates technical/biological variation" help="" expanded="false">
-            <param name="feature_stddev" argument="-algorithm:MSSim:RT:variation:feature_stddev" type="integer" optional="true" value="3" label="Standard deviation of shift in retention time [s] from predicted model (applied to every single feature independently)" help=""/>
-            <param name="affine_offset" argument="-algorithm:MSSim:RT:variation:affine_offset" type="integer" optional="true" value="0" label="Global offset in retention time [s] from predicted model" help=""/>
-            <param name="affine_scale" argument="-algorithm:MSSim:RT:variation:affine_scale" type="integer" optional="true" value="1" label="Global scaling in retention time from predicted model" help=""/>
-          </section>
-          <section name="column_condition" title="" help="" expanded="false">
-            <param name="distortion" argument="-algorithm:MSSim:RT:column_condition:distortion" type="integer" optional="true" min="0" max="10" value="0" label="Distortion of the elution profiles" help="Good presets are 0 for a perfect elution profile, 1 for a slightly distorted elution profile etc... For trapping instruments (e.g. Orbitrap) distortion should be &gt;4"/>
-          </section>
-          <section name="profile_shape" title="" help="" expanded="false">
-            <section name="width" title="Width of the EGH elution shape" help="i.e. the sigma^2 parameter, which is computed using 'value' + rnd_cauchy('variance')" expanded="false">
-              <param name="value" argument="-algorithm:MSSim:RT:profile_shape:width:value" type="float" optional="true" min="0.0" value="9.0" label="Width of the Exponential Gaussian Hybrid distribution shape of the elution profile" help="This does not correspond directly to the width in [s]"/>
-              <param name="variance" argument="-algorithm:MSSim:RT:profile_shape:width:variance" type="float" optional="true" min="0.0" value="1.6" label="Random component of the width (set to 0 to disable randomness)" help="i.e. scale parameter for the lorentzian variation of the variance (Note: The scale parameter has to be &gt;= 0)"/>
-            </section>
-            <section name="skewness" title="Skewness of the EGH elution shape" help="i.e. the tau parameter, which is computed using 'value' + rnd_cauchy('variance')" expanded="false">
-              <param name="value" argument="-algorithm:MSSim:RT:profile_shape:skewness:value" type="float" optional="true" value="0.1" label="Asymmetric component of the EGH" help="Higher absolute(!) values lead to more skewness (negative values cause fronting, positive values cause tailing). Tau parameter of the EGH, i.e. time constant of the exponential decay of the Exponential Gaussian Hybrid distribution shape of the elution profile"/>
-              <param name="variance" argument="-algorithm:MSSim:RT:profile_shape:skewness:variance" type="float" optional="true" min="0.0" value="0.3" label="Random component of skewness (set to 0 to disable randomness)" help="i.e. scale parameter for the lorentzian variation of the time constant (Note: The scale parameter has to be &gt; 0)"/>
-            </section>
-          </section>
-          <section name="CE" title="" help="" expanded="false">
-            <param name="pH" argument="-algorithm:MSSim:RT:CE:pH" type="float" optional="true" min="0.0" max="14.0" value="3.0" label="pH of buffe" help=""/>
-            <param name="alpha" argument="-algorithm:MSSim:RT:CE:alpha" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Exponent Alpha used to calculate mobility" help=""/>
-            <param name="mu_eo" argument="-algorithm:MSSim:RT:CE:mu_eo" type="float" optional="true" min="0.0" max="5.0" value="0.0" label="Electroosmotic flow" help=""/>
-            <param name="lenght_d" argument="-algorithm:MSSim:RT:CE:lenght_d" type="float" optional="true" min="0.0" max="1000.0" value="70.0" label="Length of capillary [cm] from injection site to MS" help=""/>
-            <param name="length_total" argument="-algorithm:MSSim:RT:CE:length_total" type="float" optional="true" min="0.0" max="1000.0" value="75.0" label="Total length of capillary [cm]" help=""/>
-            <param name="voltage" argument="-algorithm:MSSim:RT:CE:voltage" type="float" optional="true" min="0.0" value="1000.0" label="Voltage applied to capillary" help=""/>
-          </section>
-        </section>
-        <section name="Detectability" title="" help="" expanded="false">
-          <param name="dt_simulation_on" argument="-algorithm:MSSim:Detectability:dt_simulation_on" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Modelling detectibility enabled" help="This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count"/>
-          <param name="min_detect" argument="-algorithm:MSSim:Detectability:min_detect" type="float" optional="true" value="0.5" label="Minimum peptide detectability accepted" help="Peptides with a lower score will be removed"/>
-        </section>
-        <section name="Ionization" title="" help="" expanded="false">
-          <section name="esi" title="" help="" expanded="false">
-            <param name="ionized_residues" argument="-algorithm:MSSim:Ionization:esi:ionized_residues" multiple="true" type="select" optional="true" label="List of residues (as three letter code) that will be considered during ES ionization" help="The N-term is always assumed to carry a charge. This parameter will be ignored during MALDI ionization">
-              <option value="Ala">Ala</option>
-              <option value="Cys">Cys</option>
-              <option value="Asp">Asp</option>
-              <option value="Glu">Glu</option>
-              <option value="Phe">Phe</option>
-              <option value="Gly">Gly</option>
-              <option value="His" selected="true">His</option>
-              <option value="Ile">Ile</option>
-              <option value="Lys" selected="true">Lys</option>
-              <option value="Leu">Leu</option>
-              <option value="Met">Met</option>
-              <option value="Asn">Asn</option>
-              <option value="Pro">Pro</option>
-              <option value="Gln">Gln</option>
-              <option value="Arg" selected="true">Arg</option>
-              <option value="Sec">Sec</option>
-              <option value="Ser">Ser</option>
-              <option value="Thr">Thr</option>
-              <option value="Val">Val</option>
-              <option value="Trp">Trp</option>
-              <option value="Tyr">Tyr</option>
-              <expand macro="list_string_san" name="ionized_residues"/>
-            </param>
-            <param name="charge_impurity" argument="-algorithm:MSSim:Ionization:esi:charge_impurity" type="text" optional="true" value="H+:1" label="List of charged ions that contribute to charge with weight of occurrence (their sum is scaled to 1 internally)" help="e.g. ['H:1'] or ['H:0.7' 'Na:0.3'], ['H:4' 'Na:1'] (which internally translates to ['H:0.8' 'Na:0.2']) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
-              <expand macro="list_string_val" name="charge_impurity"/>
-              <expand macro="list_string_san" name="charge_impurity"/>
-            </param>
-            <param name="max_impurity_set_size" argument="-algorithm:MSSim:Ionization:esi:max_impurity_set_size" type="integer" optional="true" value="3" label="Maximal #combinations of charge impurities allowed (each generating one feature) per charge state" help="E.g. assuming charge=3 and this parameter is 2, then we could choose to allow '3H+, 2H+Na+' features (given a certain 'charge_impurity' constraints), but no '3H+, 2H+Na+, 3Na+'"/>
-            <param name="ionization_probability" argument="-algorithm:MSSim:Ionization:esi:ionization_probability" type="float" optional="true" value="0.8" label="Probability for the binomial distribution of the ESI charge states" help=""/>
-          </section>
-          <section name="maldi" title="" help="" expanded="false">
-            <param name="ionization_probabilities" argument="-algorithm:MSSim:Ionization:maldi:ionization_probabilities" type="text" optional="true" value="0.9 0.1 0.0" label="List of probabilities for different charge states (starting at charge=1, 2, ...) during MALDI ionization (the list must sum up to 1.0)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
-              <expand macro="list_float_valsan" name="ionization_probabilities"/>
-            </param>
-          </section>
-          <section name="mz" title="" help="" expanded="false">
-            <param name="lower_measurement_limit" argument="-algorithm:MSSim:Ionization:mz:lower_measurement_limit" type="float" optional="true" min="0.0" value="200.0" label="Lower m/z detector limit" help=""/>
-            <param name="upper_measurement_limit" argument="-algorithm:MSSim:Ionization:mz:upper_measurement_limit" type="float" optional="true" min="0.0" value="1200.0" label="Upper m/z detector limit" help=""/>
-          </section>
-        </section>
-        <section name="RawSignal" title="" help="" expanded="false">
-          <param name="enabled" argument="-algorithm:MSSim:RawSignal:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable RAW signal simulation" help="(select 'false' if you only need feature-maps)"/>
-          <param name="peak_shape" argument="-algorithm:MSSim:RawSignal:peak_shape" type="select" optional="true" label="Peak Shape used around each isotope peak (be aware that the area under the curve is constant for both types, but the maximal height will differ (~ 2:3 = Lorentz:Gaussian) due to the wider base of the Lorentzian" help="">
-            <option value="Gaussian" selected="true">Gaussian</option>
-            <option value="Lorentzian">Lorentzian</option>
-            <expand macro="list_string_san" name="peak_shape"/>
-          </param>
-          <section name="resolution" title="" help="" expanded="false">
-            <param name="value" argument="-algorithm:MSSim:RawSignal:resolution:value" type="integer" optional="true" value="50000" label="Instrument resolution at 400 Th" help=""/>
-            <param name="type" argument="-algorithm:MSSim:RawSignal:resolution:type" type="select" optional="true" label="How does resolution change with increasing m/z" help="QTOFs usually show 'constant' behavior, FTs have linear degradation, and on Orbitraps the resolution decreases with square root of mass">
-              <option value="constant">constant</option>
-              <option value="linear" selected="true">linear</option>
-              <option value="sqrt">sqrt</option>
-              <expand macro="list_string_san" name="type"/>
-            </param>
-          </section>
-          <section name="baseline" title="Baseline modeling for MALDI ionization" help="" expanded="false">
-            <param name="scaling" argument="-algorithm:MSSim:RawSignal:baseline:scaling" type="float" optional="true" min="0.0" value="0.0" label="Scale of baseline" help="Set to 0 to disable simulation of baseline"/>
-            <param name="shape" argument="-algorithm:MSSim:RawSignal:baseline:shape" type="float" optional="true" min="0.0" value="0.5" label="The baseline is modeled by an exponential probability density function (pdf) with f(x) = shape*e^(- shape*x)" help=""/>
-          </section>
-          <section name="mz" title="" help="" expanded="false">
-            <param name="sampling_points" argument="-algorithm:MSSim:RawSignal:mz:sampling_points" type="integer" optional="true" min="2" value="3" label="Number of raw data points per FWHM of the peak" help=""/>
-          </section>
-          <section name="contaminants" title="" help="" expanded="false">
-            <param name="file" argument="-algorithm:MSSim:RawSignal:contaminants:file" type="text" optional="true" value="SIMULATION/contaminants.csv" label="Contaminants file with sum formula and absolute RT interval" help="See 'share/OpenMS/SIMULATION/contaminants.txt' for details">
-              <expand macro="list_string_san" name="file"/>
-            </param>
-          </section>
-          <section name="variation" title="Random components that simulate biological and technical variations of the simulated data" help="" expanded="false">
-            <section name="mz" title="Shifts in mass to charge dimension of the simulated signals" help="" expanded="false">
-              <param name="error_mean" argument="-algorithm:MSSim:RawSignal:variation:mz:error_mean" type="float" optional="true" value="0.0" label="Average systematic m/z error (in Da)" help=""/>
-              <param name="error_stddev" argument="-algorithm:MSSim:RawSignal:variation:mz:error_stddev" type="float" optional="true" value="0.0" label="Standard deviation for m/z errors" help="Set to 0 to disable simulation of m/z errors"/>
-            </section>
-            <section name="intensity" title="Variations in intensity to model randomness in feature intensity" help="" expanded="false">
-              <param name="scale" argument="-algorithm:MSSim:RawSignal:variation:intensity:scale" type="float" optional="true" min="0.0" value="100.0" label="Constant scale factor of the feature intensity" help="Set to 1.0 to get the real intensity values provided in the FASTA file"/>
-              <param name="scale_stddev" argument="-algorithm:MSSim:RawSignal:variation:intensity:scale_stddev" type="float" optional="true" min="0.0" value="0.0" label="Standard deviation of peak intensity (relative to the scaled peak height)" help="Set to 0 to get simple rescaled intensities"/>
-            </section>
-          </section>
-          <section name="noise" title="Parameters modeling noise in mass spectrometry measurements" help="" expanded="false">
-            <section name="shot" title="Parameters of Poisson and Exponential for shot noise modeling (set :rate OR :mean = 0 to disable)" help="" expanded="false">
-              <param name="rate" argument="-algorithm:MSSim:RawSignal:noise:shot:rate" type="float" optional="true" min="0.0" value="0.0" label="Poisson rate of shot noise per unit m/z (random peaks in m/z, where the number of peaks per unit m/z follows a Poisson distribution)" help="Set this to 0 to disable simulation of shot noise"/>
-              <param name="intensity_mean" argument="-algorithm:MSSim:RawSignal:noise:shot:intensity-mean" type="float" optional="true" value="1.0" label="Shot noise intensity mean (exponentially distributed with given mean)" help=""/>
-            </section>
-            <section name="white" title="Parameters of Gaussian distribution for white noise modeling (set :mean AND :stddev = 0 to disable)" help="No new peaks are generated; only intensity of existing ones is changed" expanded="false">
-              <param name="mean" argument="-algorithm:MSSim:RawSignal:noise:white:mean" type="float" optional="true" value="0.0" label="Mean value of white noise (Gaussian) being added to each *measured* signal intensity" help=""/>
-              <param name="stddev" argument="-algorithm:MSSim:RawSignal:noise:white:stddev" type="float" optional="true" value="0.0" label="Standard deviation of white noise being added to each *measured* signal intensity" help=""/>
-            </section>
-            <section name="detector" title="Parameters of Gaussian distribution for detector noise modeling (set :mean AND :stddev = 0 to disable)" help="If enabled, ALL possible m/z positions (up to sampling frequency of detector) will receive an intensity increase/decrease according to the specified Gaussian intensity distribution (similar to a noisy baseline)" expanded="false">
-              <param name="mean" argument="-algorithm:MSSim:RawSignal:noise:detector:mean" type="float" optional="true" value="0.0" label="Mean intensity value of the detector noise (Gaussian distribution)" help=""/>
-              <param name="stddev" argument="-algorithm:MSSim:RawSignal:noise:detector:stddev" type="float" optional="true" value="0.0" label="Standard deviation of the detector noise (Gaussian distribution)" help=""/>
-            </section>
-          </section>
-        </section>
-        <section name="RawTandemSignal" title="" help="" expanded="false">
-          <param name="status" argument="-algorithm:MSSim:RawTandemSignal:status" type="select" optional="true" label="Create Tandem-MS scans?" help="">
-            <option value="disabled" selected="true">disabled</option>
-            <option value="precursor">precursor</option>
-            <option value="MS^E">MS^E</option>
-            <expand macro="list_string_san" name="status"/>
-          </param>
-          <param name="tandem_mode" argument="-algorithm:MSSim:RawTandemSignal:tandem_mode" type="integer" optional="true" min="0" max="2" value="0" label="Algorithm to generate the tandem-MS spectra" help="0 - fixed intensities, 1 - SVC prediction (abundant/missing), 2 - SVR prediction of peak intensity . "/>
-          <param name="svm_model_set_file" argument="-algorithm:MSSim:RawTandemSignal:svm_model_set_file" type="text" optional="true" value="SIMULATION/SvmModelSet.model" label="File containing the filenames of SVM Models for different charge variants" help="">
-            <expand macro="list_string_san" name="svm_model_set_file"/>
-          </param>
-          <section name="Precursor" title="" help="" expanded="false">
-            <param name="ms2_spectra_per_rt_bin" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ms2_spectra_per_rt_bin" type="integer" optional="true" min="1" value="5" label="Number of allowed MS/MS spectra in a retention time bin" help=""/>
-            <param name="min_mz_peak_distance" argument="-algorithm:MSSim:RawTandemSignal:Precursor:min_mz_peak_distance" type="float" optional="true" min="0.0001" value="2.0" label="The minimal distance (in Th) between two peaks for concurrent selection for fragmentation" help="Also used to define the m/z width of an exclusion window (distance +/- from m/z of precursor). If you set this lower than the isotopic envelope of a peptide, you might get multiple fragment spectra pointing to the same precursor"/>
-            <param name="mz_isolation_window" argument="-algorithm:MSSim:RawTandemSignal:Precursor:mz_isolation_window" type="float" optional="true" min="0.0" value="2.0" label="All peaks within a mass window (in Th) of a selected peak are also selected for fragmentation" help=""/>
-            <param name="exclude_overlapping_peaks" argument="-algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection" help=""/>
-            <param name="charge_filter" argument="-algorithm:MSSim:RawTandemSignal:Precursor:charge_filter" type="text" optional="true" value="2 3" label="Charges considered for MS2 fragmentation" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
-              <expand macro="list_integer_valsan" name="charge_filter">
-                <validator type="expression" message="a space separated list of integer values in the range 1:5 is required"><![CDATA[len(value.split(' ')) == len([_ for _ in value.split(' ') if  1 <= int(_) <= 5])
-]]></validator>
-              </expand>
-            </param>
-            <section name="Exclusion" title="" help="" expanded="false">
-              <param name="use_dynamic_exclusion" argument="-algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true dynamic exclusion is applied" help=""/>
-              <param name="exclusion_time" argument="-algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:exclusion_time" type="float" optional="true" min="0.0" value="100.0" label="The time (in seconds) a feature is excluded" help=""/>
-            </section>
-            <section name="ProteinBasedInclusion" title="" help="" expanded="false">
-              <param name="max_list_size" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:max_list_size" type="integer" optional="true" min="1" value="1000" label="The maximal number of precursors in the inclusion list" help=""/>
-              <section name="rt" title="" help="" expanded="false">
-                <param name="min_rt" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:min_rt" type="float" optional="true" min="0.0" value="960.0" label="Minimal rt in seconds" help=""/>
-                <param name="max_rt" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:max_rt" type="float" optional="true" min="0.0" value="3840.0" label="Maximal rt in seconds" help=""/>
-                <param name="rt_step_size" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_step_size" type="float" optional="true" min="1.0" value="30.0" label="rt step size in seconds" help=""/>
-                <param name="rt_window_size" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_window_size" type="integer" optional="true" min="1" value="100" label="rt window size in seconds" help=""/>
-              </section>
-              <section name="thresholds" title="" help="" expanded="false">
-                <param name="min_protein_id_probability" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="Minimal protein probability for a protein to be considered identified" help=""/>
-                <param name="min_pt_weight" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_pt_weight" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Minimal pt weight of a precurso" help=""/>
-                <param name="min_mz" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_mz" type="float" optional="true" min="0.0" value="500.0" label="Minimal mz to be considered in protein based LP formulation" help=""/>
-                <param name="max_mz" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:max_mz" type="float" optional="true" min="0.0" value="5000.0" label="Minimal mz to be considered in protein based LP formulation" help=""/>
-                <param name="use_peptide_rule" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use peptide rule instead of minimal protein id probability" help=""/>
-                <param name="min_peptide_ids" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids" type="integer" optional="true" min="1" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help=""/>
-                <param name="min_peptide_probability" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help=""/>
-              </section>
-            </section>
-          </section>
-          <section name="MS_E" title="" help="" expanded="false">
-            <param name="add_single_spectra" argument="-algorithm:MSSim:RawTandemSignal:MS_E:add_single_spectra" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, the MS2 spectra for each peptide signal are included in the output (might be a lot)" help="They will have a meta value 'MSE_DebugSpectrum' attached, so they can be filtered out. Native MS_E spectra will have 'MSE_Spectrum' instead"/>
-          </section>
-          <section name="TandemSim" title="" help="" expanded="false">
-            <section name="Simple" title="" help="" expanded="false">
-              <param name="isotope_model" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:isotope_model" type="select" optional="true" label="Model to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks" help="Note that adding isotopic peaks is very slow">
-                <option value="none" selected="true">none</option>
-                <option value="coarse">coarse</option>
-                <option value="fine">fine</option>
-                <expand macro="list_string_san" name="isotope_model"/>
-              </param>
-              <param name="max_isotope" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope" type="integer" optional="true" value="2" label="Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'" help=""/>
-              <param name="max_isotope_probability" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope_probability" type="float" optional="true" value="0.05" label="Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'" help=""/>
-              <param name="add_metainfo" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help=""/>
-              <param name="add_losses" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help=""/>
-              <param name="sort_by_position" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:sort_by_position" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Sort output by position" help=""/>
-              <param name="add_precursor_peaks" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds peaks of the unfragmented precursor ion to the spectrum" help=""/>
-              <param name="add_all_precursor_charges" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds precursor peaks with all charges in the given range" help=""/>
-              <param name="add_abundant_immonium_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add most abundant immonium ions (for Proline, Cystein, Iso/Leucine, Histidin, Phenylalanin, Tyrosine, Tryptophan)" help=""/>
-              <param name="add_first_prefix_ion" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true e.g. b1 ions are added" help=""/>
-              <param name="add_y_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Add peaks of y-ions to the spectrum" help=""/>
-              <param name="add_b_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Add peaks of b-ions to the spectrum" help=""/>
-              <param name="add_a_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of a-ions to the spectrum" help=""/>
-              <param name="add_c_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_c_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of c-ions to the spectrum" help=""/>
-              <param name="add_x_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_x_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of  x-ions to the spectrum" help=""/>
-              <param name="add_z_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of z-ions to the spectrum" help=""/>
-              <param name="y_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:y_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the y-ions" help=""/>
-              <param name="b_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:b_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the b-ions" help=""/>
-              <param name="a_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:a_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the a-ions" help=""/>
-              <param name="c_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:c_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the c-ions" help=""/>
-              <param name="x_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:x_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the x-ions" help=""/>
-              <param name="z_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:z_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the z-ions" help=""/>
-              <param name="relative_loss_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:relative_loss_intensity" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help=""/>
-              <param name="precursor_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the precursor peak" help=""/>
-              <param name="precursor_H2O_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_H2O_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the H2O loss peak of the precurso" help=""/>
-              <param name="precursor_NH3_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_NH3_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the NH3 loss peak of the precurso" help=""/>
-            </section>
-            <section name="SVM" title="" help="" expanded="false">
-              <param name="add_isotopes" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_isotopes" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to 1 isotope peaks of the product ion peaks are added" help=""/>
-              <param name="max_isotope" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:max_isotope" type="integer" optional="true" value="2" label="Defines the maximal isotopic peak which is added, add_isotopes must be set to 1" help=""/>
-              <param name="add_metainfo" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_metainfo" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help=""/>
-              <param name="add_first_prefix_ion" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_first_prefix_ion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true e.g. b1 ions are added" help=""/>
-              <param name="hide_y_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of y-ions to the spectrum" help=""/>
-              <param name="hide_y2_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y2_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of y-ions to the spectrum" help=""/>
-              <param name="hide_b_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of b-ions to the spectrum" help=""/>
-              <param name="hide_b2_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b2_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of b-ions to the spectrum" help=""/>
-              <param name="hide_a_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_a_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of a-ions to the spectrum" help=""/>
-              <param name="hide_c_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_c_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of c-ions to the spectrum" help=""/>
-              <param name="hide_x_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_x_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of  x-ions to the spectrum" help=""/>
-              <param name="hide_z_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of z-ions to the spectrum" help=""/>
-              <param name="hide_losses" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help=""/>
-              <param name="y_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:y_intensity" type="float" optional="true" value="1.0" label="Intensity of the y-ions" help=""/>
-              <param name="b_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:b_intensity" type="float" optional="true" value="1.0" label="Intensity of the b-ions" help=""/>
-              <param name="a_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:a_intensity" type="float" optional="true" value="1.0" label="Intensity of the a-ions" help=""/>
-              <param name="c_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:c_intensity" type="float" optional="true" value="1.0" label="Intensity of the c-ions" help=""/>
-              <param name="x_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:x_intensity" type="float" optional="true" value="1.0" label="Intensity of the x-ions" help=""/>
-              <param name="z_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:z_intensity" type="float" optional="true" value="1.0" label="Intensity of the z-ions" help=""/>
-              <param name="relative_loss_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity" type="float" optional="true" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help=""/>
-            </section>
-          </section>
-        </section>
-        <section name="Global" title="" help="" expanded="false">
-          <param name="ionization_type" argument="-algorithm:MSSim:Global:ionization_type" type="select" optional="true" label="Type of Ionization (MALDI or ESI)" help="">
-            <option value="MALDI">MALDI</option>
-            <option value="ESI" selected="true">ESI</option>
-            <expand macro="list_string_san" name="ionization_type"/>
-          </param>
-        </section>
-        <section name="Labeling" title="" help="" expanded="false">
-          <param name="type" argument="-algorithm:MSSim:Labeling:type" type="select" optional="true" label="Select the labeling type you want for your experiment" help="">
-            <option value="ICPL">ICPL</option>
-            <option value="SILAC">SILAC</option>
-            <option value="itraq">itraq</option>
-            <option value="labelfree" selected="true">labelfree</option>
-            <option value="o18">o18</option>
-            <expand macro="list_string_san" name="type"/>
-          </param>
-          <section name="ICPL" title="ICPL labeling on MS1 level of lysines and n-term (on protein or peptide level) with either two or three channels" help="" expanded="false">
-            <param name="ICPL_fixed_rtshift" argument="-algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift" type="float" optional="true" value="0.0" label="Fixed retention time shift between labeled pairs" help="If set to 0.0 only the retention times, computed by the RT model step are used"/>
-            <param name="label_proteins" argument="-algorithm:MSSim:Labeling:ICPL:label_proteins" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables protein-labeling" help="(select 'false' if you only need peptide-labeling)"/>
-            <param name="ICPL_light_channel_label" argument="-algorithm:MSSim:Labeling:ICPL:ICPL_light_channel_label" type="text" optional="true" value="UniMod:365" label="UniMod Id of the light channel ICPL label" help="">
-              <expand macro="list_string_san" name="ICPL_light_channel_label"/>
-            </param>
-            <param name="ICPL_medium_channel_label" argument="-algorithm:MSSim:Labeling:ICPL:ICPL_medium_channel_label" type="text" optional="true" value="UniMod:687" label="UniMod Id of the medium channel ICPL label" help="">
-              <expand macro="list_string_san" name="ICPL_medium_channel_label"/>
-            </param>
-            <param name="ICPL_heavy_channel_label" argument="-algorithm:MSSim:Labeling:ICPL:ICPL_heavy_channel_label" type="text" optional="true" value="UniMod:364" label="UniMod Id of the heavy channel ICPL label" help="">
-              <expand macro="list_string_san" name="ICPL_heavy_channel_label"/>
-            </param>
-          </section>
-          <section name="SILAC" title="SILAC labeling on MS1 level with up to 3 channels and custom modifications" help="" expanded="false">
-            <param name="fixed_rtshift" argument="-algorithm:MSSim:Labeling:SILAC:fixed_rtshift" type="float" optional="true" min="0.0" value="0.0001" label="Fixed retention time shift between labeled peptides" help="If set to 0.0 only the retention times computed by the RT model step are used"/>
-            <section name="medium_channel" title="Modifications for the medium SILAC channel" help="" expanded="false">
-              <param name="modification_lysine" argument="-algorithm:MSSim:Labeling:SILAC:medium_channel:modification_lysine" type="text" optional="true" value="UniMod:481" label="Modification of Lysine in the medium SILAC channel" help="">
-                <expand macro="list_string_san" name="modification_lysine"/>
-              </param>
-              <param name="modification_arginine" argument="-algorithm:MSSim:Labeling:SILAC:medium_channel:modification_arginine" type="text" optional="true" value="UniMod:188" label="Modification of Arginine in the medium SILAC channel" help="">
-                <expand macro="list_string_san" name="modification_arginine"/>
-              </param>
-            </section>
-            <section name="heavy_channel" title="Modifications for the heavy SILAC channel" help="If you want to use only 2 channels, just leave the Labels as they are and provide only 2 input files" expanded="false">
-              <param name="modification_lysine" argument="-algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_lysine" type="text" optional="true" value="UniMod:259" label="Modification of Lysine in the heavy SILAC channel" help="If left empty, two channelSILAC is assumed">
-                <expand macro="list_string_san" name="modification_lysine"/>
-              </param>
-              <param name="modification_arginine" argument="-algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine" type="text" optional="true" value="UniMod:267" label="Modification of Arginine in the heavy SILAC channel" help="If left empty, two-channel SILAC is assumed">
-                <expand macro="list_string_san" name="modification_arginine"/>
-              </param>
-            </section>
-          </section>
-          <section name="itraq" title="iTRAQ labeling on MS2 level with up to 4 (4plex) or 8 (8plex) channels" help="" expanded="false">
-            <param name="iTRAQ" argument="-algorithm:MSSim:Labeling:itraq:iTRAQ" type="select" optional="true" label="4plex or 8plex iTRAQ?" help="">
-              <option value="4plex" selected="true">4plex</option>
-              <option value="8plex">8plex</option>
-              <expand macro="list_string_san" name="iTRAQ"/>
-            </param>
-            <param name="reporter_mass_shift" argument="-algorithm:MSSim:Labeling:itraq:reporter_mass_shift" type="float" optional="true" min="0.0" max="0.5" value="0.1" label="Allowed shift (uniformly distributed - left to right) in Da from the expected position (of" help="e.g. 114.1, 115.1)"/>
-            <param name="channel_active_4plex" argument="-algorithm:MSSim:Labeling:itraq:channel_active_4plex" type="text" optional="true" value="114:myReference" label="Four-plex only: Each channel that was used in the experiment and its description (114-117) in format &lt;channel&gt;:&lt;name" help="e.g. &quot;114:myref&quot;,&quot;115:liver&quot; (space separated list, in order to allow for spaces in list items surround them by single quotes)">
-              <expand macro="list_string_val" name="channel_active_4plex"/>
-              <expand macro="list_string_san" name="channel_active_4plex"/>
-            </param>
-            <param name="channel_active_8plex" argument="-algorithm:MSSim:Labeling:itraq:channel_active_8plex" type="text" optional="true" value="113:myReference" label="Eight-plex only: Each channel that was used in the experiment and its description (113-121) in format &lt;channel&gt;:&lt;name" help="e.g. &quot;113:myref&quot;,&quot;115:liver&quot;,&quot;118:lung&quot; (space separated list, in order to allow for spaces in list items surround them by single quotes)">
-              <expand macro="list_string_val" name="channel_active_8plex"/>
-              <expand macro="list_string_san" name="channel_active_8plex"/>
-            </param>
-            <param name="isotope_correction_values_4plex" argument="-algorithm:MSSim:Labeling:itraq:isotope_correction_values_4plex" type="text" optional="true" value="114:0.0/1.0/5.9/0.2 115:0.0/2.0/5.6/0.1 116:0.0/3.0/4.5/0.1 117:0.1/4.0/3.5/0.1" label="override default values (see Documentation); use the following format: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ;" help="e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'  (space separated list, in order to allow for spaces in list items surround them by single quotes)">
-              <expand macro="list_string_val" name="isotope_correction_values_4plex"/>
-              <expand macro="list_string_san" name="isotope_correction_values_4plex"/>
-            </param>
-            <param name="isotope_correction_values_8plex" argument="-algorithm:MSSim:Labeling:itraq:isotope_correction_values_8plex" type="text" optional="true" value="113:0.0/0.0/6.89/0.22 114:0.0/0.94/5.9/0.16 115:0.0/1.88/4.9/0.1 116:0.0/2.82/3.9/0.07 117:0.06/3.77/2.99/0.0 118:0.09/4.71/1.88/0.0 119:0.14/5.66/0.87/0.0 121:0.27/7.44/0.18/0.0" label="override default values (see Documentation); use the following format: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ;" help="e.g. '113:0/0.3/4/0' , '116:0.1/0.3/3/0.2'  (space separated list, in order to allow for spaces in list items surround them by single quotes)">
-              <expand macro="list_string_val" name="isotope_correction_values_8plex"/>
-              <expand macro="list_string_san" name="isotope_correction_values_8plex"/>
-            </param>
-            <param name="Y_contamination" argument="-algorithm:MSSim:Labeling:itraq:Y_contamination" type="float" optional="true" min="0.0" max="1.0" value="0.3" label="Efficiency of labeling tyrosine ('Y') residues" help="0=off, 1=full labeling"/>
-          </section>
-          <section name="o18" title="18O labeling on MS1 level with 2 channels, requiring trypsin digestion" help="" expanded="false">
-            <param name="labeling_efficiency" argument="-algorithm:MSSim:Labeling:o18:labeling_efficiency" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Describes the distribution of the labeled peptide over the different states (unlabeled, mono- and di-labeled)" help=""/>
-          </section>
-        </section>
-      </section>
-      <section name="RandomNumberGenerators" title="Parameters for generating the random aspects" help="(e.g. noise) in the simulated data. The generation is separated into two parts, the technical part, like noise in the raw signal, and the biological part, like systematic deviations in the predicted retention times" expanded="false">
-        <param name="biological" argument="-algorithm:RandomNumberGenerators:biological" type="select" optional="true" label="Controls the 'biological' randomness of the generated data" help="(e.g. systematic effects like deviations in RT). If set to 'random' each experiment will look different. If set to 'reproducible' each experiment will have the same outcome (given that the input data is the same)">
-          <option value="reproducible">reproducible</option>
-          <option value="random" selected="true">random</option>
-          <expand macro="list_string_san" name="biological"/>
-        </param>
-        <param name="technical" argument="-algorithm:RandomNumberGenerators:technical" type="select" optional="true" label="Controls the 'technical' randomness of the generated data" help="(e.g. noise in the raw signal). If set to 'random' each experiment will look different. If set to 'reproducible' each experiment will have the same outcome (given that the input data is the same)">
-          <option value="reproducible">reproducible</option>
-          <option value="random" selected="true">random</option>
-          <expand macro="list_string_san" name="technical"/>
-        </param>
-      </section>
-    </section>
-    <expand macro="adv_opts_macro">
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="out_FLAG">out (output: simulated MS raw (profile) data)</option>
-      <option value="out_pm_FLAG">out_pm (output: ground-truth picked (centroided) MS data)</option>
-      <option value="out_fm_FLAG">out_fm (output: ground-truth features)</option>
-      <option value="out_cm_FLAG">out_cm (output: ground-truth features, grouping ESI charge variants of each parent peptide)</option>
-      <option value="out_lcm_FLAG">out_lcm (output: ground-truth features, grouping labeled variants)</option>
-      <option value="out_cntm_FLAG">out_cntm (output: ground-truth features caused by contaminants)</option>
-      <option value="out_id_FLAG">out_id (output: ground-truth MS2 peptide identifications)</option>
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="mzml">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="out_pm" label="${tool.name} on ${on_string}: out_pm" format="mzml">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_pm_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="out_fm" label="${tool.name} on ${on_string}: out_fm" format="featurexml">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_fm_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="out_lcm" label="${tool.name} on ${on_string}: out_lcm" format="consensusxml">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_lcm_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="out_cntm" label="${tool.name} on ${on_string}: out_cntm" format="featurexml">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_cntm_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="out_id" label="${tool.name} on ${on_string}: out_id" format="idxml">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_id_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
-      <filter>OPTIONAL_OUTPUTS is None</filter>
-    </data>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
-    <output name="out" ftype="mzml" value="MSsimulator.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/>
-    <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/>
-    <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/>
-  </test>
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter generate MALDI output for use in the test for DeMeanderize -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
-    <output name="out" ftype="mzml" value="MSsimulator_MALDI.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/>
-    <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/>
-    <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/>
-    <param name="algorithm|MSSim|Global|ionization_type" value="MALDI"/>
-  </test>
-</tests>
-  <help><![CDATA[A highly configurable simulator for mass spectrometry experiments.
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MSSimulator.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/MSstatsConverter.xml b/tools/openms/MSstatsConverter.xml
index 979ca0267..55420878b 100644
--- a/tools/openms/MSstatsConverter.xml
+++ b/tools/openms/MSstatsConverter.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [File Converter]-->
 <tool id="MSstatsConverter" name="MSstatsConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Converter to input for MSstats</description>
   <macros>
@@ -15,20 +14,22 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir in_design &&
-ln -s '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' &&
+cp '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' &&
 mkdir out &&
+## advanced options
   #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
     mkdir adv_opts.reannotate_filenames_cond.reannotate_filenames &&
     #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
     mkdir ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s'" % (i) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} && 
-    ${' '.join(["ln -s '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])}
+    ${' '.join(["cp '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])}
     #else
-    ln -s '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' &&
+    cp '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' &&
     #end if
   #end if
 
+
 ## Main program call
 
 set -o pipefail &&
@@ -41,6 +42,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)'
 -out
 'out/output.${gxy2omsext("csv")}'
+## advanced options
   #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
     -reannotate_filenames
     #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
@@ -50,6 +52,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     #end if
   #end if
 
+
 ## Postprocessing
 && mv 'out/output.${gxy2omsext("csv")}' '$out'
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
@@ -60,20 +63,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml" optional="false" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/>
-    <param argument="-in_design" type="data" format="tabular" optional="false" label="Experimental Design file" help=" select tabular data sets(s)"/>
-    <param argument="-method" type="select" optional="true" label="Method used in the experiment(label free [LFQ], isobaric labeling [ISO]))" help="">
+    <param argument="-in" type="data" format="consensusxml" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/>
+    <param argument="-in_design" type="data" format="tabular" label="Experimental Design file" help=" select tabular data sets(s)"/>
+    <param argument="-method" type="select" label="Method used in the experiment(label free [LFQ], isobaric labeling [ISO]))" help="">
       <option value="LFQ" selected="true">LFQ</option>
       <option value="ISO">ISO</option>
       <expand macro="list_string_san" name="method"/>
     </param>
-    <param argument="-msstats_bioreplicate" type="text" optional="true" value="MSstats_BioReplicate" label="Which column in the condition table should be used for MSstats 'BioReplicate'" help="">
+    <param argument="-msstats_bioreplicate" type="text" value="MSstats_BioReplicate" label="Which column in the condition table should be used for MSstats 'BioReplicate'" help="">
       <expand macro="list_string_san" name="msstats_bioreplicate"/>
     </param>
-    <param argument="-msstats_condition" type="text" optional="true" value="MSstats_Condition" label="Which column in the condition table should be used for MSstats 'Condition'" help="">
+    <param argument="-msstats_condition" type="text" value="MSstats_Condition" label="Which column in the condition table should be used for MSstats 'Condition'" help="">
       <expand macro="list_string_san" name="msstats_condition"/>
     </param>
-    <param argument="-msstats_mixture" type="text" optional="true" value="MSstats_Mixture" label="Which column in the condition table should be used for MSstats 'Mixture'" help="">
+    <param argument="-msstats_mixture" type="text" value="MSstats_Mixture" label="Which column in the condition table should be used for MSstats 'Mixture'" help="">
       <expand macro="list_string_san" name="msstats_mixture"/>
     </param>
     <param argument="-labeled_reference_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, IsotopeLabelType is 'H', else 'L'" help=""/>
@@ -87,10 +90,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param argument="-reannotate_filenames" type="data" format="mzml" multiple="true" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
         </when>
         <when value="yes">
-          <param argument="-reannotate_filenames" type="data" format="mzml" multiple="false" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
+          <param argument="-reannotate_filenames" type="data" format="mzml" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
         </when>
       </conditional>
-      <param argument="-retention_time_summarization_method" type="select" optional="true" label="How indistinguishable peptidoforms at different retention times should be treated" help="This is usually necessary for LFQ experiments and therefore defaults to 'max'. In case of TMT/iTRAQ, MSstatsTMT does the aggregation itself later and the parameter always resets to manual (i.e. is unused)">
+      <param argument="-retention_time_summarization_method" type="select" label="How indistinguishable peptidoforms at different retention times should be treated" help="This is usually necessary for LFQ experiments and therefore defaults to 'max'. In case of TMT/iTRAQ, MSstatsTMT does the aggregation itself later and the parameter always resets to manual (i.e. is unused)">
         <option value="manual">manual</option>
         <option value="max" selected="true">max</option>
         <option value="min">min</option>
@@ -99,7 +102,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <expand macro="list_string_san" name="retention_time_summarization_method"/>
       </param>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -113,7 +116,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MSstatsConverter_1 -->
+  <tests>
+    <!-- TOPP_MSstatsConverter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="retention_time_summarization_method" value="max"/>
@@ -127,13 +131,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="msstats_condition" value="MSstats_Condition"/>
       <param name="msstats_mixture" value="MSstats_Mixture"/>
       <param name="labeled_reference_peptides" value="false"/>
-      <output name="out" file="MSstatsConverter_1_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out" value="MSstatsConverter_1_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MSstatsConverter_2 -->
     <test expect_num_outputs="2">
@@ -149,13 +156,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="msstats_condition" value="MSstats_Condition"/>
       <param name="msstats_mixture" value="MSstats_Mixture"/>
       <param name="labeled_reference_peptides" value="false"/>
-      <output name="out" file="MSstatsConverter_2_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out" value="MSstatsConverter_2_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MSstatsConverter_3 -->
     <test expect_num_outputs="2">
@@ -171,18 +181,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="msstats_condition" value="MSstats_Condition"/>
       <param name="msstats_mixture" value="MSstats_Mixture"/>
       <param name="labeled_reference_peptides" value="false"/>
-      <output name="out" file="MSstatsConverter_3_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out" value="MSstatsConverter_3_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Converter to input for MSstats
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MSstatsConverter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MSstatsConverter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MaRaClusterAdapter.xml b/tools/openms/MaRaClusterAdapter.xml
deleted file mode 100644
index 04db4f91b..000000000
--- a/tools/openms/MaRaClusterAdapter.xml
+++ /dev/null
@@ -1,139 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [ID Processing]-->
-<tool id="MaRaClusterAdapter" name="MaRaClusterAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Facilitate input to MaRaCluster and reintegrate.</description>
-  <macros>
-    <token name="@EXECUTABLE@">MaRaClusterAdapter</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in_cond.in &&
-#if $in_cond.in_select == "no"
-mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
-#else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
-#end if
-#if $id_in_cond.id_in:
-  mkdir id_in_cond.id_in &&
-  #if $id_in_cond.id_in_select == "no"
-  mkdir ${' '.join(["'id_in_cond.id_in/%s'" % (i) for i, f in enumerate($id_in_cond.id_in) if f])} && 
-  ${' '.join(["ln -s '%s' 'id_in_cond.id_in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])}
-  #else
-  ln -s '$id_in_cond.id_in' 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)' &&
-  #end if
-#end if
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out &&
-#end if
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in
-#if $in_cond.in_select == "no"
-${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
-#else
-'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
-#end if
-#if $id_in_cond.id_in:
-  -id_in
-  #if $id_in_cond.id_in_select == "no"
-  ${' '.join(["'id_in_cond.id_in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])}
-  #else
-  'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)'
-  #end if
-#end if
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out
-  'out/output.${gxy2omsext("idxml")}'
-#end if
-#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
-  | tee '$stdout'
-#end if
-
-## Postprocessing
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out/output.${gxy2omsext("idxml")}' '$out'
-#end if
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"maracluster_executable": "/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
-  </configfiles>
-  <inputs>
-    <conditional name="in_cond">
-      <param name="in_select" type="select" label="Run tool in batch mode for -in">
-        <option value="no">No: process all datasets jointly</option>
-        <option value="yes">Yes: process each dataset in an independent job</option>
-      </param>
-      <when value="no">
-        <param argument="-in" type="data" format="mgf,mzml" multiple="true" optional="false" label="Input file(s)" help=" select mgf,mzml data sets(s)"/>
-      </when>
-      <when value="yes">
-        <param argument="-in" type="data" format="mgf,mzml" multiple="false" optional="false" label="Input file(s)" help=" select mgf,mzml data sets(s)"/>
-      </when>
-    </conditional>
-    <conditional name="id_in_cond">
-      <param name="id_in_select" type="select" label="Run tool in batch mode for -id_in">
-        <option value="no">No: process all datasets jointly</option>
-        <option value="yes">Yes: process each dataset in an independent job</option>
-      </param>
-      <when value="no">
-        <param argument="-id_in" type="data" format="idxml" multiple="true" optional="true" label="Optional idXML Input file(s) in the same order as mzML files - for Maracluster Cluster annotation" help=" select idxml data sets(s)"/>
-      </when>
-      <when value="yes">
-        <param argument="-id_in" type="data" format="idxml" multiple="false" optional="true" label="Optional idXML Input file(s) in the same order as mzML files - for Maracluster Cluster annotation" help=" select idxml data sets(s)"/>
-      </when>
-    </conditional>
-    <param argument="-pcut" type="float" optional="true" max="0.0" value="-10.0" label="log(p-value) cutoff, has to be &lt; 0.0" help="Default: -10.0"/>
-    <param argument="-min_cluster_size" type="integer" optional="true" min="1" value="1" label="minimum number of spectra in a cluster for consensus spectra" help=""/>
-    <expand macro="adv_opts_macro">
-      <param argument="-verbose" type="integer" optional="true" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help=""/>
-      <param argument="-precursor_tolerance" type="float" optional="true" value="20.0" label="Precursor monoisotopic mass tolerance" help=""/>
-      <param argument="-precursor_tolerance_units" type="select" optional="true" label="tolerance_mass_units 0=ppm, 1=Da" help="">
-        <option value="ppm" selected="true">ppm</option>
-        <option value="Da">Da</option>
-        <expand macro="list_string_san" name="precursor_tolerance_units"/>
-      </param>
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="out_FLAG">out (Output file in idXML format)</option>
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
-      <filter>OPTIONAL_OUTPUTS is None</filter>
-    </data>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><!-- TOPP_MaRaClusterAdapter_2 -->
-  </tests>
-  <help><![CDATA[Facilitate input to MaRaCluster and reintegrate.
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MaRaClusterAdapter.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/MapAlignerIdentification.xml b/tools/openms/MapAlignerIdentification.xml
index 93051a262..33cac9d1e 100644
--- a/tools/openms/MapAlignerIdentification.xml
+++ b/tools/openms/MapAlignerIdentification.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Map Alignment]-->
 <tool id="MapAlignerIdentification" name="MapAlignerIdentification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Corrects retention time distortions between maps based on common peptide identifications.</description>
+  <description>Corrects retention time distortions between maps based on common peptide identifications</description>
   <macros>
     <token name="@EXECUTABLE@">MapAlignerIdentification</token>
     <import>macros.xml</import>
@@ -17,9 +16,9 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
@@ -31,11 +30,11 @@ ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_id
 #end if
 #if $design:
   mkdir design &&
-  ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
+  cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
 #end if
 #if $reference.file:
   mkdir reference.file &&
-  ln -s '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' &&
+  cp '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' &&
 #end if
 
 ## Main program call
@@ -88,32 +87,32 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="consensusxml,featurexml,idxml,sqlite" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select consensusxml,featurexml,idxml,sqlite data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,featurexml,idxml,sqlite" multiple="true" label="Input files to align (all must have the same file type)" help=" select consensusxml,featurexml,idxml,sqlite data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="consensusxml,featurexml,idxml,sqlite" multiple="false" optional="false" label="Input files to align (all must have the same file type)" help=" select consensusxml,featurexml,idxml,sqlite data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,featurexml,idxml,sqlite" label="Input files to align (all must have the same file type)" help=" select consensusxml,featurexml,idxml,sqlite data sets(s)"/>
       </when>
     </conditional>
     <param argument="-design" type="data" format="tabular" optional="true" label="Input file containing the experimental design" help=" select tabular data sets(s)"/>
     <param argument="-store_original_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original retention times (before transformation) as meta data in the output?" help=""/>
     <section name="reference" title="Options to define a reference file (use either 'file' or 'index', not both)" help="" expanded="false">
       <param name="file" argument="-reference:file" type="data" format="consensusxml,featurexml,idxml,sqlite" optional="true" label="File to use as reference" help=" select consensusxml,featurexml,idxml,sqlite data sets(s)"/>
-      <param name="index" argument="-reference:index" type="integer" optional="true" min="0" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="If '0', no explicit reference is set - the algorithm will select a reference"/>
+      <param name="index" argument="-reference:index" type="integer" min="0" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="If '0', no explicit reference is set - the algorithm will select a reference"/>
     </section>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <param name="score_type" argument="-algorithm:score_type" type="text" optional="true" value="" label="Name of the score type to use for ranking and filtering (.oms input only)" help="If left empty, a score type is picked automatically">
         <expand macro="list_string_san" name="score_type"/>
       </param>
       <param name="score_cutoff" argument="-algorithm:score_cutoff" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use only IDs above a score cut-off (parameter 'min_score') for alignment?" help=""/>
-      <param name="min_score" argument="-algorithm:min_score" type="float" optional="true" value="0.05" label="If 'score_cutoff' is 'true': Minimum score for an ID to be considered" help="Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
-      <param name="min_run_occur" argument="-algorithm:min_run_occur" type="integer" optional="true" min="2" value="2" label="Minimum number of runs (incl" help="reference, if any) in which a peptide must occur to be used for the alignment.. Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
-      <param name="max_rt_shift" argument="-algorithm:max_rt_shift" type="float" optional="true" min="0.0" value="0.5" label="Maximum realistic RT difference for a peptide (median per run vs" help="reference). Peptides with higher shifts (outliers) are not used to compute the alignment.. If 0, no limit (disable filter); if &gt; 1, the final value in seconds; if &lt;= 1, taken as a fraction of the range of the reference RT scale"/>
+      <param name="min_score" argument="-algorithm:min_score" type="float" value="0.05" label="If 'score_cutoff' is 'true': Minimum score for an ID to be considered" help="Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
+      <param name="min_run_occur" argument="-algorithm:min_run_occur" type="integer" min="2" value="2" label="Minimum number of runs (incl" help="reference, if any) in which a peptide must occur to be used for the alignment.. Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
+      <param name="max_rt_shift" argument="-algorithm:max_rt_shift" type="float" min="0.0" value="0.5" label="Maximum realistic RT difference for a peptide (median per run vs" help="reference). Peptides with higher shifts (outliers) are not used to compute the alignment.. If 0, no limit (disable filter); if &gt; 1, the final value in seconds; if &lt;= 1, taken as a fraction of the range of the reference RT scale"/>
       <param name="use_unassigned_peptides" argument="-algorithm:use_unassigned_peptides" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Should unassigned peptide identifications be used when computing an alignment of feature or consensus maps" help="If 'false', only peptide IDs assigned to features will be used"/>
       <param name="use_feature_rt" argument="-algorithm:use_feature_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="When aligning feature or consensus maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to" help="If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used.. Precludes 'use_unassigned_peptides'"/>
       <param name="use_adducts" argument="-algorithm:use_adducts" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If IDs contain adducts, treat differently adducted variants of the same molecule as different" help=""/>
     </section>
     <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
-      <param name="type" argument="-model:type" type="select" optional="true" label="Type of model" help="">
+      <param name="type" argument="-model:type" type="select" label="Type of model" help="">
         <option value="linear">linear</option>
         <option value="b_spline" selected="true">b_spline</option>
         <option value="lowess">lowess</option>
@@ -122,48 +121,48 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </param>
       <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
         <param name="symmetric_regression" argument="-model:linear:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
-        <param name="x_weight" argument="-model:linear:x_weight" type="select" optional="true" label="Weight x values" help="">
+        <param name="x_weight" argument="-model:linear:x_weight" type="select" label="Weight x values" help="">
           <option value="1/x">1/x</option>
           <option value="1/x2">1/x2</option>
           <option value="ln(x)">ln(x)</option>
-          <option value=""></option>
+          <option value="x" selected="true">x</option>
           <expand macro="list_string_san" name="x_weight"/>
         </param>
-        <param name="y_weight" argument="-model:linear:y_weight" type="select" optional="true" label="Weight y values" help="">
+        <param name="y_weight" argument="-model:linear:y_weight" type="select" label="Weight y values" help="">
           <option value="1/y">1/y</option>
           <option value="1/y2">1/y2</option>
           <option value="ln(y)">ln(y)</option>
-          <option value=""></option>
+          <option value="y" selected="true">y</option>
           <expand macro="list_string_san" name="y_weight"/>
         </param>
-        <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" optional="true" value="1e-15" label="Minimum x value" help=""/>
-        <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum x value" help=""/>
-        <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" optional="true" value="1e-15" label="Minimum y value" help=""/>
-        <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum y value" help=""/>
+        <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" value="1e-15" label="Minimum x value" help=""/>
+        <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" value="1000000000000000.0" label="Maximum x value" help=""/>
+        <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" value="1e-15" label="Minimum y value" help=""/>
+        <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" value="1000000000000000.0" label="Maximum y value" help=""/>
       </section>
       <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
-        <param name="wavelength" argument="-model:b_spline:wavelength" type="float" optional="true" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
-        <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
-        <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" optional="true" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
+        <param name="wavelength" argument="-model:b_spline:wavelength" type="float" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
+        <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
+        <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
           <option value="linear" selected="true">linear</option>
           <option value="b_spline">b_spline</option>
           <option value="constant">constant</option>
           <option value="global_linear">global_linear</option>
           <expand macro="list_string_san" name="extrapolate"/>
         </param>
-        <param name="boundary_condition" argument="-model:b_spline:boundary_condition" type="integer" optional="true" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/>
+        <param name="boundary_condition" argument="-model:b_spline:boundary_condition" type="integer" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/>
       </section>
       <section name="lowess" title="Parameters for 'lowess' model" help="" expanded="false">
-        <param name="span" argument="-model:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
-        <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" optional="true" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
-        <param name="delta" argument="-model:lowess:delta" type="float" optional="true" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
-        <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" optional="true" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
+        <param name="span" argument="-model:lowess:span" type="float" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
+        <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
+        <param name="delta" argument="-model:lowess:delta" type="float" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
+        <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
           <option value="linear">linear</option>
           <option value="cspline" selected="true">cspline</option>
           <option value="akima">akima</option>
           <expand macro="list_string_san" name="interpolation_type"/>
         </param>
-        <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" optional="true" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
+        <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
           <option value="two-point-linear">two-point-linear</option>
           <option value="four-point-linear" selected="true">four-point-linear</option>
           <option value="global-linear">global-linear</option>
@@ -171,13 +170,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         </param>
       </section>
       <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
-        <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" optional="true" label="Type of interpolation to apply" help="">
+        <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" label="Type of interpolation to apply" help="">
           <option value="linear">linear</option>
           <option value="cspline" selected="true">cspline</option>
           <option value="akima">akima</option>
           <expand macro="list_string_san" name="interpolation_type"/>
         </param>
-        <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" optional="true" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
+        <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
           <option value="two-point-linear" selected="true">two-point-linear</option>
           <option value="four-point-linear">four-point-linear</option>
           <option value="global-linear">global-linear</option>
@@ -187,7 +186,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -213,7 +212,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MapAlignerIdentification_1 -->
+  <tests>
+    <!-- TOPP_MapAlignerIdentification_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -241,8 +241,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="type" value="b_spline"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -272,6 +272,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapAlignerIdentification_2 -->
     <test expect_num_outputs="2">
@@ -302,8 +305,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="type" value="b_spline"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -333,6 +336,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapAlignerIdentification_3 -->
     <test expect_num_outputs="2">
@@ -362,8 +368,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="type" value="b_spline"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -393,6 +399,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapAlignerIdentification_4 -->
     <test expect_num_outputs="2">
@@ -422,8 +431,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="type" value="b_spline"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -453,6 +462,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapAlignerIdentification_5 -->
     <test expect_num_outputs="2">
@@ -482,8 +494,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="type" value="b_spline"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -513,6 +525,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapAlignerIdentification_6 -->
     <test expect_num_outputs="2">
@@ -543,8 +558,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="type" value="b_spline"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -574,6 +589,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapAlignerIdentification_7 -->
     <test expect_num_outputs="3">
@@ -582,7 +600,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="test" value="true"/>
       </section>
       <conditional name="in_cond">
-        <param name="in" value="MapAlignerIdentification_7_input1.idXML"/>
+        <param name="in" value="MapAlignerIdentification_7_input1_0.idXML"/>
       </conditional>
       <output_collection name="out" count="1"/>
       <output_collection name="trafo_out" count="1"/>
@@ -605,8 +623,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="type" value="b_spline"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -636,6 +654,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapAlignerIdentification_8 -->
     <test expect_num_outputs="3">
@@ -667,8 +688,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="type" value="b_spline"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -698,11 +719,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Corrects retention time distortions between maps based on common peptide identifications.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapAlignerIdentification.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MapAlignerIdentification.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MapAlignerPoseClustering.xml b/tools/openms/MapAlignerPoseClustering.xml
index 6421dbfb8..cfa5bf066 100644
--- a/tools/openms/MapAlignerPoseClustering.xml
+++ b/tools/openms/MapAlignerPoseClustering.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Map Alignment]-->
 <tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Corrects retention time distortions between maps using a pose clustering approach.</description>
+  <description>Corrects retention time distortions between maps using a pose clustering approach</description>
   <macros>
     <token name="@EXECUTABLE@">MapAlignerPoseClustering</token>
     <import>macros.xml</import>
@@ -17,9 +16,9 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
@@ -31,7 +30,7 @@ ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_id
 #end if
 #if $reference.file:
   mkdir reference.file &&
-  ln -s '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' &&
+  cp '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' &&
 #end if
 
 ## Main program call
@@ -80,26 +79,26 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="featurexml,mzml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml,mzml data sets(s)"/>
+        <param argument="-in" type="data" format="featurexml,mzml" multiple="true" label="Input files to align (all must have the same file type)" help=" select featurexml,mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="featurexml,mzml" multiple="false" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml,mzml data sets(s)"/>
+        <param argument="-in" type="data" format="featurexml,mzml" label="Input files to align (all must have the same file type)" help=" select featurexml,mzml data sets(s)"/>
       </when>
     </conditional>
     <section name="reference" title="Options to define a reference file (use either 'file' or 'index', not both)" help="" expanded="false">
       <param name="file" argument="-reference:file" type="data" format="featurexml,mzml" optional="true" label="File to use as reference (same file format as input files required)" help=" select featurexml,mzml data sets(s)"/>
-      <param name="index" argument="-reference:index" type="integer" optional="true" min="0" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="If '0', no explicit reference is set - the algorithm will select a reference"/>
+      <param name="index" argument="-reference:index" type="integer" min="0" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="If '0', no explicit reference is set - the algorithm will select a reference"/>
     </section>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="max_num_peaks_considered" argument="-algorithm:max_num_peaks_considered" type="integer" optional="true" min="-1" value="1000" label="The maximal number of peaks/features to be considered per map" help="To use all, set to '-1'"/>
+      <param name="max_num_peaks_considered" argument="-algorithm:max_num_peaks_considered" type="integer" min="-1" value="1000" label="The maximal number of peaks/features to be considered per map" help="To use all, set to '-1'"/>
       <section name="superimposer" title="" help="" expanded="false">
-        <param name="mz_pair_max_distance" argument="-algorithm:superimposer:mz_pair_max_distance" type="float" optional="true" min="0.0" value="0.5" label="Maximum of m/z deviation of corresponding elements in different maps" help="This condition applies to the pairs considered in hashing"/>
-        <param name="rt_pair_distance_fraction" argument="-algorithm:superimposer:rt_pair_distance_fraction" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval" help="(i.e., max - min).  "/>
-        <param name="num_used_points" argument="-algorithm:superimposer:num_used_points" type="integer" optional="true" min="-1" value="2000" label="Maximum number of elements considered in each map (selected by intensity)" help="Use this to reduce the running time and to disregard weak signals during alignment.  For using all points, set this to -1"/>
-        <param name="scaling_bucket_size" argument="-algorithm:superimposer:scaling_bucket_size" type="float" optional="true" min="0.0" value="0.005" label="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering" help="A good choice for this would be a bit smaller than the error you would expect from repeated runs"/>
-        <param name="shift_bucket_size" argument="-algorithm:superimposer:shift_bucket_size" type="float" optional="true" min="0.0" value="3.0" label="The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering" help="A good choice for this would be about the time between consecutive MS scans"/>
-        <param name="max_shift" argument="-algorithm:superimposer:max_shift" type="float" optional="true" min="0.0" value="1000.0" label="Maximal shift which is considered during histogramming (in seconds)" help="This applies for both directions"/>
-        <param name="max_scaling" argument="-algorithm:superimposer:max_scaling" type="float" optional="true" min="1.0" value="2.0" label="Maximal scaling which is considered during histogramming" help="The minimal scaling is the reciprocal of this"/>
+        <param name="mz_pair_max_distance" argument="-algorithm:superimposer:mz_pair_max_distance" type="float" min="0.0" value="0.5" label="Maximum of m/z deviation of corresponding elements in different maps" help="This condition applies to the pairs considered in hashing"/>
+        <param name="rt_pair_distance_fraction" argument="-algorithm:superimposer:rt_pair_distance_fraction" type="float" min="0.0" max="1.0" value="0.1" label="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval" help="(i.e., max - min).  "/>
+        <param name="num_used_points" argument="-algorithm:superimposer:num_used_points" type="integer" min="-1" value="2000" label="Maximum number of elements considered in each map (selected by intensity)" help="Use this to reduce the running time and to disregard weak signals during alignment.  For using all points, set this to -1"/>
+        <param name="scaling_bucket_size" argument="-algorithm:superimposer:scaling_bucket_size" type="float" min="0.0" value="0.005" label="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering" help="A good choice for this would be a bit smaller than the error you would expect from repeated runs"/>
+        <param name="shift_bucket_size" argument="-algorithm:superimposer:shift_bucket_size" type="float" min="0.0" value="3.0" label="The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering" help="A good choice for this would be about the time between consecutive MS scans"/>
+        <param name="max_shift" argument="-algorithm:superimposer:max_shift" type="float" min="0.0" value="1000.0" label="Maximal shift which is considered during histogramming (in seconds)" help="This applies for both directions"/>
+        <param name="max_scaling" argument="-algorithm:superimposer:max_scaling" type="float" min="1.0" value="2.0" label="Maximal scaling which is considered during histogramming" help="The minimal scaling is the reciprocal of this"/>
         <param name="dump_buckets" argument="-algorithm:superimposer:dump_buckets" type="text" optional="true" value="" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to" help="A serial number for each invocation will be appended automatically">
           <expand macro="list_string_san" name="dump_buckets"/>
         </param>
@@ -108,29 +107,29 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         </param>
       </section>
       <section name="pairfinder" title="" help="" expanded="false">
-        <param name="second_nearest_gap" argument="-algorithm:pairfinder:second_nearest_gap" type="float" optional="true" min="1.0" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help=""/>
+        <param name="second_nearest_gap" argument="-algorithm:pairfinder:second_nearest_gap" type="float" min="1.0" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help=""/>
         <param name="use_identifications" argument="-algorithm:pairfinder:use_identifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" help=""/>
         <param name="ignore_charge" argument="-algorithm:pairfinder:ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help=""/>
         <param name="ignore_adduct" argument="-algorithm:pairfinder:ignore_adduct" type="boolean" truevalue="true" falsevalue="false" checked="true" label="true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts" help=""/>
         <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false">
-          <param name="max_difference" argument="-algorithm:pairfinder:distance_RT:max_difference" type="float" optional="true" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/>
-          <param name="exponent" argument="-algorithm:pairfinder:distance_RT:exponent" type="float" optional="true" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
-          <param name="weight" argument="-algorithm:pairfinder:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
+          <param name="max_difference" argument="-algorithm:pairfinder:distance_RT:max_difference" type="float" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/>
+          <param name="exponent" argument="-algorithm:pairfinder:distance_RT:exponent" type="float" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
+          <param name="weight" argument="-algorithm:pairfinder:distance_RT:weight" type="float" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
         </section>
         <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
-          <param name="max_difference" argument="-algorithm:pairfinder:distance_MZ:max_difference" type="float" optional="true" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
-          <param name="unit" argument="-algorithm:pairfinder:distance_MZ:unit" type="select" optional="true" label="Unit of the 'max_difference' paramete" help="">
+          <param name="max_difference" argument="-algorithm:pairfinder:distance_MZ:max_difference" type="float" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
+          <param name="unit" argument="-algorithm:pairfinder:distance_MZ:unit" type="select" label="Unit of the 'max_difference' paramete" help="">
             <option value="Da" selected="true">Da</option>
             <option value="ppm">ppm</option>
             <expand macro="list_string_san" name="unit"/>
           </param>
-          <param name="exponent" argument="-algorithm:pairfinder:distance_MZ:exponent" type="float" optional="true" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
-          <param name="weight" argument="-algorithm:pairfinder:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
+          <param name="exponent" argument="-algorithm:pairfinder:distance_MZ:exponent" type="float" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
+          <param name="weight" argument="-algorithm:pairfinder:distance_MZ:weight" type="float" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
         </section>
         <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
-          <param name="exponent" argument="-algorithm:pairfinder:distance_intensity:exponent" type="float" optional="true" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
-          <param name="weight" argument="-algorithm:pairfinder:distance_intensity:weight" type="float" optional="true" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
-          <param name="log_transform" argument="-algorithm:pairfinder:distance_intensity:log_transform" type="select" optional="true" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
+          <param name="exponent" argument="-algorithm:pairfinder:distance_intensity:exponent" type="float" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
+          <param name="weight" argument="-algorithm:pairfinder:distance_intensity:weight" type="float" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
+          <param name="log_transform" argument="-algorithm:pairfinder:distance_intensity:log_transform" type="select" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
             <option value="enabled">enabled</option>
             <option value="disabled" selected="true">disabled</option>
             <expand macro="list_string_san" name="log_transform"/>
@@ -140,7 +139,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -166,7 +165,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MapAlignerPoseClustering_1 -->
+  <tests>
+    <!-- TOPP_MapAlignerPoseClustering_1 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -222,6 +222,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapAlignerPoseClustering_2 -->
     <test expect_num_outputs="2">
@@ -278,6 +281,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapAlignerPoseClustering_3 -->
     <test expect_num_outputs="2">
@@ -335,6 +341,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapAlignerPoseClustering_4 -->
     <test expect_num_outputs="2">
@@ -391,11 +400,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Corrects retention time distortions between maps using a pose clustering approach.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapAlignerPoseClustering.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MapAlignerPoseClustering.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MapAlignerSpectrum.xml b/tools/openms/MapAlignerSpectrum.xml
index 04ac196f1..1912c4c97 100644
--- a/tools/openms/MapAlignerSpectrum.xml
+++ b/tools/openms/MapAlignerSpectrum.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Map Alignment]-->
 <tool id="MapAlignerSpectrum" name="MapAlignerSpectrum" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Corrects retention time distortions between maps by spectrum alignment.</description>
+  <description>Corrects retention time distortions between maps by spectrum alignment</description>
   <macros>
     <token name="@EXECUTABLE@">MapAlignerSpectrum</token>
     <import>macros.xml</import>
@@ -17,9 +16,9 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
@@ -75,27 +74,27 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" multiple="true" label="Input files to align (all must have the same file type)" help=" select mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input files to align (all must have the same file type)" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" label="Input files to align (all must have the same file type)" help=" select mzml data sets(s)"/>
       </when>
     </conditional>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="gapcost" argument="-algorithm:gapcost" type="float" optional="true" min="0.0" value="1.0" label="This Parameter stands for the cost of opening a gap in the Alignment" help="A gap means that one spectrum can not be aligned directly to another spectrum in the Map. This happens, when the similarity of both spectra a too low or even not present. Imagine it as a insert or delete of the spectrum in the map (similar to sequence alignment). The gap is necessary for aligning, if we open a gap there is a possibility that an another spectrum can be correct aligned with a higher score as before without gap. But to open a gap is a negative event and needs to carry a punishment, so a gap should only be opened if the benefits outweigh the downsides. The Parameter is to giving as a positive number, the implementation convert it to a negative number"/>
-      <param name="affinegapcost" argument="-algorithm:affinegapcost" type="float" optional="true" min="0.0" value="0.5" label="This Parameter controls the cost of extension a already open gap" help="The idea behind the affine gapcost lies under the assumption, that it is better to get a long distance of connected gaps than to have a structure of gaps interspersed with matches (gap match gap match etc.). Therefore the punishment for the extension of a gap generally should be lower than the normal gapcost. If the result of the alignment shows high compression, it is a good idea to lower either the affine gapcost or gap opening cost"/>
-      <param name="cutoff_score" argument="-algorithm:cutoff_score" type="float" optional="true" min="0.0" max="1.0" value="0.7" label="The Parameter defines the threshold which filtered spectra, these spectra are high potential candidate for deciding the interval of a sub-alignment" help="Only those pair of spectra are selected, which has a score higher or same of the threshold"/>
-      <param name="bucketsize" argument="-algorithm:bucketsize" type="integer" optional="true" min="1" value="100" label="Defines the numbers of buckets" help="It is a quantize of the interval of those points, which defines the main alignment (match points). These points have to filtered, to reduce the amount of points for the calculating a smoother spline curve"/>
-      <param name="anchorpoints" argument="-algorithm:anchorpoints" type="integer" optional="true" min="1" max="100" value="100" label="Defines the percent of numbers of match points which a selected from one bucket" help="The high score pairs are previously selected. The reduction of match points helps to get a smoother spline curve"/>
-      <param name="mismatchscore" argument="-algorithm:mismatchscore" type="float" optional="true" max="0.0" value="-5.0" label="Defines the score of two spectra if they have no similarity to each othe" help=""/>
-      <param name="scorefunction" argument="-algorithm:scorefunction" type="select" optional="true" label="The score function is the core of an alignment" help="The success of an alignment depends mostly of the elected score function. The score function return the similarity of two spectra. The score influence defines later the way of possible traceback. There are multiple spectra similarity scores available">
+      <param name="gapcost" argument="-algorithm:gapcost" type="float" min="0.0" value="1.0" label="This Parameter stands for the cost of opening a gap in the Alignment" help="A gap means that one spectrum can not be aligned directly to another spectrum in the Map. This happens, when the similarity of both spectra a too low or even not present. Imagine it as a insert or delete of the spectrum in the map (similar to sequence alignment). The gap is necessary for aligning, if we open a gap there is a possibility that an another spectrum can be correct aligned with a higher score as before without gap. But to open a gap is a negative event and needs to carry a punishment, so a gap should only be opened if the benefits outweigh the downsides. The Parameter is to giving as a positive number, the implementation convert it to a negative number"/>
+      <param name="affinegapcost" argument="-algorithm:affinegapcost" type="float" min="0.0" value="0.5" label="This Parameter controls the cost of extension a already open gap" help="The idea behind the affine gapcost lies under the assumption, that it is better to get a long distance of connected gaps than to have a structure of gaps interspersed with matches (gap match gap match etc.). Therefore the punishment for the extension of a gap generally should be lower than the normal gapcost. If the result of the alignment shows high compression, it is a good idea to lower either the affine gapcost or gap opening cost"/>
+      <param name="cutoff_score" argument="-algorithm:cutoff_score" type="float" min="0.0" max="1.0" value="0.7" label="The Parameter defines the threshold which filtered spectra, these spectra are high potential candidate for deciding the interval of a sub-alignment" help="Only those pair of spectra are selected, which has a score higher or same of the threshold"/>
+      <param name="bucketsize" argument="-algorithm:bucketsize" type="integer" min="1" value="100" label="Defines the numbers of buckets" help="It is a quantize of the interval of those points, which defines the main alignment (match points). These points have to filtered, to reduce the amount of points for the calculating a smoother spline curve"/>
+      <param name="anchorpoints" argument="-algorithm:anchorpoints" type="integer" min="1" max="100" value="100" label="Defines the percent of numbers of match points which a selected from one bucket" help="The high score pairs are previously selected. The reduction of match points helps to get a smoother spline curve"/>
+      <param name="mismatchscore" argument="-algorithm:mismatchscore" type="float" max="0.0" value="-5.0" label="Defines the score of two spectra if they have no similarity to each othe" help=""/>
+      <param name="scorefunction" argument="-algorithm:scorefunction" type="select" label="The score function is the core of an alignment" help="The success of an alignment depends mostly of the elected score function. The score function return the similarity of two spectra. The score influence defines later the way of possible traceback. There are multiple spectra similarity scores available">
         <option value="SteinScottImproveScore" selected="true">SteinScottImproveScore</option>
         <option value="ZhangSimilarityScore">ZhangSimilarityScore</option>
         <expand macro="list_string_san" name="scorefunction"/>
       </param>
     </section>
     <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
-      <param name="type" argument="-model:type" type="select" optional="true" label="Type of model" help="">
+      <param name="type" argument="-model:type" type="select" label="Type of model" help="">
         <option value="linear">linear</option>
         <option value="b_spline">b_spline</option>
         <option value="lowess">lowess</option>
@@ -104,48 +103,48 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </param>
       <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
         <param name="symmetric_regression" argument="-model:linear:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
-        <param name="x_weight" argument="-model:linear:x_weight" type="select" optional="true" label="Weight x values" help="">
+        <param name="x_weight" argument="-model:linear:x_weight" type="select" label="Weight x values" help="">
           <option value="1/x">1/x</option>
           <option value="1/x2">1/x2</option>
           <option value="ln(x)">ln(x)</option>
-          <option value=""></option>
+          <option value="x" selected="true">x</option>
           <expand macro="list_string_san" name="x_weight"/>
         </param>
-        <param name="y_weight" argument="-model:linear:y_weight" type="select" optional="true" label="Weight y values" help="">
+        <param name="y_weight" argument="-model:linear:y_weight" type="select" label="Weight y values" help="">
           <option value="1/y">1/y</option>
           <option value="1/y2">1/y2</option>
           <option value="ln(y)">ln(y)</option>
-          <option value=""></option>
+          <option value="y" selected="true">y</option>
           <expand macro="list_string_san" name="y_weight"/>
         </param>
-        <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" optional="true" value="1e-15" label="Minimum x value" help=""/>
-        <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum x value" help=""/>
-        <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" optional="true" value="1e-15" label="Minimum y value" help=""/>
-        <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum y value" help=""/>
+        <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" value="1e-15" label="Minimum x value" help=""/>
+        <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" value="1000000000000000.0" label="Maximum x value" help=""/>
+        <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" value="1e-15" label="Minimum y value" help=""/>
+        <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" value="1000000000000000.0" label="Maximum y value" help=""/>
       </section>
       <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
-        <param name="wavelength" argument="-model:b_spline:wavelength" type="float" optional="true" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
-        <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
-        <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" optional="true" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
+        <param name="wavelength" argument="-model:b_spline:wavelength" type="float" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
+        <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
+        <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
           <option value="linear" selected="true">linear</option>
           <option value="b_spline">b_spline</option>
           <option value="constant">constant</option>
           <option value="global_linear">global_linear</option>
           <expand macro="list_string_san" name="extrapolate"/>
         </param>
-        <param name="boundary_condition" argument="-model:b_spline:boundary_condition" type="integer" optional="true" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/>
+        <param name="boundary_condition" argument="-model:b_spline:boundary_condition" type="integer" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/>
       </section>
       <section name="lowess" title="Parameters for 'lowess' model" help="" expanded="false">
-        <param name="span" argument="-model:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
-        <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" optional="true" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
-        <param name="delta" argument="-model:lowess:delta" type="float" optional="true" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
-        <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" optional="true" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
+        <param name="span" argument="-model:lowess:span" type="float" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
+        <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
+        <param name="delta" argument="-model:lowess:delta" type="float" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
+        <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
           <option value="linear">linear</option>
           <option value="cspline" selected="true">cspline</option>
           <option value="akima">akima</option>
           <expand macro="list_string_san" name="interpolation_type"/>
         </param>
-        <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" optional="true" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
+        <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
           <option value="two-point-linear">two-point-linear</option>
           <option value="four-point-linear" selected="true">four-point-linear</option>
           <option value="global-linear">global-linear</option>
@@ -153,13 +152,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         </param>
       </section>
       <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
-        <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" optional="true" label="Type of interpolation to apply" help="">
+        <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" label="Type of interpolation to apply" help="">
           <option value="linear">linear</option>
           <option value="cspline" selected="true">cspline</option>
           <option value="akima">akima</option>
           <expand macro="list_string_san" name="interpolation_type"/>
         </param>
-        <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" optional="true" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
+        <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
           <option value="two-point-linear" selected="true">two-point-linear</option>
           <option value="four-point-linear">four-point-linear</option>
           <option value="global-linear">global-linear</option>
@@ -169,7 +168,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -195,7 +194,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MapAlignerSpectrum_1 -->
+  <tests>
+    <!-- TOPP_MapAlignerSpectrum_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -218,8 +218,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="type" value="interpolated"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -249,11 +249,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Corrects retention time distortions between maps by spectrum alignment.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapAlignerSpectrum.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MapAlignerSpectrum.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MapAlignerTreeGuided.xml b/tools/openms/MapAlignerTreeGuided.xml
index 2642db20b..bca21011e 100644
--- a/tools/openms/MapAlignerTreeGuided.xml
+++ b/tools/openms/MapAlignerTreeGuided.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Map Alignment]-->
 <tool id="MapAlignerTreeGuided" name="MapAlignerTreeGuided" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Tree guided correction of retention time distortions between maps.</description>
+  <description>Tree guided correction of retention time distortions between maps</description>
   <macros>
     <token name="@EXECUTABLE@">MapAlignerTreeGuided</token>
     <import>macros.xml</import>
@@ -17,9 +16,9 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
@@ -75,14 +74,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="featurexml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml data sets(s)"/>
+        <param argument="-in" type="data" format="featurexml" multiple="true" label="Input files to align (all must have the same file type)" help=" select featurexml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="featurexml" multiple="false" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml data sets(s)"/>
+        <param argument="-in" type="data" format="featurexml" label="Input files to align (all must have the same file type)" help=" select featurexml data sets(s)"/>
       </when>
     </conditional>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="model_type" argument="-algorithm:model_type" type="select" optional="true" label="Options to control the modeling of retention time transformations from data" help="">
+      <param name="model_type" argument="-algorithm:model_type" type="select" label="Options to control the modeling of retention time transformations from data" help="">
         <option value="linear">linear</option>
         <option value="b_spline" selected="true">b_spline</option>
         <option value="lowess">lowess</option>
@@ -90,7 +89,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <expand macro="list_string_san" name="model_type"/>
       </param>
       <section name="model" title="" help="" expanded="false">
-        <param name="type" argument="-algorithm:model:type" type="select" optional="true" label="Type of model" help="">
+        <param name="type" argument="-algorithm:model:type" type="select" label="Type of model" help="">
           <option value="linear">linear</option>
           <option value="b_spline" selected="true">b_spline</option>
           <option value="lowess">lowess</option>
@@ -99,48 +98,48 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         </param>
         <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
           <param name="symmetric_regression" argument="-algorithm:model:linear:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
-          <param name="x_weight" argument="-algorithm:model:linear:x_weight" type="select" optional="true" label="Weight x values" help="">
+          <param name="x_weight" argument="-algorithm:model:linear:x_weight" type="select" label="Weight x values" help="">
             <option value="1/x">1/x</option>
             <option value="1/x2">1/x2</option>
             <option value="ln(x)">ln(x)</option>
-            <option value=""></option>
+            <option value="x" selected="true">x</option>
             <expand macro="list_string_san" name="x_weight"/>
           </param>
-          <param name="y_weight" argument="-algorithm:model:linear:y_weight" type="select" optional="true" label="Weight y values" help="">
+          <param name="y_weight" argument="-algorithm:model:linear:y_weight" type="select" label="Weight y values" help="">
             <option value="1/y">1/y</option>
             <option value="1/y2">1/y2</option>
             <option value="ln(y)">ln(y)</option>
-            <option value=""></option>
+            <option value="y" selected="true">y</option>
             <expand macro="list_string_san" name="y_weight"/>
           </param>
-          <param name="x_datum_min" argument="-algorithm:model:linear:x_datum_min" type="float" optional="true" value="1e-15" label="Minimum x value" help=""/>
-          <param name="x_datum_max" argument="-algorithm:model:linear:x_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum x value" help=""/>
-          <param name="y_datum_min" argument="-algorithm:model:linear:y_datum_min" type="float" optional="true" value="1e-15" label="Minimum y value" help=""/>
-          <param name="y_datum_max" argument="-algorithm:model:linear:y_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum y value" help=""/>
+          <param name="x_datum_min" argument="-algorithm:model:linear:x_datum_min" type="float" value="1e-15" label="Minimum x value" help=""/>
+          <param name="x_datum_max" argument="-algorithm:model:linear:x_datum_max" type="float" value="1000000000000000.0" label="Maximum x value" help=""/>
+          <param name="y_datum_min" argument="-algorithm:model:linear:y_datum_min" type="float" value="1e-15" label="Minimum y value" help=""/>
+          <param name="y_datum_max" argument="-algorithm:model:linear:y_datum_max" type="float" value="1000000000000000.0" label="Maximum y value" help=""/>
         </section>
         <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
-          <param name="wavelength" argument="-algorithm:model:b_spline:wavelength" type="float" optional="true" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
-          <param name="num_nodes" argument="-algorithm:model:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
-          <param name="extrapolate" argument="-algorithm:model:b_spline:extrapolate" type="select" optional="true" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
+          <param name="wavelength" argument="-algorithm:model:b_spline:wavelength" type="float" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
+          <param name="num_nodes" argument="-algorithm:model:b_spline:num_nodes" type="integer" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
+          <param name="extrapolate" argument="-algorithm:model:b_spline:extrapolate" type="select" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
             <option value="linear" selected="true">linear</option>
             <option value="b_spline">b_spline</option>
             <option value="constant">constant</option>
             <option value="global_linear">global_linear</option>
             <expand macro="list_string_san" name="extrapolate"/>
           </param>
-          <param name="boundary_condition" argument="-algorithm:model:b_spline:boundary_condition" type="integer" optional="true" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/>
+          <param name="boundary_condition" argument="-algorithm:model:b_spline:boundary_condition" type="integer" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/>
         </section>
         <section name="lowess" title="Parameters for 'lowess' model" help="" expanded="false">
-          <param name="span" argument="-algorithm:model:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
-          <param name="num_iterations" argument="-algorithm:model:lowess:num_iterations" type="integer" optional="true" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
-          <param name="delta" argument="-algorithm:model:lowess:delta" type="float" optional="true" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
-          <param name="interpolation_type" argument="-algorithm:model:lowess:interpolation_type" type="select" optional="true" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
+          <param name="span" argument="-algorithm:model:lowess:span" type="float" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
+          <param name="num_iterations" argument="-algorithm:model:lowess:num_iterations" type="integer" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
+          <param name="delta" argument="-algorithm:model:lowess:delta" type="float" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
+          <param name="interpolation_type" argument="-algorithm:model:lowess:interpolation_type" type="select" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
             <option value="linear">linear</option>
             <option value="cspline" selected="true">cspline</option>
             <option value="akima">akima</option>
             <expand macro="list_string_san" name="interpolation_type"/>
           </param>
-          <param name="extrapolation_type" argument="-algorithm:model:lowess:extrapolation_type" type="select" optional="true" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
+          <param name="extrapolation_type" argument="-algorithm:model:lowess:extrapolation_type" type="select" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
             <option value="two-point-linear">two-point-linear</option>
             <option value="four-point-linear" selected="true">four-point-linear</option>
             <option value="global-linear">global-linear</option>
@@ -148,13 +147,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           </param>
         </section>
         <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
-          <param name="interpolation_type" argument="-algorithm:model:interpolated:interpolation_type" type="select" optional="true" label="Type of interpolation to apply" help="">
+          <param name="interpolation_type" argument="-algorithm:model:interpolated:interpolation_type" type="select" label="Type of interpolation to apply" help="">
             <option value="linear">linear</option>
             <option value="cspline" selected="true">cspline</option>
             <option value="akima">akima</option>
             <expand macro="list_string_san" name="interpolation_type"/>
           </param>
-          <param name="extrapolation_type" argument="-algorithm:model:interpolated:extrapolation_type" type="select" optional="true" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
+          <param name="extrapolation_type" argument="-algorithm:model:interpolated:extrapolation_type" type="select" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
             <option value="two-point-linear" selected="true">two-point-linear</option>
             <option value="four-point-linear">four-point-linear</option>
             <option value="global-linear">global-linear</option>
@@ -167,9 +166,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <expand macro="list_string_san" name="score_type"/>
         </param>
         <param name="score_cutoff" argument="-algorithm:align_algorithm:score_cutoff" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use only IDs above a score cut-off (parameter 'min_score') for alignment?" help=""/>
-        <param name="min_score" argument="-algorithm:align_algorithm:min_score" type="float" optional="true" value="0.05" label="If 'score_cutoff' is 'true': Minimum score for an ID to be considered" help="Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
-        <param name="min_run_occur" argument="-algorithm:align_algorithm:min_run_occur" type="integer" optional="true" min="2" value="2" label="Minimum number of runs (incl" help="reference, if any) in which a peptide must occur to be used for the alignment.. Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
-        <param name="max_rt_shift" argument="-algorithm:align_algorithm:max_rt_shift" type="float" optional="true" min="0.0" value="0.5" label="Maximum realistic RT difference for a peptide (median per run vs" help="reference). Peptides with higher shifts (outliers) are not used to compute the alignment.. If 0, no limit (disable filter); if &gt; 1, the final value in seconds; if &lt;= 1, taken as a fraction of the range of the reference RT scale"/>
+        <param name="min_score" argument="-algorithm:align_algorithm:min_score" type="float" value="0.05" label="If 'score_cutoff' is 'true': Minimum score for an ID to be considered" help="Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
+        <param name="min_run_occur" argument="-algorithm:align_algorithm:min_run_occur" type="integer" min="2" value="2" label="Minimum number of runs (incl" help="reference, if any) in which a peptide must occur to be used for the alignment.. Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
+        <param name="max_rt_shift" argument="-algorithm:align_algorithm:max_rt_shift" type="float" min="0.0" value="0.5" label="Maximum realistic RT difference for a peptide (median per run vs" help="reference). Peptides with higher shifts (outliers) are not used to compute the alignment.. If 0, no limit (disable filter); if &gt; 1, the final value in seconds; if &lt;= 1, taken as a fraction of the range of the reference RT scale"/>
         <param name="use_unassigned_peptides" argument="-algorithm:align_algorithm:use_unassigned_peptides" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Should unassigned peptide identifications be used when computing an alignment of feature or consensus maps" help="If 'false', only peptide IDs assigned to features will be used"/>
         <param name="use_feature_rt" argument="-algorithm:align_algorithm:use_feature_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="When aligning feature or consensus maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to" help="If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used.. Precludes 'use_unassigned_peptides'"/>
         <param name="use_adducts" argument="-algorithm:align_algorithm:use_adducts" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If IDs contain adducts, treat differently adducted variants of the same molecule as different" help=""/>
@@ -177,7 +176,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -203,7 +202,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MapAlignerTreeGuided_1 -->
+  <tests>
+    <!-- TOPP_MapAlignerTreeGuided_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -219,8 +219,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <param name="type" value="b_spline"/>
           <section name="linear">
             <param name="symmetric_regression" value="false"/>
-            <param name="x_weight"/>
-            <param name="y_weight"/>
+            <param name="x_weight" value="x"/>
+            <param name="y_weight" value="y"/>
             <param name="x_datum_min" value="1e-15"/>
             <param name="x_datum_max" value="1000000000000000.0"/>
             <param name="y_datum_min" value="1e-15"/>
@@ -261,6 +261,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapAlignerTreeGuided_2 -->
     <test expect_num_outputs="2">
@@ -278,8 +281,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <param name="type" value="b_spline"/>
           <section name="linear">
             <param name="symmetric_regression" value="false"/>
-            <param name="x_weight"/>
-            <param name="y_weight"/>
+            <param name="x_weight" value="x"/>
+            <param name="y_weight" value="y"/>
             <param name="x_datum_min" value="1e-15"/>
             <param name="x_datum_max" value="1000000000000000.0"/>
             <param name="y_datum_min" value="1e-15"/>
@@ -320,6 +323,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapAlignerTreeGuided_3 -->
     <test expect_num_outputs="2">
@@ -337,8 +343,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <param name="type" value="b_spline"/>
           <section name="linear">
             <param name="symmetric_regression" value="false"/>
-            <param name="x_weight"/>
-            <param name="y_weight"/>
+            <param name="x_weight" value="x"/>
+            <param name="y_weight" value="y"/>
             <param name="x_datum_min" value="1e-15"/>
             <param name="x_datum_max" value="1000000000000000.0"/>
             <param name="y_datum_min" value="1e-15"/>
@@ -379,11 +385,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Tree guided correction of retention time distortions between maps.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapAlignerTreeGuided.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MapAlignerTreeGuided.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MapNormalizer.xml b/tools/openms/MapNormalizer.xml
index 7b53c9b64..657d2e798 100644
--- a/tools/openms/MapNormalizer.xml
+++ b/tools/openms/MapNormalizer.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="MapNormalizer" name="MapNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Normalizes peak intensities in an MS run.</description>
+  <description>Normalizes peak intensities in an MS run</description>
   <macros>
     <token name="@EXECUTABLE@">MapNormalizer</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,10 +38,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -56,25 +55,29 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MapNormalizer_1 -->
+  <tests>
+    <!-- TOPP_MapNormalizer_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MapNormalizer_input.mzML"/>
-      <output name="out" file="MapNormalizer.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="MapNormalizer_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Normalizes peak intensities in an MS run.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapNormalizer.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MapNormalizer.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MapRTTransformer.xml b/tools/openms/MapRTTransformer.xml
index a4a57a566..85b0cdaca 100644
--- a/tools/openms/MapRTTransformer.xml
+++ b/tools/openms/MapRTTransformer.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Map Alignment]-->
 <tool id="MapRTTransformer" name="MapRTTransformer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies retention time transformations to maps.</description>
+  <description>Applies retention time transformations to maps</description>
   <macros>
     <token name="@EXECUTABLE@">MapRTTransformer</token>
     <import>macros.xml</import>
@@ -16,13 +15,13 @@
 ## Preprocessing
 #if $in:
   mkdir in &&
-  ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+  cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
 #end if
 mkdir trafo_in &&
-ln -s '$trafo_in' 'trafo_in/${re.sub("[^\w\-_]", "_", $trafo_in.element_identifier)}.$gxy2omsext($trafo_in.ext)' &&
+cp '$trafo_in' 'trafo_in/${re.sub("[^\w\-_]", "_", $trafo_in.element_identifier)}.$gxy2omsext($trafo_in.ext)' &&
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir trafo_out &&
 #end if
@@ -67,11 +66,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" optional="true" label="Input file to transform (separated by blanks)" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
-    <param argument="-trafo_in" type="data" format="trafoxml" optional="false" label="Transformation to apply" help=" select trafoxml data sets(s)"/>
+    <param argument="-trafo_in" type="data" format="trafoxml" label="Transformation to apply" help=" select trafoxml data sets(s)"/>
     <param argument="-invert" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Invert transformation (approximatively) before applying it" help=""/>
     <param argument="-store_original_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original retention times (before transformation) as meta data in the output file" help=""/>
     <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
-      <param name="type" argument="-model:type" type="select" optional="true" label="Type of model" help="">
+      <param name="type" argument="-model:type" type="select" label="Type of model" help="">
         <option value="none" selected="true">none</option>
         <option value="linear">linear</option>
         <option value="b_spline">b_spline</option>
@@ -81,48 +80,48 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </param>
       <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
         <param name="symmetric_regression" argument="-model:linear:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
-        <param name="x_weight" argument="-model:linear:x_weight" type="select" optional="true" label="Weight x values" help="">
+        <param name="x_weight" argument="-model:linear:x_weight" type="select" label="Weight x values" help="">
           <option value="1/x">1/x</option>
           <option value="1/x2">1/x2</option>
           <option value="ln(x)">ln(x)</option>
-          <option value=""></option>
+          <option value="x" selected="true">x</option>
           <expand macro="list_string_san" name="x_weight"/>
         </param>
-        <param name="y_weight" argument="-model:linear:y_weight" type="select" optional="true" label="Weight y values" help="">
+        <param name="y_weight" argument="-model:linear:y_weight" type="select" label="Weight y values" help="">
           <option value="1/y">1/y</option>
           <option value="1/y2">1/y2</option>
           <option value="ln(y)">ln(y)</option>
-          <option value=""></option>
+          <option value="y" selected="true">y</option>
           <expand macro="list_string_san" name="y_weight"/>
         </param>
-        <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" optional="true" value="1e-15" label="Minimum x value" help=""/>
-        <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum x value" help=""/>
-        <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" optional="true" value="1e-15" label="Minimum y value" help=""/>
-        <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum y value" help=""/>
+        <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" value="1e-15" label="Minimum x value" help=""/>
+        <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" value="1000000000000000.0" label="Maximum x value" help=""/>
+        <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" value="1e-15" label="Minimum y value" help=""/>
+        <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" value="1000000000000000.0" label="Maximum y value" help=""/>
       </section>
       <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
-        <param name="wavelength" argument="-model:b_spline:wavelength" type="float" optional="true" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
-        <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
-        <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" optional="true" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
+        <param name="wavelength" argument="-model:b_spline:wavelength" type="float" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
+        <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
+        <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
           <option value="linear" selected="true">linear</option>
           <option value="b_spline">b_spline</option>
           <option value="constant">constant</option>
           <option value="global_linear">global_linear</option>
           <expand macro="list_string_san" name="extrapolate"/>
         </param>
-        <param name="boundary_condition" argument="-model:b_spline:boundary_condition" type="integer" optional="true" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/>
+        <param name="boundary_condition" argument="-model:b_spline:boundary_condition" type="integer" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/>
       </section>
       <section name="lowess" title="Parameters for 'lowess' model" help="" expanded="false">
-        <param name="span" argument="-model:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
-        <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" optional="true" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
-        <param name="delta" argument="-model:lowess:delta" type="float" optional="true" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
-        <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" optional="true" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
+        <param name="span" argument="-model:lowess:span" type="float" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
+        <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
+        <param name="delta" argument="-model:lowess:delta" type="float" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
+        <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
           <option value="linear">linear</option>
           <option value="cspline" selected="true">cspline</option>
           <option value="akima">akima</option>
           <expand macro="list_string_san" name="interpolation_type"/>
         </param>
-        <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" optional="true" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
+        <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
           <option value="two-point-linear">two-point-linear</option>
           <option value="four-point-linear" selected="true">four-point-linear</option>
           <option value="global-linear">global-linear</option>
@@ -130,13 +129,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         </param>
       </section>
       <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
-        <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" optional="true" label="Type of interpolation to apply" help="">
+        <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" label="Type of interpolation to apply" help="">
           <option value="linear">linear</option>
           <option value="cspline" selected="true">cspline</option>
           <option value="akima">akima</option>
           <expand macro="list_string_san" name="interpolation_type"/>
         </param>
-        <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" optional="true" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
+        <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
           <option value="two-point-linear" selected="true">two-point-linear</option>
           <option value="four-point-linear">four-point-linear</option>
           <option value="global-linear">global-linear</option>
@@ -146,7 +145,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -170,14 +169,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MapRTTransformer_1 -->
+  <tests>
+    <!-- TOPP_MapRTTransformer_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MapRTTransformer_1_input.featureXML"/>
-      <output name="out" file="MapRTTransformer_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="MapRTTransformer_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
       <param name="invert" value="false"/>
       <param name="store_original_rt" value="false"/>
@@ -185,8 +185,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="type" value="none"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -216,6 +216,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapRTTransformer_2 -->
     <test expect_num_outputs="2">
@@ -224,7 +227,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MapRTTransformer_2_input.mzML"/>
-      <output name="out" file="MapRTTransformer_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="MapRTTransformer_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
       <param name="invert" value="false"/>
       <param name="store_original_rt" value="false"/>
@@ -232,8 +235,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="type" value="none"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -263,6 +266,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapRTTransformer_3 -->
     <test expect_num_outputs="2">
@@ -271,15 +277,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="trafo_in" value="MapAlignerPoseClustering_1_trafo2.trafoXML"/>
-      <output name="trafo_out" file="MapRTTransformer_3_trafo.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
+      <output name="trafo_out" value="MapRTTransformer_3_trafo.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
       <param name="invert" value="true"/>
       <param name="store_original_rt" value="false"/>
       <section name="model">
         <param name="type" value="none"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -309,6 +315,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapRTTransformer_4 -->
     <test expect_num_outputs="2">
@@ -317,7 +326,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MapRTTransformer_4_input.chrom.mzML"/>
-      <output name="out" file="MapRTTransformer_4_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="MapRTTransformer_4_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
       <param name="invert" value="false"/>
       <param name="store_original_rt" value="false"/>
@@ -325,8 +334,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="type" value="none"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -356,6 +365,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapRTTransformer_5 -->
     <test expect_num_outputs="2">
@@ -364,7 +376,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MapRTTransformer_1_input.featureXML"/>
-      <output name="out" file="MapRTTransformer_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="MapRTTransformer_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="trafo_in" value="MapRTTransformer_trafo_none.trafoXML"/>
       <param name="invert" value="false"/>
       <param name="store_original_rt" value="false"/>
@@ -372,8 +384,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="type" value="none"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -403,6 +415,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MapRTTransformer_6 -->
     <test expect_num_outputs="2">
@@ -411,7 +426,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MapRTTransformer_1_input.featureXML"/>
-      <output name="out" file="MapRTTransformer_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="MapRTTransformer_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
       <param name="invert" value="false"/>
       <param name="store_original_rt" value="true"/>
@@ -419,8 +434,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="type" value="none"/>
         <section name="linear">
           <param name="symmetric_regression" value="false"/>
-          <param name="x_weight"/>
-          <param name="y_weight"/>
+          <param name="x_weight" value="x"/>
+          <param name="y_weight" value="y"/>
           <param name="x_datum_min" value="1e-15"/>
           <param name="x_datum_max" value="1000000000000000.0"/>
           <param name="y_datum_min" value="1e-15"/>
@@ -450,11 +465,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Applies retention time transformations to maps.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapRTTransformer.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MapRTTransformer.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MapStatistics.xml b/tools/openms/MapStatistics.xml
index b55f06470..c401d3dd6 100644
--- a/tools/openms/MapStatistics.xml
+++ b/tools/openms/MapStatistics.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [File Handling]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="MapStatistics" name="MapStatistics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Extract extended statistics on the features of a map for quality control.</description>
+  <description>Extract extended statistics on the features of a map for quality control</description>
   <macros>
     <token name="@EXECUTABLE@">MapStatistics</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,14 +38,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="Input file" help=" select consensusxml,featurexml data sets(s)"/>
-    <param argument="-n" type="integer" optional="true" min="1" max="100" value="4" label="Report separate statistics for each of n RT slices of the map" help=""/>
+    <param argument="-in" type="data" format="consensusxml,featurexml" label="Input file" help=" select consensusxml,featurexml data sets(s)"/>
+    <param argument="-n" type="integer" min="1" max="100" value="4" label="Report separate statistics for each of n RT slices of the map" help=""/>
     <param argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/>
     <param argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/>
     <param argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a summary statistics of intensities, qualities, and widths" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -60,20 +59,23 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- test with a featureXML input  -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="featurexml" value="SiriusAdapter_3_input.featureXML"/>
-    <output name="out" ftype="txt" value="MapStatistics.txt"/>
-  </test>
-  <test expect_num_outputs="1"><!-- test with a consensusxml input -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/>
-    <output name="out" ftype="txt" value="MapStatistics2.txt"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- test with a featureXML input  -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="featurexml" value="SiriusAdapter_3_input.featureXML"/>
+      <output name="out" ftype="txt" value="MapStatistics.txt"/>
+    </test>
+    <test expect_num_outputs="1">
+      <!-- test with a consensusxml input -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/>
+      <output name="out" ftype="txt" value="MapStatistics2.txt"/>
+    </test>
+  </tests>
   <help><![CDATA[Extract extended statistics on the features of a map for quality control.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapStatistics.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MapStatistics.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MascotAdapter.xml b/tools/openms/MascotAdapter.xml
index 59c0c3483..67d36732a 100644
--- a/tools/openms/MascotAdapter.xml
+++ b/tools/openms/MascotAdapter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
 <tool id="MascotAdapter" name="MascotAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Annotates MS/MS spectra using Mascot.</description>
+  <description>Annotates MS/MS spectra using Mascot</description>
   <macros>
     <token name="@EXECUTABLE@">MascotAdapter</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,18 +38,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"mascot_directory": "TODO", "temp_data_directory": "\$TMP_DIR", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mascotxml,mzdata" optional="false" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="output file type (for TOPPAS)" help="">
+    <param argument="-in" type="data" format="mascotxml,mzdata" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/>
+    <param argument="-out_type" type="select" label="output file type (for TOPPAS)" help="">
       <option value="idXML">idxml</option>
       <option value="mgf">mgf</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param argument="-instrument" type="text" optional="true" value="Default" label="the instrument that was used to measure the spectra" help="">
+    <param argument="-instrument" type="text" value="Default" label="the instrument that was used to measure the spectra" help="">
       <expand macro="list_string_san" name="instrument"/>
     </param>
-    <param argument="-precursor_mass_tolerance" type="float" optional="true" value="2.0" label="the precursor mass tolerance" help=""/>
-    <param argument="-peak_mass_tolerance" type="float" optional="true" value="1.0" label="the peak mass tolerance" help=""/>
-    <param argument="-taxonomy" type="select" optional="true" label="the taxonomy" help="">
+    <param argument="-precursor_mass_tolerance" type="float" value="2.0" label="the precursor mass tolerance" help=""/>
+    <param argument="-peak_mass_tolerance" type="float" value="1.0" label="the peak mass tolerance" help=""/>
+    <param argument="-taxonomy" type="select" label="the taxonomy" help="">
       <option value="All entries" selected="true">All entries</option>
       <option value=". . Archaea (Archaeobacteria)">. . Archaea (Archaeobacteria)</option>
       <option value=". . Eukaryota (eucaryotes)">. . Eukaryota (eucaryotes)</option>
@@ -126,17 +126,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <expand macro="list_string_val" name="variable_modifications"/>
       <expand macro="list_string_san" name="variable_modifications"/>
     </param>
-    <param argument="-charges" type="text" optional="true" value="1+ 2+ 3+" label="the different charge states" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-charges" type="text" value="1+ 2+ 3+" label="the different charge states" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="charges"/>
       <expand macro="list_string_san" name="charges"/>
     </param>
-    <param argument="-db" type="text" optional="true" value="MSDB" label="the database to search in" help="">
+    <param argument="-db" type="text" value="MSDB" label="the database to search in" help="">
       <expand macro="list_string_san" name="db"/>
     </param>
-    <param argument="-hits" type="text" optional="true" value="AUTO" label="the number of hits to report" help="">
+    <param argument="-hits" type="text" value="AUTO" label="the number of hits to report" help="">
       <expand macro="list_string_san" name="hits"/>
     </param>
-    <param argument="-cleavage" type="select" optional="true" label="The enzyme descriptor to the enzyme used for digestion" help="(Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)">
+    <param argument="-cleavage" type="select" label="The enzyme descriptor to the enzyme used for digestion" help="(Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)">
       <option value="Trypsin" selected="true">Trypsin</option>
       <option value="Arg-C">Arg-C</option>
       <option value="Asp-N">Asp-N</option>
@@ -158,27 +158,27 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="None">None</option>
       <expand macro="list_string_san" name="cleavage"/>
     </param>
-    <param argument="-missed_cleavages" type="integer" optional="true" min="0" value="0" label="number of allowed missed cleavages" help=""/>
-    <param argument="-sig_threshold" type="float" optional="true" value="0.05" label="significance threshold" help=""/>
-    <param argument="-pep_homol" type="float" optional="true" value="1.0" label="peptide homology threshold" help=""/>
-    <param argument="-pep_ident" type="float" optional="true" value="1.0" label="peptide ident threshold" help=""/>
-    <param argument="-pep_rank" type="integer" optional="true" value="1" label="peptide rank" help=""/>
-    <param argument="-prot_score" type="float" optional="true" value="1.0" label="protein score" help=""/>
-    <param argument="-pep_score" type="float" optional="true" value="1.0" label="peptide score" help=""/>
-    <param argument="-pep_exp_z" type="integer" optional="true" value="1" label="peptide expected charge" help=""/>
-    <param argument="-show_unassigned" type="integer" optional="true" value="1" label="show_unassigned" help=""/>
-    <param argument="-first_dim_rt" type="float" optional="true" value="0.0" label="additional information which is added to every peptide identification as metavalue if set &gt; 0" help=""/>
+    <param argument="-missed_cleavages" type="integer" min="0" value="0" label="number of allowed missed cleavages" help=""/>
+    <param argument="-sig_threshold" type="float" value="0.05" label="significance threshold" help=""/>
+    <param argument="-pep_homol" type="float" value="1.0" label="peptide homology threshold" help=""/>
+    <param argument="-pep_ident" type="float" value="1.0" label="peptide ident threshold" help=""/>
+    <param argument="-pep_rank" type="integer" value="1" label="peptide rank" help=""/>
+    <param argument="-prot_score" type="float" value="1.0" label="protein score" help=""/>
+    <param argument="-pep_score" type="float" value="1.0" label="peptide score" help=""/>
+    <param argument="-pep_exp_z" type="integer" value="1" label="peptide expected charge" help=""/>
+    <param argument="-show_unassigned" type="integer" value="1" label="show_unassigned" help=""/>
+    <param argument="-first_dim_rt" type="float" value="0.0" label="additional information which is added to every peptide identification as metavalue if set &gt; 0" help=""/>
     <param argument="-boundary" type="text" optional="true" value="" label="MIME boundary for mascot output format" help="">
       <expand macro="list_string_san" name="boundary"/>
     </param>
-    <param argument="-mass_type" type="select" optional="true" label="mass type" help="">
+    <param argument="-mass_type" type="select" label="mass type" help="">
       <option value="Monoisotopic" selected="true">Monoisotopic</option>
       <option value="Average">Average</option>
       <expand macro="list_string_san" name="mass_type"/>
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -196,14 +196,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MascotAdapter_1 -->
+  <tests>
+    <!-- TOPP_MascotAdapter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MascotAdapter_1_input.mzData"/>
-      <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta_frac="0.7"/>
+      <output name="out" value="MascotAdapter_1_output.mascot_in" compare="sim_size" delta_frac="0.7"/>
       <param name="out_type" value="mgf"/>
       <param name="instrument" value="ESI-TRAP"/>
       <param name="precursor_mass_tolerance" value="1.3"/>
@@ -233,6 +234,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MascotAdapter_2 -->
     <test expect_num_outputs="2">
@@ -241,14 +245,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MascotAdapter_2_input.mascotXML"/>
-      <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="MascotAdapter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="instrument" value="Default"/>
       <param name="precursor_mass_tolerance" value="2.0"/>
       <param name="peak_mass_tolerance" value="1.0"/>
       <param name="taxonomy" value="All entries"/>
-      <param name="modifications" value=""/>
-      <param name="variable_modifications" value=""/>
       <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
       <param name="db" value="MSDB"/>
       <param name="hits" value="AUTO"/>
@@ -271,11 +273,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Annotates MS/MS spectra using Mascot.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MascotAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MascotAdapter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MascotAdapterOnline.xml b/tools/openms/MascotAdapterOnline.xml
index 336386cc7..2db59705d 100644
--- a/tools/openms/MascotAdapterOnline.xml
+++ b/tools/openms/MascotAdapterOnline.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
 <tool id="MascotAdapterOnline" name="MascotAdapterOnline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Annotates MS/MS spectra using Mascot.</description>
+  <description>Annotates MS/MS spectra using Mascot</description>
   <macros>
     <token name="@EXECUTABLE@">MascotAdapterOnline</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,45 +38,45 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file in mzML format.." help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file in mzML format.." help=" select mzml data sets(s)"/>
     <section name="Mascot_parameters" title="Mascot parameters used for searching" help="" expanded="false">
-      <param name="database" argument="-Mascot_parameters:database" type="text" optional="true" value="MSDB" label="Name of the sequence database" help="">
+      <param name="database" argument="-Mascot_parameters:database" type="text" value="MSDB" label="Name of the sequence database" help="">
         <expand macro="list_string_san" name="database"/>
       </param>
-      <param name="search_type" argument="-Mascot_parameters:search_type" type="select" optional="true" label="Name of the search type for the query" help="">
+      <param name="search_type" argument="-Mascot_parameters:search_type" type="select" label="Name of the search type for the query" help="">
         <option value="MIS" selected="true">MIS</option>
         <option value="SQ">SQ</option>
         <option value="PMF">PMF</option>
         <expand macro="list_string_san" name="search_type"/>
       </param>
-      <param name="enzyme" argument="-Mascot_parameters:enzyme" type="text" optional="true" value="Trypsin" label="The enzyme descriptor to the enzyme used for digestion" help="(Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)">
+      <param name="enzyme" argument="-Mascot_parameters:enzyme" type="text" value="Trypsin" label="The enzyme descriptor to the enzyme used for digestion" help="(Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)">
         <expand macro="list_string_san" name="enzyme"/>
       </param>
-      <param name="instrument" argument="-Mascot_parameters:instrument" type="text" optional="true" value="Default" label="Instrument definition which specifies the fragmentation rules" help="">
+      <param name="instrument" argument="-Mascot_parameters:instrument" type="text" value="Default" label="Instrument definition which specifies the fragmentation rules" help="">
         <expand macro="list_string_san" name="instrument"/>
       </param>
-      <param name="missed_cleavages" argument="-Mascot_parameters:missed_cleavages" type="integer" optional="true" min="0" value="1" label="Number of missed cleavages allowed for the enzyme" help=""/>
-      <param name="precursor_mass_tolerance" argument="-Mascot_parameters:precursor_mass_tolerance" type="float" optional="true" min="0.0" value="3.0" label="Tolerance of the precursor peaks" help=""/>
-      <param name="precursor_error_units" argument="-Mascot_parameters:precursor_error_units" type="select" optional="true" label="Units of the precursor mass tolerance" help="">
+      <param name="missed_cleavages" argument="-Mascot_parameters:missed_cleavages" type="integer" min="0" value="1" label="Number of missed cleavages allowed for the enzyme" help=""/>
+      <param name="precursor_mass_tolerance" argument="-Mascot_parameters:precursor_mass_tolerance" type="float" min="0.0" value="3.0" label="Tolerance of the precursor peaks" help=""/>
+      <param name="precursor_error_units" argument="-Mascot_parameters:precursor_error_units" type="select" label="Units of the precursor mass tolerance" help="">
         <option value="%">%</option>
         <option value="ppm">ppm</option>
         <option value="mmu">mmu</option>
         <option value="Da" selected="true">Da</option>
         <expand macro="list_string_san" name="precursor_error_units"/>
       </param>
-      <param name="fragment_mass_tolerance" argument="-Mascot_parameters:fragment_mass_tolerance" type="float" optional="true" min="0.0" value="0.3" label="Tolerance of the peaks in the fragment spectrum" help=""/>
-      <param name="fragment_error_units" argument="-Mascot_parameters:fragment_error_units" type="select" optional="true" label="Units of the fragment peaks tolerance" help="">
+      <param name="fragment_mass_tolerance" argument="-Mascot_parameters:fragment_mass_tolerance" type="float" min="0.0" value="0.3" label="Tolerance of the peaks in the fragment spectrum" help=""/>
+      <param name="fragment_error_units" argument="-Mascot_parameters:fragment_error_units" type="select" label="Units of the fragment peaks tolerance" help="">
         <option value="mmu">mmu</option>
         <option value="Da" selected="true">Da</option>
         <expand macro="list_string_san" name="fragment_error_units"/>
       </param>
-      <param name="charges" argument="-Mascot_parameters:charges" type="text" optional="true" value="1,2,3" label="Charge states to consider, given as a comma separated list of integers (only used for spectra without precursor charge information)" help="">
+      <param name="charges" argument="-Mascot_parameters:charges" type="text" value="1,2,3" label="Charge states to consider, given as a comma separated list of integers (only used for spectra without precursor charge information)" help="">
         <expand macro="list_string_san" name="charges"/>
       </param>
-      <param name="taxonomy" argument="-Mascot_parameters:taxonomy" type="text" optional="true" value="All entries" label="Taxonomy specification of the sequences" help="">
+      <param name="taxonomy" argument="-Mascot_parameters:taxonomy" type="text" value="All entries" label="Taxonomy specification of the sequences" help="">
         <expand macro="list_string_san" name="taxonomy"/>
       </param>
-      <param name="fixed_modifications" argument="-Mascot_parameters:fixed_modifications" multiple="true" type="select" optional="true" label="List of fixed modifications, according to UniMod definitions" help="">
+      <param name="fixed_modifications" argument="-Mascot_parameters:fixed_modifications" type="select" multiple="true" optional="true" label="List of fixed modifications, according to UniMod definitions" help="">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
         <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -87,6 +86,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="2-succinyl (C)">2-succinyl (C)</option>
         <option value="2HPG (R)">2HPG (R)</option>
         <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+        <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+        <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+        <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+        <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
         <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
         <option value="3sulfo (N-term)">3sulfo (N-term)</option>
         <option value="4-ONE (C)">4-ONE (C)</option>
@@ -176,6 +179,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
         <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
         <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+        <option value="Andro-H2O (C)">Andro-H2O (C)</option>
         <option value="Archaeol (C)">Archaeol (C)</option>
         <option value="Arg (N-term)">Arg (N-term)</option>
         <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -279,6 +283,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
         <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
         <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+        <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
         <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
         <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
         <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -311,7 +316,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="BITC (N-term)">BITC (N-term)</option>
         <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
         <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-        <option value="Bodipy (C)">Bodipy (C)</option>
         <option value="Brij35 (N-term)">Brij35 (N-term)</option>
         <option value="Brij58 (N-term)">Brij58 (N-term)</option>
         <option value="Bromo (F)">Bromo (F)</option>
@@ -743,9 +747,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Dehydrated (T)">Dehydrated (T)</option>
         <option value="Dehydrated (Y)">Dehydrated (Y)</option>
         <option value="Dehydro (C)">Dehydro (C)</option>
+        <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
         <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-        <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
         <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
         <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -755,7 +759,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
         <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
         <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-        <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
         <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
         <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -767,6 +770,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
         <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
         <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+        <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
         <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
         <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -1339,7 +1343,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Ethanolyl (C)">Ethanolyl (C)</option>
         <option value="Ethanolyl (K)">Ethanolyl (K)</option>
         <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-        <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
         <option value="Ethyl (C-term)">Ethyl (C-term)</option>
         <option value="Ethyl (D)">Ethyl (D)</option>
         <option value="Ethyl (E)">Ethyl (E)</option>
@@ -1433,6 +1436,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
         <option value="Glu (E)">Glu (E)</option>
         <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+        <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
         <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
         <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
         <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -1447,7 +1451,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
         <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
         <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
         <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -1471,6 +1474,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gly (K)">Gly (K)</option>
         <option value="Gly (S)">Gly (S)</option>
         <option value="Gly (T)">Gly (T)</option>
+        <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
         <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
         <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
         <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -1861,6 +1865,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
         <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
         <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+        <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
         <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
         <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
         <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -1872,6 +1877,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
         <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
         <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+        <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+        <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+        <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
         <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
         <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
         <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -1927,6 +1935,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
         <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
         <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+        <option value="His+O(2) (H)">His+O(2) (H)</option>
         <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
         <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
         <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -2064,11 +2073,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+        <option value="Kdo (S)">Kdo (S)</option>
+        <option value="Kdo (T)">Kdo (T)</option>
         <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
         <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
         <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
         <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
         <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+        <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
         <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
         <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
         <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -2153,13 +2165,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
         <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
         <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+        <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
         <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
         <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
         <option value="Lipoyl (K)">Lipoyl (K)</option>
         <option value="LRGG (K)">LRGG (K)</option>
         <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
         <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+        <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
         <option value="Lys (N-term)">Lys (N-term)</option>
+        <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
         <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
         <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
         <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -2194,6 +2209,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Malonyl (C)">Malonyl (C)</option>
         <option value="Malonyl (K)">Malonyl (K)</option>
         <option value="Malonyl (S)">Malonyl (S)</option>
+        <option value="MBS+peptide (C)">MBS+peptide (C)</option>
         <option value="MDCC (C)">MDCC (C)</option>
         <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
         <option value="Menadione (C)">Menadione (C)</option>
@@ -2205,6 +2221,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="MesitylOxide (H)">MesitylOxide (H)</option>
         <option value="MesitylOxide (K)">MesitylOxide (K)</option>
         <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+        <option value="Met+O(2) (H)">Met+O(2) (H)</option>
         <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
         <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
         <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -2388,7 +2405,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
         <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
         <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-        <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
         <option value="NP40 (N-term)">NP40 (N-term)</option>
         <option value="NQIGG (K)">NQIGG (K)</option>
         <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -2476,6 +2492,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
         <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
         <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+        <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+        <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+        <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+        <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
         <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
         <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
         <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -2490,6 +2510,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phospho (Y)">Phospho (Y)</option>
         <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
         <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+        <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
         <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
         <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
         <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -2521,6 +2542,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
         <option value="Piperidine (K)">Piperidine (K)</option>
         <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+        <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
         <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
         <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
         <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -2598,18 +2620,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="QTGG (K)">QTGG (K)</option>
         <option value="Quinone (W)">Quinone (W)</option>
         <option value="Quinone (Y)">Quinone (Y)</option>
+        <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+        <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+        <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+        <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+        <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+        <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+        <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+        <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+        <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+        <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+        <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+        <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+        <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+        <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+        <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+        <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+        <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+        <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+        <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+        <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
         <option value="Retinylidene (K)">Retinylidene (K)</option>
         <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
         <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
         <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-        <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-        <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-        <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-        <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-        <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-        <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-        <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-        <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
         <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
         <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
         <option value="Saligenin (H)">Saligenin (H)</option>
@@ -2637,6 +2671,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="shTMT (K)">shTMT (K)</option>
         <option value="shTMT (N-term)">shTMT (N-term)</option>
         <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+        <option value="shTMTpro (K)">shTMTpro (K)</option>
+        <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+        <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
         <option value="SMA (K)">SMA (K)</option>
         <option value="SMA (N-term)">SMA (N-term)</option>
         <option value="spermidine (Q)">spermidine (Q)</option>
@@ -2812,7 +2849,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
         <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
         <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-        <option value="Ub-amide (C)">Ub-amide (C)</option>
         <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
         <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
         <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -3007,7 +3043,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="ZQG (K)">ZQG (K)</option>
         <expand macro="list_string_san" name="fixed_modifications"/>
       </param>
-      <param name="variable_modifications" argument="-Mascot_parameters:variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications given as UniMod definitions" help="">
+      <param name="variable_modifications" argument="-Mascot_parameters:variable_modifications" type="select" multiple="true" optional="true" label="Variable modifications given as UniMod definitions" help="">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
         <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -3017,6 +3053,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="2-succinyl (C)">2-succinyl (C)</option>
         <option value="2HPG (R)">2HPG (R)</option>
         <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+        <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+        <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+        <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+        <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
         <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
         <option value="3sulfo (N-term)">3sulfo (N-term)</option>
         <option value="4-ONE (C)">4-ONE (C)</option>
@@ -3106,6 +3146,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
         <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
         <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+        <option value="Andro-H2O (C)">Andro-H2O (C)</option>
         <option value="Archaeol (C)">Archaeol (C)</option>
         <option value="Arg (N-term)">Arg (N-term)</option>
         <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -3209,6 +3250,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
         <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
         <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+        <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
         <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
         <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
         <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -3241,7 +3283,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="BITC (N-term)">BITC (N-term)</option>
         <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
         <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-        <option value="Bodipy (C)">Bodipy (C)</option>
         <option value="Brij35 (N-term)">Brij35 (N-term)</option>
         <option value="Brij58 (N-term)">Brij58 (N-term)</option>
         <option value="Bromo (F)">Bromo (F)</option>
@@ -3673,9 +3714,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Dehydrated (T)">Dehydrated (T)</option>
         <option value="Dehydrated (Y)">Dehydrated (Y)</option>
         <option value="Dehydro (C)">Dehydro (C)</option>
+        <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
         <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-        <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
         <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
         <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -3685,7 +3726,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
         <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
         <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-        <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
         <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
         <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -3697,6 +3737,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
         <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
         <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+        <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
         <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
         <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -4269,7 +4310,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Ethanolyl (C)">Ethanolyl (C)</option>
         <option value="Ethanolyl (K)">Ethanolyl (K)</option>
         <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-        <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
         <option value="Ethyl (C-term)">Ethyl (C-term)</option>
         <option value="Ethyl (D)">Ethyl (D)</option>
         <option value="Ethyl (E)">Ethyl (E)</option>
@@ -4363,6 +4403,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
         <option value="Glu (E)">Glu (E)</option>
         <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+        <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
         <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
         <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
         <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -4377,7 +4418,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
         <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
         <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
         <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -4401,6 +4441,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gly (K)">Gly (K)</option>
         <option value="Gly (S)">Gly (S)</option>
         <option value="Gly (T)">Gly (T)</option>
+        <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
         <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
         <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
         <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -4791,6 +4832,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
         <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
         <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+        <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
         <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
         <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
         <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -4802,6 +4844,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
         <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
         <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+        <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+        <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+        <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
         <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
         <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
         <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -4857,6 +4902,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
         <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
         <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+        <option value="His+O(2) (H)">His+O(2) (H)</option>
         <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
         <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
         <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -4994,11 +5040,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+        <option value="Kdo (S)">Kdo (S)</option>
+        <option value="Kdo (T)">Kdo (T)</option>
         <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
         <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
         <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
         <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
         <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+        <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
         <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
         <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
         <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -5083,13 +5132,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
         <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
         <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+        <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
         <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
         <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
         <option value="Lipoyl (K)">Lipoyl (K)</option>
         <option value="LRGG (K)">LRGG (K)</option>
         <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
         <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+        <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
         <option value="Lys (N-term)">Lys (N-term)</option>
+        <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
         <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
         <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
         <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -5124,6 +5176,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Malonyl (C)">Malonyl (C)</option>
         <option value="Malonyl (K)">Malonyl (K)</option>
         <option value="Malonyl (S)">Malonyl (S)</option>
+        <option value="MBS+peptide (C)">MBS+peptide (C)</option>
         <option value="MDCC (C)">MDCC (C)</option>
         <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
         <option value="Menadione (C)">Menadione (C)</option>
@@ -5135,6 +5188,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="MesitylOxide (H)">MesitylOxide (H)</option>
         <option value="MesitylOxide (K)">MesitylOxide (K)</option>
         <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+        <option value="Met+O(2) (H)">Met+O(2) (H)</option>
         <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
         <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
         <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -5318,7 +5372,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
         <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
         <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-        <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
         <option value="NP40 (N-term)">NP40 (N-term)</option>
         <option value="NQIGG (K)">NQIGG (K)</option>
         <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -5406,6 +5459,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
         <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
         <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+        <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+        <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+        <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+        <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
         <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
         <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
         <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -5420,6 +5477,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phospho (Y)">Phospho (Y)</option>
         <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
         <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+        <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
         <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
         <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
         <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -5451,6 +5509,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
         <option value="Piperidine (K)">Piperidine (K)</option>
         <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+        <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
         <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
         <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
         <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -5528,18 +5587,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="QTGG (K)">QTGG (K)</option>
         <option value="Quinone (W)">Quinone (W)</option>
         <option value="Quinone (Y)">Quinone (Y)</option>
+        <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+        <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+        <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+        <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+        <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+        <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+        <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+        <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+        <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+        <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+        <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+        <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+        <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+        <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+        <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+        <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+        <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+        <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+        <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+        <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
         <option value="Retinylidene (K)">Retinylidene (K)</option>
         <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
         <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
         <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-        <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-        <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-        <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-        <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-        <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-        <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-        <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-        <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
         <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
         <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
         <option value="Saligenin (H)">Saligenin (H)</option>
@@ -5567,6 +5638,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="shTMT (K)">shTMT (K)</option>
         <option value="shTMT (N-term)">shTMT (N-term)</option>
         <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+        <option value="shTMTpro (K)">shTMTpro (K)</option>
+        <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+        <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
         <option value="SMA (K)">SMA (K)</option>
         <option value="SMA (N-term)">SMA (N-term)</option>
         <option value="spermidine (Q)">spermidine (Q)</option>
@@ -5742,7 +5816,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
         <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
         <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-        <option value="Ub-amide (C)">Ub-amide (C)</option>
         <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
         <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
         <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -5937,21 +6010,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="ZQG (K)">ZQG (K)</option>
         <expand macro="list_string_san" name="variable_modifications"/>
       </param>
-      <param name="special_modifications" argument="-Mascot_parameters:special_modifications" type="text" optional="true" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)" label="Modifications with specificity groups that are used by Mascot and have to be treated specially" help="">
+      <param name="special_modifications" argument="-Mascot_parameters:special_modifications" type="text" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)" label="Modifications with specificity groups that are used by Mascot and have to be treated specially" help="">
         <expand macro="list_string_san" name="special_modifications"/>
       </param>
-      <param name="mass_type" argument="-Mascot_parameters:mass_type" type="select" optional="true" label="Defines the mass type, either monoisotopic or average" help="">
+      <param name="mass_type" argument="-Mascot_parameters:mass_type" type="select" label="Defines the mass type, either monoisotopic or average" help="">
         <option value="monoisotopic" selected="true">monoisotopic</option>
         <option value="average">average</option>
         <expand macro="list_string_san" name="mass_type"/>
       </param>
-      <param name="number_of_hits" argument="-Mascot_parameters:number_of_hits" type="integer" optional="true" min="0" value="0" label="Number of hits which should be returned, if 0 AUTO mode is enabled" help=""/>
+      <param name="number_of_hits" argument="-Mascot_parameters:number_of_hits" type="integer" min="0" value="0" label="Number of hits which should be returned, if 0 AUTO mode is enabled" help=""/>
       <param name="skip_spectrum_charges" argument="-Mascot_parameters:skip_spectrum_charges" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sometimes precursor charges are given for each spectrum but are wrong, setting this to 'true' does not write any charge information to the spectrum, the general charge information is however kept" help=""/>
       <param name="decoy" argument="-Mascot_parameters:decoy" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to true if mascot should generate the decoy database" help=""/>
-      <param name="search_title" argument="-Mascot_parameters:search_title" type="text" optional="true" value="OpenMS_search" label="Sets the title of the search" help="">
+      <param name="search_title" argument="-Mascot_parameters:search_title" type="text" value="OpenMS_search" label="Sets the title of the search" help="">
         <expand macro="list_string_san" name="search_title"/>
       </param>
-      <param name="username" argument="-Mascot_parameters:username" type="text" optional="true" value="OpenMS" label="Sets the username which is mentioned in the results file" help="">
+      <param name="username" argument="-Mascot_parameters:username" type="text" value="OpenMS" label="Sets the username which is mentioned in the results file" help="">
         <expand macro="list_string_san" name="username"/>
       </param>
       <param name="email" argument="-Mascot_parameters:email" type="text" optional="true" value="" label="Sets the email which is mentioned in the results file" help="Note: Some server require that a proper email is provided">
@@ -5962,19 +6035,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="hostname" argument="-Mascot_server:hostname" type="text" optional="true" value="" label="Address of the host where Mascot listens" help="e.g. 'mascot-server' or '127.0.0.1'">
         <expand macro="list_string_san" name="hostname"/>
       </param>
-      <param name="host_port" argument="-Mascot_server:host_port" type="integer" optional="true" min="0" value="80" label="Port where the Mascot server listens, 80 should be a good guess" help=""/>
-      <param name="server_path" argument="-Mascot_server:server_path" type="text" optional="true" value="mascot" label="Path on the server where Mascot server listens, 'mascot' should be a good guess" help="">
+      <param name="host_port" argument="-Mascot_server:host_port" type="integer" min="0" value="80" label="Port where the Mascot server listens, 80 should be a good guess" help=""/>
+      <param name="server_path" argument="-Mascot_server:server_path" type="text" value="mascot" label="Path on the server where Mascot server listens, 'mascot' should be a good guess" help="">
         <expand macro="list_string_san" name="server_path"/>
       </param>
-      <param name="timeout" argument="-Mascot_server:timeout" type="integer" optional="true" min="0" value="1500" label="Timeout in seconds, after which the query is declared as failed.This is NOT the whole time the search takes, but the time in between two progress steps" help="Some Mascot servers freeze during this (unstable network etc) and idle forever, the connection is killed. Set this to 0 to disable timeout!"/>
-      <param name="boundary" argument="-Mascot_server:boundary" type="text" optional="true" value="GZWgAaYKjHFeUaLOLEIOMq" label="Boundary for the MIME section" help="">
+      <param name="timeout" argument="-Mascot_server:timeout" type="integer" min="0" value="1500" label="Timeout in seconds, after which the query is declared as failed.This is NOT the whole time the search takes, but the time in between two progress steps" help="Some Mascot servers freeze during this (unstable network etc) and idle forever, the connection is killed. Set this to 0 to disable timeout!"/>
+      <param name="boundary" argument="-Mascot_server:boundary" type="text" value="GZWgAaYKjHFeUaLOLEIOMq" label="Boundary for the MIME section" help="">
         <expand macro="list_string_san" name="boundary"/>
       </param>
       <param name="use_proxy" argument="-Mascot_server:use_proxy" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag which enables the proxy usage for the HTTP requests, please specify at least 'proxy_host' and 'proxy_port'" help=""/>
       <param name="proxy_host" argument="-Mascot_server:proxy_host" type="text" optional="true" value="" label="Host where the proxy server runs on" help="">
         <expand macro="list_string_san" name="proxy_host"/>
       </param>
-      <param name="proxy_port" argument="-Mascot_server:proxy_port" type="integer" optional="true" min="0" value="0" label="Port where the proxy server listens" help=""/>
+      <param name="proxy_port" argument="-Mascot_server:proxy_port" type="integer" min="0" value="0" label="Port where the proxy server listens" help=""/>
       <param name="proxy_username" argument="-Mascot_server:proxy_username" type="text" optional="true" value="" label="Login name for the proxy server, if needed" help="">
         <expand macro="list_string_san" name="proxy_username"/>
       </param>
@@ -5989,15 +6062,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <expand macro="list_string_san" name="password"/>
       </param>
       <param name="use_ssl" argument="-Mascot_server:use_ssl" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag indicating whether you want to send requests to an HTTPS server or not (HTTP)" help="Requires OpenSSL to be installed (see openssl.org)"/>
-      <param name="export_params" argument="-Mascot_server:export_params" type="text" optional="true" value="_ignoreionsscorebelow=0&amp;_sigthreshold=0.99&amp;_showsubsets=1&amp;show_same_sets=1&amp;report=0&amp;percolate=0&amp;query_master=0" label="Adjustable export parameters (passed to Mascot's 'export_dat_2.pl' script)" help="Generally only parameters that control which hits to export are safe to adjust/add. Many settings that govern what types of information to include are required by OpenMS and cannot be changed. Note that setting 'query_master' to 1 may lead to incorrect protein references for peptides">
+      <param name="export_params" argument="-Mascot_server:export_params" type="text" value="_ignoreionsscorebelow=0&amp;_sigthreshold=0.99&amp;_showsubsets=1&amp;show_same_sets=1&amp;report=0&amp;percolate=0&amp;query_master=0" label="Adjustable export parameters (passed to Mascot's 'export_dat_2.pl' script)" help="Generally only parameters that control which hits to export are safe to adjust/add. Many settings that govern what types of information to include are required by OpenMS and cannot be changed. Note that setting 'query_master' to 1 may lead to incorrect protein references for peptides">
         <expand macro="list_string_san" name="export_params"/>
       </param>
       <param name="skip_export" argument="-Mascot_server:skip_export" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For use with an external Mascot Percolator (via GenericWrapper): Run the Mascot search, but do not export the results" help="The output file produced by MascotAdapterOnline will contain only the Mascot search number"/>
-      <param name="batch_size" argument="-Mascot_server:batch_size" type="integer" optional="true" min="0" value="50000" label="Number of spectra processed in one batch by Mascot (default 50000)" help=""/>
+      <param name="batch_size" argument="-Mascot_server:batch_size" type="integer" min="0" value="50000" label="Number of spectra processed in one batch by Mascot (default 50000)" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -6011,14 +6084,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MascotAdapterOnline_1 -->
+  <tests>
+    <!-- TOPP_MascotAdapterOnline_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="spectra_comet.mzML"/>
-      <output name="out" file="MascotAdapterOnline_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="MascotAdapterOnline_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <section name="Mascot_parameters">
         <param name="database" value="SwissProt"/>
         <param name="search_type" value="MIS"/>
@@ -6031,8 +6105,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="fragment_error_units" value="Da"/>
         <param name="charges" value="1,2,3"/>
         <param name="taxonomy" value="All entries"/>
-        <param name="fixed_modifications"/>
-        <param name="variable_modifications"/>
         <param name="special_modifications" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)"/>
         <param name="mass_type" value="monoisotopic"/>
         <param name="number_of_hits" value="0"/>
@@ -6067,6 +6139,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MascotAdapterOnline_2 -->
     <test expect_num_outputs="2">
@@ -6075,7 +6150,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="spectra_comet.mzML"/>
-      <output name="out" file="MascotAdapterOnline_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="MascotAdapterOnline_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <section name="Mascot_parameters">
         <param name="database" value="SwissProt"/>
         <param name="search_type" value="MIS"/>
@@ -6088,8 +6163,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="fragment_error_units" value="Da"/>
         <param name="charges" value="1,2,3"/>
         <param name="taxonomy" value="All entries"/>
-        <param name="fixed_modifications"/>
-        <param name="variable_modifications"/>
         <param name="special_modifications" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)"/>
         <param name="mass_type" value="monoisotopic"/>
         <param name="number_of_hits" value="0"/>
@@ -6124,11 +6197,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Annotates MS/MS spectra using Mascot.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MascotAdapterOnline.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MascotAdapterOnline.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MassCalculator.xml b/tools/openms/MassCalculator.xml
index e249320d1..7e4f396fa 100644
--- a/tools/openms/MassCalculator.xml
+++ b/tools/openms/MassCalculator.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Misc / Helpers]-->
 <tool id="MassCalculator" name="MassCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Calculates masses and mass-to-charge ratios of peptide sequences</description>
   <macros>
@@ -16,7 +15,7 @@
 ## Preprocessing
 #if $in:
   mkdir in &&
-  ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+  cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
@@ -57,10 +56,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <expand macro="list_string_val" name="in_seq"/>
       <expand macro="list_string_san" name="in_seq"/>
     </param>
-    <param argument="-charge" type="text" optional="true" value="0" label="List of charge states; required if 'in_seq' is given" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-charge" type="text" value="0" label="List of charge states; required if 'in_seq' is given" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_integer_valsan" name="charge"/>
     </param>
-    <param argument="-format" type="select" optional="true" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help="">
+    <param argument="-format" type="select" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help="">
       <option value="list" selected="true">list</option>
       <option value="table">table</option>
       <option value="mass_only">mass_only</option>
@@ -68,7 +67,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <expand macro="list_string_san" name="format"/>
     </param>
     <param argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) peptide masses" help=""/>
-    <param argument="-fragment_type" type="select" optional="true" label="For what type of sequence/fragment the mass should be computed" help="">
+    <param argument="-fragment_type" type="select" label="For what type of sequence/fragment the mass should be computed" help="">
       <option value="full" selected="true">full</option>
       <option value="internal">internal</option>
       <option value="N-terminal">N-terminal</option>
@@ -86,7 +85,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -106,15 +105,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_MassCalculator_1 -->
+  <tests>
+    <!-- TOPP_MassCalculator_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MassCalculator_1_input.tsv" ftype="tabular"/>
-      <param name="in_seq" value=""/>
-      <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out" value="MassCalculator_1_output.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="charge" value="0 1"/>
       <param name="format" value="table"/>
       <param name="average_mass" value="false"/>
@@ -126,15 +125,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_MassCalculator_2 -->
+    <!-- TOPP_MassCalculator_2 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in_seq" value="&quot;LDQWLC(Carbamidomethyl)EKL&quot; &quot;(Glu-&gt;pyro-Glu)EAM(Oxidation)APKHK&quot; &quot;RANVM(Oxidation)DYR&quot; &quot;FGVEQDVDMVFASFIR&quot;"/>
-      <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out" value="MassCalculator_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="charge" value="1 2 3"/>
       <param name="format" value="list"/>
       <param name="average_mass" value="false"/>
@@ -146,11 +148,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Calculates masses and mass-to-charge ratios of peptide sequences
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MassCalculator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MassCalculator.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MassTraceExtractor.xml b/tools/openms/MassTraceExtractor.xml
index d23adce9d..92f956e3f 100644
--- a/tools/openms/MassTraceExtractor.xml
+++ b/tools/openms/MassTraceExtractor.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Quantitation]-->
 <tool id="MassTraceExtractor" name="MassTraceExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Detects mass traces in centroided LC-MS data.</description>
+  <description>Detects mass traces in centroided LC-MS data</description>
   <macros>
     <token name="@EXECUTABLE@">MassTraceExtractor</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,53 +38,54 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input centroided mzML file" help=" select mzml data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="output file type -- default: determined from file extension or content" help="">
+    <param argument="-in" type="data" format="mzml" label="input centroided mzML file" help=" select mzml data sets(s)"/>
+    <param argument="-out_type" type="select" label="output file type -- default: determined from file extension or content" help="">
       <option value="consensusXML">consensusxml</option>
       <option value="featureXML">featurexml</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <section name="common" title="" help="" expanded="false">
-        <param name="noise_threshold_int" argument="-algorithm:common:noise_threshold_int" type="float" optional="true" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help=""/>
-        <param name="chrom_peak_snr" argument="-algorithm:common:chrom_peak_snr" type="float" optional="true" value="3.0" label="Minimum signal-to-noise a mass trace should have" help=""/>
-        <param name="chrom_fwhm" argument="-algorithm:common:chrom_fwhm" type="float" optional="true" value="5.0" label="Expected chromatographic peak width (in seconds)" help=""/>
+        <param name="noise_threshold_int" argument="-algorithm:common:noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help=""/>
+        <param name="chrom_peak_snr" argument="-algorithm:common:chrom_peak_snr" type="float" value="3.0" label="Minimum signal-to-noise a mass trace should have" help=""/>
+        <param name="chrom_fwhm" argument="-algorithm:common:chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)" help=""/>
       </section>
       <section name="mtd" title="" help="" expanded="false">
-        <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" optional="true" value="20.0" label="Allowed mass deviation (in ppm)" help=""/>
+        <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" value="20.0" label="Allowed mass deviation (in ppm)" help=""/>
         <param name="reestimate_mt_sd" argument="-algorithm:mtd:reestimate_mt_sd" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help=""/>
-        <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" optional="true" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace">
+        <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace">
           <option value="area" selected="true">area</option>
           <option value="median">median</option>
           <option value="max_height">max_height</option>
           <expand macro="list_string_san" name="quant_method"/>
         </param>
-        <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" optional="true" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
+        <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
           <option value="outlier" selected="true">outlier</option>
           <option value="sample_rate">sample_rate</option>
           <expand macro="list_string_san" name="trace_termination_criterion"/>
         </param>
-        <param name="trace_termination_outliers" argument="-algorithm:mtd:trace_termination_outliers" type="integer" optional="true" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help=""/>
-        <param name="min_sample_rate" argument="-algorithm:mtd:min_sample_rate" type="float" optional="true" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help=""/>
-        <param name="min_trace_length" argument="-algorithm:mtd:min_trace_length" type="float" optional="true" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help=""/>
-        <param name="max_trace_length" argument="-algorithm:mtd:max_trace_length" type="float" optional="true" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="Set to a negative value to disable maximal length check during mass trace detection"/>
+        <param name="trace_termination_outliers" argument="-algorithm:mtd:trace_termination_outliers" type="integer" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help=""/>
+        <param name="min_sample_rate" argument="-algorithm:mtd:min_sample_rate" type="float" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help=""/>
+        <param name="min_trace_length" argument="-algorithm:mtd:min_trace_length" type="float" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help=""/>
+        <param name="max_trace_length" argument="-algorithm:mtd:max_trace_length" type="float" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="Set to a negative value to disable maximal length check during mass trace detection"/>
       </section>
       <section name="epd" title="" help="" expanded="false">
-        <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" optional="true" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
+        <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
           <option value="off">off</option>
           <option value="fixed" selected="true">fixed</option>
           <option value="auto">auto</option>
           <expand macro="list_string_san" name="width_filtering"/>
         </param>
-        <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" optional="true" value="1.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
-        <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" optional="true" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
+        <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" value="1.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
+        <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
         <param name="masstrace_snr_filtering" argument="-algorithm:epd:masstrace_snr_filtering" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply post-filtering by signal-to-noise ratio after smoothing" help=""/>
         <param name="enabled" argument="-algorithm:epd:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables/disables the chromatographic peak detection of mass traces" help=""/>
       </section>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -103,14 +103,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MassTraceExtractor_1 -->
+  <tests>
+    <!-- TOPP_MassTraceExtractor_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MassTraceExtractor_1_input.mzML"/>
-      <output name="out" file="MassTraceExtractor_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="MassTraceExtractor_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <section name="algorithm">
         <section name="common">
@@ -142,6 +143,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MassTraceExtractor_2 -->
     <test expect_num_outputs="2">
@@ -150,7 +154,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MassTraceExtractor_1_input.mzML"/>
-      <output name="out" file="MassTraceExtractor_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="MassTraceExtractor_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="out_type" value="featureXML"/>
       <section name="algorithm">
         <section name="common">
@@ -182,11 +186,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Detects mass traces in centroided LC-MS data.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MassTraceExtractor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MassTraceExtractor.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MetaProSIP.xml b/tools/openms/MetaProSIP.xml
index 6b11e074b..d0bb51fdc 100644
--- a/tools/openms/MetaProSIP.xml
+++ b/tools/openms/MetaProSIP.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Quantitation]-->
 <tool id="MetaProSIP" name="MetaProSIP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
+  <description>Performs proteinSIP on peptide features for elemental flux analysis</description>
   <macros>
     <token name="@EXECUTABLE@">MetaProSIP</token>
     <import>macros.xml</import>
@@ -15,13 +14,13 @@
 
 ## Preprocessing
 mkdir in_mzML &&
-ln -s '$in_mzML' 'in_mzML/${re.sub("[^\w\-_]", "_", $in_mzML.element_identifier)}.$gxy2omsext($in_mzML.ext)' &&
+cp '$in_mzML' 'in_mzML/${re.sub("[^\w\-_]", "_", $in_mzML.element_identifier)}.$gxy2omsext($in_mzML.ext)' &&
 mkdir in_fasta &&
-ln -s '$in_fasta' 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)' &&
+cp '$in_fasta' 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)' &&
 mkdir out_csv &&
 mkdir out_peptide_centric_csv &&
 mkdir in_featureXML &&
-ln -s '$in_featureXML' 'in_featureXML/${re.sub("[^\w\-_]", "_", $in_featureXML.element_identifier)}.$gxy2omsext($in_featureXML.ext)' &&
+cp '$in_featureXML' 'in_featureXML/${re.sub("[^\w\-_]", "_", $in_featureXML.element_identifier)}.$gxy2omsext($in_featureXML.ext)' &&
 
 ## Main program call
 
@@ -51,17 +50,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"r_executable": "R", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in_mzML" type="data" format="mzml" optional="false" label="Centroided MS1 data" help=" select mzml data sets(s)"/>
-    <param argument="-in_fasta" type="data" format="fasta" optional="false" label="Protein sequence database" help=" select fasta data sets(s)"/>
-    <param argument="-in_featureXML" type="data" format="featurexml" optional="false" label="Feature data annotated with identifications (IDMapper)" help=" select featurexml data sets(s)"/>
-    <param argument="-mz_tolerance_ppm" type="float" optional="true" value="10.0" label="Tolerance in ppm" help=""/>
-    <param argument="-rt_tolerance_s" type="float" optional="true" value="30.0" label="Rolerance window around feature rt for XIC extraction" help=""/>
-    <param argument="-intensity_threshold" type="float" optional="true" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help=""/>
-    <param argument="-correlation_threshold" type="float" optional="true" value="0.7" label="Correlation threshold for reporting a RIA" help=""/>
-    <param argument="-xic_threshold" type="float" optional="true" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>
-    <param argument="-decomposition_threshold" type="float" optional="true" value="0.7" label="Minimum R-squared of decomposition that must be achieved for a peptide to be reported" help=""/>
-    <param argument="-weight_merge_window" type="float" optional="true" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help=""/>
-    <param argument="-plot_extension" type="select" optional="true" label="Extension used for plots (png|svg|pdf)" help="">
+    <param argument="-in_mzML" type="data" format="mzml" label="Centroided MS1 data" help=" select mzml data sets(s)"/>
+    <param argument="-in_fasta" type="data" format="fasta" label="Protein sequence database" help=" select fasta data sets(s)"/>
+    <param argument="-in_featureXML" type="data" format="featurexml" label="Feature data annotated with identifications (IDMapper)" help=" select featurexml data sets(s)"/>
+    <param argument="-mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help=""/>
+    <param argument="-rt_tolerance_s" type="float" value="30.0" label="Tolerance window around feature rt for XIC extraction" help=""/>
+    <param argument="-intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help=""/>
+    <param argument="-correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help=""/>
+    <param argument="-xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>
+    <param argument="-decomposition_threshold" type="float" value="0.7" label="Minimum R-squared of decomposition that must be achieved for a peptide to be reported" help=""/>
+    <param argument="-weight_merge_window" type="float" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help=""/>
+    <param argument="-plot_extension" type="select" label="Extension used for plots (png|svg|pdf)" help="">
       <option value="png" selected="true">png</option>
       <option value="svg">svg</option>
       <option value="pdf">pdf</option>
@@ -70,7 +69,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-qc_output_directory" type="text" optional="true" value="" label="Output directory for the quality report" help="">
       <expand macro="list_string_san" name="qc_output_directory"/>
     </param>
-    <param argument="-labeling_element" type="select" optional="true" label="Which element (single letter code) is labeled" help="">
+    <param argument="-labeling_element" type="select" label="Which element (single letter code) is labeled" help="">
       <option value="C" selected="true">C</option>
       <option value="N">N</option>
       <option value="H">H</option>
@@ -83,23 +82,23 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-filter_monoisotopic" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to filter out mono-isotopic patterns to improve detection of low RIA patterns" help=""/>
     <param argument="-cluster" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform grouping" help=""/>
     <expand macro="adv_opts_macro">
-      <param argument="-min_correlation_distance_to_averagine" type="float" optional="true" value="-1.0" label="Minimum difference in correlation between incorporation pattern and averagine pattern" help="Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values &lt;= -1"/>
-      <param argument="-pattern_15N_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
-      <param argument="-pattern_13C_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
-      <param argument="-pattern_2H_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
-      <param argument="-pattern_18O_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
-      <param argument="-heatmap_bins" type="integer" optional="true" value="20" label="Number of RIA bins for heat map generation" help=""/>
-      <param argument="-observed_peak_fraction" type="float" optional="true" value="0.5" label="Fraction of observed/expected peaks" help=""/>
-      <param argument="-min_consecutive_isotopes" type="integer" optional="true" value="2" label="Minimum number of consecutive isotopic intensities needed" help=""/>
-      <param argument="-score_plot_yaxis_min" type="float" optional="true" value="0.0" label="The minimum value of the score axis" help="Values smaller than zero usually only make sense if the observed peak fraction is set to 0"/>
-      <param argument="-collect_method" type="select" optional="true" label="How RIAs are collected" help="">
+      <param argument="-min_correlation_distance_to_averagine" type="float" value="-1.0" label="Minimum difference in correlation between incorporation pattern and averagine pattern" help="Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values &lt;= -1"/>
+      <param argument="-pattern_15N_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
+      <param argument="-pattern_13C_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
+      <param argument="-pattern_2H_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
+      <param argument="-pattern_18O_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
+      <param argument="-heatmap_bins" type="integer" value="20" label="Number of RIA bins for heat map generation" help=""/>
+      <param argument="-observed_peak_fraction" type="float" value="0.5" label="Fraction of observed/expected peaks" help=""/>
+      <param argument="-min_consecutive_isotopes" type="integer" value="2" label="Minimum number of consecutive isotopic intensities needed" help=""/>
+      <param argument="-score_plot_yaxis_min" type="float" value="0.0" label="The minimum value of the score axis" help="Values smaller than zero usually only make sense if the observed peak fraction is set to 0"/>
+      <param argument="-collect_method" type="select" label="How RIAs are collected" help="">
         <option value="correlation_maximum" selected="true">correlation_maximum</option>
         <option value="decomposition_maximum">decomposition_maximum</option>
         <expand macro="list_string_san" name="collect_method"/>
       </param>
-      <param argument="-lowRIA_correlation_threshold" type="float" optional="true" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="Disable and take correlation_threshold value for negative values"/>
+      <param argument="-lowRIA_correlation_threshold" type="float" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="Disable and take correlation_threshold value for negative values"/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -114,7 +113,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MetaProSIP_1 -->
+  <tests>
+    <!-- TOPP_MetaProSIP_1 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="min_correlation_distance_to_averagine" value="-1.0"/>
@@ -133,8 +133,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in_mzML" value="MetaProSIP_1_input.mzML"/>
       <param name="in_fasta" value="MetaProSIP_1_input.fasta"/>
-      <output name="out_csv" file="MetaProSIP_1_output_1.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out_csv" value="MetaProSIP_1_output_1.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out_peptide_centric_csv" value="MetaProSIP_1_output_2.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="in_featureXML" value="MetaProSIP_1_input.featureXML"/>
       <param name="mz_tolerance_ppm" value="10.0"/>
       <param name="rt_tolerance_s" value="30.0"/>
@@ -157,11 +157,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Performs proteinSIP on peptide features for elemental flux analysis.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MetaProSIP.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MetaProSIP.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MetaboliteAdductDecharger.xml b/tools/openms/MetaboliteAdductDecharger.xml
deleted file mode 100644
index 42e72b19e..000000000
--- a/tools/openms/MetaboliteAdductDecharger.xml
+++ /dev/null
@@ -1,216 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
-<tool id="MetaboliteAdductDecharger" name="MetaboliteAdductDecharger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Decharges and merges different feature charge variants of the same metabolite.</description>
-  <macros>
-    <token name="@EXECUTABLE@">MetaboliteAdductDecharger</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-#if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out_cm &&
-#end if
-#if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out_fm &&
-#end if
-#if "outpairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir outpairs &&
-#end if
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in
-'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-#if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out_cm
-  'out_cm/output.${gxy2omsext("consensusxml")}'
-#end if
-#if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out_fm
-  'out_fm/output.${gxy2omsext("featurexml")}'
-#end if
-#if "outpairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -outpairs
-  'outpairs/output.${gxy2omsext("consensusxml")}'
-#end if
-#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
-  | tee '$stdout'
-#end if
-
-## Postprocessing
-#if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
-#end if
-#if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out_fm/output.${gxy2omsext("featurexml")}' '$out_fm'
-#end if
-#if "outpairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'outpairs/output.${gxy2omsext("consensusxml")}' '$outpairs'
-#end if
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
-  </configfiles>
-  <inputs>
-    <param argument="-in" type="data" format="featurexml" optional="false" label="input file" help=" select featurexml data sets(s)"/>
-    <section name="algorithm" title="Feature decharging algorithm section" help="" expanded="false">
-      <section name="MetaboliteFeatureDeconvolution" title="" help="" expanded="false">
-        <param name="charge_min" argument="-algorithm:MetaboliteFeatureDeconvolution:charge_min" type="integer" optional="true" value="1" label="Minimal possible charge" help=""/>
-        <param name="charge_max" argument="-algorithm:MetaboliteFeatureDeconvolution:charge_max" type="integer" optional="true" value="3" label="Maximal possible charge" help=""/>
-        <param name="charge_span_max" argument="-algorithm:MetaboliteFeatureDeconvolution:charge_span_max" type="integer" optional="true" min="1" value="3" label="Maximal range of charges for a single analyte" help="i.e. observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge"/>
-        <param name="q_try" argument="-algorithm:MetaboliteFeatureDeconvolution:q_try" type="select" optional="true" label="Try different values of charge for each feature according to the above settings ('heuristic' [does not test all charges, just the likely ones] or 'all' ), or leave feature charge untouched ('feature')" help="">
-          <option value="feature" selected="true">feature</option>
-          <option value="heuristic">heuristic</option>
-          <option value="all">all</option>
-          <expand macro="list_string_san" name="q_try"/>
-        </param>
-        <param name="retention_max_diff" argument="-algorithm:MetaboliteFeatureDeconvolution:retention_max_diff" type="float" optional="true" value="1.0" label="Maximum allowed RT difference between any two features if their relation shall be determined" help=""/>
-        <param name="retention_max_diff_local" argument="-algorithm:MetaboliteFeatureDeconvolution:retention_max_diff_local" type="float" optional="true" value="1.0" label="Maximum allowed RT difference between between two co-features, after adduct shifts have been accounted for (if you do not have any adduct shifts, this value should be equal to 'retention_max_diff', otherwise it should be smaller!)" help=""/>
-        <param name="mass_max_diff" argument="-algorithm:MetaboliteFeatureDeconvolution:mass_max_diff" type="float" optional="true" min="0.0" value="0.05" label="Maximum allowed mass tolerance per feature" help="Defines a symmetric tolerance window around the feature. When looking at possible feature pairs, the allowed feature-wise errors are combined for consideration of possible adduct shifts. For ppm tolerances, each window is based on the respective observed feature mz (instead of putative experimental mzs causing the observed one)!"/>
-        <param name="unit" argument="-algorithm:MetaboliteFeatureDeconvolution:unit" type="select" optional="true" label="Unit of the 'max_difference' paramete" help="">
-          <option value="Da" selected="true">Da</option>
-          <option value="ppm">ppm</option>
-          <expand macro="list_string_san" name="unit"/>
-        </param>
-        <param name="potential_adducts" argument="-algorithm:MetaboliteFeatureDeconvolution:potential_adducts" type="text" optional="true" value="H:+:0.4 Na:+:0.25 NH4:+:0.25 K:+:0.1 H-2O-1:0:0.05" label="Adducts used to explain mass differences in format: 'Elements:Charge(+/-/0):Probability[:RTShift[:Label]]'" help="i.e. the number of '+' or '-' indicate the charge ('0' if neutral adduct), e.g. 'Ca:++:0.5' indicates +2. Probabilites have to be in (0,1]. The optional RTShift param indicates the expected RT shift caused by this adduct, e.g. '(2)H4H-4:0:1:-3' indicates a 4 deuterium label, which causes early elution by 3 seconds. As fifth parameter you can add a label for every feature with this adduct. This also determines the map number in the consensus file. Adduct element losses are written in the form 'H-2'. All provided adducts need to have the same charge sign or be neutral! Mixing of adducts with different charge directions is only allowed as neutral complexes. For example, 'H-1Na:0:0.05' can be used to model Sodium gains (with balancing deprotonation) in negative mode (space separated list, in order to allow for spaces in list items surround them by single quotes)">
-          <expand macro="list_string_val" name="potential_adducts"/>
-          <expand macro="list_string_san" name="potential_adducts"/>
-        </param>
-        <param name="max_neutrals" argument="-algorithm:MetaboliteFeatureDeconvolution:max_neutrals" type="integer" optional="true" value="1" label="Maximal number of neutral adducts(q=0) allowed" help="Add them in the 'potential_adducts' section!"/>
-        <param name="use_minority_bound" argument="-algorithm:MetaboliteFeatureDeconvolution:use_minority_bound" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Prune the considered adduct transitions by transition probabilities" help=""/>
-        <param name="max_minority_bound" argument="-algorithm:MetaboliteFeatureDeconvolution:max_minority_bound" type="integer" optional="true" min="0" value="3" label="Limits allowed adduct compositions and changes between compositions in the underlying graph optimization problem by introducing a probability-based threshold: the minority bound sets the maximum count of the least probable adduct (according to 'potential_adducts' param) within a charge variant with maximum charge only containing the most likely adduct otherwise" help="E.g., for 'charge_max' 4 and 'max_minority_bound' 2 with most probable adduct being H+ and least probable adduct being Na+, this will allow adduct compositions of '2(H+),2(Na+)' but not of '1(H+),3(Na+)'. Further, adduct compositions/changes less likely than '2(H+),2(Na+)' will be discarded as well"/>
-        <param name="min_rt_overlap" argument="-algorithm:MetaboliteFeatureDeconvolution:min_rt_overlap" type="float" optional="true" min="0.0" max="1.0" value="0.66" label="Minimum overlap of the convex hull' RT intersection measured against the union from two features (if CHs are given)" help=""/>
-        <param name="intensity_filter" argument="-algorithm:MetaboliteFeatureDeconvolution:intensity_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable the intensity filter, which will only allow edges between two equally charged features if the intensity of the feature with less likely adducts is smaller than that of the other feature" help="It is not used for features of different charge"/>
-        <param name="negative_mode" argument="-algorithm:MetaboliteFeatureDeconvolution:negative_mode" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable negative ionization mode" help=""/>
-        <param name="default_map_label" argument="-algorithm:MetaboliteFeatureDeconvolution:default_map_label" type="text" optional="true" value="decharged features" label="Label of map in output consensus file where all features are put by default" help="">
-          <expand macro="list_string_san" name="default_map_label"/>
-        </param>
-        <param name="verbose_level" argument="-algorithm:MetaboliteFeatureDeconvolution:verbose_level" type="integer" optional="true" min="0" max="3" value="0" label="Amount of debug information given during processing" help=""/>
-      </section>
-    </section>
-    <expand macro="adv_opts_macro">
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="out_cm_FLAG">out_cm (output consensus map)</option>
-      <option value="out_fm_FLAG">out_fm (output feature map)</option>
-      <option value="outpairs_FLAG">outpairs (output file)</option>
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="out_fm" label="${tool.name} on ${on_string}: out_fm" format="featurexml">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_fm_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="outpairs" label="${tool.name} on ${on_string}: outpairs" format="consensusxml">
-      <filter>OPTIONAL_OUTPUTS is not None and "outpairs_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
-      <filter>OPTIONAL_OUTPUTS is None</filter>
-    </data>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><!-- TOPP_MetaboliteAdductDecharger_1 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/>
-      <output name="out_fm" file="MetaboliteAdductDecharger_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <section name="algorithm">
-        <section name="MetaboliteFeatureDeconvolution">
-          <param name="charge_min" value="1"/>
-          <param name="charge_max" value="3"/>
-          <param name="charge_span_max" value="3"/>
-          <param name="q_try" value="feature"/>
-          <param name="retention_max_diff" value="1.0"/>
-          <param name="retention_max_diff_local" value="1.0"/>
-          <param name="mass_max_diff" value="0.05"/>
-          <param name="unit" value="Da"/>
-          <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
-          <param name="max_neutrals" value="1"/>
-          <param name="use_minority_bound" value="true"/>
-          <param name="max_minority_bound" value="3"/>
-          <param name="min_rt_overlap" value="0.66"/>
-          <param name="intensity_filter" value="false"/>
-          <param name="negative_mode" value="false"/>
-          <param name="default_map_label" value="decharged features"/>
-          <param name="verbose_level" value="0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_MetaboliteAdductDecharger_2 -->
-    <test expect_num_outputs="3">
-      <section name="adv_opts">
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/>
-      <output name="out_cm" file="MetaboliteAdductDecharger_2_output_1.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
-      <output name="outpairs" file="MetaboliteAdductDecharger_2_output_2.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
-      <section name="algorithm">
-        <section name="MetaboliteFeatureDeconvolution">
-          <param name="charge_min" value="1"/>
-          <param name="charge_max" value="3"/>
-          <param name="charge_span_max" value="3"/>
-          <param name="q_try" value="feature"/>
-          <param name="retention_max_diff" value="1.0"/>
-          <param name="retention_max_diff_local" value="1.0"/>
-          <param name="mass_max_diff" value="0.05"/>
-          <param name="unit" value="Da"/>
-          <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
-          <param name="max_neutrals" value="1"/>
-          <param name="use_minority_bound" value="true"/>
-          <param name="max_minority_bound" value="3"/>
-          <param name="min_rt_overlap" value="0.66"/>
-          <param name="intensity_filter" value="false"/>
-          <param name="negative_mode" value="false"/>
-          <param name="default_map_label" value="decharged features"/>
-          <param name="verbose_level" value="0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG,outpairs_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
-  <help><![CDATA[Decharges and merges different feature charge variants of the same metabolite.
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MetaboliteAdductDecharger.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/MetaboliteSpectralMatcher.xml b/tools/openms/MetaboliteSpectralMatcher.xml
index 1bfcd755d..6df40a19c 100644
--- a/tools/openms/MetaboliteSpectralMatcher.xml
+++ b/tools/openms/MetaboliteSpectralMatcher.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Metabolite Identification]-->
 <tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Perform a spectral library search.</description>
+  <description>Perform a spectral library search</description>
   <macros>
     <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</token>
     <import>macros.xml</import>
@@ -15,10 +14,13 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir database &&
-ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
 mkdir out &&
+#if "out_spectra_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_spectra &&
+#end if
 
 ## Main program call
 
@@ -32,9 +34,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
 -out
 'out/output.${gxy2omsext("mztab")}'
+#if "out_spectra_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_spectra
+  'out_spectra/output.${gxy2omsext("mzml")}'
+#end if
+#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
+  | tee '$stdout'
+#end if
 
 ## Postprocessing
 && mv 'out/output.${gxy2omsext("mztab")}' '$out'
+#if "out_spectra_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_spectra/output.${gxy2omsext("mzml")}' '$out_spectra'
+#end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
@@ -43,54 +55,61 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input spectra" help=" select mzml data sets(s)"/>
-    <param argument="-database" type="data" format="mzml" optional="false" label="Default spectral database" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Input spectra" help=" select mzml data sets(s)"/>
+    <param argument="-database" type="data" format="mgf,msp,mzml" label="Default spectral database" help=" select mgf,msp,mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="prec_mass_error_value" argument="-algorithm:prec_mass_error_value" type="float" optional="true" value="100.0" label="Error allowed for precursor ion mass" help=""/>
-      <param name="frag_mass_error_value" argument="-algorithm:frag_mass_error_value" type="float" optional="true" value="500.0" label="Error allowed for product ions" help=""/>
-      <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="true" label="Unit of mass error (ppm or Da)" help="">
+      <param name="prec_mass_error_value" argument="-algorithm:prec_mass_error_value" type="float" value="100.0" label="Error allowed for precursor ion mass" help=""/>
+      <param name="frag_mass_error_value" argument="-algorithm:frag_mass_error_value" type="float" value="500.0" label="Error allowed for product ions" help=""/>
+      <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" label="Unit of mass error (ppm or Da)" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_error_unit"/>
       </param>
-      <param name="report_mode" argument="-algorithm:report_mode" type="select" optional="true" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="">
+      <param name="report_mode" argument="-algorithm:report_mode" type="select" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="">
         <option value="top3" selected="true">top3</option>
         <option value="best">best</option>
         <expand macro="list_string_san" name="report_mode"/>
       </param>
-      <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="true" label="Positive or negative ionization mode?" help="">
+      <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" label="Positive or negative ionization mode?" help="">
         <option value="positive" selected="true">positive</option>
         <option value="negative">negative</option>
         <expand macro="list_string_san" name="ionization_mode"/>
       </param>
+      <param name="merge_spectra" argument="-algorithm:merge_spectra" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Merge MS2 spectra with the same precursor mass" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="out_spectra_FLAG">out_spectra (Output spectra as mzML file)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
   <outputs>
     <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
+    <data name="out_spectra" label="${tool.name} on ${on_string}: out_spectra" format="mzml">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_spectra_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML -->
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="spectra.mzML"/>
-    <param name="database" value="MetaboliteSpectralDB.mzML"/>
-    <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/>
-  </test>
-</tests>
+  <tests>
+    <!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML -->
+    <test expect_num_outputs="1">
+      <!-- same input as used in the MSGF+Adapter, used as input and database -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="mzml" value="spectra.mzML"/>
+      <param name="database" value="MetaboliteSpectralDB.mzML"/>
+      <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/>
+    </test>
+  </tests>
   <help><![CDATA[Perform a spectral library search.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MetaboliteSpectralMatcher.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MetaboliteSpectralMatcher.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MultiplexResolver.xml b/tools/openms/MultiplexResolver.xml
index 5c49bd812..a3406fdc9 100644
--- a/tools/openms/MultiplexResolver.xml
+++ b/tools/openms/MultiplexResolver.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Quantitation]-->
 <tool id="MultiplexResolver" name="MultiplexResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Completes peptide multiplets and resolves conflicts within them.</description>
+  <description>Completes peptide multiplets and resolves conflicts within them</description>
   <macros>
     <token name="@EXECUTABLE@">MultiplexResolver</token>
     <import>macros.xml</import>
@@ -15,10 +14,10 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #if $in_blacklist:
   mkdir in_blacklist &&
-  ln -s '$in_blacklist' 'in_blacklist/${re.sub("[^\w\-_]", "_", $in_blacklist.element_identifier)}.$gxy2omsext($in_blacklist.ext)' &&
+  cp '$in_blacklist' 'in_blacklist/${re.sub("[^\w\-_]", "_", $in_blacklist.element_identifier)}.$gxy2omsext($in_blacklist.ext)' &&
 #end if
 mkdir out &&
 #if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
@@ -60,36 +59,36 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml" optional="false" label="Peptide multiplets with assigned sequence information" help=" select consensusxml data sets(s)"/>
+    <param argument="-in" type="data" format="consensusxml" label="Peptide multiplets with assigned sequence information" help=" select consensusxml data sets(s)"/>
     <param argument="-in_blacklist" type="data" format="mzml" optional="true" label="Optional input containing spectral peaks blacklisted during feature detection" help="Needed for generation of dummy features select mzml data sets(s)"/>
     <section name="algorithm" title="Parameters for the algorithm" help="" expanded="false">
-      <param name="labels" argument="-algorithm:labels" type="text" optional="true" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="[...] specifies the labels for a single sample. For example.  [][Lys8,Arg10]        ... SILAC. [][Lys4,Arg6][Lys8,Arg10]        ... triple-SILAC. [Dimethyl0][Dimethyl6]        ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8]        ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10]        ... ICPL">
+      <param name="labels" argument="-algorithm:labels" type="text" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="[...] specifies the labels for a single sample. For example.  [][Lys8,Arg10]        ... SILAC. [][Lys4,Arg6][Lys8,Arg10]        ... triple-SILAC. [Dimethyl0][Dimethyl6]        ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8]        ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10]        ... ICPL">
         <expand macro="list_string_san" name="labels"/>
       </param>
-      <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
-      <param name="mass_tolerance" argument="-algorithm:mass_tolerance" type="float" optional="true" value="0.1" label="Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern" help=""/>
-      <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="integer" optional="true" value="10" label="m/z tolerance in ppm for checking if dummy feature vicinity was blacklisted" help=""/>
-      <param name="rt_tolerance" argument="-algorithm:rt_tolerance" type="integer" optional="true" value="5" label="Retention time tolerance in seconds for checking if dummy feature vicinity was blacklisted" help=""/>
+      <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
+      <param name="mass_tolerance" argument="-algorithm:mass_tolerance" type="float" value="0.1" label="Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern" help=""/>
+      <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="integer" value="10" label="m/z tolerance in ppm for checking if dummy feature vicinity was blacklisted" help=""/>
+      <param name="rt_tolerance" argument="-algorithm:rt_tolerance" type="integer" value="5" label="Retention time tolerance in seconds for checking if dummy feature vicinity was blacklisted" help=""/>
     </section>
     <section name="labels" title="Isotopic labels that can be specified in section 'algorithm:labels'" help="" expanded="false">
-      <param name="Arg6" argument="-labels:Arg6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help=""/>
-      <param name="Arg10" argument="-labels:Arg10" type="float" optional="true" min="0.0" value="10.0082686" label="Label:13C(6)15N(4)  |  C(-6) 13C(6) N(-4) 15N(4)  |  unimod #267" help=""/>
-      <param name="Lys4" argument="-labels:Lys4" type="float" optional="true" min="0.0" value="4.0251069836" label="Label:2H(4)  |  H(-4) 2H(4)  |  unimod #481" help=""/>
-      <param name="Lys6" argument="-labels:Lys6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help=""/>
-      <param name="Lys8" argument="-labels:Lys8" type="float" optional="true" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2)  |  C(-6) 13C(6) N(-2) 15N(2)  |  unimod #259" help=""/>
-      <param name="Leu3" argument="-labels:Leu3" type="float" optional="true" min="0.0" value="3.01883" label="Label:2H(3)  |  H(-3) 2H(3)  |  unimod #262" help=""/>
-      <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" optional="true" min="0.0" value="28.0313" label="Dimethyl  |  H(4) C(2)  |  unimod #36" help=""/>
-      <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" optional="true" min="0.0" value="32.056407" label="Dimethyl:2H(4)  |  2H(4) C(2)  |  unimod #199" help=""/>
-      <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" optional="true" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2)  |  2H(4) 13C(2)  |  unimod #510" help=""/>
-      <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" optional="true" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2)  |  H(-2) 2H(6) 13C(2)  |  unimod #330" help=""/>
-      <param name="ICPL0" argument="-labels:ICPL0" type="float" optional="true" min="0.0" value="105.021464" label="ICPL  |  H(3) C(6) N O  |  unimod #365" help=""/>
-      <param name="ICPL4" argument="-labels:ICPL4" type="float" optional="true" min="0.0" value="109.046571" label="ICPL:2H(4)  |  H(-1) 2H(4) C(6) N O  |  unimod #687" help=""/>
-      <param name="ICPL6" argument="-labels:ICPL6" type="float" optional="true" min="0.0" value="111.041593" label="ICPL:13C(6)  |  H(3) 13C(6) N O  |  unimod #364" help=""/>
-      <param name="ICPL10" argument="-labels:ICPL10" type="float" optional="true" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4)  |  H(-1) 2H(4) 13C(6) N O  |  unimod #866" help=""/>
+      <param name="Arg6" argument="-labels:Arg6" type="float" min="0.0" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help=""/>
+      <param name="Arg10" argument="-labels:Arg10" type="float" min="0.0" value="10.0082686" label="Label:13C(6)15N(4)  |  C(-6) 13C(6) N(-4) 15N(4)  |  unimod #267" help=""/>
+      <param name="Lys4" argument="-labels:Lys4" type="float" min="0.0" value="4.0251069836" label="Label:2H(4)  |  H(-4) 2H(4)  |  unimod #481" help=""/>
+      <param name="Lys6" argument="-labels:Lys6" type="float" min="0.0" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help=""/>
+      <param name="Lys8" argument="-labels:Lys8" type="float" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2)  |  C(-6) 13C(6) N(-2) 15N(2)  |  unimod #259" help=""/>
+      <param name="Leu3" argument="-labels:Leu3" type="float" min="0.0" value="3.01883" label="Label:2H(3)  |  H(-3) 2H(3)  |  unimod #262" help=""/>
+      <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" min="0.0" value="28.0313" label="Dimethyl  |  H(4) C(2)  |  unimod #36" help=""/>
+      <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" min="0.0" value="32.056407" label="Dimethyl:2H(4)  |  2H(4) C(2)  |  unimod #199" help=""/>
+      <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2)  |  2H(4) 13C(2)  |  unimod #510" help=""/>
+      <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2)  |  H(-2) 2H(6) 13C(2)  |  unimod #330" help=""/>
+      <param name="ICPL0" argument="-labels:ICPL0" type="float" min="0.0" value="105.021464" label="ICPL  |  H(3) C(6) N O  |  unimod #365" help=""/>
+      <param name="ICPL4" argument="-labels:ICPL4" type="float" min="0.0" value="109.046571" label="ICPL:2H(4)  |  H(-1) 2H(4) C(6) N O  |  unimod #687" help=""/>
+      <param name="ICPL6" argument="-labels:ICPL6" type="float" min="0.0" value="111.041593" label="ICPL:13C(6)  |  H(3) 13C(6) N O  |  unimod #364" help=""/>
+      <param name="ICPL10" argument="-labels:ICPL10" type="float" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4)  |  H(-1) 2H(4) 13C(6) N O  |  unimod #866" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -107,15 +106,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_MultiplexResolver_1 -->
+  <tests>
+    <!-- TOPP_MultiplexResolver_1 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MultiplexResolver_1_input.consensusXML"/>
-      <output name="out" file="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
-      <output name="out_conflicts" file="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out_conflicts" value="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="labels" value="[][Lys4,Arg6][Lys8,Arg10]"/>
         <param name="missed_cleavages" value="1"/>
@@ -145,16 +145,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_MultiplexResolver_2 -->
+    <!-- TOPP_MultiplexResolver_2 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MultiplexResolver_2_input.consensusXML"/>
-      <output name="out" file="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
-      <output name="out_conflicts" file="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out_conflicts" value="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
         <param name="missed_cleavages" value="4"/>
@@ -184,16 +187,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_MultiplexResolver_3 -->
+    <!-- TOPP_MultiplexResolver_3 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MultiplexResolver_3_input.consensusXML"/>
-      <output name="out" file="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
-      <output name="out_conflicts" file="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out_conflicts" value="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="labels" value="[][Leu3]"/>
         <param name="missed_cleavages" value="2"/>
@@ -223,8 +229,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_MultiplexResolver_4 -->
+    <!-- TOPP_MultiplexResolver_4 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -232,8 +241,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="MultiplexResolver_4_input.consensusXML"/>
       <param name="in_blacklist" value="MultiplexResolver_4_input.mzML"/>
-      <output name="out" file="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
-      <output name="out_conflicts" file="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out_conflicts" value="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <section name="algorithm">
         <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
         <param name="missed_cleavages" value="3"/>
@@ -263,11 +272,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Completes peptide multiplets and resolves conflicts within them.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MultiplexResolver.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MultiplexResolver.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MzMLSplitter.xml b/tools/openms/MzMLSplitter.xml
index 9edf27819..77d12fff0 100644
--- a/tools/openms/MzMLSplitter.xml
+++ b/tools/openms/MzMLSplitter.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="MzMLSplitter" name="MzMLSplitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Splits an mzML file into multiple parts</description>
   <macros>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -38,10 +37,10 @@ out/
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
-    <param argument="-parts" type="integer" optional="true" min="1" value="1" label="Number of parts to split into (takes precedence over 'size' if set)" help=""/>
-    <param argument="-size" type="integer" optional="true" min="0" value="0" label="Approximate upper limit for resulting file sizes (in 'unit')" help=""/>
-    <param argument="-unit" type="select" optional="true" label="Unit for 'size' (base 1024)" help="">
+    <param argument="-in" type="data" format="mzml" label="Input file" help=" select mzml data sets(s)"/>
+    <param argument="-parts" type="integer" min="1" value="1" label="Number of parts to split into (takes precedence over 'size' if set)" help=""/>
+    <param argument="-size" type="integer" min="0" value="0" label="Approximate upper limit for resulting file sizes (in 'unit')" help=""/>
+    <param argument="-unit" type="select" label="Unit for 'size' (base 1024)" help="">
       <option value="KB">KB</option>
       <option value="MB" selected="true">MB</option>
       <option value="GB">GB</option>
@@ -51,7 +50,7 @@ out/
     <param argument="-no_spec" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove spectra, keep only chromatograms" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -67,54 +66,55 @@ out/
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_MzMLSplitter_1 -->
-    <!-- UTILS_MzMLSplitter_2 -->
-  <test expect_num_outputs="2">
-  <section name="adv_opts">
-    <param name="test" value="true"/>
-  </section>
-  <param name="in" value="FileFilter_1_input.mzML"/>
-  <param name="parts" value="2"/>
-  <param name="size" value="0"/>
-  <param name="unit" value="MB"/>
-  <param name="no_chrom" value="false"/>
-  <param name="no_spec" value="false"/>
-  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-  <output_collection name="out" type="list" count="2">
-    <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/>
-    <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/>
-  </output_collection>
-</test>
-<test expect_num_outputs="2">
-  <section name="adv_opts">
-    <param name="test" value="true"/>
-  </section>
-  <param name="in" value="FileFilter_1_input.mzML"/>
-  <param name="parts" value="1"/>
-  <param name="size" value="40"/>
-  <param name="unit" value="KB"/>
-  <param name="no_chrom" value="false"/>
-  <param name="no_spec" value="false"/>
-  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-  <output_collection name="out" type="list" count="2">
-    <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/>
-    <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/>
-  </output_collection>
-</test>
-</tests>
+  <tests>
+    <!-- TOPP_MzMLSplitter_1 -->
+    <!-- TOPP_MzMLSplitter_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="FileFilter_1_input.mzML"/>
+      <param name="parts" value="2"/>
+      <param name="size" value="0"/>
+      <param name="unit" value="MB"/>
+      <param name="no_chrom" value="false"/>
+      <param name="no_spec" value="false"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <output_collection name="out" type="list" count="2">
+        <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/>
+        <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/>
+      </output_collection>
+    </test>
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="FileFilter_1_input.mzML"/>
+      <param name="parts" value="1"/>
+      <param name="size" value="40"/>
+      <param name="unit" value="KB"/>
+      <param name="no_chrom" value="false"/>
+      <param name="no_spec" value="false"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <output_collection name="out" type="list" count="2">
+        <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/>
+        <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/>
+      </output_collection>
+    </test>
+  </tests>
   <help><![CDATA[Splits an mzML file into multiple parts
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MzMLSplitter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MzMLSplitter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/MzTabExporter.xml b/tools/openms/MzTabExporter.xml
index 7b083641f..34c22f633 100644
--- a/tools/openms/MzTabExporter.xml
+++ b/tools/openms/MzTabExporter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [File Handling]-->
+<!--Proposed Tool Section: [File Converter]-->
 <tool id="MzTabExporter" name="MzTabExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Exports various XML formats to an mzTab file.</description>
+  <description>Exports various XML formats to an mzTab file</description>
   <macros>
     <token name="@EXECUTABLE@">MzTabExporter</token>
     <import>macros.xml</import>
@@ -16,7 +15,7 @@
 ## Preprocessing
 #if $in:
   mkdir in &&
-  ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+  cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #end if
 mkdir out &&
 
@@ -44,7 +43,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzid" optional="true" label="Input files used to generate the mzTab file" help=" select consensusxml,featurexml,idxml,mzid data sets(s)"/>
-    <param argument="-opt_columns" display="checkboxes" multiple="true" type="select" optional="true" label="Add optional columns which are not part of the mzTab standard" help="">
+    <param argument="-opt_columns" type="select" multiple="true" optional="false" label="Add optional columns which are not part of the mzTab standard" help="">
       <option value="subfeatures" selected="true">subfeatures</option>
       <expand macro="list_string_san" name="opt_columns"/>
     </param>
@@ -52,7 +51,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param argument="-first_run_inference_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Does the first IdentificationRun in the file only represent (protein) inference results" help="If so, read peptide information only from second to last runs"/>
       <param argument="-export_all_psms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Export all PSMs instead of only the best per spectrum" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -66,7 +65,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MzTabExporter_1 -->
+  <tests>
+    <!-- TOPP_MzTabExporter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="first_run_inference_only" value="false"/>
@@ -75,7 +75,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MzTabExporter_1_input.consensusXML"/>
-      <output name="out" file="MzTabExporter_1_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="out" value="MzTabExporter_1_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
       <param name="opt_columns" value="subfeatures"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -83,6 +83,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MzTabExporter_2 -->
     <test expect_num_outputs="2">
@@ -93,7 +96,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MzTabExporter_2_input.idXML"/>
-      <output name="out" file="MzTabExporter_2_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="out" value="MzTabExporter_2_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
       <param name="opt_columns" value="subfeatures"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -101,6 +104,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MzTabExporter_3 -->
     <test expect_num_outputs="2">
@@ -111,7 +117,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MzTabExporter_3_input.featureXML"/>
-      <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="out" value="MzTabExporter_3_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
       <param name="opt_columns" value="subfeatures"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -119,6 +125,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MzTabExporter_4 -->
     <test expect_num_outputs="2">
@@ -129,7 +138,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="Epifany_2_out.consensusXML"/>
-      <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="out" value="MzTabExporter_4_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
       <param name="opt_columns" value="subfeatures"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -137,6 +146,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MzTabExporter_5 -->
     <test expect_num_outputs="2">
@@ -147,7 +159,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MzTabExporter_5_in.consensusXML"/>
-      <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="out" value="MzTabExporter_5_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
       <param name="opt_columns" value="subfeatures"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -155,6 +167,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MzTabExporter_6 -->
     <test expect_num_outputs="2">
@@ -165,7 +180,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MzTabExporter_6_input.idXML"/>
-      <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="out" value="MzTabExporter_6_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
       <param name="opt_columns" value="subfeatures"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -173,6 +188,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MzTabExporter_7 -->
     <test expect_num_outputs="2">
@@ -183,7 +201,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MzTabExporter_7_input.consensusXML"/>
-      <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="out" value="MzTabExporter_7_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
       <param name="opt_columns" value="subfeatures"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -191,6 +209,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_MzTabExporter_8 -->
     <test expect_num_outputs="2">
@@ -201,7 +222,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MzTabExporter_6_input.idXML"/>
-      <output name="out" file="MzTabExporter_8_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="out" value="MzTabExporter_8_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
       <param name="opt_columns" value="subfeatures"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -209,11 +230,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Exports various XML formats to an mzTab file.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MzTabExporter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MzTabExporter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/NoiseFilterGaussian.xml b/tools/openms/NoiseFilterGaussian.xml
index 0141b5923..0b412f7f0 100644
--- a/tools/openms/NoiseFilterGaussian.xml
+++ b/tools/openms/NoiseFilterGaussian.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="NoiseFilterGaussian" name="NoiseFilterGaussian" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).</description>
+  <description>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data)</description>
   <macros>
     <token name="@EXECUTABLE@">NoiseFilterGaussian</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,21 +38,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input raw data file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="gaussian_width" argument="-algorithm:gaussian_width" type="float" optional="true" value="0.2" label="Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z)" help=""/>
-      <param name="ppm_tolerance" argument="-algorithm:ppm_tolerance" type="float" optional="true" value="10.0" label="Gaussian width, depending on the m/z position" help="The higher the value, the wider the peak and therefore the wider the gaussian"/>
+      <param name="gaussian_width" argument="-algorithm:gaussian_width" type="float" value="0.2" label="Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z)" help=""/>
+      <param name="ppm_tolerance" argument="-algorithm:ppm_tolerance" type="float" value="10.0" label="Gaussian width, depending on the m/z position" help="The higher the value, the wider the peak and therefore the wider the gaussian"/>
       <param name="use_ppm_tolerance" argument="-algorithm:use_ppm_tolerance" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, instead of the gaussian_width value, the ppm_tolerance is used" help="The gaussian is calculated in each step anew, so this is much slower"/>
       <param name="write_log_messages" argument="-algorithm:write_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="true: Warn if no signal was found by the Gauss filter algorithm" help=""/>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-processOption" type="select" optional="true" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
+      <param argument="-processOption" type="select" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
         <option value="inmemory" selected="true">inmemory</option>
         <option value="lowmemory">lowmemory</option>
         <expand macro="list_string_san" name="processOption"/>
       </param>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -67,7 +66,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_NoiseFilterGaussian_1 -->
+  <tests>
+    <!-- TOPP_NoiseFilterGaussian_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="processOption" value="inmemory"/>
@@ -75,7 +75,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
-      <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="gaussian_width" value="1.0"/>
         <param name="ppm_tolerance" value="10.0"/>
@@ -88,6 +88,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_NoiseFilterGaussian_2 -->
     <test expect_num_outputs="2">
@@ -97,7 +100,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
-      <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="gaussian_width" value="50.0"/>
         <param name="ppm_tolerance" value="10.0"/>
@@ -110,6 +113,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_NoiseFilterGaussian_3 -->
     <test expect_num_outputs="2">
@@ -119,7 +125,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
-      <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="gaussian_width" value="1.0"/>
         <param name="ppm_tolerance" value="10.0"/>
@@ -132,6 +138,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_NoiseFilterGaussian_4 -->
     <test expect_num_outputs="2">
@@ -141,7 +150,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
-      <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="gaussian_width" value="50.0"/>
         <param name="ppm_tolerance" value="10.0"/>
@@ -154,11 +163,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_NoiseFilterGaussian.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_NoiseFilterGaussian.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/NoiseFilterSGolay.xml b/tools/openms/NoiseFilterSGolay.xml
index 4a499304a..d7817a49b 100644
--- a/tools/openms/NoiseFilterSGolay.xml
+++ b/tools/openms/NoiseFilterSGolay.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="NoiseFilterSGolay" name="NoiseFilterSGolay" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.</description>
+  <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data</description>
   <macros>
     <token name="@EXECUTABLE@">NoiseFilterSGolay</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,19 +38,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input raw data file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="frame_length" argument="-algorithm:frame_length" type="integer" optional="true" value="11" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
-      <param name="polynomial_order" argument="-algorithm:polynomial_order" type="integer" optional="true" value="4" label="Order or the polynomial that is fitted" help=""/>
+      <param name="frame_length" argument="-algorithm:frame_length" type="integer" value="11" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
+      <param name="polynomial_order" argument="-algorithm:polynomial_order" type="integer" value="4" label="Order or the polynomial that is fitted" help=""/>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-processOption" type="select" optional="true" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
+      <param argument="-processOption" type="select" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
         <option value="inmemory" selected="true">inmemory</option>
         <option value="lowmemory">lowmemory</option>
         <expand macro="list_string_san" name="processOption"/>
       </param>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -65,7 +64,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_NoiseFilterSGolay_1 -->
+  <tests>
+    <!-- TOPP_NoiseFilterSGolay_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="processOption" value="inmemory"/>
@@ -73,7 +73,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="NoiseFilterSGolay_1_input.mzML"/>
-      <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="frame_length" value="9"/>
         <param name="polynomial_order" value="4"/>
@@ -84,6 +84,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_NoiseFilterSGolay_2 -->
     <test expect_num_outputs="2">
@@ -93,7 +96,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/>
-      <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="frame_length" value="11"/>
         <param name="polynomial_order" value="4"/>
@@ -104,6 +107,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_NoiseFilterSGolay_3 -->
     <test expect_num_outputs="2">
@@ -113,7 +119,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="NoiseFilterSGolay_1_input.mzML"/>
-      <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="frame_length" value="9"/>
         <param name="polynomial_order" value="4"/>
@@ -124,6 +130,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_NoiseFilterSGolay_4 -->
     <test expect_num_outputs="2">
@@ -133,7 +142,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/>
-      <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="frame_length" value="11"/>
         <param name="polynomial_order" value="4"/>
@@ -144,11 +153,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_NoiseFilterSGolay.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_NoiseFilterSGolay.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/NovorAdapter.xml b/tools/openms/NovorAdapter.xml
index 8469a8129..a296b9cea 100644
--- a/tools/openms/NovorAdapter.xml
+++ b/tools/openms/NovorAdapter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
 <tool id="NovorAdapter" name="NovorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Performs de novo sequencing of peptides from MS/MS data with Novor.</description>
+  <description>Performs de novo sequencing of peptides from MS/MS data with Novor</description>
   <macros>
     <token name="@EXECUTABLE@">NovorAdapter</token>
     <import>macros.xml</import>
@@ -15,11 +14,11 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if $novorFile:
   mkdir novorFile &&
-  ln -s '$novorFile' 'novorFile/${re.sub("[^\w\-_]", "_", $novorFile.element_identifier)}.$gxy2omsext($novorFile.ext)' &&
+  cp '$novorFile' 'novorFile/${re.sub("[^\w\-_]", "_", $novorFile.element_identifier)}.$gxy2omsext($novorFile.ext)' &&
 #end if
 
 ## Main program call
@@ -47,30 +46,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"executable": "/home/berntm/Downloads/novor/lib/novor.jar", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
-    <param argument="-enzyme" type="select" optional="true" label="Digestion enzyme - currently only Trypsin is supported" help="">
+    <param argument="-in" type="data" format="mzml" label="MzML Input file" help=" select mzml data sets(s)"/>
+    <param argument="-enzyme" type="select" label="Digestion enzyme - currently only Trypsin is supported" help="">
       <option value="Trypsin" selected="true">Trypsin</option>
       <expand macro="list_string_san" name="enzyme"/>
     </param>
-    <param argument="-fragmentation" type="select" optional="true" label="Fragmentation method" help="">
+    <param argument="-fragmentation" type="select" label="Fragmentation method" help="">
       <option value="CID" selected="true">CID</option>
       <option value="HCD">HCD</option>
       <expand macro="list_string_san" name="fragmentation"/>
     </param>
-    <param argument="-massAnalyzer" type="select" optional="true" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)">
+    <param argument="-massAnalyzer" type="select" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)">
       <option value="Trap" selected="true">Trap</option>
       <option value="TOF">TOF</option>
       <option value="FT">FT</option>
       <expand macro="list_string_san" name="massAnalyzer"/>
     </param>
-    <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Fragmentation error tolerance  (Da)" help=""/>
-    <param argument="-precursor_mass_tolerance" type="float" optional="true" value="15.0" label="Precursor error tolerance  (ppm or Da)" help=""/>
-    <param argument="-precursor_error_units" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
+    <param argument="-fragment_mass_tolerance" type="float" value="0.5" label="Fragmentation error tolerance  (Da)" help=""/>
+    <param argument="-precursor_mass_tolerance" type="float" value="15.0" label="Precursor error tolerance  (ppm or Da)" help=""/>
+    <param argument="-precursor_error_units" type="select" label="Unit of precursor mass tolerance" help="">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
       <expand macro="list_string_san" name="precursor_error_units"/>
     </param>
-    <param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications" help="">
+    <param argument="-variable_modifications" type="select" multiple="true" optional="true" label="Variable modifications" help="">
       <option value="Acetyl (K)">Acetyl (K)</option>
       <option value="Acetyl (N-term)">Acetyl (N-term)</option>
       <option value="Amidated (C-term)">Amidated (C-term)</option>
@@ -99,7 +98,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Trimethyl (RK)">Trimethyl (RK)</option>
       <expand macro="list_string_san" name="variable_modifications"/>
     </param>
-    <param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications" help="">
+    <param argument="-fixed_modifications" type="select" multiple="true" optional="true" label="Fixed modifications" help="">
       <option value="Acetyl (K)">Acetyl (K)</option>
       <option value="Acetyl (N-term)">Acetyl (N-term)</option>
       <option value="Amidated (C-term)">Amidated (C-term)</option>
@@ -128,7 +127,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Trimethyl (RK)">Trimethyl (RK)</option>
       <expand macro="list_string_san" name="fixed_modifications"/>
     </param>
-    <param argument="-forbiddenResidues" display="checkboxes" multiple="true" type="select" optional="true" label="Forbidden Resiudes" help="">
+    <param argument="-forbiddenResidues" type="select" multiple="true" optional="true" label="Forbidden Resiudes" help="">
       <option value="I">I</option>
       <option value="U">U</option>
       <expand macro="list_string_san" name="forbiddenResidues"/>
@@ -136,7 +135,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-novorFile" type="data" format="txt" optional="true" label="File to introduce customized algorithm parameters for advanced users (otional .novor file)" help=" select txt data sets(s)"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -150,11 +149,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_NovorAdapter_1 -->
+  <tests>
+    <!-- TOPP_NovorAdapter_1 -->
   </tests>
   <help><![CDATA[Performs de novo sequencing of peptides from MS/MS data with Novor.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_NovorAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_NovorAdapter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/NucleicAcidSearchEngine.xml b/tools/openms/NucleicAcidSearchEngine.xml
index 7e534b2b5..31821754e 100644
--- a/tools/openms/NucleicAcidSearchEngine.xml
+++ b/tools/openms/NucleicAcidSearchEngine.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [RNA]-->
 <tool id="NucleicAcidSearchEngine" name="NucleicAcidSearchEngine" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Annotate nucleic acid identifications to MS/MS spectra.</description>
+  <description>Annotate nucleic acid identifications to MS/MS spectra</description>
   <macros>
     <token name="@EXECUTABLE@">NucleicAcidSearchEngine</token>
     <import>macros.xml</import>
@@ -15,14 +14,14 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #if $database:
   mkdir database &&
-  ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+  cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
 #end if
 #if $digest:
   mkdir digest &&
-  ln -s '$digest' 'digest/${re.sub("[^\w\-_]", "_", $digest.element_identifier)}.$gxy2omsext($digest.ext)' &&
+  cp '$digest' 'digest/${re.sub("[^\w\-_]", "_", $digest.element_identifier)}.$gxy2omsext($digest.ext)' &&
 #end if
 mkdir out &&
 #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
@@ -118,37 +117,37 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file: spectra" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Input file: spectra" help=" select mzml data sets(s)"/>
     <param argument="-database" type="data" format="fasta" optional="true" label="Input file: sequence database" help="Required unless 'digest' is set select fasta data sets(s)"/>
     <param argument="-digest" type="data" format="sqlite" optional="true" label="Input file: pre-digested sequence database" help="Can be used instead of 'database'. Sets all 'oligo:...' parameters select sqlite data sets(s)"/>
     <section name="precursor" title="Precursor (parent ion) options" help="" expanded="false">
-      <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Precursor mass tolerance (+/- around uncharged precursor mass)" help=""/>
-      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
+      <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" value="10.0" label="Precursor mass tolerance (+/- around uncharged precursor mass)" help=""/>
+      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
       </param>
-      <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="-1" label="Minimum precursor charge to be considered" help=""/>
-      <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="-20" label="Maximum precursor charge to be considered" help=""/>
+      <param name="min_charge" argument="-precursor:min_charge" type="integer" value="-1" label="Minimum precursor charge to be considered" help=""/>
+      <param name="max_charge" argument="-precursor:max_charge" type="integer" value="-20" label="Maximum precursor charge to be considered" help=""/>
       <param name="include_unknown_charge" argument="-precursor:include_unknown_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include MS2 spectra with unknown precursor charge - try to match them in any possible charge between 'min_charge' and 'max_charge', at the risk of a higher error rate" help=""/>
       <param name="use_avg_mass" argument="-precursor:use_avg_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use average instead of monoisotopic precursor masses (appropriate for low-resolution instruments)" help=""/>
       <param name="use_adducts" argument="-precursor:use_adducts" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Consider possible salt adducts (see 'precursor:potential_adducts') when matching precursor masses" help=""/>
-      <param name="potential_adducts" argument="-precursor:potential_adducts" type="text" optional="true" value="Na:+" label="Adducts considered to explain mass differences" help="Format: 'Element:Charge(+/-)', i.e. the number of '+' or '-' indicates the charge, e.g. 'Ca:++' indicates +2. Only used if 'precursor:use_adducts' is set (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="potential_adducts" argument="-precursor:potential_adducts" type="text" value="Na:+" label="Adducts considered to explain mass differences" help="Format: 'Element:Charge(+/-)', i.e. the number of '+' or '-' indicates the charge, e.g. 'Ca:++' indicates +2. Only used if 'precursor:use_adducts' is set (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="potential_adducts"/>
         <expand macro="list_string_san" name="potential_adducts"/>
       </param>
-      <param name="isotopes" argument="-precursor:isotopes" type="text" optional="true" value="0 1 2 3 4" label="Correct for mono-isotopic peak misassignments" help="E.g.: 1 = precursor may be misassigned to the first isotopic peak. Ignored if 'use_avg_mass' is set (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="isotopes" argument="-precursor:isotopes" type="text" value="0 1 2 3 4" label="Correct for mono-isotopic peak misassignments" help="E.g.: 1 = precursor may be misassigned to the first isotopic peak. Ignored if 'use_avg_mass' is set (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_integer_valsan" name="isotopes"/>
       </param>
     </section>
     <section name="fragment" title="Fragment (Product Ion) Options" help="" expanded="false">
-      <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/>
-      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="true" label="Unit of fragment mass tolerance" help="">
+      <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/>
+      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" label="Unit of fragment mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
       </param>
-      <param name="ions" argument="-fragment:ions" multiple="true" type="select" optional="true" label="Fragment ions to include in theoretical spectra" help="">
+      <param name="ions" argument="-fragment:ions" type="select" multiple="true" optional="false" label="Fragment ions to include in theoretical spectra" help="">
         <option value="a-B" selected="true">a-B</option>
         <option value="a" selected="true">a</option>
         <option value="b" selected="true">b</option>
@@ -162,182 +161,337 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </param>
     </section>
     <section name="modifications" title="Modification options" help="" expanded="false">
-      <param name="variable" argument="-modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications" help="">
-        <option value="m1Am">m1Am</option>
-        <option value="m1Gm">m1Gm</option>
-        <option value="m1Im">m1Im</option>
-        <option value="m1acp3Y">m1acp3Y</option>
-        <option value="m1A">m1A</option>
-        <option value="m1G">m1G</option>
-        <option value="m1I">m1I</option>
-        <option value="m1Y">m1Y</option>
-        <option value="m28A">m28A</option>
-        <option value="msms2i6A">msms2i6A</option>
-        <option value="ges2U">ges2U</option>
+      <param name="variable" argument="-modifications:variable" type="select" multiple="true" optional="true" label="Variable modifications" help="">
+        <option value="io6A">io6A</option>
+        <option value="s2U">s2U</option>
         <option value="k2C">k2C</option>
-        <option value="m2A">m2A</option>
-        <option value="ms2ct6A">ms2ct6A</option>
-        <option value="ms2io6A">ms2io6A</option>
-        <option value="ms2hn6A">ms2hn6A</option>
-        <option value="ms2i6A">ms2i6A</option>
-        <option value="ms2m6A">ms2m6A</option>
-        <option value="ms2t6A">ms2t6A</option>
-        <option value="se2U">se2U</option>
+        <option value="m2Gm">m2Gm</option>
+        <option value="Ym">Ym</option>
+        <option value="f5Cm">f5Cm</option>
+        <option value="Qbase">Qbase</option>
+        <option value="ac4Cm">ac4Cm</option>
+        <option value="imG-14">imG-14</option>
+        <option value="cm5s2U">cm5s2U</option>
+        <option value="mnm5s2U">mnm5s2U</option>
+        <option value="m227G">m227G</option>
+        <option value="yW-58">yW-58</option>
+        <option value="I">I</option>
+        <option value="g6A">g6A</option>
+        <option value="nm5U">nm5U</option>
+        <option value="m7G">m7G</option>
         <option value="s2Um">s2Um</option>
-        <option value="s2C">s2C</option>
-        <option value="s2U">s2U</option>
+        <option value="Y">Y</option>
+        <option value="hm5C">hm5C</option>
+        <option value="m5U">m5U</option>
+        <option value="preQ0">preQ0</option>
+        <option value="o2yW">o2yW</option>
+        <option value="m5Um">m5Um</option>
+        <option value="preQ1">preQ1</option>
+        <option value="m66Am">m66Am</option>
+        <option value="ac6A">ac6A</option>
+        <option value="ms2io6A">ms2io6A</option>
         <option value="Am">Am</option>
-        <option value="Cm">Cm</option>
-        <option value="Gm">Gm</option>
         <option value="Im">Im</option>
-        <option value="Ym">Ym</option>
-        <option value="Um">Um</option>
-        <option value="mcmo5Um">mcmo5Um</option>
-        <option value="Ar(p)">Ar(p)</option>
-        <option value="Gr(p)">Gr(p)</option>
-        <option value="(pN)2'3'&gt;p">(pN)2'3'&gt;p</option>
-        <option value="hm5Cm">hm5Cm</option>
-        <option value="m3Um">m3Um</option>
+        <option value="mnm5U">mnm5U</option>
+        <option value="m22G">m22G</option>
+        <option value="t6A">t6A</option>
+        <option value="m8A">m8A</option>
+        <option value="m7GpppN">m7GpppN</option>
+        <option value="m27GpppN">m27GpppN</option>
+        <option value="m227GpppN">m227GpppN</option>
+        <option value="mpppN">mpppN</option>
+        <option value="m28A">m28A</option>
         <option value="acp3D">acp3D</option>
         <option value="acp3Y">acp3Y</option>
-        <option value="acp3U">acp3U</option>
-        <option value="m3C">m3C</option>
-        <option value="m3Y">m3Y</option>
-        <option value="m3U">m3U</option>
-        <option value="imG-14">imG-14</option>
-        <option value="s4U">s4U</option>
-        <option value="m5Cm">m5Cm</option>
-        <option value="m5Um">m5Um</option>
-        <option value="mchm5Um">mchm5Um</option>
-        <option value="mchm5U">mchm5U</option>
-        <option value="inm5s2U">inm5s2U</option>
-        <option value="inm5Um">inm5Um</option>
+        <option value="imG">imG</option>
+        <option value="D">D</option>
+        <option value="N">N</option>
+        <option value="C+">C+</option>
+        <option value="m27Gm">m27Gm</option>
+        <option value="ho5C">ho5C</option>
         <option value="inm5U">inm5U</option>
-        <option value="nm5ges2U">nm5ges2U</option>
-        <option value="nm5se2U">nm5se2U</option>
-        <option value="nm5s2U">nm5s2U</option>
-        <option value="nm5U">nm5U</option>
-        <option value="nchm5U">nchm5U</option>
+        <option value="inm5Um">inm5Um</option>
+        <option value="inm5s2U">inm5s2U</option>
+        <option value="pppN">pppN</option>
+        <option value="GpppN">GpppN</option>
+        <option value="CoApN">CoApN</option>
+        <option value="m44C">m44C</option>
+        <option value="acCoApN">acCoApN</option>
+        <option value="malonyl-CoApN">malonyl-CoApN</option>
+        <option value="succinyl-CoApN">succinyl-CoApN</option>
+        <option value="ppN">ppN</option>
+        <option value="NADpN">NADpN</option>
+        <option value="m6t6A">m6t6A</option>
+        <option value="OHyWy">OHyWy</option>
+        <option value="pG(pN)">pG(pN)</option>
         <option value="ncm5s2U">ncm5s2U</option>
-        <option value="ncm5Um">ncm5Um</option>
-        <option value="ncm5U">ncm5U</option>
-        <option value="chm5U">chm5U</option>
-        <option value="cm5s2U">cm5s2U</option>
+        <option value="nchm5U">nchm5U</option>
+        <option value="mchm5Um">mchm5Um</option>
+        <option value="pN">pN</option>
+        <option value="ges2U">ges2U</option>
         <option value="cmnm5ges2U">cmnm5ges2U</option>
-        <option value="cmnm5se2U">cmnm5se2U</option>
-        <option value="cmnm5s2U">cmnm5s2U</option>
-        <option value="cmnm5Um">cmnm5Um</option>
-        <option value="cmnm5U">cmnm5U</option>
-        <option value="cm5U">cm5U</option>
-        <option value="cnm5U">cnm5U</option>
-        <option value="f5Cm">f5Cm</option>
-        <option value="f5C">f5C</option>
-        <option value="ho5C">ho5C</option>
-        <option value="hm5C">hm5C</option>
-        <option value="ho5U">ho5U</option>
-        <option value="mcm5s2U">mcm5s2U</option>
-        <option value="mcm5Um">mcm5Um</option>
-        <option value="mcm5U">mcm5U</option>
-        <option value="mo5U">mo5U</option>
-        <option value="m5s2U">m5s2U</option>
         <option value="mnm5ges2U">mnm5ges2U</option>
-        <option value="mnm5se2U">mnm5se2U</option>
-        <option value="mnm5s2U">mnm5s2U</option>
-        <option value="mnm5U">mnm5U</option>
-        <option value="m5C">m5C</option>
+        <option value="nm5ges2U">nm5ges2U</option>
         <option value="m5D">m5D</option>
-        <option value="m5U">m5U</option>
-        <option value="tm5s2U">tm5s2U</option>
-        <option value="tm5U">tm5U</option>
-        <option value="CoA(pN)">CoA(pN)</option>
-        <option value="acCoA(pN)">acCoA(pN)</option>
-        <option value="malonyl-CoA(pN)">malonyl-CoA(pN)</option>
-        <option value="succinyl-CoA(pN)">succinyl-CoA(pN)</option>
-        <option value="p(pN)">p(pN)</option>
+        <option value="mmpN">mmpN</option>
+        <option value="mpN">mpN</option>
         <option value="5'-OH-N">5'-OH-N</option>
-        <option value="(pN)">(pN)</option>
-        <option value="NAD(pN)">NAD(pN)</option>
-        <option value="pp(pN)">pp(pN)</option>
-        <option value="yW-86">yW-86</option>
-        <option value="yW-72">yW-72</option>
-        <option value="yW-58">yW-58</option>
-        <option value="preQ1tRNA">preQ1tRNA</option>
-        <option value="preQ0tRNA">preQ0tRNA</option>
-        <option value="m7G">m7G</option>
-        <option value="m7Gpp(pN)">m7Gpp(pN)</option>
-        <option value="m8A">m8A</option>
-        <option value="m2Gm">m2Gm</option>
-        <option value="m27Gm">m27Gm</option>
-        <option value="m27G">m27G</option>
-        <option value="m27Gpp(pN)">m27Gpp(pN)</option>
-        <option value="m22Gm">m22Gm</option>
-        <option value="m227G">m227G</option>
-        <option value="m227Gpp(pN)">m227Gpp(pN)</option>
-        <option value="m22G">m22G</option>
+        <option value="N2'3'cp">N2'3'cp</option>
+        <option value="ct6A">ct6A</option>
+        <option value="hm6A">hm6A</option>
+        <option value="f6A">f6A</option>
+        <option value="cnm5U">cnm5U</option>
+        <option value="mcmo5Um">mcmo5Um</option>
+        <option value="m5C">m5C</option>
+        <option value="ms2ct6A">ms2ct6A</option>
+        <option value="ht6A">ht6A</option>
+        <option value="msms2i6A">msms2i6A</option>
+        <option value="hm5Cm">hm5Cm</option>
+        <option value="pY">pY</option>
+        <option value="pm5C">pm5C</option>
+        <option value="ps2U">ps2U</option>
+        <option value="hn6A">hn6A</option>
+        <option value="pD">pD</option>
+        <option value="pm2G">pm2G</option>
+        <option value="pm66A">pm66A</option>
+        <option value="pGm">pGm</option>
+        <option value="pm5U">pm5U</option>
+        <option value="pm22G">pm22G</option>
+        <option value="pm3U">pm3U</option>
+        <option value="m5Cm">m5Cm</option>
+        <option value="Ar(p)">Ar(p)</option>
+        <option value="pac4C">pac4C</option>
+        <option value="pCm">pCm</option>
+        <option value="pppG">pppG</option>
+        <option value="pm7G">pm7G</option>
+        <option value="pm1A">pm1A</option>
+        <option value="pUm">pUm</option>
+        <option value="pAm">pAm</option>
+        <option value="pm4Cm">pm4Cm</option>
+        <option value="pC2'3'cp">pC2'3'cp</option>
+        <option value="tm5U">tm5U</option>
+        <option value="pm6A">pm6A</option>
+        <option value="pyW">pyW</option>
+        <option value="pm1G">pm1G</option>
+        <option value="pA2'3'cp">pA2'3'cp</option>
+        <option value="ps4U">ps4U</option>
+        <option value="pI">pI</option>
+        <option value="ppG">ppG</option>
+        <option value="pm2A">pm2A</option>
+        <option value="m1G">m1G</option>
+        <option value="pmcm5s2U">pmcm5s2U</option>
+        <option value="cmnm5Um">cmnm5Um</option>
+        <option value="pse2U">pse2U</option>
+        <option value="pt6A">pt6A</option>
+        <option value="pf5C">pf5C</option>
+        <option value="pppA">pppA</option>
+        <option value="pG">pG</option>
+        <option value="pG2'3'cp">pG2'3'cp</option>
+        <option value="pms2i6A">pms2i6A</option>
+        <option value="pcmo5U">pcmo5U</option>
+        <option value="Xm">Xm</option>
+        <option value="pm44C">pm44C</option>
+        <option value="pi6A">pi6A</option>
+        <option value="phm5C">phm5C</option>
+        <option value="pU">pU</option>
+        <option value="pAr(p)">pAr(p)</option>
+        <option value="pac4Cm">pac4Cm</option>
+        <option value="pGp">pGp</option>
+        <option value="m1I">m1I</option>
+        <option value="pU2'3'cp">pU2'3'cp</option>
+        <option value="mcm5U">mcm5U</option>
+        <option value="Gm">Gm</option>
+        <option value="pm4C">pm4C</option>
+        <option value="ncm5Um">ncm5Um</option>
+        <option value="pm5Um">pm5Um</option>
+        <option value="pmnm5U">pmnm5U</option>
+        <option value="pm3C">pm3C</option>
+        <option value="m5s2U">m5s2U</option>
+        <option value="yW">yW</option>
+        <option value="pC">pC</option>
+        <option value="pm6t6A">pm6t6A</option>
+        <option value="f5C">f5C</option>
+        <option value="pAp">pAp</option>
+        <option value="m1Am">m1Am</option>
+        <option value="m1Im">m1Im</option>
+        <option value="ApppN">ApppN</option>
+        <option value="AppppN">AppppN</option>
+        <option value="ApppppN">ApppppN</option>
+        <option value="m6ApppN">m6ApppN</option>
+        <option value="m6AppppN">m6AppppN</option>
+        <option value="m6ApppppN">m6ApppppN</option>
+        <option value="m7GppppN">m7GppppN</option>
+        <option value="Gr(p)">Gr(p)</option>
+        <option value="pm1Am">pm1Am</option>
+        <option value="pm1Gm">pm1Gm</option>
+        <option value="pm1Im">pm1Im</option>
+        <option value="pm1acp3Y">pm1acp3Y</option>
+        <option value="pm1I">pm1I</option>
+        <option value="pm1Y">pm1Y</option>
+        <option value="pk2C">pk2C</option>
+        <option value="ps2C">ps2C</option>
+        <option value="pm3Y">pm3Y</option>
+        <option value="nm5s2U">nm5s2U</option>
+        <option value="pm5Cm">pm5Cm</option>
+        <option value="pmchm5U">pmchm5U</option>
+        <option value="pinm5Um">pinm5Um</option>
+        <option value="pinm5s2U">pinm5s2U</option>
+        <option value="pinm5U">pinm5U</option>
+        <option value="pnm5U">pnm5U</option>
+        <option value="pncm5U">pncm5U</option>
+        <option value="pchm5U">pchm5U</option>
+        <option value="pcmnm5U">pcmnm5U</option>
+        <option value="pcm5U">pcm5U</option>
         <option value="m2G">m2G</option>
+        <option value="pho5U">pho5U</option>
+        <option value="pmcm5Um">pmcm5Um</option>
+        <option value="pmcm5U">pmcm5U</option>
+        <option value="pmo5U">pmo5U</option>
+        <option value="pm5D">pm5D</option>
+        <option value="pmimG">pmimG</option>
+        <option value="phm5Cm">phm5Cm</option>
+        <option value="pIm">pIm</option>
+        <option value="pYm">pYm</option>
+        <option value="pmcmo5Um">pmcmo5Um</option>
+        <option value="m2A">m2A</option>
+        <option value="pGr(p)">pGr(p)</option>
+        <option value="pm28A">pm28A</option>
+        <option value="pmsms2i6A">pmsms2i6A</option>
+        <option value="pges2U">pges2U</option>
+        <option value="pms2ct6A">pms2ct6A</option>
+        <option value="pms2io6A">pms2io6A</option>
+        <option value="pms2hn6A">pms2hn6A</option>
+        <option value="pms2m6A">pms2m6A</option>
+        <option value="pms2t6A">pms2t6A</option>
+        <option value="ps2Um">ps2Um</option>
+        <option value="pm3Um">pm3Um</option>
+        <option value="pacp3D">pacp3D</option>
+        <option value="pacp3U">pacp3U</option>
+        <option value="pimG-14">pimG-14</option>
+        <option value="pmchm5Um">pmchm5Um</option>
+        <option value="pnm5ges2U">pnm5ges2U</option>
+        <option value="pnm5se2U">pnm5se2U</option>
+        <option value="pnm5s2U">pnm5s2U</option>
+        <option value="pnchm5U">pnchm5U</option>
+        <option value="pncm5Um">pncm5Um</option>
         <option value="m4Cm">m4Cm</option>
-        <option value="m44Cm">m44Cm</option>
-        <option value="m44C">m44C</option>
-        <option value="ac4Cm">ac4Cm</option>
-        <option value="ac4C">ac4C</option>
-        <option value="m4C">m4C</option>
-        <option value="m6Am">m6Am</option>
-        <option value="m66Am">m66Am</option>
+        <option value="pncm5s2U">pncm5s2U</option>
+        <option value="pcm5s2U">pcm5s2U</option>
+        <option value="pcmnm5Um">pcmnm5Um</option>
+        <option value="pcmnm5ges2U">pcmnm5ges2U</option>
+        <option value="pcmnm5se2U">pcmnm5se2U</option>
+        <option value="pcmnm5s2U">pcmnm5s2U</option>
+        <option value="pcnm5U">pcnm5U</option>
+        <option value="pf5Cm">pf5Cm</option>
+        <option value="pho5C">pho5C</option>
+        <option value="pm5s2U">pm5s2U</option>
+        <option value="m27G">m27G</option>
+        <option value="m22Gm">m22Gm</option>
+        <option value="pmnm5ges2U">pmnm5ges2U</option>
+        <option value="pmnm5se2U">pmnm5se2U</option>
+        <option value="pmnm5s2U">pmnm5s2U</option>
+        <option value="ptm5s2U">ptm5s2U</option>
+        <option value="ptm5U">ptm5U</option>
+        <option value="pyW-86">pyW-86</option>
+        <option value="pyW-72">pyW-72</option>
+        <option value="pyW-58">pyW-58</option>
+        <option value="ppreQ1">ppreQ1</option>
+        <option value="ppreQ0">ppreQ0</option>
         <option value="m66A">m66A</option>
-        <option value="io6A">io6A</option>
-        <option value="ac6A">ac6A</option>
-        <option value="f6A">f6A</option>
-        <option value="g6A">g6A</option>
-        <option value="hm6A">hm6A</option>
-        <option value="hn6A">hn6A</option>
+        <option value="pm8A">pm8A</option>
+        <option value="pC+">pC+</option>
+        <option value="pG+">pG+</option>
+        <option value="pct6A">pct6A</option>
+        <option value="poQ">poQ</option>
+        <option value="pgalQ">pgalQ</option>
+        <option value="pgluQ">pgluQ</option>
+        <option value="pht6A">pht6A</option>
+        <option value="pOHyW">pOHyW</option>
+        <option value="pimG2">pimG2</option>
+        <option value="gluQ">gluQ</option>
+        <option value="pmanQ">pmanQ</option>
+        <option value="pOHyWy">pOHyWy</option>
+        <option value="pm27Gm">pm27Gm</option>
+        <option value="pQ">pQ</option>
+        <option value="pOHyWx">pOHyWx</option>
+        <option value="pmcmo5U">pmcmo5U</option>
+        <option value="pimG">pimG</option>
+        <option value="pm44Cm">pm44Cm</option>
+        <option value="pm2Gm">pm2Gm</option>
+        <option value="pm22Gm">pm22Gm</option>
+        <option value="ncm5U">ncm5U</option>
+        <option value="pm6Am">pm6Am</option>
+        <option value="pm66Am">pm66Am</option>
+        <option value="pio6A">pio6A</option>
+        <option value="pac6A">pac6A</option>
+        <option value="pf6A">pf6A</option>
+        <option value="pg6A">pg6A</option>
+        <option value="phm6A">phm6A</option>
+        <option value="phn6A">phn6A</option>
+        <option value="cm5U">cm5U</option>
+        <option value="pm27G">pm27G</option>
+        <option value="pm227G">pm227G</option>
+        <option value="pA">pA</option>
+        <option value="cmnm5s2U">cmnm5s2U</option>
+        <option value="cmo5U">cmo5U</option>
+        <option value="m3Y">m3Y</option>
+        <option value="m3U">m3U</option>
+        <option value="ms2m6A">ms2m6A</option>
+        <option value="Um">Um</option>
+        <option value="ms2i6A">ms2i6A</option>
+        <option value="m3C">m3C</option>
+        <option value="cmnm5se2U">cmnm5se2U</option>
+        <option value="ms2t6A">ms2t6A</option>
         <option value="i6A">i6A</option>
-        <option value="m6t6A">m6t6A</option>
-        <option value="m6A">m6A</option>
-        <option value="t6A">t6A</option>
-        <option value="Qbase">Qbase</option>
-        <option value="C+">C+</option>
-        <option value="mm(pN)">mm(pN)</option>
-        <option value="m(pN)">m(pN)</option>
-        <option value="G+">G+</option>
-        <option value="ct6A">ct6A</option>
-        <option value="D">D</option>
+        <option value="m3Um">m3Um</option>
+        <option value="mcmo5U">mcmo5U</option>
+        <option value="mimG">mimG</option>
         <option value="oQ">oQ</option>
+        <option value="preQ1base">preQ1base</option>
+        <option value="nm5se2U">nm5se2U</option>
+        <option value="m1Gm">m1Gm</option>
+        <option value="ho5U">ho5U</option>
+        <option value="Q">Q</option>
+        <option value="xG">xG</option>
+        <option value="mcm5s2U">mcm5s2U</option>
+        <option value="m44Cm">m44Cm</option>
+        <option value="s4U">s4U</option>
+        <option value="xC">xC</option>
+        <option value="yW-86">yW-86</option>
+        <option value="xA">xA</option>
+        <option value="chm5U">chm5U</option>
+        <option value="mo5U">mo5U</option>
+        <option value="acp3U">acp3U</option>
+        <option value="xU">xU</option>
+        <option value="yW-72">yW-72</option>
+        <option value="mnm5se2U">mnm5se2U</option>
+        <option value="ms2hn6A">ms2hn6A</option>
+        <option value="m1acp3Y">m1acp3Y</option>
+        <option value="mcm5Um">mcm5Um</option>
+        <option value="ac4C">ac4C</option>
+        <option value="m6Am">m6Am</option>
+        <option value="m1A">m1A</option>
+        <option value="Cm">Cm</option>
+        <option value="mchm5U">mchm5U</option>
         <option value="galQ">galQ</option>
-        <option value="mpp(pN)">mpp(pN)</option>
-        <option value="gluQ">gluQ</option>
-        <option value="pG(pN)">pG(pN)</option>
-        <option value="Gpp(pN)">Gpp(pN)</option>
-        <option value="ht6A">ht6A</option>
-        <option value="OHyW">OHyW</option>
-        <option value="I">I</option>
+        <option value="cmnm5U">cmnm5U</option>
+        <option value="m1Y">m1Y</option>
         <option value="imG2">imG2</option>
+        <option value="m4C">m4C</option>
         <option value="manQ">manQ</option>
-        <option value="OHyWy">OHyWy</option>
-        <option value="mimG">mimG</option>
-        <option value="o2yW">o2yW</option>
-        <option value="preQ0base">preQ0base</option>
-        <option value="preQ1base">preQ1base</option>
-        <option value="Y">Y</option>
-        <option value="Q">Q</option>
+        <option value="tm5s2U">tm5s2U</option>
+        <option value="s2C">s2C</option>
         <option value="OHyWx">OHyWx</option>
-        <option value="Xm">Xm</option>
+        <option value="se2U">se2U</option>
+        <option value="preQ0base">preQ0base</option>
+        <option value="m6A">m6A</option>
+        <option value="OHyW">OHyW</option>
         <option value="xX">xX</option>
-        <option value="xA">xA</option>
-        <option value="xC">xC</option>
-        <option value="xG">xG</option>
-        <option value="xU">xU</option>
-        <option value="N">N</option>
-        <option value="cmo5U">cmo5U</option>
-        <option value="mcmo5U">mcmo5U</option>
-        <option value="yW">yW</option>
-        <option value="imG">imG</option>
-        <option value="dA">dA</option>
-        <option value="dC">dC</option>
-        <option value="dG">dG</option>
-        <option value="dU">dU</option>
-        <option value="dT">dT</option>
+        <option value="G+">G+</option>
         <option value="3'-p">3'-p</option>
         <option value="5'-p">5'-p</option>
+        <option value="5'-p*">5'-p*</option>
+        <option value="3'-c">3'-c</option>
         <option value="mA">mA</option>
         <option value="mC">mC</option>
         <option value="mG">mG</option>
@@ -365,43 +519,57 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="mmmG?">mmmG?</option>
         <option value="ac4C/f5Cm?">ac4C/f5Cm?</option>
         <option value="acp3U/cmnm5Um?">acp3U/cmnm5Um?</option>
+        <option value="dA">dA</option>
+        <option value="dC">dC</option>
+        <option value="dG">dG</option>
+        <option value="dU">dU</option>
+        <option value="dT">dT</option>
+        <option value="A*">A*</option>
+        <option value="C*">C*</option>
+        <option value="G*">G*</option>
+        <option value="U*">U*</option>
+        <option value="dA*">dA*</option>
+        <option value="dC*">dC*</option>
+        <option value="dG*">dG*</option>
+        <option value="dU*">dU*</option>
+        <option value="dT*">dT*</option>
         <expand macro="list_string_san" name="variable"/>
       </param>
-      <param name="variable_max_per_oligo" argument="-modifications:variable_max_per_oligo" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate oligonucleotide" help=""/>
+      <param name="variable_max_per_oligo" argument="-modifications:variable_max_per_oligo" type="integer" value="2" label="Maximum number of residues carrying a variable modification per candidate oligonucleotide" help=""/>
       <param name="resolve_ambiguities" argument="-modifications:resolve_ambiguities" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Attempt to resolve ambiguous modifications" help="(e.g. 'mA?' for 'mA'/'Am') based on a-B ions.. This incurs a performance cost because two modifications have to be considered for each case.. Requires a-B ions to be enabled in parameter 'fragment:ions'"/>
     </section>
     <section name="oligo" title="Oligonucleotide (digestion) options (ignored if 'digest' input is used)" help="" expanded="false">
-      <param name="min_size" argument="-oligo:min_size" type="integer" optional="true" value="5" label="Minimum size an oligonucleotide must have after digestion to be considered in the search" help=""/>
-      <param name="max_size" argument="-oligo:max_size" type="integer" optional="true" value="0" label="Maximum size an oligonucleotide must have after digestion to be considered in the search, leave at 0 for no limit" help=""/>
-      <param name="missed_cleavages" argument="-oligo:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/>
-      <param name="enzyme" argument="-oligo:enzyme" type="select" optional="true" label="The enzyme used for RNA digestion" help="">
-        <option value="RNase_T1">RNase_T1</option>
-        <option value="cusativin">cusativin</option>
+      <param name="min_size" argument="-oligo:min_size" type="integer" value="5" label="Minimum size an oligonucleotide must have after digestion to be considered in the search" help=""/>
+      <param name="max_size" argument="-oligo:max_size" type="integer" value="0" label="Maximum size an oligonucleotide must have after digestion to be considered in the search, leave at 0 for no limit" help=""/>
+      <param name="missed_cleavages" argument="-oligo:missed_cleavages" type="integer" value="1" label="Number of missed cleavages" help=""/>
+      <param name="enzyme" argument="-oligo:enzyme" type="select" label="The enzyme used for RNA digestion" help="">
+        <option value="RNase_A">RNase_A</option>
+        <option value="RNase_MC1">RNase_MC1</option>
         <option value="RNase_H">RNase_H</option>
         <option value="mazF">mazF</option>
+        <option value="cusativin">cusativin</option>
+        <option value="RNase_T1">RNase_T1</option>
         <option value="colicin_E5">colicin_E5</option>
         <option value="no cleavage" selected="true">no cleavage</option>
-        <option value="RNase_U2">RNase_U2</option>
-        <option value="RNase_A">RNase_A</option>
-        <option value="RNase_MC1">RNase_MC1</option>
         <option value="unspecific cleavage">unspecific cleavage</option>
+        <option value="RNase_U2">RNase_U2</option>
         <expand macro="list_string_san" name="enzyme"/>
       </param>
     </section>
     <section name="report" title="Reporting Options" help="" expanded="false">
-      <param name="top_hits" argument="-report:top_hits" type="integer" optional="true" min="0" value="1" label="Maximum number of top-scoring hits per spectrum that are reported ('0' for all hits)" help=""/>
+      <param name="top_hits" argument="-report:top_hits" type="integer" min="0" value="1" label="Maximum number of top-scoring hits per spectrum that are reported ('0' for all hits)" help=""/>
     </section>
     <section name="fdr" title="False Discovery Rate options" help="" expanded="false">
       <param name="decoy_pattern" argument="-fdr:decoy_pattern" type="text" optional="true" value="" label="String used as part of the accession to annotate decoy sequences" help="(e.g. 'DECOY_'). Leave empty to skip the FDR/q-value calculation">
         <expand macro="list_string_san" name="decoy_pattern"/>
       </param>
-      <param name="cutoff" argument="-fdr:cutoff" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Cut-off for FDR filtering; search hits with higher q-values will be removed" help=""/>
+      <param name="cutoff" argument="-fdr:cutoff" type="float" min="0.0" max="1.0" value="1.0" label="Cut-off for FDR filtering; search hits with higher q-values will be removed" help=""/>
       <param name="remove_decoys" argument="-fdr:remove_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not score hits to decoy sequences and remove them when filtering" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-decharge_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decharge the MS2 spectra for scoring" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -439,7 +607,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_NucleicAcidSearchEngine_1 -->
+  <tests>
+    <!-- TOPP_NucleicAcidSearchEngine_1 -->
     <test expect_num_outputs="5">
       <section name="adv_opts">
         <param name="decharge_ms2" value="false"/>
@@ -448,10 +617,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="NucleicAcidSearchEngine_1.mzML"/>
       <param name="database" value="NucleicAcidSearchEngine_1.fasta"/>
-      <output name="out" file="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <output name="id_out" file="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <output name="db_out" file="NucleicAcidSearchEngine_13_out.tmp" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
-      <output name="digest_out" file="NucleicAcidSearchEngine_1_digest.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
+      <output name="out" value="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="id_out" value="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="db_out" value="NucleicAcidSearchEngine_13_out.tmp" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
+      <output name="digest_out" value="NucleicAcidSearchEngine_1_digest.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
       <section name="precursor">
         <param name="mass_tolerance" value="5.0"/>
         <param name="mass_tolerance_unit" value="ppm"/>
@@ -459,7 +628,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="max_charge" value="-14"/>
         <param name="include_unknown_charge" value="true"/>
         <param name="use_avg_mass" value="false"/>
-        <param name="use_adducts" value="false"/>
+        <param name="use_adducts" value="true"/>
         <param name="potential_adducts" value="&quot;K:+&quot; &quot;Na:+&quot; &quot;Na2:++&quot; &quot;K2:++&quot; &quot;NaK:++&quot; &quot;K3:+++&quot; &quot;Na3:+++&quot; &quot;NaK2:+++&quot; &quot;Na2K:+++&quot;"/>
         <param name="isotopes" value="0 1 2"/>
       </section>
@@ -469,7 +638,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="ions" value="a-B,c,w,y"/>
       </section>
       <section name="modifications">
-        <param name="variable"/>
         <param name="variable_max_per_oligo" value="2"/>
         <param name="resolve_ambiguities" value="false"/>
       </section>
@@ -493,8 +661,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_NucleicAcidSearchEngine_2 -->
+    <!-- TOPP_NucleicAcidSearchEngine_2 -->
     <test expect_num_outputs="4">
       <section name="adv_opts">
         <param name="decharge_ms2" value="false"/>
@@ -503,9 +674,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="NucleicAcidSearchEngine_1.mzML"/>
       <param name="digest" value="NucleicAcidSearchEngine_1_digest.oms"/>
-      <output name="out" file="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <output name="id_out" file="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <output name="db_out" file="NucleicAcidSearchEngine_23_out.tmp" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
+      <output name="out" value="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="id_out" value="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="db_out" value="NucleicAcidSearchEngine_23_out.tmp" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
       <section name="precursor">
         <param name="mass_tolerance" value="5.0"/>
         <param name="mass_tolerance_unit" value="ppm"/>
@@ -513,7 +684,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="max_charge" value="-14"/>
         <param name="include_unknown_charge" value="true"/>
         <param name="use_avg_mass" value="false"/>
-        <param name="use_adducts" value="false"/>
+        <param name="use_adducts" value="true"/>
         <param name="potential_adducts" value="&quot;K:+&quot; &quot;Na:+&quot; &quot;Na2:++&quot; &quot;K2:++&quot; &quot;NaK:++&quot; &quot;K3:+++&quot; &quot;Na3:+++&quot; &quot;NaK2:+++&quot; &quot;Na2K:+++&quot;"/>
         <param name="isotopes" value="0 1 2"/>
       </section>
@@ -523,7 +694,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="ions" value="a-B,c,w,y"/>
       </section>
       <section name="modifications">
-        <param name="variable"/>
         <param name="variable_max_per_oligo" value="2"/>
         <param name="resolve_ambiguities" value="false"/>
       </section>
@@ -547,11 +717,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Annotate nucleic acid identifications to MS/MS spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_NucleicAcidSearchEngine.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_NucleicAcidSearchEngine.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/OMSSAAdapter.xml b/tools/openms/OMSSAAdapter.xml
deleted file mode 100644
index 53d23e6ea..000000000
--- a/tools/openms/OMSSAAdapter.xml
+++ /dev/null
@@ -1,6044 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
-<tool id="OMSSAAdapter" name="OMSSAAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Annotates MS/MS spectra using OMSSA.</description>
-  <macros>
-    <token name="@EXECUTABLE@">OMSSAAdapter</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-mkdir out &&
-mkdir database &&
-ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
-
-makeblastdb -dbtype prot -blastdb_version 4 -in 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in
-'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
--out
-'out/output.${gxy2omsext("idxml")}'
--database
-'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
-
-## Postprocessing
-&& mv 'out/output.${gxy2omsext("idxml")}' '$out'
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"omssa_executable": "\$(dirname \$(realpath \$(which omssacl)))/omssacl", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
-  </configfiles>
-  <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
-    <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance" help=""/>
-    <param argument="-precursor_error_units" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
-      <option value="Da">Da</option>
-      <option value="ppm" selected="true">ppm</option>
-      <expand macro="list_string_san" name="precursor_error_units"/>
-    </param>
-    <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.3" label="Fragment mass error in Dalton" help=""/>
-    <param argument="-database" type="data" format="fasta" optional="false" label="NCBI formatted FASTA files" help="The .psq filename should be given, e.g. 'SwissProt.fasta.psq'. If the filename does not end in '.psq' (e.g., SwissProt.fasta) the psq suffix will be added automatically. Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir' select fasta data sets(s)"/>
-    <param argument="-min_precursor_charge" type="integer" optional="true" value="1" label="Minimum precursor ion charge" help=""/>
-    <param argument="-max_precursor_charge" type="integer" optional="true" value="3" label="Maximum precursor ion charge" help=""/>
-    <param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
-      <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
-      <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
-      <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
-      <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
-      <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
-      <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
-      <option value="2-succinyl (C)">2-succinyl (C)</option>
-      <option value="2HPG (R)">2HPG (R)</option>
-      <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
-      <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
-      <option value="3sulfo (N-term)">3sulfo (N-term)</option>
-      <option value="4-ONE (C)">4-ONE (C)</option>
-      <option value="4-ONE (H)">4-ONE (H)</option>
-      <option value="4-ONE (K)">4-ONE (K)</option>
-      <option value="4-ONE+Delta:H(-2)O(-1) (C)">4-ONE+Delta:H(-2)O(-1) (C)</option>
-      <option value="4-ONE+Delta:H(-2)O(-1) (H)">4-ONE+Delta:H(-2)O(-1) (H)</option>
-      <option value="4-ONE+Delta:H(-2)O(-1) (K)">4-ONE+Delta:H(-2)O(-1) (K)</option>
-      <option value="4AcAllylGal (C)">4AcAllylGal (C)</option>
-      <option value="a-type-ion (C-term)">a-type-ion (C-term)</option>
-      <option value="AccQTag (K)">AccQTag (K)</option>
-      <option value="AccQTag (N-term)">AccQTag (N-term)</option>
-      <option value="Acetyl (C)">Acetyl (C)</option>
-      <option value="Acetyl (H)">Acetyl (H)</option>
-      <option value="Acetyl (K)">Acetyl (K)</option>
-      <option value="Acetyl (N-term)">Acetyl (N-term)</option>
-      <option value="Acetyl (Protein N-term)">Acetyl (Protein N-term)</option>
-      <option value="Acetyl (R)">Acetyl (R)</option>
-      <option value="Acetyl (S)">Acetyl (S)</option>
-      <option value="Acetyl (T)">Acetyl (T)</option>
-      <option value="Acetyl (Y)">Acetyl (Y)</option>
-      <option value="Acetyl:13C(2) (K)">Acetyl:13C(2) (K)</option>
-      <option value="Acetyl:13C(2) (Protein N-term)">Acetyl:13C(2) (Protein N-term)</option>
-      <option value="Acetyl:2H(3) (H)">Acetyl:2H(3) (H)</option>
-      <option value="Acetyl:2H(3) (K)">Acetyl:2H(3) (K)</option>
-      <option value="Acetyl:2H(3) (N-term)">Acetyl:2H(3) (N-term)</option>
-      <option value="Acetyl:2H(3) (Protein N-term)">Acetyl:2H(3) (Protein N-term)</option>
-      <option value="Acetyl:2H(3) (S)">Acetyl:2H(3) (S)</option>
-      <option value="Acetyl:2H(3) (T)">Acetyl:2H(3) (T)</option>
-      <option value="Acetyl:2H(3) (Y)">Acetyl:2H(3) (Y)</option>
-      <option value="Acetyldeoxyhypusine (K)">Acetyldeoxyhypusine (K)</option>
-      <option value="Acetylhypusine (K)">Acetylhypusine (K)</option>
-      <option value="ADP-Ribosyl (C)">ADP-Ribosyl (C)</option>
-      <option value="ADP-Ribosyl (D)">ADP-Ribosyl (D)</option>
-      <option value="ADP-Ribosyl (E)">ADP-Ribosyl (E)</option>
-      <option value="ADP-Ribosyl (K)">ADP-Ribosyl (K)</option>
-      <option value="ADP-Ribosyl (N)">ADP-Ribosyl (N)</option>
-      <option value="ADP-Ribosyl (R)">ADP-Ribosyl (R)</option>
-      <option value="ADP-Ribosyl (S)">ADP-Ribosyl (S)</option>
-      <option value="ADP-Ribosyl (T)">ADP-Ribosyl (T)</option>
-      <option value="AEBS (H)">AEBS (H)</option>
-      <option value="AEBS (K)">AEBS (K)</option>
-      <option value="AEBS (Protein N-term)">AEBS (Protein N-term)</option>
-      <option value="AEBS (S)">AEBS (S)</option>
-      <option value="AEBS (Y)">AEBS (Y)</option>
-      <option value="AEC-MAEC (S)">AEC-MAEC (S)</option>
-      <option value="AEC-MAEC (T)">AEC-MAEC (T)</option>
-      <option value="AEC-MAEC:2H(4) (S)">AEC-MAEC:2H(4) (S)</option>
-      <option value="AEC-MAEC:2H(4) (T)">AEC-MAEC:2H(4) (T)</option>
-      <option value="AFB1_Dialdehyde (K)">AFB1_Dialdehyde (K)</option>
-      <option value="AHA-Alkyne (M)">AHA-Alkyne (M)</option>
-      <option value="AHA-Alkyne-KDDDD (M)">AHA-Alkyne-KDDDD (M)</option>
-      <option value="AHA-SS (M)">AHA-SS (M)</option>
-      <option value="AHA-SS_CAM (M)">AHA-SS_CAM (M)</option>
-      <option value="Ahx2+Hsl (C-term)">Ahx2+Hsl (C-term)</option>
-      <option value="Ala-&gt;Arg (A)">Ala-&gt;Arg (A)</option>
-      <option value="Ala-&gt;Asn (A)">Ala-&gt;Asn (A)</option>
-      <option value="Ala-&gt;Asp (A)">Ala-&gt;Asp (A)</option>
-      <option value="Ala-&gt;Cys (A)">Ala-&gt;Cys (A)</option>
-      <option value="Ala-&gt;Gln (A)">Ala-&gt;Gln (A)</option>
-      <option value="Ala-&gt;Glu (A)">Ala-&gt;Glu (A)</option>
-      <option value="Ala-&gt;Gly (A)">Ala-&gt;Gly (A)</option>
-      <option value="Ala-&gt;His (A)">Ala-&gt;His (A)</option>
-      <option value="Ala-&gt;Lys (A)">Ala-&gt;Lys (A)</option>
-      <option value="Ala-&gt;Met (A)">Ala-&gt;Met (A)</option>
-      <option value="Ala-&gt;Phe (A)">Ala-&gt;Phe (A)</option>
-      <option value="Ala-&gt;Pro (A)">Ala-&gt;Pro (A)</option>
-      <option value="Ala-&gt;Ser (A)">Ala-&gt;Ser (A)</option>
-      <option value="Ala-&gt;Thr (A)">Ala-&gt;Thr (A)</option>
-      <option value="Ala-&gt;Trp (A)">Ala-&gt;Trp (A)</option>
-      <option value="Ala-&gt;Tyr (A)">Ala-&gt;Tyr (A)</option>
-      <option value="Ala-&gt;Val (A)">Ala-&gt;Val (A)</option>
-      <option value="Ala-&gt;Xle (A)">Ala-&gt;Xle (A)</option>
-      <option value="Amidated (C-term)">Amidated (C-term)</option>
-      <option value="Amidated (Protein C-term)">Amidated (Protein C-term)</option>
-      <option value="Amidine (K)">Amidine (K)</option>
-      <option value="Amidine (N-term)">Amidine (N-term)</option>
-      <option value="Amidino (C)">Amidino (C)</option>
-      <option value="Amino (Y)">Amino (Y)</option>
-      <option value="Ammonia-loss (N)">Ammonia-loss (N)</option>
-      <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
-      <option value="Ammonia-loss (Protein N-term S)">Ammonia-loss (Protein N-term S)</option>
-      <option value="Ammonia-loss (Protein N-term T)">Ammonia-loss (Protein N-term T)</option>
-      <option value="Ammonium (C-term)">Ammonium (C-term)</option>
-      <option value="Ammonium (D)">Ammonium (D)</option>
-      <option value="Ammonium (E)">Ammonium (E)</option>
-      <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
-      <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
-      <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
-      <option value="Archaeol (C)">Archaeol (C)</option>
-      <option value="Arg (N-term)">Arg (N-term)</option>
-      <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
-      <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
-      <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
-      <option value="Arg-&gt;Cys (R)">Arg-&gt;Cys (R)</option>
-      <option value="Arg-&gt;Gln (R)">Arg-&gt;Gln (R)</option>
-      <option value="Arg-&gt;Glu (R)">Arg-&gt;Glu (R)</option>
-      <option value="Arg-&gt;GluSA (R)">Arg-&gt;GluSA (R)</option>
-      <option value="Arg-&gt;Gly (R)">Arg-&gt;Gly (R)</option>
-      <option value="Arg-&gt;His (R)">Arg-&gt;His (R)</option>
-      <option value="Arg-&gt;Lys (R)">Arg-&gt;Lys (R)</option>
-      <option value="Arg-&gt;Met (R)">Arg-&gt;Met (R)</option>
-      <option value="Arg-&gt;Npo (R)">Arg-&gt;Npo (R)</option>
-      <option value="Arg-&gt;Orn (R)">Arg-&gt;Orn (R)</option>
-      <option value="Arg-&gt;Phe (R)">Arg-&gt;Phe (R)</option>
-      <option value="Arg-&gt;Pro (R)">Arg-&gt;Pro (R)</option>
-      <option value="Arg-&gt;Ser (R)">Arg-&gt;Ser (R)</option>
-      <option value="Arg-&gt;Thr (R)">Arg-&gt;Thr (R)</option>
-      <option value="Arg-&gt;Trp (R)">Arg-&gt;Trp (R)</option>
-      <option value="Arg-&gt;Tyr (R)">Arg-&gt;Tyr (R)</option>
-      <option value="Arg-&gt;Val (R)">Arg-&gt;Val (R)</option>
-      <option value="Arg-&gt;Xle (R)">Arg-&gt;Xle (R)</option>
-      <option value="Arg-loss (C-term R)">Arg-loss (C-term R)</option>
-      <option value="Arg2PG (R)">Arg2PG (R)</option>
-      <option value="Argbiotinhydrazide (R)">Argbiotinhydrazide (R)</option>
-      <option value="AROD (C)">AROD (C)</option>
-      <option value="Asn-&gt;Ala (N)">Asn-&gt;Ala (N)</option>
-      <option value="Asn-&gt;Arg (N)">Asn-&gt;Arg (N)</option>
-      <option value="Asn-&gt;Asp (N)">Asn-&gt;Asp (N)</option>
-      <option value="Asn-&gt;Cys (N)">Asn-&gt;Cys (N)</option>
-      <option value="Asn-&gt;Gln (N)">Asn-&gt;Gln (N)</option>
-      <option value="Asn-&gt;Glu (N)">Asn-&gt;Glu (N)</option>
-      <option value="Asn-&gt;Gly (N)">Asn-&gt;Gly (N)</option>
-      <option value="Asn-&gt;His (N)">Asn-&gt;His (N)</option>
-      <option value="Asn-&gt;Lys (N)">Asn-&gt;Lys (N)</option>
-      <option value="Asn-&gt;Met (N)">Asn-&gt;Met (N)</option>
-      <option value="Asn-&gt;Phe (N)">Asn-&gt;Phe (N)</option>
-      <option value="Asn-&gt;Pro (N)">Asn-&gt;Pro (N)</option>
-      <option value="Asn-&gt;Ser (N)">Asn-&gt;Ser (N)</option>
-      <option value="Asn-&gt;Thr (N)">Asn-&gt;Thr (N)</option>
-      <option value="Asn-&gt;Trp (N)">Asn-&gt;Trp (N)</option>
-      <option value="Asn-&gt;Tyr (N)">Asn-&gt;Tyr (N)</option>
-      <option value="Asn-&gt;Val (N)">Asn-&gt;Val (N)</option>
-      <option value="Asn-&gt;Xle (N)">Asn-&gt;Xle (N)</option>
-      <option value="Asp-&gt;Ala (D)">Asp-&gt;Ala (D)</option>
-      <option value="Asp-&gt;Arg (D)">Asp-&gt;Arg (D)</option>
-      <option value="Asp-&gt;Asn (D)">Asp-&gt;Asn (D)</option>
-      <option value="Asp-&gt;Cys (D)">Asp-&gt;Cys (D)</option>
-      <option value="Asp-&gt;Gln (D)">Asp-&gt;Gln (D)</option>
-      <option value="Asp-&gt;Glu (D)">Asp-&gt;Glu (D)</option>
-      <option value="Asp-&gt;Gly (D)">Asp-&gt;Gly (D)</option>
-      <option value="Asp-&gt;His (D)">Asp-&gt;His (D)</option>
-      <option value="Asp-&gt;Lys (D)">Asp-&gt;Lys (D)</option>
-      <option value="Asp-&gt;Met (D)">Asp-&gt;Met (D)</option>
-      <option value="Asp-&gt;Phe (D)">Asp-&gt;Phe (D)</option>
-      <option value="Asp-&gt;Pro (D)">Asp-&gt;Pro (D)</option>
-      <option value="Asp-&gt;Ser (D)">Asp-&gt;Ser (D)</option>
-      <option value="Asp-&gt;Thr (D)">Asp-&gt;Thr (D)</option>
-      <option value="Asp-&gt;Trp (D)">Asp-&gt;Trp (D)</option>
-      <option value="Asp-&gt;Tyr (D)">Asp-&gt;Tyr (D)</option>
-      <option value="Asp-&gt;Val (D)">Asp-&gt;Val (D)</option>
-      <option value="Asp-&gt;Xle (D)">Asp-&gt;Xle (D)</option>
-      <option value="Aspartylurea (H)">Aspartylurea (H)</option>
-      <option value="Atto495Maleimide (C)">Atto495Maleimide (C)</option>
-      <option value="AzidoF (F)">AzidoF (F)</option>
-      <option value="azole (C)">azole (C)</option>
-      <option value="azole (S)">azole (S)</option>
-      <option value="Bacillosamine (N)">Bacillosamine (N)</option>
-      <option value="BADGE (C)">BADGE (C)</option>
-      <option value="BDMAPP (H)">BDMAPP (H)</option>
-      <option value="BDMAPP (K)">BDMAPP (K)</option>
-      <option value="BDMAPP (Protein N-term)">BDMAPP (Protein N-term)</option>
-      <option value="BDMAPP (W)">BDMAPP (W)</option>
-      <option value="BDMAPP (Y)">BDMAPP (Y)</option>
-      <option value="BEMAD_C (C)">BEMAD_C (C)</option>
-      <option value="BEMAD_C:2H(6) (C)">BEMAD_C:2H(6) (C)</option>
-      <option value="BEMAD_ST (S)">BEMAD_ST (S)</option>
-      <option value="BEMAD_ST (T)">BEMAD_ST (T)</option>
-      <option value="BEMAD_ST:2H(6) (S)">BEMAD_ST:2H(6) (S)</option>
-      <option value="BEMAD_ST:2H(6) (T)">BEMAD_ST:2H(6) (T)</option>
-      <option value="Benzoyl (K)">Benzoyl (K)</option>
-      <option value="Benzoyl (N-term)">Benzoyl (N-term)</option>
-      <option value="benzylguanidine (K)">benzylguanidine (K)</option>
-      <option value="betaFNA (C)">betaFNA (C)</option>
-      <option value="betaFNA (K)">betaFNA (K)</option>
-      <option value="BHT (C)">BHT (C)</option>
-      <option value="BHT (H)">BHT (H)</option>
-      <option value="BHT (K)">BHT (K)</option>
-      <option value="BHTOH (C)">BHTOH (C)</option>
-      <option value="BHTOH (H)">BHTOH (H)</option>
-      <option value="BHTOH (K)">BHTOH (K)</option>
-      <option value="Biotin (K)">Biotin (K)</option>
-      <option value="Biotin (N-term)">Biotin (N-term)</option>
-      <option value="Biotin-HPDP (C)">Biotin-HPDP (C)</option>
-      <option value="Biotin-PEG-PRA (M)">Biotin-PEG-PRA (M)</option>
-      <option value="Biotin-PEO-Amine (D)">Biotin-PEO-Amine (D)</option>
-      <option value="Biotin-PEO-Amine (E)">Biotin-PEO-Amine (E)</option>
-      <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
-      <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
-      <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
-      <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
-      <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
-      <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
-      <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
-      <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
-      <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
-      <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
-      <option value="Biotin:Thermo-21328 (K)">Biotin:Thermo-21328 (K)</option>
-      <option value="Biotin:Thermo-21328 (N-term)">Biotin:Thermo-21328 (N-term)</option>
-      <option value="Biotin:Thermo-21330 (K)">Biotin:Thermo-21330 (K)</option>
-      <option value="Biotin:Thermo-21330 (N-term)">Biotin:Thermo-21330 (N-term)</option>
-      <option value="Biotin:Thermo-21345 (Q)">Biotin:Thermo-21345 (Q)</option>
-      <option value="Biotin:Thermo-21360 (X)">Biotin:Thermo-21360 (X)</option>
-      <option value="Biotin:Thermo-21901+2H2O (C)">Biotin:Thermo-21901+2H2O (C)</option>
-      <option value="Biotin:Thermo-21901+H2O (C)">Biotin:Thermo-21901+H2O (C)</option>
-      <option value="Biotin:Thermo-21911 (C)">Biotin:Thermo-21911 (C)</option>
-      <option value="Biotin:Thermo-33033 (X)">Biotin:Thermo-33033 (X)</option>
-      <option value="Biotin:Thermo-33033-H (X)">Biotin:Thermo-33033-H (X)</option>
-      <option value="Biotin:Thermo-88310 (K)">Biotin:Thermo-88310 (K)</option>
-      <option value="Biotin:Thermo-88317 (S)">Biotin:Thermo-88317 (S)</option>
-      <option value="Biotin:Thermo-88317 (Y)">Biotin:Thermo-88317 (Y)</option>
-      <option value="biotinAcrolein298 (C)">biotinAcrolein298 (C)</option>
-      <option value="biotinAcrolein298 (H)">biotinAcrolein298 (H)</option>
-      <option value="biotinAcrolein298 (K)">biotinAcrolein298 (K)</option>
-      <option value="biotinAcrolein298 (Protein N-term)">biotinAcrolein298 (Protein N-term)</option>
-      <option value="BisANS (K)">BisANS (K)</option>
-      <option value="bisANS-sulfonates (K)">bisANS-sulfonates (K)</option>
-      <option value="bisANS-sulfonates (S)">bisANS-sulfonates (S)</option>
-      <option value="bisANS-sulfonates (T)">bisANS-sulfonates (T)</option>
-      <option value="BITC (C)">BITC (C)</option>
-      <option value="BITC (K)">BITC (K)</option>
-      <option value="BITC (N-term)">BITC (N-term)</option>
-      <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
-      <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-      <option value="Bodipy (C)">Bodipy (C)</option>
-      <option value="Brij35 (N-term)">Brij35 (N-term)</option>
-      <option value="Brij58 (N-term)">Brij58 (N-term)</option>
-      <option value="Bromo (F)">Bromo (F)</option>
-      <option value="Bromo (H)">Bromo (H)</option>
-      <option value="Bromo (W)">Bromo (W)</option>
-      <option value="Bromo (Y)">Bromo (Y)</option>
-      <option value="Bromobimane (C)">Bromobimane (C)</option>
-      <option value="Butyryl (K)">Butyryl (K)</option>
-      <option value="C8-QAT (K)">C8-QAT (K)</option>
-      <option value="C8-QAT (N-term)">C8-QAT (N-term)</option>
-      <option value="CAF (N-term)">CAF (N-term)</option>
-      <option value="CAMthiopropanoyl (K)">CAMthiopropanoyl (K)</option>
-      <option value="CAMthiopropanoyl (Protein N-term)">CAMthiopropanoyl (Protein N-term)</option>
-      <option value="Can-FP-biotin (S)">Can-FP-biotin (S)</option>
-      <option value="Can-FP-biotin (T)">Can-FP-biotin (T)</option>
-      <option value="Can-FP-biotin (Y)">Can-FP-biotin (Y)</option>
-      <option value="Carbamidomethyl (C)" selected="true">Carbamidomethyl (C)</option>
-      <option value="Carbamidomethyl (D)">Carbamidomethyl (D)</option>
-      <option value="Carbamidomethyl (E)">Carbamidomethyl (E)</option>
-      <option value="Carbamidomethyl (H)">Carbamidomethyl (H)</option>
-      <option value="Carbamidomethyl (K)">Carbamidomethyl (K)</option>
-      <option value="Carbamidomethyl (M)">Carbamidomethyl (M)</option>
-      <option value="Carbamidomethyl (N-term)">Carbamidomethyl (N-term)</option>
-      <option value="Carbamidomethyl (S)">Carbamidomethyl (S)</option>
-      <option value="Carbamidomethyl (T)">Carbamidomethyl (T)</option>
-      <option value="Carbamidomethyl (U)">Carbamidomethyl (U)</option>
-      <option value="Carbamidomethyl (Y)">Carbamidomethyl (Y)</option>
-      <option value="CarbamidomethylDTT (C)">CarbamidomethylDTT (C)</option>
-      <option value="Carbamyl (C)">Carbamyl (C)</option>
-      <option value="Carbamyl (K)">Carbamyl (K)</option>
-      <option value="Carbamyl (M)">Carbamyl (M)</option>
-      <option value="Carbamyl (N-term)">Carbamyl (N-term)</option>
-      <option value="Carbamyl (Protein N-term)">Carbamyl (Protein N-term)</option>
-      <option value="Carbamyl (R)">Carbamyl (R)</option>
-      <option value="Carbamyl (S)">Carbamyl (S)</option>
-      <option value="Carbamyl (T)">Carbamyl (T)</option>
-      <option value="Carbamyl (Y)">Carbamyl (Y)</option>
-      <option value="Carbofuran (S)">Carbofuran (S)</option>
-      <option value="Carbonyl (A)">Carbonyl (A)</option>
-      <option value="Carbonyl (E)">Carbonyl (E)</option>
-      <option value="Carbonyl (I)">Carbonyl (I)</option>
-      <option value="Carbonyl (L)">Carbonyl (L)</option>
-      <option value="Carbonyl (Q)">Carbonyl (Q)</option>
-      <option value="Carbonyl (R)">Carbonyl (R)</option>
-      <option value="Carbonyl (S)">Carbonyl (S)</option>
-      <option value="Carbonyl (V)">Carbonyl (V)</option>
-      <option value="Carboxy (D)">Carboxy (D)</option>
-      <option value="Carboxy (E)">Carboxy (E)</option>
-      <option value="Carboxy (K)">Carboxy (K)</option>
-      <option value="Carboxy (Protein N-term M)">Carboxy (Protein N-term M)</option>
-      <option value="Carboxy (W)">Carboxy (W)</option>
-      <option value="Carboxy-&gt;Thiocarboxy (Protein C-term G)">Carboxy-&gt;Thiocarboxy (Protein C-term G)</option>
-      <option value="Carboxyethyl (H)">Carboxyethyl (H)</option>
-      <option value="Carboxyethyl (K)">Carboxyethyl (K)</option>
-      <option value="Carboxyethylpyrrole (K)">Carboxyethylpyrrole (K)</option>
-      <option value="Carboxymethyl (C)">Carboxymethyl (C)</option>
-      <option value="Carboxymethyl (K)">Carboxymethyl (K)</option>
-      <option value="Carboxymethyl (N-term)">Carboxymethyl (N-term)</option>
-      <option value="Carboxymethyl (U)">Carboxymethyl (U)</option>
-      <option value="Carboxymethyl (W)">Carboxymethyl (W)</option>
-      <option value="Carboxymethyl:13C(2) (C)">Carboxymethyl:13C(2) (C)</option>
-      <option value="CarboxymethylDMAP (N-term)">CarboxymethylDMAP (N-term)</option>
-      <option value="CarboxymethylDTT (C)">CarboxymethylDTT (C)</option>
-      <option value="Cation:Ag (C-term)">Cation:Ag (C-term)</option>
-      <option value="Cation:Ag (D)">Cation:Ag (D)</option>
-      <option value="Cation:Ag (E)">Cation:Ag (E)</option>
-      <option value="Cation:Al[III] (C-term)">Cation:Al[III] (C-term)</option>
-      <option value="Cation:Al[III] (D)">Cation:Al[III] (D)</option>
-      <option value="Cation:Al[III] (E)">Cation:Al[III] (E)</option>
-      <option value="Cation:Ca[II] (C-term)">Cation:Ca[II] (C-term)</option>
-      <option value="Cation:Ca[II] (D)">Cation:Ca[II] (D)</option>
-      <option value="Cation:Ca[II] (E)">Cation:Ca[II] (E)</option>
-      <option value="Cation:Cu[I] (C-term)">Cation:Cu[I] (C-term)</option>
-      <option value="Cation:Cu[I] (D)">Cation:Cu[I] (D)</option>
-      <option value="Cation:Cu[I] (E)">Cation:Cu[I] (E)</option>
-      <option value="Cation:Cu[I] (H)">Cation:Cu[I] (H)</option>
-      <option value="Cation:Fe[II] (C-term)">Cation:Fe[II] (C-term)</option>
-      <option value="Cation:Fe[II] (D)">Cation:Fe[II] (D)</option>
-      <option value="Cation:Fe[II] (E)">Cation:Fe[II] (E)</option>
-      <option value="Cation:Fe[III] (C-term)">Cation:Fe[III] (C-term)</option>
-      <option value="Cation:Fe[III] (D)">Cation:Fe[III] (D)</option>
-      <option value="Cation:Fe[III] (E)">Cation:Fe[III] (E)</option>
-      <option value="Cation:K (C-term)">Cation:K (C-term)</option>
-      <option value="Cation:K (D)">Cation:K (D)</option>
-      <option value="Cation:K (E)">Cation:K (E)</option>
-      <option value="Cation:Li (C-term)">Cation:Li (C-term)</option>
-      <option value="Cation:Li (D)">Cation:Li (D)</option>
-      <option value="Cation:Li (E)">Cation:Li (E)</option>
-      <option value="Cation:Mg[II] (C-term)">Cation:Mg[II] (C-term)</option>
-      <option value="Cation:Mg[II] (D)">Cation:Mg[II] (D)</option>
-      <option value="Cation:Mg[II] (E)">Cation:Mg[II] (E)</option>
-      <option value="Cation:Na (C-term)">Cation:Na (C-term)</option>
-      <option value="Cation:Na (D)">Cation:Na (D)</option>
-      <option value="Cation:Na (E)">Cation:Na (E)</option>
-      <option value="Cation:Ni[II] (C-term)">Cation:Ni[II] (C-term)</option>
-      <option value="Cation:Ni[II] (D)">Cation:Ni[II] (D)</option>
-      <option value="Cation:Ni[II] (E)">Cation:Ni[II] (E)</option>
-      <option value="Cation:Zn[II] (C-term)">Cation:Zn[II] (C-term)</option>
-      <option value="Cation:Zn[II] (D)">Cation:Zn[II] (D)</option>
-      <option value="Cation:Zn[II] (E)">Cation:Zn[II] (E)</option>
-      <option value="Cation:Zn[II] (H)">Cation:Zn[II] (H)</option>
-      <option value="cGMP (C)">cGMP (C)</option>
-      <option value="cGMP (S)">cGMP (S)</option>
-      <option value="cGMP+RMP-loss (C)">cGMP+RMP-loss (C)</option>
-      <option value="cGMP+RMP-loss (S)">cGMP+RMP-loss (S)</option>
-      <option value="CHDH (D)">CHDH (D)</option>
-      <option value="Chlorination (W)">Chlorination (W)</option>
-      <option value="Chlorination (Y)">Chlorination (Y)</option>
-      <option value="Cholesterol (Protein C-term)">Cholesterol (Protein C-term)</option>
-      <option value="CIGG (K)">CIGG (K)</option>
-      <option value="CLIP_TRAQ_2 (K)">CLIP_TRAQ_2 (K)</option>
-      <option value="CLIP_TRAQ_2 (N-term)">CLIP_TRAQ_2 (N-term)</option>
-      <option value="CLIP_TRAQ_2 (Y)">CLIP_TRAQ_2 (Y)</option>
-      <option value="CLIP_TRAQ_3 (K)">CLIP_TRAQ_3 (K)</option>
-      <option value="CLIP_TRAQ_3 (N-term)">CLIP_TRAQ_3 (N-term)</option>
-      <option value="CLIP_TRAQ_3 (Y)">CLIP_TRAQ_3 (Y)</option>
-      <option value="CLIP_TRAQ_4 (K)">CLIP_TRAQ_4 (K)</option>
-      <option value="CLIP_TRAQ_4 (N-term)">CLIP_TRAQ_4 (N-term)</option>
-      <option value="CLIP_TRAQ_4 (Y)">CLIP_TRAQ_4 (Y)</option>
-      <option value="CoenzymeA (C)">CoenzymeA (C)</option>
-      <option value="Cresylphosphate (H)">Cresylphosphate (H)</option>
-      <option value="Cresylphosphate (K)">Cresylphosphate (K)</option>
-      <option value="Cresylphosphate (R)">Cresylphosphate (R)</option>
-      <option value="Cresylphosphate (S)">Cresylphosphate (S)</option>
-      <option value="Cresylphosphate (T)">Cresylphosphate (T)</option>
-      <option value="Cresylphosphate (Y)">Cresylphosphate (Y)</option>
-      <option value="CresylSaligeninPhosphate (H)">CresylSaligeninPhosphate (H)</option>
-      <option value="CresylSaligeninPhosphate (K)">CresylSaligeninPhosphate (K)</option>
-      <option value="CresylSaligeninPhosphate (R)">CresylSaligeninPhosphate (R)</option>
-      <option value="CresylSaligeninPhosphate (S)">CresylSaligeninPhosphate (S)</option>
-      <option value="CresylSaligeninPhosphate (T)">CresylSaligeninPhosphate (T)</option>
-      <option value="CresylSaligeninPhosphate (Y)">CresylSaligeninPhosphate (Y)</option>
-      <option value="Crotonaldehyde (C)">Crotonaldehyde (C)</option>
-      <option value="Crotonaldehyde (H)">Crotonaldehyde (H)</option>
-      <option value="Crotonaldehyde (K)">Crotonaldehyde (K)</option>
-      <option value="Crotonyl (K)">Crotonyl (K)</option>
-      <option value="CuSMo (C)">CuSMo (C)</option>
-      <option value="CUSTOM0 (A)">CUSTOM0 (A)</option>
-      <option value="CUSTOM0 (C)">CUSTOM0 (C)</option>
-      <option value="CUSTOM0 (C-term)">CUSTOM0 (C-term)</option>
-      <option value="CUSTOM0 (D)">CUSTOM0 (D)</option>
-      <option value="CUSTOM0 (E)">CUSTOM0 (E)</option>
-      <option value="CUSTOM0 (F)">CUSTOM0 (F)</option>
-      <option value="CUSTOM0 (G)">CUSTOM0 (G)</option>
-      <option value="CUSTOM0 (H)">CUSTOM0 (H)</option>
-      <option value="CUSTOM0 (I)">CUSTOM0 (I)</option>
-      <option value="CUSTOM0 (K)">CUSTOM0 (K)</option>
-      <option value="CUSTOM0 (L)">CUSTOM0 (L)</option>
-      <option value="CUSTOM0 (M)">CUSTOM0 (M)</option>
-      <option value="CUSTOM0 (N)">CUSTOM0 (N)</option>
-      <option value="CUSTOM0 (N-term)">CUSTOM0 (N-term)</option>
-      <option value="CUSTOM0 (P)">CUSTOM0 (P)</option>
-      <option value="CUSTOM0 (Q)">CUSTOM0 (Q)</option>
-      <option value="CUSTOM0 (R)">CUSTOM0 (R)</option>
-      <option value="CUSTOM0 (S)">CUSTOM0 (S)</option>
-      <option value="CUSTOM0 (T)">CUSTOM0 (T)</option>
-      <option value="CUSTOM0 (V)">CUSTOM0 (V)</option>
-      <option value="CUSTOM0 (W)">CUSTOM0 (W)</option>
-      <option value="CUSTOM0 (Y)">CUSTOM0 (Y)</option>
-      <option value="CUSTOM1 (A)">CUSTOM1 (A)</option>
-      <option value="CUSTOM1 (C)">CUSTOM1 (C)</option>
-      <option value="CUSTOM1 (C-term)">CUSTOM1 (C-term)</option>
-      <option value="CUSTOM1 (D)">CUSTOM1 (D)</option>
-      <option value="CUSTOM1 (E)">CUSTOM1 (E)</option>
-      <option value="CUSTOM1 (F)">CUSTOM1 (F)</option>
-      <option value="CUSTOM1 (G)">CUSTOM1 (G)</option>
-      <option value="CUSTOM1 (H)">CUSTOM1 (H)</option>
-      <option value="CUSTOM1 (I)">CUSTOM1 (I)</option>
-      <option value="CUSTOM1 (K)">CUSTOM1 (K)</option>
-      <option value="CUSTOM1 (L)">CUSTOM1 (L)</option>
-      <option value="CUSTOM1 (M)">CUSTOM1 (M)</option>
-      <option value="CUSTOM1 (N)">CUSTOM1 (N)</option>
-      <option value="CUSTOM1 (N-term)">CUSTOM1 (N-term)</option>
-      <option value="CUSTOM1 (P)">CUSTOM1 (P)</option>
-      <option value="CUSTOM1 (Q)">CUSTOM1 (Q)</option>
-      <option value="CUSTOM1 (R)">CUSTOM1 (R)</option>
-      <option value="CUSTOM1 (S)">CUSTOM1 (S)</option>
-      <option value="CUSTOM1 (T)">CUSTOM1 (T)</option>
-      <option value="CUSTOM1 (V)">CUSTOM1 (V)</option>
-      <option value="CUSTOM1 (W)">CUSTOM1 (W)</option>
-      <option value="CUSTOM1 (Y)">CUSTOM1 (Y)</option>
-      <option value="CUSTOM2 (A)">CUSTOM2 (A)</option>
-      <option value="CUSTOM2 (C)">CUSTOM2 (C)</option>
-      <option value="CUSTOM2 (C-term)">CUSTOM2 (C-term)</option>
-      <option value="CUSTOM2 (D)">CUSTOM2 (D)</option>
-      <option value="CUSTOM2 (E)">CUSTOM2 (E)</option>
-      <option value="CUSTOM2 (F)">CUSTOM2 (F)</option>
-      <option value="CUSTOM2 (G)">CUSTOM2 (G)</option>
-      <option value="CUSTOM2 (H)">CUSTOM2 (H)</option>
-      <option value="CUSTOM2 (I)">CUSTOM2 (I)</option>
-      <option value="CUSTOM2 (K)">CUSTOM2 (K)</option>
-      <option value="CUSTOM2 (L)">CUSTOM2 (L)</option>
-      <option value="CUSTOM2 (M)">CUSTOM2 (M)</option>
-      <option value="CUSTOM2 (N)">CUSTOM2 (N)</option>
-      <option value="CUSTOM2 (N-term)">CUSTOM2 (N-term)</option>
-      <option value="CUSTOM2 (P)">CUSTOM2 (P)</option>
-      <option value="CUSTOM2 (Q)">CUSTOM2 (Q)</option>
-      <option value="CUSTOM2 (R)">CUSTOM2 (R)</option>
-      <option value="CUSTOM2 (S)">CUSTOM2 (S)</option>
-      <option value="CUSTOM2 (T)">CUSTOM2 (T)</option>
-      <option value="CUSTOM2 (V)">CUSTOM2 (V)</option>
-      <option value="CUSTOM2 (W)">CUSTOM2 (W)</option>
-      <option value="CUSTOM2 (Y)">CUSTOM2 (Y)</option>
-      <option value="CUSTOM3 (A)">CUSTOM3 (A)</option>
-      <option value="CUSTOM3 (C)">CUSTOM3 (C)</option>
-      <option value="CUSTOM3 (C-term)">CUSTOM3 (C-term)</option>
-      <option value="CUSTOM3 (D)">CUSTOM3 (D)</option>
-      <option value="CUSTOM3 (E)">CUSTOM3 (E)</option>
-      <option value="CUSTOM3 (F)">CUSTOM3 (F)</option>
-      <option value="CUSTOM3 (G)">CUSTOM3 (G)</option>
-      <option value="CUSTOM3 (H)">CUSTOM3 (H)</option>
-      <option value="CUSTOM3 (I)">CUSTOM3 (I)</option>
-      <option value="CUSTOM3 (K)">CUSTOM3 (K)</option>
-      <option value="CUSTOM3 (L)">CUSTOM3 (L)</option>
-      <option value="CUSTOM3 (M)">CUSTOM3 (M)</option>
-      <option value="CUSTOM3 (N)">CUSTOM3 (N)</option>
-      <option value="CUSTOM3 (N-term)">CUSTOM3 (N-term)</option>
-      <option value="CUSTOM3 (P)">CUSTOM3 (P)</option>
-      <option value="CUSTOM3 (Q)">CUSTOM3 (Q)</option>
-      <option value="CUSTOM3 (R)">CUSTOM3 (R)</option>
-      <option value="CUSTOM3 (S)">CUSTOM3 (S)</option>
-      <option value="CUSTOM3 (T)">CUSTOM3 (T)</option>
-      <option value="CUSTOM3 (V)">CUSTOM3 (V)</option>
-      <option value="CUSTOM3 (W)">CUSTOM3 (W)</option>
-      <option value="CUSTOM3 (Y)">CUSTOM3 (Y)</option>
-      <option value="CUSTOM4 (A)">CUSTOM4 (A)</option>
-      <option value="CUSTOM4 (C)">CUSTOM4 (C)</option>
-      <option value="CUSTOM4 (C-term)">CUSTOM4 (C-term)</option>
-      <option value="CUSTOM4 (D)">CUSTOM4 (D)</option>
-      <option value="CUSTOM4 (E)">CUSTOM4 (E)</option>
-      <option value="CUSTOM4 (F)">CUSTOM4 (F)</option>
-      <option value="CUSTOM4 (G)">CUSTOM4 (G)</option>
-      <option value="CUSTOM4 (H)">CUSTOM4 (H)</option>
-      <option value="CUSTOM4 (I)">CUSTOM4 (I)</option>
-      <option value="CUSTOM4 (K)">CUSTOM4 (K)</option>
-      <option value="CUSTOM4 (L)">CUSTOM4 (L)</option>
-      <option value="CUSTOM4 (M)">CUSTOM4 (M)</option>
-      <option value="CUSTOM4 (N)">CUSTOM4 (N)</option>
-      <option value="CUSTOM4 (N-term)">CUSTOM4 (N-term)</option>
-      <option value="CUSTOM4 (P)">CUSTOM4 (P)</option>
-      <option value="CUSTOM4 (Q)">CUSTOM4 (Q)</option>
-      <option value="CUSTOM4 (R)">CUSTOM4 (R)</option>
-      <option value="CUSTOM4 (S)">CUSTOM4 (S)</option>
-      <option value="CUSTOM4 (T)">CUSTOM4 (T)</option>
-      <option value="CUSTOM4 (V)">CUSTOM4 (V)</option>
-      <option value="CUSTOM4 (W)">CUSTOM4 (W)</option>
-      <option value="CUSTOM4 (Y)">CUSTOM4 (Y)</option>
-      <option value="CUSTOM5 (A)">CUSTOM5 (A)</option>
-      <option value="CUSTOM5 (C)">CUSTOM5 (C)</option>
-      <option value="CUSTOM5 (C-term)">CUSTOM5 (C-term)</option>
-      <option value="CUSTOM5 (D)">CUSTOM5 (D)</option>
-      <option value="CUSTOM5 (E)">CUSTOM5 (E)</option>
-      <option value="CUSTOM5 (F)">CUSTOM5 (F)</option>
-      <option value="CUSTOM5 (G)">CUSTOM5 (G)</option>
-      <option value="CUSTOM5 (H)">CUSTOM5 (H)</option>
-      <option value="CUSTOM5 (I)">CUSTOM5 (I)</option>
-      <option value="CUSTOM5 (K)">CUSTOM5 (K)</option>
-      <option value="CUSTOM5 (L)">CUSTOM5 (L)</option>
-      <option value="CUSTOM5 (M)">CUSTOM5 (M)</option>
-      <option value="CUSTOM5 (N)">CUSTOM5 (N)</option>
-      <option value="CUSTOM5 (N-term)">CUSTOM5 (N-term)</option>
-      <option value="CUSTOM5 (P)">CUSTOM5 (P)</option>
-      <option value="CUSTOM5 (Q)">CUSTOM5 (Q)</option>
-      <option value="CUSTOM5 (R)">CUSTOM5 (R)</option>
-      <option value="CUSTOM5 (S)">CUSTOM5 (S)</option>
-      <option value="CUSTOM5 (T)">CUSTOM5 (T)</option>
-      <option value="CUSTOM5 (V)">CUSTOM5 (V)</option>
-      <option value="CUSTOM5 (W)">CUSTOM5 (W)</option>
-      <option value="CUSTOM5 (Y)">CUSTOM5 (Y)</option>
-      <option value="CUSTOM6 (A)">CUSTOM6 (A)</option>
-      <option value="CUSTOM6 (C)">CUSTOM6 (C)</option>
-      <option value="CUSTOM6 (C-term)">CUSTOM6 (C-term)</option>
-      <option value="CUSTOM6 (D)">CUSTOM6 (D)</option>
-      <option value="CUSTOM6 (E)">CUSTOM6 (E)</option>
-      <option value="CUSTOM6 (F)">CUSTOM6 (F)</option>
-      <option value="CUSTOM6 (G)">CUSTOM6 (G)</option>
-      <option value="CUSTOM6 (H)">CUSTOM6 (H)</option>
-      <option value="CUSTOM6 (I)">CUSTOM6 (I)</option>
-      <option value="CUSTOM6 (K)">CUSTOM6 (K)</option>
-      <option value="CUSTOM6 (L)">CUSTOM6 (L)</option>
-      <option value="CUSTOM6 (M)">CUSTOM6 (M)</option>
-      <option value="CUSTOM6 (N)">CUSTOM6 (N)</option>
-      <option value="CUSTOM6 (N-term)">CUSTOM6 (N-term)</option>
-      <option value="CUSTOM6 (P)">CUSTOM6 (P)</option>
-      <option value="CUSTOM6 (Q)">CUSTOM6 (Q)</option>
-      <option value="CUSTOM6 (R)">CUSTOM6 (R)</option>
-      <option value="CUSTOM6 (S)">CUSTOM6 (S)</option>
-      <option value="CUSTOM6 (T)">CUSTOM6 (T)</option>
-      <option value="CUSTOM6 (V)">CUSTOM6 (V)</option>
-      <option value="CUSTOM6 (W)">CUSTOM6 (W)</option>
-      <option value="CUSTOM6 (Y)">CUSTOM6 (Y)</option>
-      <option value="CUSTOM7 (A)">CUSTOM7 (A)</option>
-      <option value="CUSTOM7 (C)">CUSTOM7 (C)</option>
-      <option value="CUSTOM7 (C-term)">CUSTOM7 (C-term)</option>
-      <option value="CUSTOM7 (D)">CUSTOM7 (D)</option>
-      <option value="CUSTOM7 (E)">CUSTOM7 (E)</option>
-      <option value="CUSTOM7 (F)">CUSTOM7 (F)</option>
-      <option value="CUSTOM7 (G)">CUSTOM7 (G)</option>
-      <option value="CUSTOM7 (H)">CUSTOM7 (H)</option>
-      <option value="CUSTOM7 (I)">CUSTOM7 (I)</option>
-      <option value="CUSTOM7 (K)">CUSTOM7 (K)</option>
-      <option value="CUSTOM7 (L)">CUSTOM7 (L)</option>
-      <option value="CUSTOM7 (M)">CUSTOM7 (M)</option>
-      <option value="CUSTOM7 (N)">CUSTOM7 (N)</option>
-      <option value="CUSTOM7 (N-term)">CUSTOM7 (N-term)</option>
-      <option value="CUSTOM7 (P)">CUSTOM7 (P)</option>
-      <option value="CUSTOM7 (Q)">CUSTOM7 (Q)</option>
-      <option value="CUSTOM7 (R)">CUSTOM7 (R)</option>
-      <option value="CUSTOM7 (S)">CUSTOM7 (S)</option>
-      <option value="CUSTOM7 (T)">CUSTOM7 (T)</option>
-      <option value="CUSTOM7 (V)">CUSTOM7 (V)</option>
-      <option value="CUSTOM7 (W)">CUSTOM7 (W)</option>
-      <option value="CUSTOM7 (Y)">CUSTOM7 (Y)</option>
-      <option value="CUSTOM8 (A)">CUSTOM8 (A)</option>
-      <option value="CUSTOM8 (C)">CUSTOM8 (C)</option>
-      <option value="CUSTOM8 (C-term)">CUSTOM8 (C-term)</option>
-      <option value="CUSTOM8 (D)">CUSTOM8 (D)</option>
-      <option value="CUSTOM8 (E)">CUSTOM8 (E)</option>
-      <option value="CUSTOM8 (F)">CUSTOM8 (F)</option>
-      <option value="CUSTOM8 (G)">CUSTOM8 (G)</option>
-      <option value="CUSTOM8 (H)">CUSTOM8 (H)</option>
-      <option value="CUSTOM8 (I)">CUSTOM8 (I)</option>
-      <option value="CUSTOM8 (K)">CUSTOM8 (K)</option>
-      <option value="CUSTOM8 (L)">CUSTOM8 (L)</option>
-      <option value="CUSTOM8 (M)">CUSTOM8 (M)</option>
-      <option value="CUSTOM8 (N)">CUSTOM8 (N)</option>
-      <option value="CUSTOM8 (N-term)">CUSTOM8 (N-term)</option>
-      <option value="CUSTOM8 (P)">CUSTOM8 (P)</option>
-      <option value="CUSTOM8 (Q)">CUSTOM8 (Q)</option>
-      <option value="CUSTOM8 (R)">CUSTOM8 (R)</option>
-      <option value="CUSTOM8 (S)">CUSTOM8 (S)</option>
-      <option value="CUSTOM8 (T)">CUSTOM8 (T)</option>
-      <option value="CUSTOM8 (V)">CUSTOM8 (V)</option>
-      <option value="CUSTOM8 (W)">CUSTOM8 (W)</option>
-      <option value="CUSTOM8 (Y)">CUSTOM8 (Y)</option>
-      <option value="CUSTOM9 (A)">CUSTOM9 (A)</option>
-      <option value="CUSTOM9 (C)">CUSTOM9 (C)</option>
-      <option value="CUSTOM9 (C-term)">CUSTOM9 (C-term)</option>
-      <option value="CUSTOM9 (D)">CUSTOM9 (D)</option>
-      <option value="CUSTOM9 (E)">CUSTOM9 (E)</option>
-      <option value="CUSTOM9 (F)">CUSTOM9 (F)</option>
-      <option value="CUSTOM9 (G)">CUSTOM9 (G)</option>
-      <option value="CUSTOM9 (H)">CUSTOM9 (H)</option>
-      <option value="CUSTOM9 (I)">CUSTOM9 (I)</option>
-      <option value="CUSTOM9 (K)">CUSTOM9 (K)</option>
-      <option value="CUSTOM9 (L)">CUSTOM9 (L)</option>
-      <option value="CUSTOM9 (M)">CUSTOM9 (M)</option>
-      <option value="CUSTOM9 (N)">CUSTOM9 (N)</option>
-      <option value="CUSTOM9 (N-term)">CUSTOM9 (N-term)</option>
-      <option value="CUSTOM9 (P)">CUSTOM9 (P)</option>
-      <option value="CUSTOM9 (Q)">CUSTOM9 (Q)</option>
-      <option value="CUSTOM9 (R)">CUSTOM9 (R)</option>
-      <option value="CUSTOM9 (S)">CUSTOM9 (S)</option>
-      <option value="CUSTOM9 (T)">CUSTOM9 (T)</option>
-      <option value="CUSTOM9 (V)">CUSTOM9 (V)</option>
-      <option value="CUSTOM9 (W)">CUSTOM9 (W)</option>
-      <option value="CUSTOM9 (Y)">CUSTOM9 (Y)</option>
-      <option value="Cy3-maleimide (C)">Cy3-maleimide (C)</option>
-      <option value="Cy3b-maleimide (C)">Cy3b-maleimide (C)</option>
-      <option value="Cyano (C)">Cyano (C)</option>
-      <option value="CyDye-Cy3 (C)">CyDye-Cy3 (C)</option>
-      <option value="CyDye-Cy5 (C)">CyDye-Cy5 (C)</option>
-      <option value="Cys-&gt;Ala (C)">Cys-&gt;Ala (C)</option>
-      <option value="Cys-&gt;Arg (C)">Cys-&gt;Arg (C)</option>
-      <option value="Cys-&gt;Asn (C)">Cys-&gt;Asn (C)</option>
-      <option value="Cys-&gt;Asp (C)">Cys-&gt;Asp (C)</option>
-      <option value="Cys-&gt;CamSec (C)">Cys-&gt;CamSec (C)</option>
-      <option value="Cys-&gt;Dha (C)">Cys-&gt;Dha (C)</option>
-      <option value="Cys-&gt;ethylaminoAla (C)">Cys-&gt;ethylaminoAla (C)</option>
-      <option value="Cys-&gt;Gln (C)">Cys-&gt;Gln (C)</option>
-      <option value="Cys-&gt;Glu (C)">Cys-&gt;Glu (C)</option>
-      <option value="Cys-&gt;Gly (C)">Cys-&gt;Gly (C)</option>
-      <option value="Cys-&gt;His (C)">Cys-&gt;His (C)</option>
-      <option value="Cys-&gt;Lys (C)">Cys-&gt;Lys (C)</option>
-      <option value="Cys-&gt;Met (C)">Cys-&gt;Met (C)</option>
-      <option value="Cys-&gt;methylaminoAla (C)">Cys-&gt;methylaminoAla (C)</option>
-      <option value="Cys-&gt;Oxoalanine (C)">Cys-&gt;Oxoalanine (C)</option>
-      <option value="Cys-&gt;Phe (C)">Cys-&gt;Phe (C)</option>
-      <option value="Cys-&gt;Pro (C)">Cys-&gt;Pro (C)</option>
-      <option value="Cys-&gt;PyruvicAcid (Protein N-term C)">Cys-&gt;PyruvicAcid (Protein N-term C)</option>
-      <option value="Cys-&gt;SecNEM (C)">Cys-&gt;SecNEM (C)</option>
-      <option value="Cys-&gt;SecNEM:2H(5) (C)">Cys-&gt;SecNEM:2H(5) (C)</option>
-      <option value="Cys-&gt;Ser (C)">Cys-&gt;Ser (C)</option>
-      <option value="Cys-&gt;Thr (C)">Cys-&gt;Thr (C)</option>
-      <option value="Cys-&gt;Trp (C)">Cys-&gt;Trp (C)</option>
-      <option value="Cys-&gt;Tyr (C)">Cys-&gt;Tyr (C)</option>
-      <option value="Cys-&gt;Val (C)">Cys-&gt;Val (C)</option>
-      <option value="Cys-&gt;Xle (C)">Cys-&gt;Xle (C)</option>
-      <option value="Cysteinyl (C)">Cysteinyl (C)</option>
-      <option value="cysTMT (C)">cysTMT (C)</option>
-      <option value="cysTMT6plex (C)">cysTMT6plex (C)</option>
-      <option value="Cytopiloyne (C)">Cytopiloyne (C)</option>
-      <option value="Cytopiloyne (K)">Cytopiloyne (K)</option>
-      <option value="Cytopiloyne (N-term)">Cytopiloyne (N-term)</option>
-      <option value="Cytopiloyne (P)">Cytopiloyne (P)</option>
-      <option value="Cytopiloyne (R)">Cytopiloyne (R)</option>
-      <option value="Cytopiloyne (S)">Cytopiloyne (S)</option>
-      <option value="Cytopiloyne (Y)">Cytopiloyne (Y)</option>
-      <option value="Cytopiloyne+water (C)">Cytopiloyne+water (C)</option>
-      <option value="Cytopiloyne+water (K)">Cytopiloyne+water (K)</option>
-      <option value="Cytopiloyne+water (N-term)">Cytopiloyne+water (N-term)</option>
-      <option value="Cytopiloyne+water (R)">Cytopiloyne+water (R)</option>
-      <option value="Cytopiloyne+water (S)">Cytopiloyne+water (S)</option>
-      <option value="Cytopiloyne+water (T)">Cytopiloyne+water (T)</option>
-      <option value="Cytopiloyne+water (Y)">Cytopiloyne+water (Y)</option>
-      <option value="DAET (S)">DAET (S)</option>
-      <option value="DAET (T)">DAET (T)</option>
-      <option value="Dansyl (K)">Dansyl (K)</option>
-      <option value="Dansyl (N-term)">Dansyl (N-term)</option>
-      <option value="Dap-DSP (A)">Dap-DSP (A)</option>
-      <option value="Dap-DSP (E)">Dap-DSP (E)</option>
-      <option value="Dap-DSP (K)">Dap-DSP (K)</option>
-      <option value="Deamidated (N)">Deamidated (N)</option>
-      <option value="Deamidated (Protein N-term F)">Deamidated (Protein N-term F)</option>
-      <option value="Deamidated (Q)">Deamidated (Q)</option>
-      <option value="Deamidated (R)">Deamidated (R)</option>
-      <option value="Deamidated:18O(1) (N)">Deamidated:18O(1) (N)</option>
-      <option value="Deamidated:18O(1) (Q)">Deamidated:18O(1) (Q)</option>
-      <option value="Decanoyl (S)">Decanoyl (S)</option>
-      <option value="Decanoyl (T)">Decanoyl (T)</option>
-      <option value="Decarboxylation (D)">Decarboxylation (D)</option>
-      <option value="Decarboxylation (E)">Decarboxylation (E)</option>
-      <option value="DEDGFLYMVYASQETFG (K)">DEDGFLYMVYASQETFG (K)</option>
-      <option value="Dehydrated (D)">Dehydrated (D)</option>
-      <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
-      <option value="Dehydrated (Protein C-term N)">Dehydrated (Protein C-term N)</option>
-      <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
-      <option value="Dehydrated (S)">Dehydrated (S)</option>
-      <option value="Dehydrated (T)">Dehydrated (T)</option>
-      <option value="Dehydrated (Y)">Dehydrated (Y)</option>
-      <option value="Dehydro (C)">Dehydro (C)</option>
-      <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
-      <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-      <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
-      <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
-      <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
-      <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
-      <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
-      <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
-      <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
-      <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
-      <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
-      <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-      <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
-      <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
-      <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
-      <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
-      <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
-      <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
-      <option value="Delta:H(4)C(3) (K)">Delta:H(4)C(3) (K)</option>
-      <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
-      <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
-      <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
-      <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
-      <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
-      <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
-      <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
-      <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
-      <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
-      <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
-      <option value="Delta:H(6)C(3)O(1) (K)">Delta:H(6)C(3)O(1) (K)</option>
-      <option value="Delta:H(6)C(3)O(1) (Protein N-term)">Delta:H(6)C(3)O(1) (Protein N-term)</option>
-      <option value="Delta:H(6)C(6)O(1) (K)">Delta:H(6)C(6)O(1) (K)</option>
-      <option value="Delta:H(6)C(7)O(4) (R)">Delta:H(6)C(7)O(4) (R)</option>
-      <option value="Delta:H(8)C(6)O(1) (K)">Delta:H(8)C(6)O(1) (K)</option>
-      <option value="Delta:H(8)C(6)O(1) (Protein N-term)">Delta:H(8)C(6)O(1) (Protein N-term)</option>
-      <option value="Delta:H(8)C(6)O(2) (K)">Delta:H(8)C(6)O(2) (K)</option>
-      <option value="Delta:Hg(1) (C)">Delta:Hg(1) (C)</option>
-      <option value="Delta:O(4) (W)">Delta:O(4) (W)</option>
-      <option value="Delta:S(-1)Se(1) (C)">Delta:S(-1)Se(1) (C)</option>
-      <option value="Delta:S(-1)Se(1) (M)">Delta:S(-1)Se(1) (M)</option>
-      <option value="Delta:Se(1) (C)">Delta:Se(1) (C)</option>
-      <option value="Deoxy (D)">Deoxy (D)</option>
-      <option value="Deoxy (S)">Deoxy (S)</option>
-      <option value="Deoxy (T)">Deoxy (T)</option>
-      <option value="Deoxyhypusine (K)">Deoxyhypusine (K)</option>
-      <option value="Deoxyhypusine (Q)">Deoxyhypusine (Q)</option>
-      <option value="DeStreak (C)">DeStreak (C)</option>
-      <option value="Dethiomethyl (M)">Dethiomethyl (M)</option>
-      <option value="dHex (N)">dHex (N)</option>
-      <option value="dHex (S)">dHex (S)</option>
-      <option value="dHex (T)">dHex (T)</option>
-      <option value="dHex(1)Hex(1) (S)">dHex(1)Hex(1) (S)</option>
-      <option value="dHex(1)Hex(1) (T)">dHex(1)Hex(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexA(1)HexNAc(3) (S)">dHex(1)Hex(1)HexA(1)HexNAc(3) (S)</option>
-      <option value="dHex(1)Hex(1)HexA(1)HexNAc(3) (T)">dHex(1)Hex(1)HexA(1)HexNAc(3) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)Kdn(1) (S)">dHex(1)Hex(1)HexNAc(1)Kdn(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)Kdn(1) (T)">dHex(1)Hex(1)HexNAc(1)Kdn(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(1)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(1)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3) (S)">dHex(1)Hex(1)HexNAc(3) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3) (T)">dHex(1)Hex(1)HexNAc(3) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(4) (S)">dHex(1)Hex(1)HexNAc(4) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(4) (T)">dHex(1)Hex(1)HexNAc(4) (T)</option>
-      <option value="dHex(1)Hex(2) (S)">dHex(1)Hex(2) (S)</option>
-      <option value="dHex(1)Hex(2) (T)">dHex(1)Hex(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexA(1) (S)">dHex(1)Hex(2)HexA(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexA(1) (T)">dHex(1)Hex(2)HexA(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(1) (S)">dHex(1)Hex(2)HexA(1)HexNAc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(1) (T)">dHex(1)Hex(2)HexA(1)HexNAc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (S)">dHex(1)Hex(2)HexA(1)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (T)">dHex(1)Hex(2)HexA(1)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1) (S)">dHex(1)Hex(2)HexNAc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1) (T)">dHex(1)Hex(2)HexNAc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)Pent(1) (N)">dHex(1)Hex(2)HexNAc(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3) (N)">dHex(1)Hex(2)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3) (S)">dHex(1)Hex(2)HexNAc(3) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3) (T)">dHex(1)Hex(2)HexNAc(3) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4) (N)">dHex(1)Hex(2)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4) (S)">dHex(1)Hex(2)HexNAc(4) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4) (T)">dHex(1)Hex(2)HexNAc(4) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-      <option value="dHex(1)Hex(3) (S)">dHex(1)Hex(3) (S)</option>
-      <option value="dHex(1)Hex(3) (T)">dHex(1)Hex(3) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(2) (S)">dHex(1)Hex(3)HexA(1)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(2) (T)">dHex(1)Hex(3)HexA(1)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(2)HexNAc(2) (S)">dHex(1)Hex(3)HexA(2)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(2)HexNAc(2) (T)">dHex(1)Hex(3)HexA(2)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(1) (S)">dHex(1)Hex(3)HexNAc(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(1) (T)">dHex(1)Hex(3)HexNAc(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2) (N)">dHex(1)Hex(3)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2) (S)">dHex(1)Hex(3)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2) (T)">dHex(1)Hex(3)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)Pent(1) (N)">dHex(1)Hex(3)HexNAc(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3) (N)">dHex(1)Hex(3)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3) (S)">dHex(1)Hex(3)HexNAc(3) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3) (T)">dHex(1)Hex(3)HexNAc(3) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Pent(1) (N)">dHex(1)Hex(3)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Pent(2) (N)">dHex(1)Hex(3)HexNAc(3)Pent(2) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Pent(3) (N)">dHex(1)Hex(3)HexNAc(3)Pent(3) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4) (N)">dHex(1)Hex(3)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4) (S)">dHex(1)Hex(3)HexNAc(4) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4) (T)">dHex(1)Hex(3)HexNAc(4) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)Pent(1) (N)">dHex(1)Hex(3)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)Pent(2) (N)">dHex(1)Hex(3)HexNAc(4)Pent(2) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)Pent(3) (N)">dHex(1)Hex(3)HexNAc(4)Pent(3) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5) (N)">dHex(1)Hex(3)HexNAc(5) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5) (S)">dHex(1)Hex(3)HexNAc(5) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5) (T)">dHex(1)Hex(3)HexNAc(5) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(5)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(6) (N)">dHex(1)Hex(3)HexNAc(6) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(6) (S)">dHex(1)Hex(3)HexNAc(6) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(6) (T)">dHex(1)Hex(3)HexNAc(6) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4) (S)">dHex(1)Hex(4) (S)</option>
-      <option value="dHex(1)Hex(4) (T)">dHex(1)Hex(4) (T)</option>
-      <option value="dHex(1)Hex(4)HexA(1) (S)">dHex(1)Hex(4)HexA(1) (S)</option>
-      <option value="dHex(1)Hex(4)HexA(1) (T)">dHex(1)Hex(4)HexA(1) (T)</option>
-      <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (S)">dHex(1)Hex(4)HexA(1)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (T)">dHex(1)Hex(4)HexA(1)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(1)Pent(1) (N)">dHex(1)Hex(4)HexNAc(1)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(2) (N)">dHex(1)Hex(4)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(2) (S)">dHex(1)Hex(4)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(4)HexNAc(2) (T)">dHex(1)Hex(4)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(2)Pent(1) (N)">dHex(1)Hex(4)HexNAc(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3) (N)">dHex(1)Hex(4)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)Pent(1) (N)">dHex(1)Hex(4)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4) (N)">dHex(1)Hex(4)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4) (S)">dHex(1)Hex(4)HexNAc(4) (S)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4) (T)">dHex(1)Hex(4)HexNAc(4) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)Pent(1) (N)">dHex(1)Hex(4)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(5) (N)">dHex(1)Hex(4)HexNAc(5) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(5)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(5)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5) (S)">dHex(1)Hex(5) (S)</option>
-      <option value="dHex(1)Hex(5) (T)">dHex(1)Hex(5) (T)</option>
-      <option value="dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N)">dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(2) (N)">dHex(1)Hex(5)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(2)Pent(1) (N)">dHex(1)Hex(5)HexNAc(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3) (N)">dHex(1)Hex(5)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4) (N)">dHex(1)Hex(5)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N)">dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N)">dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)Pent(1) (N)">dHex(1)Hex(5)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)Sulf(2) (N)">dHex(1)Hex(5)HexNAc(4)Sulf(2) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(5) (N)">dHex(1)Hex(5)HexNAc(5) (N)</option>
-      <option value="dHex(1)Hex(6) (S)">dHex(1)Hex(6) (S)</option>
-      <option value="dHex(1)Hex(6) (T)">dHex(1)Hex(6) (T)</option>
-      <option value="dHex(1)Hex(6)HexNAc(2) (N)">dHex(1)Hex(6)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(6)HexNAc(3) (N)">dHex(1)Hex(6)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(6)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(6)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(6)HexNAc(4) (N)">dHex(1)Hex(6)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(2) (N)">dHex(1)Hex(7)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(3) (N)">dHex(1)Hex(7)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(3)Phos(1) (N)">dHex(1)Hex(7)HexNAc(3)Phos(1) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(4) (N)">dHex(1)Hex(7)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(8)HexNAc(2) (N)">dHex(1)Hex(8)HexNAc(2) (N)</option>
-      <option value="dHex(1)HexNAc(3) (S)">dHex(1)HexNAc(3) (S)</option>
-      <option value="dHex(1)HexNAc(3) (T)">dHex(1)HexNAc(3) (T)</option>
-      <option value="dHex(1)HexNAc(4) (S)">dHex(1)HexNAc(4) (S)</option>
-      <option value="dHex(1)HexNAc(4) (T)">dHex(1)HexNAc(4) (T)</option>
-      <option value="dHex(1)HexNAc(5) (S)">dHex(1)HexNAc(5) (S)</option>
-      <option value="dHex(1)HexNAc(5) (T)">dHex(1)HexNAc(5) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(1)Kdn(1) (S)">dHex(2)Hex(1)HexNAc(1)Kdn(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(1)Kdn(1) (T)">dHex(2)Hex(1)HexNAc(1)Kdn(1) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(2)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(2)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)NeuAc(1) (S)">dHex(2)Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)NeuAc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(3) (S)">dHex(2)Hex(1)HexNAc(3) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(3) (T)">dHex(2)Hex(1)HexNAc(3) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2) (S)">dHex(2)Hex(2) (S)</option>
-      <option value="dHex(2)Hex(2) (T)">dHex(2)Hex(2) (T)</option>
-      <option value="dHex(2)Hex(2)HexA(1) (S)">dHex(2)Hex(2)HexA(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexA(1) (T)">dHex(2)Hex(2)HexA(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexA(1)HexNAc(1) (S)">dHex(2)Hex(2)HexA(1)HexNAc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexA(1)HexNAc(1) (T)">dHex(2)Hex(2)HexA(1)HexNAc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(1) (S)">dHex(2)Hex(2)HexNAc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(1) (T)">dHex(2)Hex(2)HexNAc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2) (N)">dHex(2)Hex(2)HexNAc(2) (N)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2) (S)">dHex(2)Hex(2)HexNAc(2) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2) (T)">dHex(2)Hex(2)HexNAc(2) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(2)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(2)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(2)Sulf(2) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(2)Sulf(2) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3) (N)">dHex(2)Hex(2)HexNAc(3) (N)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3) (S)">dHex(2)Hex(2)HexNAc(3) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3) (T)">dHex(2)Hex(2)HexNAc(3) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)NeuAc(1) (S)">dHex(2)Hex(2)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(2)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)NeuGc(1) (S)">dHex(2)Hex(2)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)NeuGc(1) (T)">dHex(2)Hex(2)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(4) (S)">dHex(2)Hex(2)HexNAc(4) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(4) (T)">dHex(2)Hex(2)HexNAc(4) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(5) (S)">dHex(2)Hex(2)HexNAc(5) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(5) (T)">dHex(2)Hex(2)HexNAc(5) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3) (S)">dHex(2)Hex(3) (S)</option>
-      <option value="dHex(2)Hex(3) (T)">dHex(2)Hex(3) (T)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(1)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2) (N)">dHex(2)Hex(3)HexNAc(2) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2) (S)">dHex(2)Hex(3)HexNAc(2) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2) (T)">dHex(2)Hex(3)HexNAc(2) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(3)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(3)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3) (N)">dHex(2)Hex(3)HexNAc(3) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3) (S)">dHex(2)Hex(3)HexNAc(3) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3) (T)">dHex(2)Hex(3)HexNAc(3) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)Pent(1) (N)">dHex(2)Hex(3)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)Pent(2) (N)">dHex(2)Hex(3)HexNAc(3)Pent(2) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4) (N)">dHex(2)Hex(3)HexNAc(4) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4) (S)">dHex(2)Hex(3)HexNAc(4) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4) (T)">dHex(2)Hex(3)HexNAc(4) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4)Pent(1) (N)">dHex(2)Hex(3)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4)Pent(2) (N)">dHex(2)Hex(3)HexNAc(4)Pent(2) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(5) (N)">dHex(2)Hex(3)HexNAc(5) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(5) (S)">dHex(2)Hex(3)HexNAc(5) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(5) (T)">dHex(2)Hex(3)HexNAc(5) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(6) (N)">dHex(2)Hex(3)HexNAc(6) (N)</option>
-      <option value="dHex(2)Hex(4) (S)">dHex(2)Hex(4) (S)</option>
-      <option value="dHex(2)Hex(4) (T)">dHex(2)Hex(4) (T)</option>
-      <option value="dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(4)HexNAc(1) (S)">dHex(2)Hex(4)HexNAc(1) (S)</option>
-      <option value="dHex(2)Hex(4)HexNAc(1) (T)">dHex(2)Hex(4)HexNAc(1) (T)</option>
-      <option value="dHex(2)Hex(4)HexNAc(2) (N)">dHex(2)Hex(4)HexNAc(2) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(2) (S)">dHex(2)Hex(4)HexNAc(2) (S)</option>
-      <option value="dHex(2)Hex(4)HexNAc(2) (T)">dHex(2)Hex(4)HexNAc(2) (T)</option>
-      <option value="dHex(2)Hex(4)HexNAc(3) (N)">dHex(2)Hex(4)HexNAc(3) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(3)Pent(1) (N)">dHex(2)Hex(4)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4) (N)">dHex(2)Hex(4)HexNAc(4) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4) (S)">dHex(2)Hex(4)HexNAc(4) (S)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4) (T)">dHex(2)Hex(4)HexNAc(4) (T)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4)Pent(1) (N)">dHex(2)Hex(4)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(2)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(5) (N)">dHex(2)Hex(4)HexNAc(5) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(5) (S)">dHex(2)Hex(4)HexNAc(5) (S)</option>
-      <option value="dHex(2)Hex(4)HexNAc(5) (T)">dHex(2)Hex(4)HexNAc(5) (T)</option>
-      <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (S)">dHex(2)Hex(5)HexNAc(2)Me(1) (S)</option>
-      <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (T)">dHex(2)Hex(5)HexNAc(2)Me(1) (T)</option>
-      <option value="dHex(2)Hex(5)HexNAc(3)Pent(1) (N)">dHex(2)Hex(5)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(5)HexNAc(4) (N)">dHex(2)Hex(5)HexNAc(4) (N)</option>
-      <option value="dHex(2)HexNAc(2)Kdn(1) (S)">dHex(2)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(2)HexNAc(2)Kdn(1) (T)">dHex(2)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(2)HexNAc(5) (S)">dHex(2)HexNAc(5) (S)</option>
-      <option value="dHex(2)HexNAc(5) (T)">dHex(2)HexNAc(5) (T)</option>
-      <option value="dHex(2)HexNAc(7) (S)">dHex(2)HexNAc(7) (S)</option>
-      <option value="dHex(2)HexNAc(7) (T)">dHex(2)HexNAc(7) (T)</option>
-      <option value="dHex(3)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(3)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(3)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(3)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(3)Hex(1)HexNAc(3)Kdn(1) (S)">dHex(3)Hex(1)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(3)Hex(1)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(1)HexNAc(3)Kdn(1) (T)</option>
-      <option value="dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(2) (S)">dHex(3)Hex(2)HexNAc(2) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(2) (T)">dHex(3)Hex(2)HexNAc(2) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(3)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(3) (S)">dHex(3)Hex(2)HexNAc(3) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(3) (T)">dHex(3)Hex(2)HexNAc(3) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (S)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(4) (S)">dHex(3)Hex(2)HexNAc(4) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(4) (T)">dHex(3)Hex(2)HexNAc(4) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(1) (S)">dHex(3)Hex(3)HexNAc(1) (S)</option>
-      <option value="dHex(3)Hex(3)HexNAc(1) (T)">dHex(3)Hex(3)HexNAc(1) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(2) (S)">dHex(3)Hex(3)HexNAc(2) (S)</option>
-      <option value="dHex(3)Hex(3)HexNAc(2) (T)">dHex(3)Hex(3)HexNAc(2) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3) (S)">dHex(3)Hex(3)HexNAc(3) (S)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3) (T)">dHex(3)Hex(3)HexNAc(3) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3)Pent(1) (N)">dHex(3)Hex(3)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(3)Hex(3)HexNAc(4) (N)">dHex(3)Hex(3)HexNAc(4) (N)</option>
-      <option value="dHex(3)Hex(3)HexNAc(4)Pent(1) (N)">dHex(3)Hex(3)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(3)Hex(4)HexNAc(4) (N)">dHex(3)Hex(4)HexNAc(4) (N)</option>
-      <option value="dHex(3)Hex(4)HexNAc(4) (S)">dHex(3)Hex(4)HexNAc(4) (S)</option>
-      <option value="dHex(3)Hex(4)HexNAc(4) (T)">dHex(3)Hex(4)HexNAc(4) (T)</option>
-      <option value="dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(3)HexNAc(3)Kdn(1) (S)">dHex(3)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(3)HexNAc(3)Kdn(1) (T)">dHex(3)HexNAc(3)Kdn(1) (T)</option>
-      <option value="dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)">dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)</option>
-      <option value="dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)">dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)</option>
-      <option value="dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)">dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)">dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)</option>
-      <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(4)Hex(2)HexNAc(3) (S)">dHex(4)Hex(2)HexNAc(3) (S)</option>
-      <option value="dHex(4)Hex(2)HexNAc(3) (T)">dHex(4)Hex(2)HexNAc(3) (T)</option>
-      <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="dHex(4)Hex(3)HexNAc(3) (S)">dHex(4)Hex(3)HexNAc(3) (S)</option>
-      <option value="dHex(4)Hex(3)HexNAc(3) (T)">dHex(4)Hex(3)HexNAc(3) (T)</option>
-      <option value="dHex(4)HexNAc(3)Kdn(1) (S)">dHex(4)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(4)HexNAc(3)Kdn(1) (T)">dHex(4)HexNAc(3)Kdn(1) (T)</option>
-      <option value="DHP (C)">DHP (C)</option>
-      <option value="Diacylglycerol (C)">Diacylglycerol (C)</option>
-      <option value="DiART6plex (K)">DiART6plex (K)</option>
-      <option value="DiART6plex (N-term)">DiART6plex (N-term)</option>
-      <option value="DiART6plex (Protein N-term)">DiART6plex (Protein N-term)</option>
-      <option value="DiART6plex (Y)">DiART6plex (Y)</option>
-      <option value="DiART6plex115 (K)">DiART6plex115 (K)</option>
-      <option value="DiART6plex115 (N-term)">DiART6plex115 (N-term)</option>
-      <option value="DiART6plex115 (Protein N-term)">DiART6plex115 (Protein N-term)</option>
-      <option value="DiART6plex115 (Y)">DiART6plex115 (Y)</option>
-      <option value="DiART6plex116/119 (K)">DiART6plex116/119 (K)</option>
-      <option value="DiART6plex116/119 (N-term)">DiART6plex116/119 (N-term)</option>
-      <option value="DiART6plex116/119 (Protein N-term)">DiART6plex116/119 (Protein N-term)</option>
-      <option value="DiART6plex116/119 (Y)">DiART6plex116/119 (Y)</option>
-      <option value="DiART6plex117 (K)">DiART6plex117 (K)</option>
-      <option value="DiART6plex117 (N-term)">DiART6plex117 (N-term)</option>
-      <option value="DiART6plex117 (Protein N-term)">DiART6plex117 (Protein N-term)</option>
-      <option value="DiART6plex117 (Y)">DiART6plex117 (Y)</option>
-      <option value="DiART6plex118 (K)">DiART6plex118 (K)</option>
-      <option value="DiART6plex118 (N-term)">DiART6plex118 (N-term)</option>
-      <option value="DiART6plex118 (Protein N-term)">DiART6plex118 (Protein N-term)</option>
-      <option value="DiART6plex118 (Y)">DiART6plex118 (Y)</option>
-      <option value="Dibromo (Y)">Dibromo (Y)</option>
-      <option value="Dicarbamidomethyl (C)">Dicarbamidomethyl (C)</option>
-      <option value="Dicarbamidomethyl (H)">Dicarbamidomethyl (H)</option>
-      <option value="Dicarbamidomethyl (K)">Dicarbamidomethyl (K)</option>
-      <option value="Dicarbamidomethyl (N-term)">Dicarbamidomethyl (N-term)</option>
-      <option value="Dicarbamidomethyl (R)">Dicarbamidomethyl (R)</option>
-      <option value="dichlorination (C)">dichlorination (C)</option>
-      <option value="dichlorination (Y)">dichlorination (Y)</option>
-      <option value="Didehydro (C-term K)">Didehydro (C-term K)</option>
-      <option value="Didehydro (S)">Didehydro (S)</option>
-      <option value="Didehydro (T)">Didehydro (T)</option>
-      <option value="Didehydro (Y)">Didehydro (Y)</option>
-      <option value="Didehydroretinylidene (K)">Didehydroretinylidene (K)</option>
-      <option value="Diethyl (K)">Diethyl (K)</option>
-      <option value="Diethyl (N-term)">Diethyl (N-term)</option>
-      <option value="Diethylphosphate (C)">Diethylphosphate (C)</option>
-      <option value="Diethylphosphate (H)">Diethylphosphate (H)</option>
-      <option value="Diethylphosphate (K)">Diethylphosphate (K)</option>
-      <option value="Diethylphosphate (N-term)">Diethylphosphate (N-term)</option>
-      <option value="Diethylphosphate (S)">Diethylphosphate (S)</option>
-      <option value="Diethylphosphate (T)">Diethylphosphate (T)</option>
-      <option value="Diethylphosphate (Y)">Diethylphosphate (Y)</option>
-      <option value="Diethylphosphothione (C)">Diethylphosphothione (C)</option>
-      <option value="Diethylphosphothione (H)">Diethylphosphothione (H)</option>
-      <option value="Diethylphosphothione (K)">Diethylphosphothione (K)</option>
-      <option value="Diethylphosphothione (S)">Diethylphosphothione (S)</option>
-      <option value="Diethylphosphothione (T)">Diethylphosphothione (T)</option>
-      <option value="Diethylphosphothione (Y)">Diethylphosphothione (Y)</option>
-      <option value="Difuran (Y)">Difuran (Y)</option>
-      <option value="Dihydroxyimidazolidine (R)">Dihydroxyimidazolidine (R)</option>
-      <option value="Diiodo (H)">Diiodo (H)</option>
-      <option value="Diiodo (Y)">Diiodo (Y)</option>
-      <option value="Diironsubcluster (C)">Diironsubcluster (C)</option>
-      <option value="Diisopropylphosphate (K)">Diisopropylphosphate (K)</option>
-      <option value="Diisopropylphosphate (N-term)">Diisopropylphosphate (N-term)</option>
-      <option value="Diisopropylphosphate (S)">Diisopropylphosphate (S)</option>
-      <option value="Diisopropylphosphate (T)">Diisopropylphosphate (T)</option>
-      <option value="Diisopropylphosphate (Y)">Diisopropylphosphate (Y)</option>
-      <option value="DiLeu4plex (K)">DiLeu4plex (K)</option>
-      <option value="DiLeu4plex (N-term)">DiLeu4plex (N-term)</option>
-      <option value="DiLeu4plex (Y)">DiLeu4plex (Y)</option>
-      <option value="DiLeu4plex115 (K)">DiLeu4plex115 (K)</option>
-      <option value="DiLeu4plex115 (N-term)">DiLeu4plex115 (N-term)</option>
-      <option value="DiLeu4plex115 (Y)">DiLeu4plex115 (Y)</option>
-      <option value="DiLeu4plex117 (K)">DiLeu4plex117 (K)</option>
-      <option value="DiLeu4plex117 (N-term)">DiLeu4plex117 (N-term)</option>
-      <option value="DiLeu4plex117 (Y)">DiLeu4plex117 (Y)</option>
-      <option value="DiLeu4plex118 (K)">DiLeu4plex118 (K)</option>
-      <option value="DiLeu4plex118 (N-term)">DiLeu4plex118 (N-term)</option>
-      <option value="DiLeu4plex118 (Y)">DiLeu4plex118 (Y)</option>
-      <option value="Dimethyl (K)">Dimethyl (K)</option>
-      <option value="Dimethyl (N)">Dimethyl (N)</option>
-      <option value="Dimethyl (N-term)">Dimethyl (N-term)</option>
-      <option value="Dimethyl (Protein N-term P)">Dimethyl (Protein N-term P)</option>
-      <option value="Dimethyl (Protein N-term)">Dimethyl (Protein N-term)</option>
-      <option value="Dimethyl (R)">Dimethyl (R)</option>
-      <option value="Dimethyl:2H(2)13C (K)">Dimethyl:2H(2)13C (K)</option>
-      <option value="Dimethyl:2H(2)13C (N)">Dimethyl:2H(2)13C (N)</option>
-      <option value="Dimethyl:2H(2)13C (N-term)">Dimethyl:2H(2)13C (N-term)</option>
-      <option value="Dimethyl:2H(2)13C (Protein N-term P)">Dimethyl:2H(2)13C (Protein N-term P)</option>
-      <option value="Dimethyl:2H(2)13C (R)">Dimethyl:2H(2)13C (R)</option>
-      <option value="Dimethyl:2H(4) (K)">Dimethyl:2H(4) (K)</option>
-      <option value="Dimethyl:2H(4) (N-term)">Dimethyl:2H(4) (N-term)</option>
-      <option value="Dimethyl:2H(4) (Protein N-term)">Dimethyl:2H(4) (Protein N-term)</option>
-      <option value="Dimethyl:2H(4) (R)">Dimethyl:2H(4) (R)</option>
-      <option value="Dimethyl:2H(4)13C(2) (K)">Dimethyl:2H(4)13C(2) (K)</option>
-      <option value="Dimethyl:2H(4)13C(2) (N-term)">Dimethyl:2H(4)13C(2) (N-term)</option>
-      <option value="Dimethyl:2H(4)13C(2) (Protein N-term)">Dimethyl:2H(4)13C(2) (Protein N-term)</option>
-      <option value="Dimethyl:2H(4)13C(2) (R)">Dimethyl:2H(4)13C(2) (R)</option>
-      <option value="Dimethyl:2H(6) (K)">Dimethyl:2H(6) (K)</option>
-      <option value="Dimethyl:2H(6) (N-term)">Dimethyl:2H(6) (N-term)</option>
-      <option value="Dimethyl:2H(6) (R)">Dimethyl:2H(6) (R)</option>
-      <option value="Dimethyl:2H(6)13C(2) (K)">Dimethyl:2H(6)13C(2) (K)</option>
-      <option value="Dimethyl:2H(6)13C(2) (N-term)">Dimethyl:2H(6)13C(2) (N-term)</option>
-      <option value="Dimethyl:2H(6)13C(2) (Protein N-term)">Dimethyl:2H(6)13C(2) (Protein N-term)</option>
-      <option value="Dimethyl:2H(6)13C(2) (R)">Dimethyl:2H(6)13C(2) (R)</option>
-      <option value="DimethylamineGMBS (C)">DimethylamineGMBS (C)</option>
-      <option value="Dimethylaminoethyl (C)">Dimethylaminoethyl (C)</option>
-      <option value="DimethylArsino (C)">DimethylArsino (C)</option>
-      <option value="Dimethylphosphothione (C)">Dimethylphosphothione (C)</option>
-      <option value="Dimethylphosphothione (H)">Dimethylphosphothione (H)</option>
-      <option value="Dimethylphosphothione (K)">Dimethylphosphothione (K)</option>
-      <option value="Dimethylphosphothione (S)">Dimethylphosphothione (S)</option>
-      <option value="Dimethylphosphothione (T)">Dimethylphosphothione (T)</option>
-      <option value="Dimethylphosphothione (Y)">Dimethylphosphothione (Y)</option>
-      <option value="DimethylpyrroleAdduct (K)">DimethylpyrroleAdduct (K)</option>
-      <option value="Dioxidation (C)">Dioxidation (C)</option>
-      <option value="Dioxidation (E)">Dioxidation (E)</option>
-      <option value="Dioxidation (F)">Dioxidation (F)</option>
-      <option value="Dioxidation (I)">Dioxidation (I)</option>
-      <option value="Dioxidation (K)">Dioxidation (K)</option>
-      <option value="Dioxidation (L)">Dioxidation (L)</option>
-      <option value="Dioxidation (M)">Dioxidation (M)</option>
-      <option value="Dioxidation (P)">Dioxidation (P)</option>
-      <option value="Dioxidation (R)">Dioxidation (R)</option>
-      <option value="Dioxidation (U)">Dioxidation (U)</option>
-      <option value="Dioxidation (V)">Dioxidation (V)</option>
-      <option value="Dioxidation (W)">Dioxidation (W)</option>
-      <option value="Dioxidation (Y)">Dioxidation (Y)</option>
-      <option value="Diphthamide (H)">Diphthamide (H)</option>
-      <option value="Dipyridyl (C)">Dipyridyl (C)</option>
-      <option value="Dipyrrolylmethanemethyl (C)">Dipyrrolylmethanemethyl (C)</option>
-      <option value="DMPO (C)">DMPO (C)</option>
-      <option value="DMPO (H)">DMPO (H)</option>
-      <option value="DMPO (Y)">DMPO (Y)</option>
-      <option value="DNCB_hapten (C)">DNCB_hapten (C)</option>
-      <option value="DNCB_hapten (H)">DNCB_hapten (H)</option>
-      <option value="DNCB_hapten (K)">DNCB_hapten (K)</option>
-      <option value="DNCB_hapten (Y)">DNCB_hapten (Y)</option>
-      <option value="dNIC (K)">dNIC (K)</option>
-      <option value="dNIC (N-term)">dNIC (N-term)</option>
-      <option value="DNPS (C)">DNPS (C)</option>
-      <option value="DNPS (W)">DNPS (W)</option>
-      <option value="DTT (C)">DTT (C)</option>
-      <option value="DyLight-maleimide (C)">DyLight-maleimide (C)</option>
-      <option value="DYn-2 (C)">DYn-2 (C)</option>
-      <option value="EDEDTIDVFQQQTGG (K)">EDEDTIDVFQQQTGG (K)</option>
-      <option value="EDT-iodoacetyl-PEO-biotin (S)">EDT-iodoacetyl-PEO-biotin (S)</option>
-      <option value="EDT-iodoacetyl-PEO-biotin (T)">EDT-iodoacetyl-PEO-biotin (T)</option>
-      <option value="EDT-maleimide-PEO-biotin (S)">EDT-maleimide-PEO-biotin (S)</option>
-      <option value="EDT-maleimide-PEO-biotin (T)">EDT-maleimide-PEO-biotin (T)</option>
-      <option value="EEEDVIEVYQEQTGG (K)">EEEDVIEVYQEQTGG (K)</option>
-      <option value="EGCG1 (C)">EGCG1 (C)</option>
-      <option value="EGCG2 (C)">EGCG2 (C)</option>
-      <option value="EHD-diphenylpentanone (C)">EHD-diphenylpentanone (C)</option>
-      <option value="EHD-diphenylpentanone (M)">EHD-diphenylpentanone (M)</option>
-      <option value="EQAT (C)">EQAT (C)</option>
-      <option value="EQAT:2H(5) (C)">EQAT:2H(5) (C)</option>
-      <option value="EQIGG (K)">EQIGG (K)</option>
-      <option value="ESP (K)">ESP (K)</option>
-      <option value="ESP (N-term)">ESP (N-term)</option>
-      <option value="ESP:2H(10) (K)">ESP:2H(10) (K)</option>
-      <option value="ESP:2H(10) (N-term)">ESP:2H(10) (N-term)</option>
-      <option value="Ethanedithiol (S)">Ethanedithiol (S)</option>
-      <option value="Ethanedithiol (T)">Ethanedithiol (T)</option>
-      <option value="Ethanolamine (C)">Ethanolamine (C)</option>
-      <option value="Ethanolamine (C-term)">Ethanolamine (C-term)</option>
-      <option value="Ethanolamine (D)">Ethanolamine (D)</option>
-      <option value="Ethanolamine (E)">Ethanolamine (E)</option>
-      <option value="Ethanolyl (C)">Ethanolyl (C)</option>
-      <option value="Ethanolyl (K)">Ethanolyl (K)</option>
-      <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-      <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
-      <option value="Ethyl (C-term)">Ethyl (C-term)</option>
-      <option value="Ethyl (D)">Ethyl (D)</option>
-      <option value="Ethyl (E)">Ethyl (E)</option>
-      <option value="Ethyl (K)">Ethyl (K)</option>
-      <option value="Ethyl (N-term)">Ethyl (N-term)</option>
-      <option value="Ethyl (Protein N-term)">Ethyl (Protein N-term)</option>
-      <option value="Ethyl+Deamidated (N)">Ethyl+Deamidated (N)</option>
-      <option value="Ethyl+Deamidated (Q)">Ethyl+Deamidated (Q)</option>
-      <option value="ethylamino (S)">ethylamino (S)</option>
-      <option value="ethylamino (T)">ethylamino (T)</option>
-      <option value="Ethylphosphate (K)">Ethylphosphate (K)</option>
-      <option value="Ethylphosphate (N-term)">Ethylphosphate (N-term)</option>
-      <option value="Ethylphosphate (S)">Ethylphosphate (S)</option>
-      <option value="Ethylphosphate (T)">Ethylphosphate (T)</option>
-      <option value="Ethylphosphate (Y)">Ethylphosphate (Y)</option>
-      <option value="ethylsulfonylethyl (C)">ethylsulfonylethyl (C)</option>
-      <option value="ethylsulfonylethyl (H)">ethylsulfonylethyl (H)</option>
-      <option value="ethylsulfonylethyl (K)">ethylsulfonylethyl (K)</option>
-      <option value="ExacTagAmine (K)">ExacTagAmine (K)</option>
-      <option value="ExacTagThiol (C)">ExacTagThiol (C)</option>
-      <option value="FAD (C)">FAD (C)</option>
-      <option value="FAD (H)">FAD (H)</option>
-      <option value="FAD (Y)">FAD (Y)</option>
-      <option value="Farnesyl (C)">Farnesyl (C)</option>
-      <option value="Fluorescein (C)">Fluorescein (C)</option>
-      <option value="Fluorescein-tyramine (Y)">Fluorescein-tyramine (Y)</option>
-      <option value="Fluoro (A)">Fluoro (A)</option>
-      <option value="Fluoro (F)">Fluoro (F)</option>
-      <option value="Fluoro (W)">Fluoro (W)</option>
-      <option value="Fluoro (Y)">Fluoro (Y)</option>
-      <option value="FMN (S)">FMN (S)</option>
-      <option value="FMN (T)">FMN (T)</option>
-      <option value="FMNC (C)">FMNC (C)</option>
-      <option value="FMNH (C)">FMNH (C)</option>
-      <option value="FMNH (H)">FMNH (H)</option>
-      <option value="FNEM (C)">FNEM (C)</option>
-      <option value="Formyl (K)">Formyl (K)</option>
-      <option value="Formyl (N-term)">Formyl (N-term)</option>
-      <option value="Formyl (Protein N-term)">Formyl (Protein N-term)</option>
-      <option value="Formyl (S)">Formyl (S)</option>
-      <option value="Formyl (T)">Formyl (T)</option>
-      <option value="Formylasparagine (H)">Formylasparagine (H)</option>
-      <option value="FormylMet (Protein N-term)">FormylMet (Protein N-term)</option>
-      <option value="FP-Biotin (K)">FP-Biotin (K)</option>
-      <option value="FP-Biotin (S)">FP-Biotin (S)</option>
-      <option value="FP-Biotin (T)">FP-Biotin (T)</option>
-      <option value="FP-Biotin (Y)">FP-Biotin (Y)</option>
-      <option value="FTC (C)">FTC (C)</option>
-      <option value="FTC (K)">FTC (K)</option>
-      <option value="FTC (P)">FTC (P)</option>
-      <option value="FTC (R)">FTC (R)</option>
-      <option value="FTC (S)">FTC (S)</option>
-      <option value="Furan (Y)">Furan (Y)</option>
-      <option value="G-H1 (R)">G-H1 (R)</option>
-      <option value="Galactosyl (K)">Galactosyl (K)</option>
-      <option value="Galactosyl (N-term)">Galactosyl (N-term)</option>
-      <option value="GEE (Q)">GEE (Q)</option>
-      <option value="GeranylGeranyl (C)">GeranylGeranyl (C)</option>
-      <option value="GG (C)">GG (C)</option>
-      <option value="GG (K)">GG (K)</option>
-      <option value="GG (Protein N-term)">GG (Protein N-term)</option>
-      <option value="GG (S)">GG (S)</option>
-      <option value="GG (T)">GG (T)</option>
-      <option value="GGQ (K)">GGQ (K)</option>
-      <option value="GIST-Quat (K)">GIST-Quat (K)</option>
-      <option value="GIST-Quat (N-term)">GIST-Quat (N-term)</option>
-      <option value="GIST-Quat:2H(3) (K)">GIST-Quat:2H(3) (K)</option>
-      <option value="GIST-Quat:2H(3) (N-term)">GIST-Quat:2H(3) (N-term)</option>
-      <option value="GIST-Quat:2H(6) (K)">GIST-Quat:2H(6) (K)</option>
-      <option value="GIST-Quat:2H(6) (N-term)">GIST-Quat:2H(6) (N-term)</option>
-      <option value="GIST-Quat:2H(9) (K)">GIST-Quat:2H(9) (K)</option>
-      <option value="GIST-Quat:2H(9) (N-term)">GIST-Quat:2H(9) (N-term)</option>
-      <option value="Gln-&gt;Ala (Q)">Gln-&gt;Ala (Q)</option>
-      <option value="Gln-&gt;Arg (Q)">Gln-&gt;Arg (Q)</option>
-      <option value="Gln-&gt;Asn (Q)">Gln-&gt;Asn (Q)</option>
-      <option value="Gln-&gt;Asp (Q)">Gln-&gt;Asp (Q)</option>
-      <option value="Gln-&gt;Cys (Q)">Gln-&gt;Cys (Q)</option>
-      <option value="Gln-&gt;Glu (Q)">Gln-&gt;Glu (Q)</option>
-      <option value="Gln-&gt;Gly (Q)">Gln-&gt;Gly (Q)</option>
-      <option value="Gln-&gt;His (Q)">Gln-&gt;His (Q)</option>
-      <option value="Gln-&gt;Lys (Q)">Gln-&gt;Lys (Q)</option>
-      <option value="Gln-&gt;Met (Q)">Gln-&gt;Met (Q)</option>
-      <option value="Gln-&gt;Phe (Q)">Gln-&gt;Phe (Q)</option>
-      <option value="Gln-&gt;Pro (Q)">Gln-&gt;Pro (Q)</option>
-      <option value="Gln-&gt;pyro-Glu (N-term Q)">Gln-&gt;pyro-Glu (N-term Q)</option>
-      <option value="Gln-&gt;Ser (Q)">Gln-&gt;Ser (Q)</option>
-      <option value="Gln-&gt;Thr (Q)">Gln-&gt;Thr (Q)</option>
-      <option value="Gln-&gt;Trp (Q)">Gln-&gt;Trp (Q)</option>
-      <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
-      <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
-      <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
-      <option value="Glu (E)">Glu (E)</option>
-      <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
-      <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
-      <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
-      <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
-      <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
-      <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
-      <option value="Glu-&gt;Gln (E)">Glu-&gt;Gln (E)</option>
-      <option value="Glu-&gt;Gly (E)">Glu-&gt;Gly (E)</option>
-      <option value="Glu-&gt;His (E)">Glu-&gt;His (E)</option>
-      <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
-      <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
-      <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
-      <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
-      <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
-      <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
-      <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
-      <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
-      <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
-      <option value="Glu-&gt;Val (E)">Glu-&gt;Val (E)</option>
-      <option value="Glu-&gt;Xle (E)">Glu-&gt;Xle (E)</option>
-      <option value="glucosone (R)">glucosone (R)</option>
-      <option value="Glucosylgalactosyl (K)">Glucosylgalactosyl (K)</option>
-      <option value="Glucuronyl (Protein N-term)">Glucuronyl (Protein N-term)</option>
-      <option value="Glucuronyl (S)">Glucuronyl (S)</option>
-      <option value="Glucuronyl (T)">Glucuronyl (T)</option>
-      <option value="GluGlu (E)">GluGlu (E)</option>
-      <option value="GluGlu (Protein C-term)">GluGlu (Protein C-term)</option>
-      <option value="GluGluGlu (E)">GluGluGlu (E)</option>
-      <option value="GluGluGlu (Protein C-term)">GluGluGlu (Protein C-term)</option>
-      <option value="GluGluGluGlu (E)">GluGluGluGlu (E)</option>
-      <option value="GluGluGluGlu (Protein C-term)">GluGluGluGlu (Protein C-term)</option>
-      <option value="Gluratylation (K)">Gluratylation (K)</option>
-      <option value="Glutathione (C)">Glutathione (C)</option>
-      <option value="Gly (K)">Gly (K)</option>
-      <option value="Gly (S)">Gly (S)</option>
-      <option value="Gly (T)">Gly (T)</option>
-      <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
-      <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
-      <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
-      <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
-      <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
-      <option value="Gly-&gt;Gln (G)">Gly-&gt;Gln (G)</option>
-      <option value="Gly-&gt;Glu (G)">Gly-&gt;Glu (G)</option>
-      <option value="Gly-&gt;His (G)">Gly-&gt;His (G)</option>
-      <option value="Gly-&gt;Lys (G)">Gly-&gt;Lys (G)</option>
-      <option value="Gly-&gt;Met (G)">Gly-&gt;Met (G)</option>
-      <option value="Gly-&gt;Phe (G)">Gly-&gt;Phe (G)</option>
-      <option value="Gly-&gt;Pro (G)">Gly-&gt;Pro (G)</option>
-      <option value="Gly-&gt;Ser (G)">Gly-&gt;Ser (G)</option>
-      <option value="Gly-&gt;Thr (G)">Gly-&gt;Thr (G)</option>
-      <option value="Gly-&gt;Trp (G)">Gly-&gt;Trp (G)</option>
-      <option value="Gly-&gt;Tyr (G)">Gly-&gt;Tyr (G)</option>
-      <option value="Gly-&gt;Val (G)">Gly-&gt;Val (G)</option>
-      <option value="Gly-&gt;Xle (G)">Gly-&gt;Xle (G)</option>
-      <option value="Gly-loss+Amide (C-term G)">Gly-loss+Amide (C-term G)</option>
-      <option value="Glycerophospho (S)">Glycerophospho (S)</option>
-      <option value="GlycerylPE (E)">GlycerylPE (E)</option>
-      <option value="glycidamide (K)">glycidamide (K)</option>
-      <option value="glycidamide (N-term)">glycidamide (N-term)</option>
-      <option value="Glycosyl (P)">Glycosyl (P)</option>
-      <option value="glyoxalAGE (R)">glyoxalAGE (R)</option>
-      <option value="GNLLFLACYCIGG (K)">GNLLFLACYCIGG (K)</option>
-      <option value="GPIanchor (Protein C-term)">GPIanchor (Protein C-term)</option>
-      <option value="Guanidinyl (K)">Guanidinyl (K)</option>
-      <option value="Guanidinyl (N-term)">Guanidinyl (N-term)</option>
-      <option value="Haloxon (C)">Haloxon (C)</option>
-      <option value="Haloxon (H)">Haloxon (H)</option>
-      <option value="Haloxon (K)">Haloxon (K)</option>
-      <option value="Haloxon (S)">Haloxon (S)</option>
-      <option value="Haloxon (T)">Haloxon (T)</option>
-      <option value="Haloxon (Y)">Haloxon (Y)</option>
-      <option value="HCysteinyl (C)">HCysteinyl (C)</option>
-      <option value="HCysThiolactone (K)">HCysThiolactone (K)</option>
-      <option value="Heme (C)">Heme (C)</option>
-      <option value="Heme (H)">Heme (H)</option>
-      <option value="Hep (K)">Hep (K)</option>
-      <option value="Hep (N)">Hep (N)</option>
-      <option value="Hep (Q)">Hep (Q)</option>
-      <option value="Hep (R)">Hep (R)</option>
-      <option value="Hep (S)">Hep (S)</option>
-      <option value="Hep (T)">Hep (T)</option>
-      <option value="Hex (C)">Hex (C)</option>
-      <option value="Hex (K)">Hex (K)</option>
-      <option value="Hex (N)">Hex (N)</option>
-      <option value="Hex (N-term)">Hex (N-term)</option>
-      <option value="Hex (R)">Hex (R)</option>
-      <option value="Hex (S)">Hex (S)</option>
-      <option value="Hex (T)">Hex (T)</option>
-      <option value="Hex (W)">Hex (W)</option>
-      <option value="Hex (Y)">Hex (Y)</option>
-      <option value="Hex(1)HexA(1) (S)">Hex(1)HexA(1) (S)</option>
-      <option value="Hex(1)HexA(1) (T)">Hex(1)HexA(1) (T)</option>
-      <option value="Hex(1)HexA(1)HexNAc(1) (S)">Hex(1)HexA(1)HexNAc(1) (S)</option>
-      <option value="Hex(1)HexA(1)HexNAc(1) (T)">Hex(1)HexA(1)HexNAc(1) (T)</option>
-      <option value="Hex(1)HexA(1)HexNAc(2) (S)">Hex(1)HexA(1)HexNAc(2) (S)</option>
-      <option value="Hex(1)HexA(1)HexNAc(2) (T)">Hex(1)HexA(1)HexNAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(1) (N)">Hex(1)HexNAc(1) (N)</option>
-      <option value="Hex(1)HexNAc(1) (S)">Hex(1)HexNAc(1) (S)</option>
-      <option value="Hex(1)HexNAc(1) (T)">Hex(1)HexNAc(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1) (N)">Hex(1)HexNAc(1)dHex(1) (N)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1) (S)">Hex(1)HexNAc(1)dHex(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1) (T)">Hex(1)HexNAc(1)dHex(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1)Me(1) (S)">Hex(1)HexNAc(1)dHex(1)Me(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1)Me(1) (T)">Hex(1)HexNAc(1)dHex(1)Me(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1)Me(2) (S)">Hex(1)HexNAc(1)dHex(1)Me(2) (S)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1)Me(2) (T)">Hex(1)HexNAc(1)dHex(1)Me(2) (T)</option>
-      <option value="Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S)">Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T)">Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1) (N)">Hex(1)HexNAc(1)NeuAc(1) (N)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1) (S)">Hex(1)HexNAc(1)NeuAc(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1) (T)">Hex(1)HexNAc(1)NeuAc(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S)">Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T)">Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S)">Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T)">Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T)">Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2) (N)">Hex(1)HexNAc(1)NeuAc(2) (N)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2) (S)">Hex(1)HexNAc(1)NeuAc(2) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2) (T)">Hex(1)HexNAc(1)NeuAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S)">Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T)">Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S)">Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T)">Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(3) (S)">Hex(1)HexNAc(1)NeuAc(3) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(3) (T)">Hex(1)HexNAc(1)NeuAc(3) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(1) (S)">Hex(1)HexNAc(1)NeuGc(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(1) (T)">Hex(1)HexNAc(1)NeuGc(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(2) (S)">Hex(1)HexNAc(1)NeuGc(2) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(2) (T)">Hex(1)HexNAc(1)NeuGc(2) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(3) (S)">Hex(1)HexNAc(1)NeuGc(3) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(3) (T)">Hex(1)HexNAc(1)NeuGc(3) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(4) (S)">Hex(1)HexNAc(1)NeuGc(4) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(4) (T)">Hex(1)HexNAc(1)NeuGc(4) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(5) (S)">Hex(1)HexNAc(1)NeuGc(5) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(5) (T)">Hex(1)HexNAc(1)NeuGc(5) (T)</option>
-      <option value="Hex(1)HexNAc(1)Phos(1) (S)">Hex(1)HexNAc(1)Phos(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)Phos(1) (T)">Hex(1)HexNAc(1)Phos(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)Sulf(1) (S)">Hex(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)Sulf(1) (T)">Hex(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(2) (N)">Hex(1)HexNAc(2) (N)</option>
-      <option value="Hex(1)HexNAc(2) (S)">Hex(1)HexNAc(2) (S)</option>
-      <option value="Hex(1)HexNAc(2) (T)">Hex(1)HexNAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(2)dHex(1) (N)">Hex(1)HexNAc(2)dHex(1) (N)</option>
-      <option value="Hex(1)HexNAc(2)dHex(1) (S)">Hex(1)HexNAc(2)dHex(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)dHex(1) (T)">Hex(1)HexNAc(2)dHex(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)dHex(1)Pent(1) (N)">Hex(1)HexNAc(2)dHex(1)Pent(1) (N)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2) (N)">Hex(1)HexNAc(2)dHex(2) (N)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2) (S)">Hex(1)HexNAc(2)dHex(2) (S)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2) (T)">Hex(1)HexNAc(2)dHex(2) (T)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(1) (S)">Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(1) (T)">Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(2) (S)">Hex(1)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(2) (T)">Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T)">Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuGc(1) (S)">Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuGc(1) (T)">Hex(1)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)Pent(1) (N)">Hex(1)HexNAc(2)Pent(1) (N)</option>
-      <option value="Hex(1)HexNAc(2)Sulf(1) (S)">Hex(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)Sulf(1) (T)">Hex(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(3) (S)">Hex(1)HexNAc(3) (S)</option>
-      <option value="Hex(1)HexNAc(3) (T)">Hex(1)HexNAc(3) (T)</option>
-      <option value="Hex(1)HexNAc(3)NeuAc(1) (S)">Hex(1)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="Hex(1)HexNAc(3)NeuAc(1) (T)">Hex(1)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="Hex(1)HexNAc(3)NeuAc(2) (S)">Hex(1)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="Hex(1)HexNAc(3)NeuAc(2) (T)">Hex(1)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(3)NeuGc(1) (S)">Hex(1)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="Hex(1)HexNAc(3)NeuGc(1) (T)">Hex(1)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="Hex(1)HexNAc(3)Sulf(1) (S)">Hex(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(3)Sulf(1) (T)">Hex(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)</option>
-      <option value="Hex(1)NeuAc(1) (S)">Hex(1)NeuAc(1) (S)</option>
-      <option value="Hex(1)NeuAc(1) (T)">Hex(1)NeuAc(1) (T)</option>
-      <option value="Hex(1)NeuAc(1)Pent(1) (S)">Hex(1)NeuAc(1)Pent(1) (S)</option>
-      <option value="Hex(1)NeuAc(1)Pent(1) (T)">Hex(1)NeuAc(1)Pent(1) (T)</option>
-      <option value="Hex(1)NeuGc(1) (S)">Hex(1)NeuGc(1) (S)</option>
-      <option value="Hex(1)NeuGc(1) (T)">Hex(1)NeuGc(1) (T)</option>
-      <option value="Hex(1)Pent(1) (S)">Hex(1)Pent(1) (S)</option>
-      <option value="Hex(1)Pent(1) (T)">Hex(1)Pent(1) (T)</option>
-      <option value="Hex(1)Pent(2) (S)">Hex(1)Pent(2) (S)</option>
-      <option value="Hex(1)Pent(2) (T)">Hex(1)Pent(2) (T)</option>
-      <option value="Hex(1)Pent(2)Me(1) (S)">Hex(1)Pent(2)Me(1) (S)</option>
-      <option value="Hex(1)Pent(2)Me(1) (T)">Hex(1)Pent(2)Me(1) (T)</option>
-      <option value="Hex(1)Pent(3) (S)">Hex(1)Pent(3) (S)</option>
-      <option value="Hex(1)Pent(3) (T)">Hex(1)Pent(3) (T)</option>
-      <option value="Hex(1)Pent(3)Me(1) (S)">Hex(1)Pent(3)Me(1) (S)</option>
-      <option value="Hex(1)Pent(3)Me(1) (T)">Hex(1)Pent(3)Me(1) (T)</option>
-      <option value="Hex(10)HexNAc(1) (N)">Hex(10)HexNAc(1) (N)</option>
-      <option value="Hex(10)Phos(3) (S)">Hex(10)Phos(3) (S)</option>
-      <option value="Hex(10)Phos(3) (T)">Hex(10)Phos(3) (T)</option>
-      <option value="Hex(2) (K)">Hex(2) (K)</option>
-      <option value="Hex(2) (R)">Hex(2) (R)</option>
-      <option value="Hex(2) (S)">Hex(2) (S)</option>
-      <option value="Hex(2) (T)">Hex(2) (T)</option>
-      <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)Pent(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)Pent(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(1) (N)">Hex(2)HexNAc(1) (N)</option>
-      <option value="Hex(2)HexNAc(1) (S)">Hex(2)HexNAc(1) (S)</option>
-      <option value="Hex(2)HexNAc(1) (T)">Hex(2)HexNAc(1) (T)</option>
-      <option value="Hex(2)HexNAc(1)Me(1) (S)">Hex(2)HexNAc(1)Me(1) (S)</option>
-      <option value="Hex(2)HexNAc(1)Me(1) (T)">Hex(2)HexNAc(1)Me(1) (T)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(1) (S)">Hex(2)HexNAc(1)NeuGc(1) (S)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(1) (T)">Hex(2)HexNAc(1)NeuGc(1) (T)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(2) (S)">Hex(2)HexNAc(1)NeuGc(2) (S)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(2) (T)">Hex(2)HexNAc(1)NeuGc(2) (T)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(3) (S)">Hex(2)HexNAc(1)NeuGc(3) (S)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(3) (T)">Hex(2)HexNAc(1)NeuGc(3) (T)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(4) (S)">Hex(2)HexNAc(1)NeuGc(4) (S)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(4) (T)">Hex(2)HexNAc(1)NeuGc(4) (T)</option>
-      <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (S)">Hex(2)HexNAc(1)Pent(1)HexA(1) (S)</option>
-      <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (T)">Hex(2)HexNAc(1)Pent(1)HexA(1) (T)</option>
-      <option value="Hex(2)HexNAc(1)Sulf(1) (S)">Hex(2)HexNAc(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(1)Sulf(1) (T)">Hex(2)HexNAc(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(2) (N)">Hex(2)HexNAc(2) (N)</option>
-      <option value="Hex(2)HexNAc(2) (S)">Hex(2)HexNAc(2) (S)</option>
-      <option value="Hex(2)HexNAc(2) (T)">Hex(2)HexNAc(2) (T)</option>
-      <option value="Hex(2)HexNAc(2)dHex(1) (N)">Hex(2)HexNAc(2)dHex(1) (N)</option>
-      <option value="Hex(2)HexNAc(2)dHex(1) (S)">Hex(2)HexNAc(2)dHex(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)dHex(1) (T)">Hex(2)HexNAc(2)dHex(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1) (N)">Hex(2)HexNAc(2)NeuAc(1) (N)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1) (S)">Hex(2)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1) (T)">Hex(2)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(2) (S)">Hex(2)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(2) (T)">Hex(2)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuGc(1) (S)">Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuGc(1) (T)">Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)Pent(1) (N)">Hex(2)HexNAc(2)Pent(1) (N)</option>
-      <option value="Hex(2)HexNAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(3) (N)">Hex(2)HexNAc(3) (N)</option>
-      <option value="Hex(2)HexNAc(3) (S)">Hex(2)HexNAc(3) (S)</option>
-      <option value="Hex(2)HexNAc(3) (T)">Hex(2)HexNAc(3) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(2) (S)">Hex(2)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(2) (T)">Hex(2)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(3) (S)">Hex(2)HexNAc(3)NeuAc(3) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(3) (T)">Hex(2)HexNAc(3)NeuAc(3) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(1) (T)">Hex(2)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(2) (S)">Hex(2)HexNAc(3)NeuGc(2) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(2) (T)">Hex(2)HexNAc(3)NeuGc(2) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(3) (S)">Hex(2)HexNAc(3)NeuGc(3) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(3) (T)">Hex(2)HexNAc(3)NeuGc(3) (T)</option>
-      <option value="Hex(2)HexNAc(3)Sulf(1) (S)">Hex(2)HexNAc(3)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(3)Sulf(1) (T)">Hex(2)HexNAc(3)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(4) (N)">Hex(2)HexNAc(4) (N)</option>
-      <option value="Hex(2)HexNAc(4) (S)">Hex(2)HexNAc(4) (S)</option>
-      <option value="Hex(2)HexNAc(4) (T)">Hex(2)HexNAc(4) (T)</option>
-      <option value="Hex(2)HexNAc(4)NeuAc(1) (S)">Hex(2)HexNAc(4)NeuAc(1) (S)</option>
-      <option value="Hex(2)HexNAc(4)NeuAc(1) (T)">Hex(2)HexNAc(4)NeuAc(1) (T)</option>
-      <option value="Hex(2)HexNAc(5) (S)">Hex(2)HexNAc(5) (S)</option>
-      <option value="Hex(2)HexNAc(5) (T)">Hex(2)HexNAc(5) (T)</option>
-      <option value="Hex(2)NeuAc(1) (S)">Hex(2)NeuAc(1) (S)</option>
-      <option value="Hex(2)NeuAc(1) (T)">Hex(2)NeuAc(1) (T)</option>
-      <option value="Hex(2)Pent(2) (S)">Hex(2)Pent(2) (S)</option>
-      <option value="Hex(2)Pent(2) (T)">Hex(2)Pent(2) (T)</option>
-      <option value="Hex(2)Pent(2)Me(1) (S)">Hex(2)Pent(2)Me(1) (S)</option>
-      <option value="Hex(2)Pent(2)Me(1) (T)">Hex(2)Pent(2)Me(1) (T)</option>
-      <option value="Hex(2)Sulf(1) (S)">Hex(2)Sulf(1) (S)</option>
-      <option value="Hex(2)Sulf(1) (T)">Hex(2)Sulf(1) (T)</option>
-      <option value="Hex(3) (N)">Hex(3) (N)</option>
-      <option value="Hex(3) (S)">Hex(3) (S)</option>
-      <option value="Hex(3) (T)">Hex(3) (T)</option>
-      <option value="Hex(3)HexNAc(1) (N)">Hex(3)HexNAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(1) (S)">Hex(3)HexNAc(1) (S)</option>
-      <option value="Hex(3)HexNAc(1) (T)">Hex(3)HexNAc(1) (T)</option>
-      <option value="Hex(3)HexNAc(1)HexA(1) (S)">Hex(3)HexNAc(1)HexA(1) (S)</option>
-      <option value="Hex(3)HexNAc(1)HexA(1) (T)">Hex(3)HexNAc(1)HexA(1) (T)</option>
-      <option value="Hex(3)HexNAc(1)Me(1) (S)">Hex(3)HexNAc(1)Me(1) (S)</option>
-      <option value="Hex(3)HexNAc(1)Me(1) (T)">Hex(3)HexNAc(1)Me(1) (T)</option>
-      <option value="Hex(3)HexNAc(1)Pent(1) (N)">Hex(3)HexNAc(1)Pent(1) (N)</option>
-      <option value="Hex(3)HexNAc(2) (N)">Hex(3)HexNAc(2) (N)</option>
-      <option value="Hex(3)HexNAc(2) (S)">Hex(3)HexNAc(2) (S)</option>
-      <option value="Hex(3)HexNAc(2) (T)">Hex(3)HexNAc(2) (T)</option>
-      <option value="Hex(3)HexNAc(2)NeuAc(1) (N)">Hex(3)HexNAc(2)NeuAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(2)NeuAc(2) (S)">Hex(3)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="Hex(3)HexNAc(2)NeuAc(2) (T)">Hex(3)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="Hex(3)HexNAc(2)Pent(1) (N)">Hex(3)HexNAc(2)Pent(1) (N)</option>
-      <option value="Hex(3)HexNAc(2)Phos(1) (N)">Hex(3)HexNAc(2)Phos(1) (N)</option>
-      <option value="Hex(3)HexNAc(3) (N)">Hex(3)HexNAc(3) (N)</option>
-      <option value="Hex(3)HexNAc(3) (S)">Hex(3)HexNAc(3) (S)</option>
-      <option value="Hex(3)HexNAc(3) (T)">Hex(3)HexNAc(3) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(1) (S)">Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(1) (T)">Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(2) (S)">Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(2) (T)">Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(3) (S)">Hex(3)HexNAc(3)NeuAc(3) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(3) (T)">Hex(3)HexNAc(3)NeuAc(3) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuGc(1) (S)">Hex(3)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuGc(1) (T)">Hex(3)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)Pent(1) (N)">Hex(3)HexNAc(3)Pent(1) (N)</option>
-      <option value="Hex(3)HexNAc(3)Sulf(1) (N)">Hex(3)HexNAc(3)Sulf(1) (N)</option>
-      <option value="Hex(3)HexNAc(3)Sulf(1) (S)">Hex(3)HexNAc(3)Sulf(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)Sulf(1) (T)">Hex(3)HexNAc(3)Sulf(1) (T)</option>
-      <option value="Hex(3)HexNAc(4) (N)">Hex(3)HexNAc(4) (N)</option>
-      <option value="Hex(3)HexNAc(4) (S)">Hex(3)HexNAc(4) (S)</option>
-      <option value="Hex(3)HexNAc(4) (T)">Hex(3)HexNAc(4) (T)</option>
-      <option value="Hex(3)HexNAc(4)NeuAc(1) (N)">Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(4)NeuAc(2) (N)">Hex(3)HexNAc(4)NeuAc(2) (N)</option>
-      <option value="Hex(3)HexNAc(4)Pent(1) (N)">Hex(3)HexNAc(4)Pent(1) (N)</option>
-      <option value="Hex(3)HexNAc(4)Sulf(1) (N)">Hex(3)HexNAc(4)Sulf(1) (N)</option>
-      <option value="Hex(3)HexNAc(5) (N)">Hex(3)HexNAc(5) (N)</option>
-      <option value="Hex(3)HexNAc(5) (S)">Hex(3)HexNAc(5) (S)</option>
-      <option value="Hex(3)HexNAc(5) (T)">Hex(3)HexNAc(5) (T)</option>
-      <option value="Hex(3)HexNAc(5)NeuAc(1) (N)">Hex(3)HexNAc(5)NeuAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(5)Sulf(1) (N)">Hex(3)HexNAc(5)Sulf(1) (N)</option>
-      <option value="Hex(3)HexNAc(6) (N)">Hex(3)HexNAc(6) (N)</option>
-      <option value="Hex(3)HexNAc(6) (S)">Hex(3)HexNAc(6) (S)</option>
-      <option value="Hex(3)HexNAc(6) (T)">Hex(3)HexNAc(6) (T)</option>
-      <option value="Hex(3)HexNAc(6)NeuAc(1) (N)">Hex(3)HexNAc(6)NeuAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(6)Sulf(1) (N)">Hex(3)HexNAc(6)Sulf(1) (N)</option>
-      <option value="Hex(3)HexNAc(6)Sulf(2) (N)">Hex(3)HexNAc(6)Sulf(2) (N)</option>
-      <option value="Hex(3)HexNAc(7) (N)">Hex(3)HexNAc(7) (N)</option>
-      <option value="Hex(3)HexNAc(7)Sulf(1) (N)">Hex(3)HexNAc(7)Sulf(1) (N)</option>
-      <option value="Hex(4) (S)">Hex(4) (S)</option>
-      <option value="Hex(4) (T)">Hex(4) (T)</option>
-      <option value="Hex(4)HexA(1) (S)">Hex(4)HexA(1) (S)</option>
-      <option value="Hex(4)HexA(1) (T)">Hex(4)HexA(1) (T)</option>
-      <option value="Hex(4)HexA(1)HexNAc(1) (S)">Hex(4)HexA(1)HexNAc(1) (S)</option>
-      <option value="Hex(4)HexA(1)HexNAc(1) (T)">Hex(4)HexA(1)HexNAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(1) (N)">Hex(4)HexNAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(1) (S)">Hex(4)HexNAc(1) (S)</option>
-      <option value="Hex(4)HexNAc(1) (T)">Hex(4)HexNAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(2) (N)">Hex(4)HexNAc(2) (N)</option>
-      <option value="Hex(4)HexNAc(2)NeuAc(1) (N)">Hex(4)HexNAc(2)NeuAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(2)NeuAc(1) (S)">Hex(4)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="Hex(4)HexNAc(2)NeuAc(1) (T)">Hex(4)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(2)Pent(1) (N)">Hex(4)HexNAc(2)Pent(1) (N)</option>
-      <option value="Hex(4)HexNAc(3) (N)">Hex(4)HexNAc(3) (N)</option>
-      <option value="Hex(4)HexNAc(3) (S)">Hex(4)HexNAc(3) (S)</option>
-      <option value="Hex(4)HexNAc(3) (T)">Hex(4)HexNAc(3) (T)</option>
-      <option value="Hex(4)HexNAc(3)NeuAc(1) (N)">Hex(4)HexNAc(3)NeuAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(3)NeuAc(1) (S)">Hex(4)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="Hex(4)HexNAc(3)NeuAc(1) (T)">Hex(4)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(3)NeuAc(2) (N)">Hex(4)HexNAc(3)NeuAc(2) (N)</option>
-      <option value="Hex(4)HexNAc(3)NeuGc(1) (N)">Hex(4)HexNAc(3)NeuGc(1) (N)</option>
-      <option value="Hex(4)HexNAc(3)Pent(1) (N)">Hex(4)HexNAc(3)Pent(1) (N)</option>
-      <option value="Hex(4)HexNAc(4) (N)">Hex(4)HexNAc(4) (N)</option>
-      <option value="Hex(4)HexNAc(4) (S)">Hex(4)HexNAc(4) (S)</option>
-      <option value="Hex(4)HexNAc(4) (T)">Hex(4)HexNAc(4) (T)</option>
-      <option value="Hex(4)HexNAc(4)Me(2)Pent(1) (N)">Hex(4)HexNAc(4)Me(2)Pent(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1) (N)">Hex(4)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1) (S)">Hex(4)HexNAc(4)NeuAc(1) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1) (T)">Hex(4)HexNAc(4)NeuAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1) (N)">Hex(4)HexNAc(4)NeuGc(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1) (S)">Hex(4)HexNAc(4)NeuGc(1) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1) (T)">Hex(4)HexNAc(4)NeuGc(1) (T)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)</option>
-      <option value="Hex(4)HexNAc(4)Pent(1) (N)">Hex(4)HexNAc(4)Pent(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)Sulf(1) (N)">Hex(4)HexNAc(4)Sulf(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)Sulf(2) (S)">Hex(4)HexNAc(4)Sulf(2) (S)</option>
-      <option value="Hex(4)HexNAc(4)Sulf(2) (T)">Hex(4)HexNAc(4)Sulf(2) (T)</option>
-      <option value="Hex(4)HexNAc(5) (N)">Hex(4)HexNAc(5) (N)</option>
-      <option value="Hex(4)HexNAc(5)NeuAc(1) (N)">Hex(4)HexNAc(5)NeuAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(5)Sulf(1) (N)">Hex(4)HexNAc(5)Sulf(1) (N)</option>
-      <option value="Hex(4)HexNAc(6) (N)">Hex(4)HexNAc(6) (N)</option>
-      <option value="Hex(4)Phos(1) (S)">Hex(4)Phos(1) (S)</option>
-      <option value="Hex(4)Phos(1) (T)">Hex(4)Phos(1) (T)</option>
-      <option value="Hex(5) (S)">Hex(5) (S)</option>
-      <option value="Hex(5) (T)">Hex(5) (T)</option>
-      <option value="Hex(5)HexA(1) (S)">Hex(5)HexA(1) (S)</option>
-      <option value="Hex(5)HexA(1) (T)">Hex(5)HexA(1) (T)</option>
-      <option value="Hex(5)HexNAc(1) (N)">Hex(5)HexNAc(1) (N)</option>
-      <option value="Hex(5)HexNAc(1) (S)">Hex(5)HexNAc(1) (S)</option>
-      <option value="Hex(5)HexNAc(1) (T)">Hex(5)HexNAc(1) (T)</option>
-      <option value="Hex(5)HexNAc(2) (N)">Hex(5)HexNAc(2) (N)</option>
-      <option value="Hex(5)HexNAc(2)Phos(1) (N)">Hex(5)HexNAc(2)Phos(1) (N)</option>
-      <option value="Hex(5)HexNAc(3) (N)">Hex(5)HexNAc(3) (N)</option>
-      <option value="Hex(5)HexNAc(3)Pent(1) (N)">Hex(5)HexNAc(3)Pent(1) (N)</option>
-      <option value="Hex(5)HexNAc(4) (N)">Hex(5)HexNAc(4) (N)</option>
-      <option value="Hex(5)HexNAc(4) (S)">Hex(5)HexNAc(4) (S)</option>
-      <option value="Hex(5)HexNAc(4) (T)">Hex(5)HexNAc(4) (T)</option>
-      <option value="Hex(5)HexNAc(4)Me(2)Pent(1) (N)">Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(1) (N)">Hex(5)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(2) (N)">Hex(5)HexNAc(4)NeuAc(2) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuGc(1) (N)">Hex(5)HexNAc(4)NeuGc(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)Sulf(1) (N)">Hex(5)HexNAc(4)Sulf(1) (N)</option>
-      <option value="Hex(5)HexNAc(5) (N)">Hex(5)HexNAc(5) (N)</option>
-      <option value="Hex(5)HexNAc(5) (S)">Hex(5)HexNAc(5) (S)</option>
-      <option value="Hex(5)HexNAc(5) (T)">Hex(5)HexNAc(5) (T)</option>
-      <option value="Hex(5)Phos(1) (S)">Hex(5)Phos(1) (S)</option>
-      <option value="Hex(5)Phos(1) (T)">Hex(5)Phos(1) (T)</option>
-      <option value="Hex(5)Phos(3) (S)">Hex(5)Phos(3) (S)</option>
-      <option value="Hex(5)Phos(3) (T)">Hex(5)Phos(3) (T)</option>
-      <option value="Hex(6)HexNAc(1) (N)">Hex(6)HexNAc(1) (N)</option>
-      <option value="Hex(6)HexNAc(2) (N)">Hex(6)HexNAc(2) (N)</option>
-      <option value="Hex(6)HexNAc(2)Phos(1) (N)">Hex(6)HexNAc(2)Phos(1) (N)</option>
-      <option value="Hex(6)HexNAc(3) (N)">Hex(6)HexNAc(3) (N)</option>
-      <option value="Hex(6)HexNAc(3)Phos(1) (N)">Hex(6)HexNAc(3)Phos(1) (N)</option>
-      <option value="Hex(6)HexNAc(4) (N)">Hex(6)HexNAc(4) (N)</option>
-      <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
-      <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
-      <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
-      <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
-      <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
-      <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
-      <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
-      <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
-      <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
-      <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
-      <option value="Hex(7)HexNAc(2) (N)">Hex(7)HexNAc(2) (N)</option>
-      <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
-      <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
-      <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
-      <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
-      <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
-      <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
-      <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
-      <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
-      <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
-      <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
-      <option value="Hex(8)Phos(3) (T)">Hex(8)Phos(3) (T)</option>
-      <option value="Hex(9) (N)">Hex(9) (N)</option>
-      <option value="Hex(9)HexNAc(1) (N)">Hex(9)HexNAc(1) (N)</option>
-      <option value="Hex(9)HexNAc(2) (N)">Hex(9)HexNAc(2) (N)</option>
-      <option value="Hex(9)Phos(3) (S)">Hex(9)Phos(3) (S)</option>
-      <option value="Hex(9)Phos(3) (T)">Hex(9)Phos(3) (T)</option>
-      <option value="HexA(2)HexNAc(3) (S)">HexA(2)HexNAc(3) (S)</option>
-      <option value="HexA(2)HexNAc(3) (T)">HexA(2)HexNAc(3) (T)</option>
-      <option value="HexN (K)">HexN (K)</option>
-      <option value="HexN (N)">HexN (N)</option>
-      <option value="HexN (S)">HexN (S)</option>
-      <option value="HexN (T)">HexN (T)</option>
-      <option value="HexN (W)">HexN (W)</option>
-      <option value="HexNAc (C)">HexNAc (C)</option>
-      <option value="HexNAc (N)">HexNAc (N)</option>
-      <option value="HexNAc (S)">HexNAc (S)</option>
-      <option value="HexNAc (T)">HexNAc (T)</option>
-      <option value="HexNAc(1)dHex(1) (N)">HexNAc(1)dHex(1) (N)</option>
-      <option value="HexNAc(1)dHex(1) (S)">HexNAc(1)dHex(1) (S)</option>
-      <option value="HexNAc(1)dHex(1) (T)">HexNAc(1)dHex(1) (T)</option>
-      <option value="HexNAc(1)dHex(2) (N)">HexNAc(1)dHex(2) (N)</option>
-      <option value="HexNAc(1)Kdn(2) (S)">HexNAc(1)Kdn(2) (S)</option>
-      <option value="HexNAc(1)Kdn(2) (T)">HexNAc(1)Kdn(2) (T)</option>
-      <option value="HexNAc(1)NeuAc(1) (S)">HexNAc(1)NeuAc(1) (S)</option>
-      <option value="HexNAc(1)NeuAc(1) (T)">HexNAc(1)NeuAc(1) (T)</option>
-      <option value="HexNAc(1)NeuGc(1) (S)">HexNAc(1)NeuGc(1) (S)</option>
-      <option value="HexNAc(1)NeuGc(1) (T)">HexNAc(1)NeuGc(1) (T)</option>
-      <option value="HexNAc(1)NeuGc(2) (S)">HexNAc(1)NeuGc(2) (S)</option>
-      <option value="HexNAc(1)NeuGc(2) (T)">HexNAc(1)NeuGc(2) (T)</option>
-      <option value="HexNAc(2) (N)">HexNAc(2) (N)</option>
-      <option value="HexNAc(2) (S)">HexNAc(2) (S)</option>
-      <option value="HexNAc(2) (T)">HexNAc(2) (T)</option>
-      <option value="HexNAc(2)dHex(1) (N)">HexNAc(2)dHex(1) (N)</option>
-      <option value="HexNAc(2)dHex(2) (N)">HexNAc(2)dHex(2) (N)</option>
-      <option value="HexNAc(2)NeuAc(1) (S)">HexNAc(2)NeuAc(1) (S)</option>
-      <option value="HexNAc(2)NeuAc(1) (T)">HexNAc(2)NeuAc(1) (T)</option>
-      <option value="HexNAc(2)NeuAc(1)Sulf(1) (S)">HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="HexNAc(2)NeuAc(1)Sulf(1) (T)">HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="HexNAc(2)NeuGc(1) (S)">HexNAc(2)NeuGc(1) (S)</option>
-      <option value="HexNAc(2)NeuGc(1) (T)">HexNAc(2)NeuGc(1) (T)</option>
-      <option value="HexNAc(2)Sulf(1) (S)">HexNAc(2)Sulf(1) (S)</option>
-      <option value="HexNAc(2)Sulf(1) (T)">HexNAc(2)Sulf(1) (T)</option>
-      <option value="HexNAc(3) (S)">HexNAc(3) (S)</option>
-      <option value="HexNAc(3) (T)">HexNAc(3) (T)</option>
-      <option value="HexNAc(3)Sulf(1) (S)">HexNAc(3)Sulf(1) (S)</option>
-      <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
-      <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
-      <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
-      <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
-      <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
-      <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
-      <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
-      <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
-      <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
-      <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
-      <option value="His-&gt;Gln (H)">His-&gt;Gln (H)</option>
-      <option value="His-&gt;Glu (H)">His-&gt;Glu (H)</option>
-      <option value="His-&gt;Gly (H)">His-&gt;Gly (H)</option>
-      <option value="His-&gt;Lys (H)">His-&gt;Lys (H)</option>
-      <option value="His-&gt;Met (H)">His-&gt;Met (H)</option>
-      <option value="His-&gt;Phe (H)">His-&gt;Phe (H)</option>
-      <option value="His-&gt;Pro (H)">His-&gt;Pro (H)</option>
-      <option value="His-&gt;Ser (H)">His-&gt;Ser (H)</option>
-      <option value="His-&gt;Thr (H)">His-&gt;Thr (H)</option>
-      <option value="His-&gt;Trp (H)">His-&gt;Trp (H)</option>
-      <option value="His-&gt;Tyr (H)">His-&gt;Tyr (H)</option>
-      <option value="His-&gt;Val (H)">His-&gt;Val (H)</option>
-      <option value="His-&gt;Xle (H)">His-&gt;Xle (H)</option>
-      <option value="HMVK (C)">HMVK (C)</option>
-      <option value="HN2_mustard (C)">HN2_mustard (C)</option>
-      <option value="HN2_mustard (H)">HN2_mustard (H)</option>
-      <option value="HN2_mustard (K)">HN2_mustard (K)</option>
-      <option value="HN3_mustard (C)">HN3_mustard (C)</option>
-      <option value="HN3_mustard (H)">HN3_mustard (H)</option>
-      <option value="HN3_mustard (K)">HN3_mustard (K)</option>
-      <option value="HNE (A)">HNE (A)</option>
-      <option value="HNE (C)">HNE (C)</option>
-      <option value="HNE (H)">HNE (H)</option>
-      <option value="HNE (K)">HNE (K)</option>
-      <option value="HNE (L)">HNE (L)</option>
-      <option value="HNE+Delta:H(2) (C)">HNE+Delta:H(2) (C)</option>
-      <option value="HNE+Delta:H(2) (H)">HNE+Delta:H(2) (H)</option>
-      <option value="HNE+Delta:H(2) (K)">HNE+Delta:H(2) (K)</option>
-      <option value="HNE-BAHAH (C)">HNE-BAHAH (C)</option>
-      <option value="HNE-BAHAH (H)">HNE-BAHAH (H)</option>
-      <option value="HNE-BAHAH (K)">HNE-BAHAH (K)</option>
-      <option value="HNE-Delta:H(2)O (C)">HNE-Delta:H(2)O (C)</option>
-      <option value="HNE-Delta:H(2)O (H)">HNE-Delta:H(2)O (H)</option>
-      <option value="HNE-Delta:H(2)O (K)">HNE-Delta:H(2)O (K)</option>
-      <option value="Homocysteic_acid (M)">Homocysteic_acid (M)</option>
-      <option value="HPG (R)">HPG (R)</option>
-      <option value="Hydroxamic_acid (D)">Hydroxamic_acid (D)</option>
-      <option value="Hydroxamic_acid (E)">Hydroxamic_acid (E)</option>
-      <option value="Hydroxycinnamyl (C)">Hydroxycinnamyl (C)</option>
-      <option value="Hydroxyfarnesyl (C)">Hydroxyfarnesyl (C)</option>
-      <option value="Hydroxyheme (E)">Hydroxyheme (E)</option>
-      <option value="hydroxyisobutyryl (K)">hydroxyisobutyryl (K)</option>
-      <option value="Hydroxymethyl (N)">Hydroxymethyl (N)</option>
-      <option value="HydroxymethylOP (K)">HydroxymethylOP (K)</option>
-      <option value="Hydroxytrimethyl (K)">Hydroxytrimethyl (K)</option>
-      <option value="Hypusine (K)">Hypusine (K)</option>
-      <option value="IASD (C)">IASD (C)</option>
-      <option value="IBTP (C)">IBTP (C)</option>
-      <option value="ICAT-C (C)">ICAT-C (C)</option>
-      <option value="ICAT-C:13C(9) (C)">ICAT-C:13C(9) (C)</option>
-      <option value="ICAT-D (C)">ICAT-D (C)</option>
-      <option value="ICAT-D:2H(8) (C)">ICAT-D:2H(8) (C)</option>
-      <option value="ICAT-G (C)">ICAT-G (C)</option>
-      <option value="ICAT-G:2H(8) (C)">ICAT-G:2H(8) (C)</option>
-      <option value="ICAT-H (C)">ICAT-H (C)</option>
-      <option value="ICAT-H:13C(6) (C)">ICAT-H:13C(6) (C)</option>
-      <option value="ICDID (C)">ICDID (C)</option>
-      <option value="ICDID:2H(6) (C)">ICDID:2H(6) (C)</option>
-      <option value="ICPL (K)">ICPL (K)</option>
-      <option value="ICPL (N-term)">ICPL (N-term)</option>
-      <option value="ICPL (Protein N-term)">ICPL (Protein N-term)</option>
-      <option value="ICPL:13C(6) (K)">ICPL:13C(6) (K)</option>
-      <option value="ICPL:13C(6) (N-term)">ICPL:13C(6) (N-term)</option>
-      <option value="ICPL:13C(6) (Protein N-term)">ICPL:13C(6) (Protein N-term)</option>
-      <option value="ICPL:13C(6)2H(4) (K)">ICPL:13C(6)2H(4) (K)</option>
-      <option value="ICPL:13C(6)2H(4) (N-term)">ICPL:13C(6)2H(4) (N-term)</option>
-      <option value="ICPL:13C(6)2H(4) (Protein N-term)">ICPL:13C(6)2H(4) (Protein N-term)</option>
-      <option value="ICPL:2H(4) (K)">ICPL:2H(4) (K)</option>
-      <option value="ICPL:2H(4) (N-term)">ICPL:2H(4) (N-term)</option>
-      <option value="ICPL:2H(4) (Protein N-term)">ICPL:2H(4) (Protein N-term)</option>
-      <option value="IDEnT (C)">IDEnT (C)</option>
-      <option value="IED-Biotin (C)">IED-Biotin (C)</option>
-      <option value="IGBP (C)">IGBP (C)</option>
-      <option value="IGBP:13C(2) (C)">IGBP:13C(2) (C)</option>
-      <option value="IMEHex(2)NeuAc(1) (K)">IMEHex(2)NeuAc(1) (K)</option>
-      <option value="IMID (K)">IMID (K)</option>
-      <option value="IMID:2H(4) (K)">IMID:2H(4) (K)</option>
-      <option value="Iminobiotin (K)">Iminobiotin (K)</option>
-      <option value="Iminobiotin (N-term)">Iminobiotin (N-term)</option>
-      <option value="Iodo (H)">Iodo (H)</option>
-      <option value="Iodo (Y)">Iodo (Y)</option>
-      <option value="Iodoacetanilide (C)">Iodoacetanilide (C)</option>
-      <option value="Iodoacetanilide (K)">Iodoacetanilide (K)</option>
-      <option value="Iodoacetanilide (N-term)">Iodoacetanilide (N-term)</option>
-      <option value="Iodoacetanilide:13C(6) (C)">Iodoacetanilide:13C(6) (C)</option>
-      <option value="Iodoacetanilide:13C(6) (K)">Iodoacetanilide:13C(6) (K)</option>
-      <option value="Iodoacetanilide:13C(6) (N-term)">Iodoacetanilide:13C(6) (N-term)</option>
-      <option value="iodoTMT (C)">iodoTMT (C)</option>
-      <option value="iodoTMT (D)">iodoTMT (D)</option>
-      <option value="iodoTMT (E)">iodoTMT (E)</option>
-      <option value="iodoTMT (H)">iodoTMT (H)</option>
-      <option value="iodoTMT (K)">iodoTMT (K)</option>
-      <option value="iodoTMT6plex (C)">iodoTMT6plex (C)</option>
-      <option value="iodoTMT6plex (D)">iodoTMT6plex (D)</option>
-      <option value="iodoTMT6plex (E)">iodoTMT6plex (E)</option>
-      <option value="iodoTMT6plex (H)">iodoTMT6plex (H)</option>
-      <option value="iodoTMT6plex (K)">iodoTMT6plex (K)</option>
-      <option value="IodoU-AMP (F)">IodoU-AMP (F)</option>
-      <option value="IodoU-AMP (W)">IodoU-AMP (W)</option>
-      <option value="IodoU-AMP (Y)">IodoU-AMP (Y)</option>
-      <option value="ISD_z+2_ion (N-term)">ISD_z+2_ion (N-term)</option>
-      <option value="Isopropylphospho (S)">Isopropylphospho (S)</option>
-      <option value="Isopropylphospho (T)">Isopropylphospho (T)</option>
-      <option value="Isopropylphospho (Y)">Isopropylphospho (Y)</option>
-      <option value="iTRAQ4plex (C)">iTRAQ4plex (C)</option>
-      <option value="iTRAQ4plex (H)">iTRAQ4plex (H)</option>
-      <option value="iTRAQ4plex (K)">iTRAQ4plex (K)</option>
-      <option value="iTRAQ4plex (N-term)">iTRAQ4plex (N-term)</option>
-      <option value="iTRAQ4plex (Protein N-term)">iTRAQ4plex (Protein N-term)</option>
-      <option value="iTRAQ4plex (S)">iTRAQ4plex (S)</option>
-      <option value="iTRAQ4plex (T)">iTRAQ4plex (T)</option>
-      <option value="iTRAQ4plex (Y)">iTRAQ4plex (Y)</option>
-      <option value="iTRAQ4plex114 (C)">iTRAQ4plex114 (C)</option>
-      <option value="iTRAQ4plex114 (K)">iTRAQ4plex114 (K)</option>
-      <option value="iTRAQ4plex114 (N-term)">iTRAQ4plex114 (N-term)</option>
-      <option value="iTRAQ4plex114 (Y)">iTRAQ4plex114 (Y)</option>
-      <option value="iTRAQ4plex115 (C)">iTRAQ4plex115 (C)</option>
-      <option value="iTRAQ4plex115 (K)">iTRAQ4plex115 (K)</option>
-      <option value="iTRAQ4plex115 (N-term)">iTRAQ4plex115 (N-term)</option>
-      <option value="iTRAQ4plex115 (Y)">iTRAQ4plex115 (Y)</option>
-      <option value="iTRAQ8plex (C)">iTRAQ8plex (C)</option>
-      <option value="iTRAQ8plex (H)">iTRAQ8plex (H)</option>
-      <option value="iTRAQ8plex (K)">iTRAQ8plex (K)</option>
-      <option value="iTRAQ8plex (N-term)">iTRAQ8plex (N-term)</option>
-      <option value="iTRAQ8plex (Protein N-term)">iTRAQ8plex (Protein N-term)</option>
-      <option value="iTRAQ8plex (S)">iTRAQ8plex (S)</option>
-      <option value="iTRAQ8plex (T)">iTRAQ8plex (T)</option>
-      <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
-      <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
-      <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
-      <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
-      <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
-      <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
-      <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
-      <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
-      <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
-      <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
-      <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
-      <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
-      <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
-      <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
-      <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
-      <option value="Label:13C(5)15N(1) (E)">Label:13C(5)15N(1) (E)</option>
-      <option value="Label:13C(5)15N(1) (M)">Label:13C(5)15N(1) (M)</option>
-      <option value="Label:13C(5)15N(1) (P)">Label:13C(5)15N(1) (P)</option>
-      <option value="Label:13C(5)15N(1) (V)">Label:13C(5)15N(1) (V)</option>
-      <option value="Label:13C(6) (I)">Label:13C(6) (I)</option>
-      <option value="Label:13C(6) (K)">Label:13C(6) (K)</option>
-      <option value="Label:13C(6) (L)">Label:13C(6) (L)</option>
-      <option value="Label:13C(6) (R)">Label:13C(6) (R)</option>
-      <option value="Label:13C(6)+Acetyl (K)">Label:13C(6)+Acetyl (K)</option>
-      <option value="Label:13C(6)+Dimethyl (K)">Label:13C(6)+Dimethyl (K)</option>
-      <option value="Label:13C(6)+GG (K)">Label:13C(6)+GG (K)</option>
-      <option value="Label:13C(6)15N(1) (I)">Label:13C(6)15N(1) (I)</option>
-      <option value="Label:13C(6)15N(1) (L)">Label:13C(6)15N(1) (L)</option>
-      <option value="Label:13C(6)15N(2) (K)">Label:13C(6)15N(2) (K)</option>
-      <option value="Label:13C(6)15N(2)+Acetyl (K)">Label:13C(6)15N(2)+Acetyl (K)</option>
-      <option value="Label:13C(6)15N(2)+Dimethyl (K)">Label:13C(6)15N(2)+Dimethyl (K)</option>
-      <option value="Label:13C(6)15N(2)+GG (K)">Label:13C(6)15N(2)+GG (K)</option>
-      <option value="Label:13C(6)15N(4) (R)">Label:13C(6)15N(4) (R)</option>
-      <option value="Label:13C(6)15N(4)+Dimethyl (R)">Label:13C(6)15N(4)+Dimethyl (R)</option>
-      <option value="Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R)">Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R)</option>
-      <option value="Label:13C(6)15N(4)+Methyl (R)">Label:13C(6)15N(4)+Methyl (R)</option>
-      <option value="Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R)">Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R)</option>
-      <option value="Label:13C(9) (F)">Label:13C(9) (F)</option>
-      <option value="Label:13C(9) (Y)">Label:13C(9) (Y)</option>
-      <option value="Label:13C(9)+Phospho (Y)">Label:13C(9)+Phospho (Y)</option>
-      <option value="Label:13C(9)15N(1) (F)">Label:13C(9)15N(1) (F)</option>
-      <option value="Label:15N(1) (A)">Label:15N(1) (A)</option>
-      <option value="Label:15N(1) (C)">Label:15N(1) (C)</option>
-      <option value="Label:15N(1) (D)">Label:15N(1) (D)</option>
-      <option value="Label:15N(1) (E)">Label:15N(1) (E)</option>
-      <option value="Label:15N(1) (F)">Label:15N(1) (F)</option>
-      <option value="Label:15N(1) (G)">Label:15N(1) (G)</option>
-      <option value="Label:15N(1) (I)">Label:15N(1) (I)</option>
-      <option value="Label:15N(1) (L)">Label:15N(1) (L)</option>
-      <option value="Label:15N(1) (M)">Label:15N(1) (M)</option>
-      <option value="Label:15N(1) (P)">Label:15N(1) (P)</option>
-      <option value="Label:15N(1) (S)">Label:15N(1) (S)</option>
-      <option value="Label:15N(1) (T)">Label:15N(1) (T)</option>
-      <option value="Label:15N(1) (V)">Label:15N(1) (V)</option>
-      <option value="Label:15N(1) (Y)">Label:15N(1) (Y)</option>
-      <option value="Label:15N(2) (K)">Label:15N(2) (K)</option>
-      <option value="Label:15N(2) (N)">Label:15N(2) (N)</option>
-      <option value="Label:15N(2) (Q)">Label:15N(2) (Q)</option>
-      <option value="Label:15N(2) (W)">Label:15N(2) (W)</option>
-      <option value="Label:15N(2)2H(9) (K)">Label:15N(2)2H(9) (K)</option>
-      <option value="Label:15N(3) (H)">Label:15N(3) (H)</option>
-      <option value="Label:15N(4) (R)">Label:15N(4) (R)</option>
-      <option value="Label:18O(1) (C-term)">Label:18O(1) (C-term)</option>
-      <option value="Label:18O(1) (S)">Label:18O(1) (S)</option>
-      <option value="Label:18O(1) (T)">Label:18O(1) (T)</option>
-      <option value="Label:18O(1) (Y)">Label:18O(1) (Y)</option>
-      <option value="Label:18O(2) (C-term)">Label:18O(2) (C-term)</option>
-      <option value="Label:2H(10) (L)">Label:2H(10) (L)</option>
-      <option value="Label:2H(3) (L)">Label:2H(3) (L)</option>
-      <option value="Label:2H(3) (M)">Label:2H(3) (M)</option>
-      <option value="Label:2H(3)+Oxidation (M)">Label:2H(3)+Oxidation (M)</option>
-      <option value="Label:2H(4) (A)">Label:2H(4) (A)</option>
-      <option value="Label:2H(4) (F)">Label:2H(4) (F)</option>
-      <option value="Label:2H(4) (K)">Label:2H(4) (K)</option>
-      <option value="Label:2H(4) (U)">Label:2H(4) (U)</option>
-      <option value="Label:2H(4) (Y)">Label:2H(4) (Y)</option>
-      <option value="Label:2H(4)+Acetyl (K)">Label:2H(4)+Acetyl (K)</option>
-      <option value="Label:2H(4)+GG (K)">Label:2H(4)+GG (K)</option>
-      <option value="Label:2H(4)13C(1) (R)">Label:2H(4)13C(1) (R)</option>
-      <option value="Label:2H(6)15N(1) (P)">Label:2H(6)15N(1) (P)</option>
-      <option value="Label:2H(7)15N(4) (R)">Label:2H(7)15N(4) (R)</option>
-      <option value="Label:2H(9)13C(6)15N(2) (K)">Label:2H(9)13C(6)15N(2) (K)</option>
-      <option value="lapachenole (C)">lapachenole (C)</option>
-      <option value="Leu-&gt;MetOx (L)">Leu-&gt;MetOx (L)</option>
-      <option value="LG-anhydrolactam (K)">LG-anhydrolactam (K)</option>
-      <option value="LG-anhydrolactam (N-term)">LG-anhydrolactam (N-term)</option>
-      <option value="LG-anhyropyrrole (K)">LG-anhyropyrrole (K)</option>
-      <option value="LG-anhyropyrrole (N-term)">LG-anhyropyrrole (N-term)</option>
-      <option value="LG-Hlactam-K (K)">LG-Hlactam-K (K)</option>
-      <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
-      <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
-      <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
-      <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
-      <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
-      <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
-      <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
-      <option value="Lipoyl (K)">Lipoyl (K)</option>
-      <option value="LRGG (K)">LRGG (K)</option>
-      <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
-      <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
-      <option value="Lys (N-term)">Lys (N-term)</option>
-      <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
-      <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
-      <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
-      <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
-      <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
-      <option value="Lys-&gt;Asp (K)">Lys-&gt;Asp (K)</option>
-      <option value="Lys-&gt;CamCys (K)">Lys-&gt;CamCys (K)</option>
-      <option value="Lys-&gt;Cys (K)">Lys-&gt;Cys (K)</option>
-      <option value="Lys-&gt;Gln (K)">Lys-&gt;Gln (K)</option>
-      <option value="Lys-&gt;Glu (K)">Lys-&gt;Glu (K)</option>
-      <option value="Lys-&gt;Gly (K)">Lys-&gt;Gly (K)</option>
-      <option value="Lys-&gt;His (K)">Lys-&gt;His (K)</option>
-      <option value="Lys-&gt;Met (K)">Lys-&gt;Met (K)</option>
-      <option value="Lys-&gt;MetOx (K)">Lys-&gt;MetOx (K)</option>
-      <option value="Lys-&gt;Phe (K)">Lys-&gt;Phe (K)</option>
-      <option value="Lys-&gt;Pro (K)">Lys-&gt;Pro (K)</option>
-      <option value="Lys-&gt;Ser (K)">Lys-&gt;Ser (K)</option>
-      <option value="Lys-&gt;Thr (K)">Lys-&gt;Thr (K)</option>
-      <option value="Lys-&gt;Trp (K)">Lys-&gt;Trp (K)</option>
-      <option value="Lys-&gt;Tyr (K)">Lys-&gt;Tyr (K)</option>
-      <option value="Lys-&gt;Val (K)">Lys-&gt;Val (K)</option>
-      <option value="Lys-&gt;Xle (K)">Lys-&gt;Xle (K)</option>
-      <option value="Lys-loss (Protein C-term K)">Lys-loss (Protein C-term K)</option>
-      <option value="Lysbiotinhydrazide (K)">Lysbiotinhydrazide (K)</option>
-      <option value="maleimide (C)">maleimide (C)</option>
-      <option value="maleimide (K)">maleimide (K)</option>
-      <option value="Maleimide-PEO2-Biotin (C)">Maleimide-PEO2-Biotin (C)</option>
-      <option value="maleimide3 (C)">maleimide3 (C)</option>
-      <option value="maleimide3 (K)">maleimide3 (K)</option>
-      <option value="maleimide5 (C)">maleimide5 (C)</option>
-      <option value="maleimide5 (K)">maleimide5 (K)</option>
-      <option value="Malonyl (C)">Malonyl (C)</option>
-      <option value="Malonyl (K)">Malonyl (K)</option>
-      <option value="Malonyl (S)">Malonyl (S)</option>
-      <option value="MDCC (C)">MDCC (C)</option>
-      <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
-      <option value="Menadione (C)">Menadione (C)</option>
-      <option value="Menadione (K)">Menadione (K)</option>
-      <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
-      <option value="Menadione-HQ (K)">Menadione-HQ (K)</option>
-      <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
-      <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
-      <option value="MesitylOxide (H)">MesitylOxide (H)</option>
-      <option value="MesitylOxide (K)">MesitylOxide (K)</option>
-      <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
-      <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
-      <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
-      <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
-      <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
-      <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
-      <option value="Met-&gt;AspSA (M)">Met-&gt;AspSA (M)</option>
-      <option value="Met-&gt;Cys (M)">Met-&gt;Cys (M)</option>
-      <option value="Met-&gt;Gln (M)">Met-&gt;Gln (M)</option>
-      <option value="Met-&gt;Glu (M)">Met-&gt;Glu (M)</option>
-      <option value="Met-&gt;Gly (M)">Met-&gt;Gly (M)</option>
-      <option value="Met-&gt;His (M)">Met-&gt;His (M)</option>
-      <option value="Met-&gt;Hpg (M)">Met-&gt;Hpg (M)</option>
-      <option value="Met-&gt;Hse (C-term M)">Met-&gt;Hse (C-term M)</option>
-      <option value="Met-&gt;Hsl (C-term M)">Met-&gt;Hsl (C-term M)</option>
-      <option value="Met-&gt;Lys (M)">Met-&gt;Lys (M)</option>
-      <option value="Met-&gt;Phe (M)">Met-&gt;Phe (M)</option>
-      <option value="Met-&gt;Pro (M)">Met-&gt;Pro (M)</option>
-      <option value="Met-&gt;Ser (M)">Met-&gt;Ser (M)</option>
-      <option value="Met-&gt;Thr (M)">Met-&gt;Thr (M)</option>
-      <option value="Met-&gt;Trp (M)">Met-&gt;Trp (M)</option>
-      <option value="Met-&gt;Tyr (M)">Met-&gt;Tyr (M)</option>
-      <option value="Met-&gt;Val (M)">Met-&gt;Val (M)</option>
-      <option value="Met-&gt;Xle (M)">Met-&gt;Xle (M)</option>
-      <option value="Met-loss (Protein N-term M)">Met-loss (Protein N-term M)</option>
-      <option value="Met-loss+Acetyl (Protein N-term M)">Met-loss+Acetyl (Protein N-term M)</option>
-      <option value="Methamidophos-O (C)">Methamidophos-O (C)</option>
-      <option value="Methamidophos-O (H)">Methamidophos-O (H)</option>
-      <option value="Methamidophos-O (K)">Methamidophos-O (K)</option>
-      <option value="Methamidophos-O (S)">Methamidophos-O (S)</option>
-      <option value="Methamidophos-O (T)">Methamidophos-O (T)</option>
-      <option value="Methamidophos-O (Y)">Methamidophos-O (Y)</option>
-      <option value="Methamidophos-S (C)">Methamidophos-S (C)</option>
-      <option value="Methamidophos-S (H)">Methamidophos-S (H)</option>
-      <option value="Methamidophos-S (K)">Methamidophos-S (K)</option>
-      <option value="Methamidophos-S (S)">Methamidophos-S (S)</option>
-      <option value="Methamidophos-S (T)">Methamidophos-S (T)</option>
-      <option value="Methamidophos-S (Y)">Methamidophos-S (Y)</option>
-      <option value="Methyl (C)">Methyl (C)</option>
-      <option value="Methyl (C-term)">Methyl (C-term)</option>
-      <option value="Methyl (D)">Methyl (D)</option>
-      <option value="Methyl (E)">Methyl (E)</option>
-      <option value="Methyl (H)">Methyl (H)</option>
-      <option value="Methyl (I)">Methyl (I)</option>
-      <option value="Methyl (K)">Methyl (K)</option>
-      <option value="Methyl (L)">Methyl (L)</option>
-      <option value="Methyl (N)">Methyl (N)</option>
-      <option value="Methyl (N-term)">Methyl (N-term)</option>
-      <option value="Methyl (Protein N-term)">Methyl (Protein N-term)</option>
-      <option value="Methyl (Q)">Methyl (Q)</option>
-      <option value="Methyl (R)">Methyl (R)</option>
-      <option value="Methyl (S)">Methyl (S)</option>
-      <option value="Methyl (T)">Methyl (T)</option>
-      <option value="Methyl+Acetyl:2H(3) (K)">Methyl+Acetyl:2H(3) (K)</option>
-      <option value="Methyl+Deamidated (N)">Methyl+Deamidated (N)</option>
-      <option value="Methyl+Deamidated (Q)">Methyl+Deamidated (Q)</option>
-      <option value="Methyl-PEO12-Maleimide (C)">Methyl-PEO12-Maleimide (C)</option>
-      <option value="Methyl:2H(2) (K)">Methyl:2H(2) (K)</option>
-      <option value="Methyl:2H(2) (N-term)">Methyl:2H(2) (N-term)</option>
-      <option value="Methyl:2H(2)13C (C)">Methyl:2H(2)13C (C)</option>
-      <option value="Methyl:2H(2)13C (C-term)">Methyl:2H(2)13C (C-term)</option>
-      <option value="Methyl:2H(2)13C (D)">Methyl:2H(2)13C (D)</option>
-      <option value="Methyl:2H(2)13C (E)">Methyl:2H(2)13C (E)</option>
-      <option value="Methyl:2H(2)13C (H)">Methyl:2H(2)13C (H)</option>
-      <option value="Methyl:2H(2)13C (I)">Methyl:2H(2)13C (I)</option>
-      <option value="Methyl:2H(2)13C (K)">Methyl:2H(2)13C (K)</option>
-      <option value="Methyl:2H(2)13C (L)">Methyl:2H(2)13C (L)</option>
-      <option value="Methyl:2H(2)13C (N)">Methyl:2H(2)13C (N)</option>
-      <option value="Methyl:2H(2)13C (N-term)">Methyl:2H(2)13C (N-term)</option>
-      <option value="Methyl:2H(2)13C (Protein N-term)">Methyl:2H(2)13C (Protein N-term)</option>
-      <option value="Methyl:2H(2)13C (Q)">Methyl:2H(2)13C (Q)</option>
-      <option value="Methyl:2H(2)13C (R)">Methyl:2H(2)13C (R)</option>
-      <option value="Methyl:2H(2)13C (S)">Methyl:2H(2)13C (S)</option>
-      <option value="Methyl:2H(2)13C (T)">Methyl:2H(2)13C (T)</option>
-      <option value="Methyl:2H(3) (D)">Methyl:2H(3) (D)</option>
-      <option value="Methyl:2H(3) (E)">Methyl:2H(3) (E)</option>
-      <option value="Methyl:2H(3) (K)">Methyl:2H(3) (K)</option>
-      <option value="Methyl:2H(3) (R)">Methyl:2H(3) (R)</option>
-      <option value="Methyl:2H(3) (X)">Methyl:2H(3) (X)</option>
-      <option value="Methyl:2H(3)+Acetyl:2H(3) (K)">Methyl:2H(3)+Acetyl:2H(3) (K)</option>
-      <option value="Methyl:2H(3)13C(1) (K)">Methyl:2H(3)13C(1) (K)</option>
-      <option value="Methyl:2H(3)13C(1) (N-term)">Methyl:2H(3)13C(1) (N-term)</option>
-      <option value="Methyl:2H(3)13C(1) (R)">Methyl:2H(3)13C(1) (R)</option>
-      <option value="Methylamine (S)">Methylamine (S)</option>
-      <option value="Methylamine (T)">Methylamine (T)</option>
-      <option value="Methylmalonylation (S)">Methylmalonylation (S)</option>
-      <option value="methylol (K)">methylol (K)</option>
-      <option value="methylol (W)">methylol (W)</option>
-      <option value="methylol (Y)">methylol (Y)</option>
-      <option value="Methylphosphonate (S)">Methylphosphonate (S)</option>
-      <option value="Methylphosphonate (T)">Methylphosphonate (T)</option>
-      <option value="Methylphosphonate (Y)">Methylphosphonate (Y)</option>
-      <option value="Methylpyrroline (K)">Methylpyrroline (K)</option>
-      <option value="methylsulfonylethyl (C)">methylsulfonylethyl (C)</option>
-      <option value="methylsulfonylethyl (H)">methylsulfonylethyl (H)</option>
-      <option value="methylsulfonylethyl (K)">methylsulfonylethyl (K)</option>
-      <option value="Methylthio (C)">Methylthio (C)</option>
-      <option value="Methylthio (D)">Methylthio (D)</option>
-      <option value="Methylthio (K)">Methylthio (K)</option>
-      <option value="Methylthio (N)">Methylthio (N)</option>
-      <option value="Methylthio (N-term)">Methylthio (N-term)</option>
-      <option value="MG-H1 (R)">MG-H1 (R)</option>
-      <option value="Microcin (Protein C-term)">Microcin (Protein C-term)</option>
-      <option value="MicrocinC7 (Protein C-term)">MicrocinC7 (Protein C-term)</option>
-      <option value="MM-diphenylpentanone (C)">MM-diphenylpentanone (C)</option>
-      <option value="Molybdopterin (C)">Molybdopterin (C)</option>
-      <option value="MolybdopterinGD (C)">MolybdopterinGD (C)</option>
-      <option value="MolybdopterinGD (D)">MolybdopterinGD (D)</option>
-      <option value="MolybdopterinGD (U)">MolybdopterinGD (U)</option>
-      <option value="MolybdopterinGD+Delta:S(-1)Se(1) (C)">MolybdopterinGD+Delta:S(-1)Se(1) (C)</option>
-      <option value="monomethylphosphothione (C)">monomethylphosphothione (C)</option>
-      <option value="monomethylphosphothione (H)">monomethylphosphothione (H)</option>
-      <option value="monomethylphosphothione (K)">monomethylphosphothione (K)</option>
-      <option value="monomethylphosphothione (S)">monomethylphosphothione (S)</option>
-      <option value="monomethylphosphothione (T)">monomethylphosphothione (T)</option>
-      <option value="monomethylphosphothione (Y)">monomethylphosphothione (Y)</option>
-      <option value="mTRAQ (H)">mTRAQ (H)</option>
-      <option value="mTRAQ (K)">mTRAQ (K)</option>
-      <option value="mTRAQ (N-term)">mTRAQ (N-term)</option>
-      <option value="mTRAQ (S)">mTRAQ (S)</option>
-      <option value="mTRAQ (T)">mTRAQ (T)</option>
-      <option value="mTRAQ (Y)">mTRAQ (Y)</option>
-      <option value="mTRAQ:13C(3)15N(1) (H)">mTRAQ:13C(3)15N(1) (H)</option>
-      <option value="mTRAQ:13C(3)15N(1) (K)">mTRAQ:13C(3)15N(1) (K)</option>
-      <option value="mTRAQ:13C(3)15N(1) (N-term)">mTRAQ:13C(3)15N(1) (N-term)</option>
-      <option value="mTRAQ:13C(3)15N(1) (S)">mTRAQ:13C(3)15N(1) (S)</option>
-      <option value="mTRAQ:13C(3)15N(1) (T)">mTRAQ:13C(3)15N(1) (T)</option>
-      <option value="mTRAQ:13C(3)15N(1) (Y)">mTRAQ:13C(3)15N(1) (Y)</option>
-      <option value="mTRAQ:13C(6)15N(2) (H)">mTRAQ:13C(6)15N(2) (H)</option>
-      <option value="mTRAQ:13C(6)15N(2) (K)">mTRAQ:13C(6)15N(2) (K)</option>
-      <option value="mTRAQ:13C(6)15N(2) (N-term)">mTRAQ:13C(6)15N(2) (N-term)</option>
-      <option value="mTRAQ:13C(6)15N(2) (S)">mTRAQ:13C(6)15N(2) (S)</option>
-      <option value="mTRAQ:13C(6)15N(2) (T)">mTRAQ:13C(6)15N(2) (T)</option>
-      <option value="mTRAQ:13C(6)15N(2) (Y)">mTRAQ:13C(6)15N(2) (Y)</option>
-      <option value="MTSL (C)">MTSL (C)</option>
-      <option value="MurNAc (A)">MurNAc (A)</option>
-      <option value="Myristoleyl (Protein N-term G)">Myristoleyl (Protein N-term G)</option>
-      <option value="Myristoyl (C)">Myristoyl (C)</option>
-      <option value="Myristoyl (K)">Myristoyl (K)</option>
-      <option value="Myristoyl (N-term G)">Myristoyl (N-term G)</option>
-      <option value="Myristoyl+Delta:H(-4) (Protein N-term G)">Myristoyl+Delta:H(-4) (Protein N-term G)</option>
-      <option value="N-dimethylphosphate (S)">N-dimethylphosphate (S)</option>
-      <option value="NA-LNO2 (C)">NA-LNO2 (C)</option>
-      <option value="NA-LNO2 (H)">NA-LNO2 (H)</option>
-      <option value="NA-OA-NO2 (C)">NA-OA-NO2 (C)</option>
-      <option value="NA-OA-NO2 (H)">NA-OA-NO2 (H)</option>
-      <option value="NBS (W)">NBS (W)</option>
-      <option value="NBS:13C(6) (W)">NBS:13C(6) (W)</option>
-      <option value="NDA (K)">NDA (K)</option>
-      <option value="NDA (N-term)">NDA (N-term)</option>
-      <option value="NEIAA (C)">NEIAA (C)</option>
-      <option value="NEIAA (Y)">NEIAA (Y)</option>
-      <option value="NEIAA:2H(5) (C)">NEIAA:2H(5) (C)</option>
-      <option value="NEIAA:2H(5) (Y)">NEIAA:2H(5) (Y)</option>
-      <option value="NEM:2H(5) (C)">NEM:2H(5) (C)</option>
-      <option value="NEM:2H(5)+H2O (C)">NEM:2H(5)+H2O (C)</option>
-      <option value="NEMsulfur (C)">NEMsulfur (C)</option>
-      <option value="NEMsulfurWater (C)">NEMsulfurWater (C)</option>
-      <option value="Nethylmaleimide (C)">Nethylmaleimide (C)</option>
-      <option value="Nethylmaleimide+water (C)">Nethylmaleimide+water (C)</option>
-      <option value="Nethylmaleimide+water (K)">Nethylmaleimide+water (K)</option>
-      <option value="NeuAc (N)">NeuAc (N)</option>
-      <option value="NeuAc (S)">NeuAc (S)</option>
-      <option value="NeuAc (T)">NeuAc (T)</option>
-      <option value="NeuGc (N)">NeuGc (N)</option>
-      <option value="NeuGc (S)">NeuGc (S)</option>
-      <option value="NeuGc (T)">NeuGc (T)</option>
-      <option value="NHS-fluorescein (K)">NHS-fluorescein (K)</option>
-      <option value="NHS-LC-Biotin (K)">NHS-LC-Biotin (K)</option>
-      <option value="NHS-LC-Biotin (N-term)">NHS-LC-Biotin (N-term)</option>
-      <option value="NIC (K)">NIC (K)</option>
-      <option value="NIC (N-term)">NIC (N-term)</option>
-      <option value="NIPCAM (C)">NIPCAM (C)</option>
-      <option value="Nitrene (Y)">Nitrene (Y)</option>
-      <option value="Nitro (F)">Nitro (F)</option>
-      <option value="Nitro (W)">Nitro (W)</option>
-      <option value="Nitro (Y)">Nitro (Y)</option>
-      <option value="Nitrosyl (C)">Nitrosyl (C)</option>
-      <option value="Nitrosyl (Y)">Nitrosyl (Y)</option>
-      <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
-      <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
-      <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
-      <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
-      <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-      <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
-      <option value="NP40 (N-term)">NP40 (N-term)</option>
-      <option value="NQIGG (K)">NQIGG (K)</option>
-      <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
-      <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
-      <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
-      <option value="O-Et-N-diMePhospho (S)">O-Et-N-diMePhospho (S)</option>
-      <option value="O-Isopropylmethylphosphonate (S)">O-Isopropylmethylphosphonate (S)</option>
-      <option value="O-Isopropylmethylphosphonate (T)">O-Isopropylmethylphosphonate (T)</option>
-      <option value="O-Isopropylmethylphosphonate (Y)">O-Isopropylmethylphosphonate (Y)</option>
-      <option value="O-Methylphosphate (S)">O-Methylphosphate (S)</option>
-      <option value="O-Methylphosphate (T)">O-Methylphosphate (T)</option>
-      <option value="O-Methylphosphate (Y)">O-Methylphosphate (Y)</option>
-      <option value="O-pinacolylmethylphosphonate (H)">O-pinacolylmethylphosphonate (H)</option>
-      <option value="O-pinacolylmethylphosphonate (K)">O-pinacolylmethylphosphonate (K)</option>
-      <option value="O-pinacolylmethylphosphonate (S)">O-pinacolylmethylphosphonate (S)</option>
-      <option value="O-pinacolylmethylphosphonate (T)">O-pinacolylmethylphosphonate (T)</option>
-      <option value="O-pinacolylmethylphosphonate (Y)">O-pinacolylmethylphosphonate (Y)</option>
-      <option value="Octanoyl (C)">Octanoyl (C)</option>
-      <option value="Octanoyl (S)">Octanoyl (S)</option>
-      <option value="Octanoyl (T)">Octanoyl (T)</option>
-      <option value="OxArgBiotin (R)">OxArgBiotin (R)</option>
-      <option value="OxArgBiotinRed (R)">OxArgBiotinRed (R)</option>
-      <option value="Oxidation (C)">Oxidation (C)</option>
-      <option value="Oxidation (C-term G)">Oxidation (C-term G)</option>
-      <option value="Oxidation (D)">Oxidation (D)</option>
-      <option value="Oxidation (E)">Oxidation (E)</option>
-      <option value="Oxidation (F)">Oxidation (F)</option>
-      <option value="Oxidation (H)">Oxidation (H)</option>
-      <option value="Oxidation (I)">Oxidation (I)</option>
-      <option value="Oxidation (K)">Oxidation (K)</option>
-      <option value="Oxidation (L)">Oxidation (L)</option>
-      <option value="Oxidation (M)">Oxidation (M)</option>
-      <option value="Oxidation (N)">Oxidation (N)</option>
-      <option value="Oxidation (P)">Oxidation (P)</option>
-      <option value="Oxidation (Q)">Oxidation (Q)</option>
-      <option value="Oxidation (R)">Oxidation (R)</option>
-      <option value="Oxidation (S)">Oxidation (S)</option>
-      <option value="Oxidation (T)">Oxidation (T)</option>
-      <option value="Oxidation (U)">Oxidation (U)</option>
-      <option value="Oxidation (V)">Oxidation (V)</option>
-      <option value="Oxidation (W)">Oxidation (W)</option>
-      <option value="Oxidation (Y)">Oxidation (Y)</option>
-      <option value="Oxidation+NEM (C)">Oxidation+NEM (C)</option>
-      <option value="OxLysBiotin (K)">OxLysBiotin (K)</option>
-      <option value="OxLysBiotinRed (K)">OxLysBiotinRed (K)</option>
-      <option value="OxProBiotin (P)">OxProBiotin (P)</option>
-      <option value="OxProBiotinRed (P)">OxProBiotinRed (P)</option>
-      <option value="Palmitoleyl (C)">Palmitoleyl (C)</option>
-      <option value="Palmitoleyl (S)">Palmitoleyl (S)</option>
-      <option value="Palmitoleyl (T)">Palmitoleyl (T)</option>
-      <option value="Palmitoyl (C)">Palmitoyl (C)</option>
-      <option value="Palmitoyl (K)">Palmitoyl (K)</option>
-      <option value="Palmitoyl (Protein N-term)">Palmitoyl (Protein N-term)</option>
-      <option value="Palmitoyl (S)">Palmitoyl (S)</option>
-      <option value="Palmitoyl (T)">Palmitoyl (T)</option>
-      <option value="PEITC (C)">PEITC (C)</option>
-      <option value="PEITC (K)">PEITC (K)</option>
-      <option value="PEITC (N-term)">PEITC (N-term)</option>
-      <option value="Pent(1)HexNAc(1) (S)">Pent(1)HexNAc(1) (S)</option>
-      <option value="Pent(1)HexNAc(1) (T)">Pent(1)HexNAc(1) (T)</option>
-      <option value="Pent(2) (S)">Pent(2) (S)</option>
-      <option value="Pent(2) (T)">Pent(2) (T)</option>
-      <option value="Pentose (S)">Pentose (S)</option>
-      <option value="Pentose (T)">Pentose (T)</option>
-      <option value="Pentylamine (Q)">Pentylamine (Q)</option>
-      <option value="PEO-Iodoacetyl-LC-Biotin (C)">PEO-Iodoacetyl-LC-Biotin (C)</option>
-      <option value="PET (S)">PET (S)</option>
-      <option value="PET (T)">PET (T)</option>
-      <option value="Phe-&gt;Ala (F)">Phe-&gt;Ala (F)</option>
-      <option value="Phe-&gt;Arg (F)">Phe-&gt;Arg (F)</option>
-      <option value="Phe-&gt;Asn (F)">Phe-&gt;Asn (F)</option>
-      <option value="Phe-&gt;Asp (F)">Phe-&gt;Asp (F)</option>
-      <option value="Phe-&gt;CamCys (F)">Phe-&gt;CamCys (F)</option>
-      <option value="Phe-&gt;Cys (F)">Phe-&gt;Cys (F)</option>
-      <option value="Phe-&gt;Gln (F)">Phe-&gt;Gln (F)</option>
-      <option value="Phe-&gt;Glu (F)">Phe-&gt;Glu (F)</option>
-      <option value="Phe-&gt;Gly (F)">Phe-&gt;Gly (F)</option>
-      <option value="Phe-&gt;His (F)">Phe-&gt;His (F)</option>
-      <option value="Phe-&gt;Lys (F)">Phe-&gt;Lys (F)</option>
-      <option value="Phe-&gt;Met (F)">Phe-&gt;Met (F)</option>
-      <option value="Phe-&gt;Pro (F)">Phe-&gt;Pro (F)</option>
-      <option value="Phe-&gt;Ser (F)">Phe-&gt;Ser (F)</option>
-      <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
-      <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
-      <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
-      <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
-      <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
-      <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
-      <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
-      <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
-      <option value="Phospho (C)">Phospho (C)</option>
-      <option value="Phospho (D)">Phospho (D)</option>
-      <option value="Phospho (E)">Phospho (E)</option>
-      <option value="Phospho (H)">Phospho (H)</option>
-      <option value="Phospho (K)">Phospho (K)</option>
-      <option value="Phospho (R)">Phospho (R)</option>
-      <option value="Phospho (S)">Phospho (S)</option>
-      <option value="Phospho (T)">Phospho (T)</option>
-      <option value="Phospho (Y)">Phospho (Y)</option>
-      <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
-      <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
-      <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
-      <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
-      <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
-      <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
-      <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
-      <option value="Phosphogluconoylation (K)">Phosphogluconoylation (K)</option>
-      <option value="Phosphogluconoylation (N-term)">Phosphogluconoylation (N-term)</option>
-      <option value="Phosphoguanosine (H)">Phosphoguanosine (H)</option>
-      <option value="Phosphoguanosine (K)">Phosphoguanosine (K)</option>
-      <option value="PhosphoHex (S)">PhosphoHex (S)</option>
-      <option value="PhosphoHex (T)">PhosphoHex (T)</option>
-      <option value="PhosphoHex(2) (N)">PhosphoHex(2) (N)</option>
-      <option value="PhosphoHex(2) (S)">PhosphoHex(2) (S)</option>
-      <option value="PhosphoHex(2) (T)">PhosphoHex(2) (T)</option>
-      <option value="PhosphoHexNAc (S)">PhosphoHexNAc (S)</option>
-      <option value="PhosphoHexNAc (T)">PhosphoHexNAc (T)</option>
-      <option value="Phosphopantetheine (S)">Phosphopantetheine (S)</option>
-      <option value="Phosphopropargyl (S)">Phosphopropargyl (S)</option>
-      <option value="Phosphopropargyl (T)">Phosphopropargyl (T)</option>
-      <option value="Phosphopropargyl (Y)">Phosphopropargyl (Y)</option>
-      <option value="phosphoRibosyl (D)">phosphoRibosyl (D)</option>
-      <option value="phosphoRibosyl (E)">phosphoRibosyl (E)</option>
-      <option value="phosphoRibosyl (R)">phosphoRibosyl (R)</option>
-      <option value="PhosphoribosyldephosphoCoA (S)">PhosphoribosyldephosphoCoA (S)</option>
-      <option value="PhosphoUridine (H)">PhosphoUridine (H)</option>
-      <option value="PhosphoUridine (Y)">PhosphoUridine (Y)</option>
-      <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
-      <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
-      <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
-      <option value="Piperidine (K)">Piperidine (K)</option>
-      <option value="Piperidine (N-term)">Piperidine (N-term)</option>
-      <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
-      <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
-      <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
-      <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
-      <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
-      <option value="Pro-&gt;Gln (P)">Pro-&gt;Gln (P)</option>
-      <option value="Pro-&gt;Glu (P)">Pro-&gt;Glu (P)</option>
-      <option value="Pro-&gt;Gly (P)">Pro-&gt;Gly (P)</option>
-      <option value="Pro-&gt;HAVA (P)">Pro-&gt;HAVA (P)</option>
-      <option value="Pro-&gt;His (P)">Pro-&gt;His (P)</option>
-      <option value="Pro-&gt;Lys (P)">Pro-&gt;Lys (P)</option>
-      <option value="Pro-&gt;Met (P)">Pro-&gt;Met (P)</option>
-      <option value="Pro-&gt;Phe (P)">Pro-&gt;Phe (P)</option>
-      <option value="Pro-&gt;pyro-Glu (P)">Pro-&gt;pyro-Glu (P)</option>
-      <option value="Pro-&gt;Pyrrolidinone (P)">Pro-&gt;Pyrrolidinone (P)</option>
-      <option value="Pro-&gt;Pyrrolidone (P)">Pro-&gt;Pyrrolidone (P)</option>
-      <option value="Pro-&gt;Ser (P)">Pro-&gt;Ser (P)</option>
-      <option value="Pro-&gt;Thr (P)">Pro-&gt;Thr (P)</option>
-      <option value="Pro-&gt;Trp (P)">Pro-&gt;Trp (P)</option>
-      <option value="Pro-&gt;Tyr (P)">Pro-&gt;Tyr (P)</option>
-      <option value="Pro-&gt;Val (P)">Pro-&gt;Val (P)</option>
-      <option value="Pro-&gt;Xle (P)">Pro-&gt;Xle (P)</option>
-      <option value="probiotinhydrazide (P)">probiotinhydrazide (P)</option>
-      <option value="Propargylamine (C-term)">Propargylamine (C-term)</option>
-      <option value="Propargylamine (D)">Propargylamine (D)</option>
-      <option value="Propargylamine (E)">Propargylamine (E)</option>
-      <option value="Propionamide (C)">Propionamide (C)</option>
-      <option value="Propionamide (K)">Propionamide (K)</option>
-      <option value="Propionamide (N-term)">Propionamide (N-term)</option>
-      <option value="Propionamide:2H(3) (C)">Propionamide:2H(3) (C)</option>
-      <option value="Propionyl (K)">Propionyl (K)</option>
-      <option value="Propionyl (N-term)">Propionyl (N-term)</option>
-      <option value="Propionyl (Protein N-term)">Propionyl (Protein N-term)</option>
-      <option value="Propionyl (S)">Propionyl (S)</option>
-      <option value="Propionyl (T)">Propionyl (T)</option>
-      <option value="Propionyl:13C(3) (K)">Propionyl:13C(3) (K)</option>
-      <option value="Propionyl:13C(3) (N-term)">Propionyl:13C(3) (N-term)</option>
-      <option value="Propiophenone (C)">Propiophenone (C)</option>
-      <option value="Propiophenone (H)">Propiophenone (H)</option>
-      <option value="Propiophenone (K)">Propiophenone (K)</option>
-      <option value="Propiophenone (R)">Propiophenone (R)</option>
-      <option value="Propiophenone (S)">Propiophenone (S)</option>
-      <option value="Propiophenone (T)">Propiophenone (T)</option>
-      <option value="Propiophenone (W)">Propiophenone (W)</option>
-      <option value="Propyl (C-term)">Propyl (C-term)</option>
-      <option value="Propyl (D)">Propyl (D)</option>
-      <option value="Propyl (E)">Propyl (E)</option>
-      <option value="Propyl (K)">Propyl (K)</option>
-      <option value="Propyl (N-term)">Propyl (N-term)</option>
-      <option value="Propyl (Protein C-term)">Propyl (Protein C-term)</option>
-      <option value="Propyl:2H(6) (K)">Propyl:2H(6) (K)</option>
-      <option value="Propyl:2H(6) (N-term)">Propyl:2H(6) (N-term)</option>
-      <option value="PropylNAGthiazoline (C)">PropylNAGthiazoline (C)</option>
-      <option value="PS_Hapten (C)">PS_Hapten (C)</option>
-      <option value="PS_Hapten (H)">PS_Hapten (H)</option>
-      <option value="PS_Hapten (K)">PS_Hapten (K)</option>
-      <option value="pupylation (K)">pupylation (K)</option>
-      <option value="Puromycin (C-term)">Puromycin (C-term)</option>
-      <option value="PyMIC (N-term)">PyMIC (N-term)</option>
-      <option value="PyridoxalPhosphate (K)">PyridoxalPhosphate (K)</option>
-      <option value="PyridoxalPhosphateH2 (K)">PyridoxalPhosphateH2 (K)</option>
-      <option value="Pyridylacetyl (K)">Pyridylacetyl (K)</option>
-      <option value="Pyridylacetyl (N-term)">Pyridylacetyl (N-term)</option>
-      <option value="Pyridylethyl (C)">Pyridylethyl (C)</option>
-      <option value="Pyro-carbamidomethyl (N-term C)">Pyro-carbamidomethyl (N-term C)</option>
-      <option value="pyrophospho (S)">pyrophospho (S)</option>
-      <option value="pyrophospho (T)">pyrophospho (T)</option>
-      <option value="PyruvicAcidIminyl (K)">PyruvicAcidIminyl (K)</option>
-      <option value="PyruvicAcidIminyl (Protein N-term C)">PyruvicAcidIminyl (Protein N-term C)</option>
-      <option value="PyruvicAcidIminyl (Protein N-term V)">PyruvicAcidIminyl (Protein N-term V)</option>
-      <option value="QAT (C)">QAT (C)</option>
-      <option value="QAT:2H(3) (C)">QAT:2H(3) (C)</option>
-      <option value="QEQTGG (K)">QEQTGG (K)</option>
-      <option value="QQQTGG (K)">QQQTGG (K)</option>
-      <option value="QTGG (K)">QTGG (K)</option>
-      <option value="Quinone (W)">Quinone (W)</option>
-      <option value="Quinone (Y)">Quinone (Y)</option>
-      <option value="Retinylidene (K)">Retinylidene (K)</option>
-      <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
-      <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
-      <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-      <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-      <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-      <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-      <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-      <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-      <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-      <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-      <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
-      <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
-      <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
-      <option value="Saligenin (H)">Saligenin (H)</option>
-      <option value="Saligenin (K)">Saligenin (K)</option>
-      <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
-      <option value="Ser-&gt;Arg (S)">Ser-&gt;Arg (S)</option>
-      <option value="Ser-&gt;Asn (S)">Ser-&gt;Asn (S)</option>
-      <option value="Ser-&gt;Asp (S)">Ser-&gt;Asp (S)</option>
-      <option value="Ser-&gt;Cys (S)">Ser-&gt;Cys (S)</option>
-      <option value="Ser-&gt;Gln (S)">Ser-&gt;Gln (S)</option>
-      <option value="Ser-&gt;Glu (S)">Ser-&gt;Glu (S)</option>
-      <option value="Ser-&gt;Gly (S)">Ser-&gt;Gly (S)</option>
-      <option value="Ser-&gt;His (S)">Ser-&gt;His (S)</option>
-      <option value="Ser-&gt;LacticAcid (Protein N-term S)">Ser-&gt;LacticAcid (Protein N-term S)</option>
-      <option value="Ser-&gt;Lys (S)">Ser-&gt;Lys (S)</option>
-      <option value="Ser-&gt;Met (S)">Ser-&gt;Met (S)</option>
-      <option value="Ser-&gt;Phe (S)">Ser-&gt;Phe (S)</option>
-      <option value="Ser-&gt;Pro (S)">Ser-&gt;Pro (S)</option>
-      <option value="Ser-&gt;Thr (S)">Ser-&gt;Thr (S)</option>
-      <option value="Ser-&gt;Trp (S)">Ser-&gt;Trp (S)</option>
-      <option value="Ser-&gt;Tyr (S)">Ser-&gt;Tyr (S)</option>
-      <option value="Ser-&gt;Val (S)">Ser-&gt;Val (S)</option>
-      <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
-      <option value="serotonylation (Q)">serotonylation (Q)</option>
-      <option value="shTMT (K)">shTMT (K)</option>
-      <option value="shTMT (N-term)">shTMT (N-term)</option>
-      <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
-      <option value="SMA (K)">SMA (K)</option>
-      <option value="SMA (N-term)">SMA (N-term)</option>
-      <option value="spermidine (Q)">spermidine (Q)</option>
-      <option value="spermine (Q)">spermine (Q)</option>
-      <option value="SPITC (K)">SPITC (K)</option>
-      <option value="SPITC (N-term)">SPITC (N-term)</option>
-      <option value="SPITC:13C(6) (K)">SPITC:13C(6) (K)</option>
-      <option value="SPITC:13C(6) (N-term)">SPITC:13C(6) (N-term)</option>
-      <option value="Succinyl (K)">Succinyl (K)</option>
-      <option value="Succinyl (N-term)">Succinyl (N-term)</option>
-      <option value="Succinyl (Protein N-term)">Succinyl (Protein N-term)</option>
-      <option value="Succinyl:13C(4) (K)">Succinyl:13C(4) (K)</option>
-      <option value="Succinyl:13C(4) (N-term)">Succinyl:13C(4) (N-term)</option>
-      <option value="Succinyl:2H(4) (K)">Succinyl:2H(4) (K)</option>
-      <option value="Succinyl:2H(4) (N-term)">Succinyl:2H(4) (N-term)</option>
-      <option value="SulfanilicAcid (C-term)">SulfanilicAcid (C-term)</option>
-      <option value="SulfanilicAcid (D)">SulfanilicAcid (D)</option>
-      <option value="SulfanilicAcid (E)">SulfanilicAcid (E)</option>
-      <option value="SulfanilicAcid:13C(6) (C-term)">SulfanilicAcid:13C(6) (C-term)</option>
-      <option value="SulfanilicAcid:13C(6) (D)">SulfanilicAcid:13C(6) (D)</option>
-      <option value="SulfanilicAcid:13C(6) (E)">SulfanilicAcid:13C(6) (E)</option>
-      <option value="Sulfide (C)">Sulfide (C)</option>
-      <option value="Sulfide (D)">Sulfide (D)</option>
-      <option value="Sulfide (W)">Sulfide (W)</option>
-      <option value="Sulfo (C)">Sulfo (C)</option>
-      <option value="Sulfo (S)">Sulfo (S)</option>
-      <option value="Sulfo (T)">Sulfo (T)</option>
-      <option value="Sulfo (Y)">Sulfo (Y)</option>
-      <option value="sulfo+amino (Y)">sulfo+amino (Y)</option>
-      <option value="Sulfo-NHS-LC-LC-Biotin (K)">Sulfo-NHS-LC-LC-Biotin (K)</option>
-      <option value="Sulfo-NHS-LC-LC-Biotin (N-term)">Sulfo-NHS-LC-LC-Biotin (N-term)</option>
-      <option value="SulfoGMBS (C)">SulfoGMBS (C)</option>
-      <option value="SulfurDioxide (C)">SulfurDioxide (C)</option>
-      <option value="SUMO2135 (K)">SUMO2135 (K)</option>
-      <option value="SUMO3549 (K)">SUMO3549 (K)</option>
-      <option value="TAMRA-FP (S)">TAMRA-FP (S)</option>
-      <option value="TAMRA-FP (Y)">TAMRA-FP (Y)</option>
-      <option value="Thiadiazole (C)">Thiadiazole (C)</option>
-      <option value="Thiazolidine (C)">Thiazolidine (C)</option>
-      <option value="Thiazolidine (F)">Thiazolidine (F)</option>
-      <option value="Thiazolidine (H)">Thiazolidine (H)</option>
-      <option value="Thiazolidine (K)">Thiazolidine (K)</option>
-      <option value="Thiazolidine (Protein N-term)">Thiazolidine (Protein N-term)</option>
-      <option value="Thiazolidine (R)">Thiazolidine (R)</option>
-      <option value="Thiazolidine (W)">Thiazolidine (W)</option>
-      <option value="Thiazolidine (Y)">Thiazolidine (Y)</option>
-      <option value="thioacylPA (K)">thioacylPA (K)</option>
-      <option value="Thiophos-S-S-biotin (S)">Thiophos-S-S-biotin (S)</option>
-      <option value="Thiophos-S-S-biotin (T)">Thiophos-S-S-biotin (T)</option>
-      <option value="Thiophos-S-S-biotin (Y)">Thiophos-S-S-biotin (Y)</option>
-      <option value="Thiophospho (S)">Thiophospho (S)</option>
-      <option value="Thiophospho (T)">Thiophospho (T)</option>
-      <option value="Thiophospho (Y)">Thiophospho (Y)</option>
-      <option value="Thr-&gt;Ala (T)">Thr-&gt;Ala (T)</option>
-      <option value="Thr-&gt;Arg (T)">Thr-&gt;Arg (T)</option>
-      <option value="Thr-&gt;Asn (T)">Thr-&gt;Asn (T)</option>
-      <option value="Thr-&gt;Asp (T)">Thr-&gt;Asp (T)</option>
-      <option value="Thr-&gt;Cys (T)">Thr-&gt;Cys (T)</option>
-      <option value="Thr-&gt;Gln (T)">Thr-&gt;Gln (T)</option>
-      <option value="Thr-&gt;Glu (T)">Thr-&gt;Glu (T)</option>
-      <option value="Thr-&gt;Gly (T)">Thr-&gt;Gly (T)</option>
-      <option value="Thr-&gt;His (T)">Thr-&gt;His (T)</option>
-      <option value="Thr-&gt;Lys (T)">Thr-&gt;Lys (T)</option>
-      <option value="Thr-&gt;Met (T)">Thr-&gt;Met (T)</option>
-      <option value="Thr-&gt;Phe (T)">Thr-&gt;Phe (T)</option>
-      <option value="Thr-&gt;Pro (T)">Thr-&gt;Pro (T)</option>
-      <option value="Thr-&gt;Ser (T)">Thr-&gt;Ser (T)</option>
-      <option value="Thr-&gt;Trp (T)">Thr-&gt;Trp (T)</option>
-      <option value="Thr-&gt;Tyr (T)">Thr-&gt;Tyr (T)</option>
-      <option value="Thr-&gt;Val (T)">Thr-&gt;Val (T)</option>
-      <option value="Thr-&gt;Xle (T)">Thr-&gt;Xle (T)</option>
-      <option value="Thrbiotinhydrazide (T)">Thrbiotinhydrazide (T)</option>
-      <option value="Thyroxine (Y)">Thyroxine (Y)</option>
-      <option value="TMAB (K)">TMAB (K)</option>
-      <option value="TMAB (N-term)">TMAB (N-term)</option>
-      <option value="TMAB:2H(9) (K)">TMAB:2H(9) (K)</option>
-      <option value="TMAB:2H(9) (N-term)">TMAB:2H(9) (N-term)</option>
-      <option value="TMPP-Ac (K)">TMPP-Ac (K)</option>
-      <option value="TMPP-Ac (N-term)">TMPP-Ac (N-term)</option>
-      <option value="TMPP-Ac (Y)">TMPP-Ac (Y)</option>
-      <option value="TMPP-Ac:13C(9) (K)">TMPP-Ac:13C(9) (K)</option>
-      <option value="TMPP-Ac:13C(9) (N-term)">TMPP-Ac:13C(9) (N-term)</option>
-      <option value="TMPP-Ac:13C(9) (Y)">TMPP-Ac:13C(9) (Y)</option>
-      <option value="TMT (H)">TMT (H)</option>
-      <option value="TMT (K)">TMT (K)</option>
-      <option value="TMT (N-term)">TMT (N-term)</option>
-      <option value="TMT (Protein N-term)">TMT (Protein N-term)</option>
-      <option value="TMT (S)">TMT (S)</option>
-      <option value="TMT (T)">TMT (T)</option>
-      <option value="TMT2plex (H)">TMT2plex (H)</option>
-      <option value="TMT2plex (K)">TMT2plex (K)</option>
-      <option value="TMT2plex (N-term)">TMT2plex (N-term)</option>
-      <option value="TMT2plex (Protein N-term)">TMT2plex (Protein N-term)</option>
-      <option value="TMT2plex (S)">TMT2plex (S)</option>
-      <option value="TMT2plex (T)">TMT2plex (T)</option>
-      <option value="TMT6plex (H)">TMT6plex (H)</option>
-      <option value="TMT6plex (K)">TMT6plex (K)</option>
-      <option value="TMT6plex (N-term)">TMT6plex (N-term)</option>
-      <option value="TMT6plex (Protein N-term)">TMT6plex (Protein N-term)</option>
-      <option value="TMT6plex (S)">TMT6plex (S)</option>
-      <option value="TMT6plex (T)">TMT6plex (T)</option>
-      <option value="TMTpro (H)">TMTpro (H)</option>
-      <option value="TMTpro (K)">TMTpro (K)</option>
-      <option value="TMTpro (N-term)">TMTpro (N-term)</option>
-      <option value="TMTpro (Protein N-term)">TMTpro (Protein N-term)</option>
-      <option value="TMTpro (S)">TMTpro (S)</option>
-      <option value="TMTpro (T)">TMTpro (T)</option>
-      <option value="TMTpro_zero (H)">TMTpro_zero (H)</option>
-      <option value="TMTpro_zero (K)">TMTpro_zero (K)</option>
-      <option value="TMTpro_zero (N-term)">TMTpro_zero (N-term)</option>
-      <option value="TMTpro_zero (Protein N-term)">TMTpro_zero (Protein N-term)</option>
-      <option value="TMTpro_zero (S)">TMTpro_zero (S)</option>
-      <option value="TMTpro_zero (T)">TMTpro_zero (T)</option>
-      <option value="TNBS (K)">TNBS (K)</option>
-      <option value="TNBS (N-term)">TNBS (N-term)</option>
-      <option value="trifluoro (L)">trifluoro (L)</option>
-      <option value="Triiodo (Y)">Triiodo (Y)</option>
-      <option value="Triiodothyronine (Y)">Triiodothyronine (Y)</option>
-      <option value="Trimethyl (K)">Trimethyl (K)</option>
-      <option value="Trimethyl (Protein N-term A)">Trimethyl (Protein N-term A)</option>
-      <option value="Trimethyl (R)">Trimethyl (R)</option>
-      <option value="Trimethyl:13C(3)2H(9) (K)">Trimethyl:13C(3)2H(9) (K)</option>
-      <option value="Trimethyl:13C(3)2H(9) (R)">Trimethyl:13C(3)2H(9) (R)</option>
-      <option value="Trimethyl:2H(9) (K)">Trimethyl:2H(9) (K)</option>
-      <option value="Trimethyl:2H(9) (R)">Trimethyl:2H(9) (R)</option>
-      <option value="Trioxidation (C)">Trioxidation (C)</option>
-      <option value="Trioxidation (F)">Trioxidation (F)</option>
-      <option value="Trioxidation (W)">Trioxidation (W)</option>
-      <option value="Trioxidation (Y)">Trioxidation (Y)</option>
-      <option value="Tripalmitate (Protein N-term C)">Tripalmitate (Protein N-term C)</option>
-      <option value="Tris (N)">Tris (N)</option>
-      <option value="Triton (C-term)">Triton (C-term)</option>
-      <option value="Triton (N-term)">Triton (N-term)</option>
-      <option value="Trp-&gt;Ala (W)">Trp-&gt;Ala (W)</option>
-      <option value="Trp-&gt;Arg (W)">Trp-&gt;Arg (W)</option>
-      <option value="Trp-&gt;Asn (W)">Trp-&gt;Asn (W)</option>
-      <option value="Trp-&gt;Asp (W)">Trp-&gt;Asp (W)</option>
-      <option value="Trp-&gt;Cys (W)">Trp-&gt;Cys (W)</option>
-      <option value="Trp-&gt;Gln (W)">Trp-&gt;Gln (W)</option>
-      <option value="Trp-&gt;Glu (W)">Trp-&gt;Glu (W)</option>
-      <option value="Trp-&gt;Gly (W)">Trp-&gt;Gly (W)</option>
-      <option value="Trp-&gt;His (W)">Trp-&gt;His (W)</option>
-      <option value="Trp-&gt;Hydroxykynurenin (W)">Trp-&gt;Hydroxykynurenin (W)</option>
-      <option value="Trp-&gt;Kynurenin (W)">Trp-&gt;Kynurenin (W)</option>
-      <option value="Trp-&gt;Lys (W)">Trp-&gt;Lys (W)</option>
-      <option value="Trp-&gt;Met (W)">Trp-&gt;Met (W)</option>
-      <option value="Trp-&gt;Oxolactone (W)">Trp-&gt;Oxolactone (W)</option>
-      <option value="Trp-&gt;Phe (W)">Trp-&gt;Phe (W)</option>
-      <option value="Trp-&gt;Pro (W)">Trp-&gt;Pro (W)</option>
-      <option value="Trp-&gt;Ser (W)">Trp-&gt;Ser (W)</option>
-      <option value="Trp-&gt;Thr (W)">Trp-&gt;Thr (W)</option>
-      <option value="Trp-&gt;Tyr (W)">Trp-&gt;Tyr (W)</option>
-      <option value="Trp-&gt;Val (W)">Trp-&gt;Val (W)</option>
-      <option value="Trp-&gt;Xle (W)">Trp-&gt;Xle (W)</option>
-      <option value="Tween20 (N-term)">Tween20 (N-term)</option>
-      <option value="Tween80 (C-term)">Tween80 (C-term)</option>
-      <option value="Tyr-&gt;Ala (Y)">Tyr-&gt;Ala (Y)</option>
-      <option value="Tyr-&gt;Arg (Y)">Tyr-&gt;Arg (Y)</option>
-      <option value="Tyr-&gt;Asn (Y)">Tyr-&gt;Asn (Y)</option>
-      <option value="Tyr-&gt;Asp (Y)">Tyr-&gt;Asp (Y)</option>
-      <option value="Tyr-&gt;Cys (Y)">Tyr-&gt;Cys (Y)</option>
-      <option value="Tyr-&gt;Dha (Y)">Tyr-&gt;Dha (Y)</option>
-      <option value="Tyr-&gt;Gln (Y)">Tyr-&gt;Gln (Y)</option>
-      <option value="Tyr-&gt;Glu (Y)">Tyr-&gt;Glu (Y)</option>
-      <option value="Tyr-&gt;Gly (Y)">Tyr-&gt;Gly (Y)</option>
-      <option value="Tyr-&gt;His (Y)">Tyr-&gt;His (Y)</option>
-      <option value="Tyr-&gt;Lys (Y)">Tyr-&gt;Lys (Y)</option>
-      <option value="Tyr-&gt;Met (Y)">Tyr-&gt;Met (Y)</option>
-      <option value="Tyr-&gt;Phe (Y)">Tyr-&gt;Phe (Y)</option>
-      <option value="Tyr-&gt;Pro (Y)">Tyr-&gt;Pro (Y)</option>
-      <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
-      <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
-      <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
-      <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
-      <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-      <option value="Ub-amide (C)">Ub-amide (C)</option>
-      <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
-      <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
-      <option value="Ub-VME (C)">Ub-VME (C)</option>
-      <option value="UgiJoullie (D)">UgiJoullie (D)</option>
-      <option value="UgiJoullie (E)">UgiJoullie (E)</option>
-      <option value="UgiJoullieProGly (D)">UgiJoullieProGly (D)</option>
-      <option value="UgiJoullieProGly (E)">UgiJoullieProGly (E)</option>
-      <option value="UgiJoullieProGlyProGly (D)">UgiJoullieProGlyProGly (D)</option>
-      <option value="UgiJoullieProGlyProGly (E)">UgiJoullieProGlyProGly (E)</option>
-      <option value="Unknown:162 (C-term)">Unknown:162 (C-term)</option>
-      <option value="Unknown:162 (D)">Unknown:162 (D)</option>
-      <option value="Unknown:162 (E)">Unknown:162 (E)</option>
-      <option value="Unknown:162 (N-term)">Unknown:162 (N-term)</option>
-      <option value="Unknown:177 (C-term)">Unknown:177 (C-term)</option>
-      <option value="Unknown:177 (D)">Unknown:177 (D)</option>
-      <option value="Unknown:177 (E)">Unknown:177 (E)</option>
-      <option value="Unknown:177 (N-term)">Unknown:177 (N-term)</option>
-      <option value="Unknown:210 (C-term)">Unknown:210 (C-term)</option>
-      <option value="Unknown:210 (D)">Unknown:210 (D)</option>
-      <option value="Unknown:210 (E)">Unknown:210 (E)</option>
-      <option value="Unknown:210 (N-term)">Unknown:210 (N-term)</option>
-      <option value="Unknown:216 (C-term)">Unknown:216 (C-term)</option>
-      <option value="Unknown:216 (D)">Unknown:216 (D)</option>
-      <option value="Unknown:216 (E)">Unknown:216 (E)</option>
-      <option value="Unknown:216 (N-term)">Unknown:216 (N-term)</option>
-      <option value="Unknown:234 (C-term)">Unknown:234 (C-term)</option>
-      <option value="Unknown:234 (D)">Unknown:234 (D)</option>
-      <option value="Unknown:234 (E)">Unknown:234 (E)</option>
-      <option value="Unknown:234 (N-term)">Unknown:234 (N-term)</option>
-      <option value="Unknown:248 (C-term)">Unknown:248 (C-term)</option>
-      <option value="Unknown:248 (D)">Unknown:248 (D)</option>
-      <option value="Unknown:248 (E)">Unknown:248 (E)</option>
-      <option value="Unknown:248 (N-term)">Unknown:248 (N-term)</option>
-      <option value="Unknown:250 (C-term)">Unknown:250 (C-term)</option>
-      <option value="Unknown:250 (D)">Unknown:250 (D)</option>
-      <option value="Unknown:250 (E)">Unknown:250 (E)</option>
-      <option value="Unknown:250 (N-term)">Unknown:250 (N-term)</option>
-      <option value="Unknown:302 (C-term)">Unknown:302 (C-term)</option>
-      <option value="Unknown:302 (D)">Unknown:302 (D)</option>
-      <option value="Unknown:302 (E)">Unknown:302 (E)</option>
-      <option value="Unknown:302 (N-term)">Unknown:302 (N-term)</option>
-      <option value="Unknown:306 (C-term)">Unknown:306 (C-term)</option>
-      <option value="Unknown:306 (D)">Unknown:306 (D)</option>
-      <option value="Unknown:306 (E)">Unknown:306 (E)</option>
-      <option value="Unknown:306 (N-term)">Unknown:306 (N-term)</option>
-      <option value="Unknown:420 (C-term)">Unknown:420 (C-term)</option>
-      <option value="Unknown:420 (N-term)">Unknown:420 (N-term)</option>
-      <option value="Val-&gt;Ala (V)">Val-&gt;Ala (V)</option>
-      <option value="Val-&gt;Arg (V)">Val-&gt;Arg (V)</option>
-      <option value="Val-&gt;Asn (V)">Val-&gt;Asn (V)</option>
-      <option value="Val-&gt;Asp (V)">Val-&gt;Asp (V)</option>
-      <option value="Val-&gt;Cys (V)">Val-&gt;Cys (V)</option>
-      <option value="Val-&gt;Gln (V)">Val-&gt;Gln (V)</option>
-      <option value="Val-&gt;Glu (V)">Val-&gt;Glu (V)</option>
-      <option value="Val-&gt;Gly (V)">Val-&gt;Gly (V)</option>
-      <option value="Val-&gt;His (V)">Val-&gt;His (V)</option>
-      <option value="Val-&gt;Lys (V)">Val-&gt;Lys (V)</option>
-      <option value="Val-&gt;Met (V)">Val-&gt;Met (V)</option>
-      <option value="Val-&gt;Phe (V)">Val-&gt;Phe (V)</option>
-      <option value="Val-&gt;Pro (V)">Val-&gt;Pro (V)</option>
-      <option value="Val-&gt;Ser (V)">Val-&gt;Ser (V)</option>
-      <option value="Val-&gt;Thr (V)">Val-&gt;Thr (V)</option>
-      <option value="Val-&gt;Trp (V)">Val-&gt;Trp (V)</option>
-      <option value="Val-&gt;Tyr (V)">Val-&gt;Tyr (V)</option>
-      <option value="Val-&gt;Xle (V)">Val-&gt;Xle (V)</option>
-      <option value="VFQQQTGG (K)">VFQQQTGG (K)</option>
-      <option value="VIEVYQEQTGG (K)">VIEVYQEQTGG (K)</option>
-      <option value="Withaferin (C)">Withaferin (C)</option>
-      <option value="Xle-&gt;Ala (I)">Xle-&gt;Ala (I)</option>
-      <option value="Xle-&gt;Ala (L)">Xle-&gt;Ala (L)</option>
-      <option value="Xle-&gt;Arg (I)">Xle-&gt;Arg (I)</option>
-      <option value="Xle-&gt;Arg (L)">Xle-&gt;Arg (L)</option>
-      <option value="Xle-&gt;Asn (I)">Xle-&gt;Asn (I)</option>
-      <option value="Xle-&gt;Asn (L)">Xle-&gt;Asn (L)</option>
-      <option value="Xle-&gt;Asp (I)">Xle-&gt;Asp (I)</option>
-      <option value="Xle-&gt;Asp (L)">Xle-&gt;Asp (L)</option>
-      <option value="Xle-&gt;Cys (I)">Xle-&gt;Cys (I)</option>
-      <option value="Xle-&gt;Cys (L)">Xle-&gt;Cys (L)</option>
-      <option value="Xle-&gt;Gln (I)">Xle-&gt;Gln (I)</option>
-      <option value="Xle-&gt;Gln (L)">Xle-&gt;Gln (L)</option>
-      <option value="Xle-&gt;Glu (I)">Xle-&gt;Glu (I)</option>
-      <option value="Xle-&gt;Glu (L)">Xle-&gt;Glu (L)</option>
-      <option value="Xle-&gt;Gly (I)">Xle-&gt;Gly (I)</option>
-      <option value="Xle-&gt;Gly (L)">Xle-&gt;Gly (L)</option>
-      <option value="Xle-&gt;His (I)">Xle-&gt;His (I)</option>
-      <option value="Xle-&gt;His (L)">Xle-&gt;His (L)</option>
-      <option value="Xle-&gt;Lys (I)">Xle-&gt;Lys (I)</option>
-      <option value="Xle-&gt;Lys (L)">Xle-&gt;Lys (L)</option>
-      <option value="Xle-&gt;Met (I)">Xle-&gt;Met (I)</option>
-      <option value="Xle-&gt;Met (L)">Xle-&gt;Met (L)</option>
-      <option value="Xle-&gt;Phe (I)">Xle-&gt;Phe (I)</option>
-      <option value="Xle-&gt;Phe (L)">Xle-&gt;Phe (L)</option>
-      <option value="Xle-&gt;Pro (I)">Xle-&gt;Pro (I)</option>
-      <option value="Xle-&gt;Pro (L)">Xle-&gt;Pro (L)</option>
-      <option value="Xle-&gt;Ser (I)">Xle-&gt;Ser (I)</option>
-      <option value="Xle-&gt;Ser (L)">Xle-&gt;Ser (L)</option>
-      <option value="Xle-&gt;Thr (I)">Xle-&gt;Thr (I)</option>
-      <option value="Xle-&gt;Thr (L)">Xle-&gt;Thr (L)</option>
-      <option value="Xle-&gt;Trp (I)">Xle-&gt;Trp (I)</option>
-      <option value="Xle-&gt;Trp (L)">Xle-&gt;Trp (L)</option>
-      <option value="Xle-&gt;Tyr (I)">Xle-&gt;Tyr (I)</option>
-      <option value="Xle-&gt;Tyr (L)">Xle-&gt;Tyr (L)</option>
-      <option value="Xle-&gt;Val (I)">Xle-&gt;Val (I)</option>
-      <option value="Xle-&gt;Val (L)">Xle-&gt;Val (L)</option>
-      <option value="Xlink:B10621 (C)">Xlink:B10621 (C)</option>
-      <option value="Xlink:BMOE (C)">Xlink:BMOE (C)</option>
-      <option value="Xlink:BS2G[113] (K)">Xlink:BS2G[113] (K)</option>
-      <option value="Xlink:BS2G[113] (Protein N-term)">Xlink:BS2G[113] (Protein N-term)</option>
-      <option value="Xlink:BS2G[114] (K)">Xlink:BS2G[114] (K)</option>
-      <option value="Xlink:BS2G[114] (Protein N-term)">Xlink:BS2G[114] (Protein N-term)</option>
-      <option value="Xlink:BS2G[217] (K)">Xlink:BS2G[217] (K)</option>
-      <option value="Xlink:BS2G[217] (Protein N-term)">Xlink:BS2G[217] (Protein N-term)</option>
-      <option value="Xlink:BS2G[96] (K)">Xlink:BS2G[96] (K)</option>
-      <option value="Xlink:BS2G[96] (Protein N-term)">Xlink:BS2G[96] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[111] (K)">Xlink:BuUrBu[111] (K)</option>
-      <option value="Xlink:BuUrBu[111] (Protein N-term)">Xlink:BuUrBu[111] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[196] (K)">Xlink:BuUrBu[196] (K)</option>
-      <option value="Xlink:BuUrBu[196] (Protein N-term)">Xlink:BuUrBu[196] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[213] (K)">Xlink:BuUrBu[213] (K)</option>
-      <option value="Xlink:BuUrBu[213] (Protein N-term)">Xlink:BuUrBu[213] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[214] (K)">Xlink:BuUrBu[214] (K)</option>
-      <option value="Xlink:BuUrBu[214] (Protein N-term)">Xlink:BuUrBu[214] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[317] (K)">Xlink:BuUrBu[317] (K)</option>
-      <option value="Xlink:BuUrBu[317] (Protein N-term)">Xlink:BuUrBu[317] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[85] (K)">Xlink:BuUrBu[85] (K)</option>
-      <option value="Xlink:BuUrBu[85] (Protein N-term)">Xlink:BuUrBu[85] (Protein N-term)</option>
-      <option value="Xlink:DFDNB (K)">Xlink:DFDNB (K)</option>
-      <option value="Xlink:DFDNB (N)">Xlink:DFDNB (N)</option>
-      <option value="Xlink:DFDNB (Q)">Xlink:DFDNB (Q)</option>
-      <option value="Xlink:DFDNB (R)">Xlink:DFDNB (R)</option>
-      <option value="Xlink:DMP[122] (K)">Xlink:DMP[122] (K)</option>
-      <option value="Xlink:DMP[122] (Protein N-term)">Xlink:DMP[122] (Protein N-term)</option>
-      <option value="Xlink:DMP[139] (K)">Xlink:DMP[139] (K)</option>
-      <option value="Xlink:DMP[139] (Protein N-term)">Xlink:DMP[139] (Protein N-term)</option>
-      <option value="Xlink:DMP[140] (K)">Xlink:DMP[140] (K)</option>
-      <option value="Xlink:DMP[140] (Protein N-term)">Xlink:DMP[140] (Protein N-term)</option>
-      <option value="Xlink:DMP[154] (K)">Xlink:DMP[154] (K)</option>
-      <option value="Xlink:DMP[154] (Protein N-term)">Xlink:DMP[154] (Protein N-term)</option>
-      <option value="Xlink:DSS[138] (K)">Xlink:DSS[138] (K)</option>
-      <option value="Xlink:DSS[138] (Protein N-term)">Xlink:DSS[138] (Protein N-term)</option>
-      <option value="Xlink:DSS[155] (K)">Xlink:DSS[155] (K)</option>
-      <option value="Xlink:DSS[155] (Protein N-term)">Xlink:DSS[155] (Protein N-term)</option>
-      <option value="Xlink:DSS[156] (K)">Xlink:DSS[156] (K)</option>
-      <option value="Xlink:DSS[156] (Protein N-term)">Xlink:DSS[156] (Protein N-term)</option>
-      <option value="Xlink:DSS[259] (K)">Xlink:DSS[259] (K)</option>
-      <option value="Xlink:DSS[259] (Protein N-term)">Xlink:DSS[259] (Protein N-term)</option>
-      <option value="Xlink:DSSO[104] (K)">Xlink:DSSO[104] (K)</option>
-      <option value="Xlink:DSSO[104] (Protein N-term)">Xlink:DSSO[104] (Protein N-term)</option>
-      <option value="Xlink:DSSO[158] (K)">Xlink:DSSO[158] (K)</option>
-      <option value="Xlink:DSSO[158] (Protein N-term)">Xlink:DSSO[158] (Protein N-term)</option>
-      <option value="Xlink:DSSO[175] (K)">Xlink:DSSO[175] (K)</option>
-      <option value="Xlink:DSSO[175] (Protein N-term)">Xlink:DSSO[175] (Protein N-term)</option>
-      <option value="Xlink:DSSO[176] (K)">Xlink:DSSO[176] (K)</option>
-      <option value="Xlink:DSSO[176] (Protein N-term)">Xlink:DSSO[176] (Protein N-term)</option>
-      <option value="Xlink:DSSO[279] (K)">Xlink:DSSO[279] (K)</option>
-      <option value="Xlink:DSSO[279] (Protein N-term)">Xlink:DSSO[279] (Protein N-term)</option>
-      <option value="Xlink:DSSO[54] (K)">Xlink:DSSO[54] (K)</option>
-      <option value="Xlink:DSSO[54] (Protein N-term)">Xlink:DSSO[54] (Protein N-term)</option>
-      <option value="Xlink:DSSO[86] (K)">Xlink:DSSO[86] (K)</option>
-      <option value="Xlink:DSSO[86] (Protein N-term)">Xlink:DSSO[86] (Protein N-term)</option>
-      <option value="Xlink:DST[114] (K)">Xlink:DST[114] (K)</option>
-      <option value="Xlink:DST[114] (Protein N-term)">Xlink:DST[114] (Protein N-term)</option>
-      <option value="Xlink:DST[132] (K)">Xlink:DST[132] (K)</option>
-      <option value="Xlink:DST[132] (Protein N-term)">Xlink:DST[132] (Protein N-term)</option>
-      <option value="Xlink:DST[56] (K)">Xlink:DST[56] (K)</option>
-      <option value="Xlink:DST[56] (Protein N-term)">Xlink:DST[56] (Protein N-term)</option>
-      <option value="Xlink:DTBP[172] (K)">Xlink:DTBP[172] (K)</option>
-      <option value="Xlink:DTBP[172] (Protein N-term)">Xlink:DTBP[172] (Protein N-term)</option>
-      <option value="Xlink:DTBP[87] (K)">Xlink:DTBP[87] (K)</option>
-      <option value="Xlink:DTBP[87] (Protein N-term)">Xlink:DTBP[87] (Protein N-term)</option>
-      <option value="Xlink:DTSSP[174] (K)">Xlink:DTSSP[174] (K)</option>
-      <option value="Xlink:DTSSP[174] (Protein N-term)">Xlink:DTSSP[174] (Protein N-term)</option>
-      <option value="Xlink:DTSSP[192] (K)">Xlink:DTSSP[192] (K)</option>
-      <option value="Xlink:DTSSP[192] (Protein N-term)">Xlink:DTSSP[192] (Protein N-term)</option>
-      <option value="Xlink:DTSSP[88] (K)">Xlink:DTSSP[88] (K)</option>
-      <option value="Xlink:DTSSP[88] (Protein N-term)">Xlink:DTSSP[88] (Protein N-term)</option>
-      <option value="Xlink:EGS[115] (K)">Xlink:EGS[115] (K)</option>
-      <option value="Xlink:EGS[115] (Protein N-term)">Xlink:EGS[115] (Protein N-term)</option>
-      <option value="Xlink:EGS[226] (K)">Xlink:EGS[226] (K)</option>
-      <option value="Xlink:EGS[226] (Protein N-term)">Xlink:EGS[226] (Protein N-term)</option>
-      <option value="Xlink:EGS[244] (K)">Xlink:EGS[244] (K)</option>
-      <option value="Xlink:EGS[244] (Protein N-term)">Xlink:EGS[244] (Protein N-term)</option>
-      <option value="Xlink:SMCC[219] (C)">Xlink:SMCC[219] (C)</option>
-      <option value="Xlink:SMCC[219] (K)">Xlink:SMCC[219] (K)</option>
-      <option value="Xlink:SMCC[219] (Protein N-term)">Xlink:SMCC[219] (Protein N-term)</option>
-      <option value="Xlink:SMCC[237] (C)">Xlink:SMCC[237] (C)</option>
-      <option value="Xlink:SMCC[237] (K)">Xlink:SMCC[237] (K)</option>
-      <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
-      <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
-      <option value="ZGB (K)">ZGB (K)</option>
-      <option value="ZGB (N-term)">ZGB (N-term)</option>
-      <option value="ZQG (K)">ZQG (K)</option>
-      <expand macro="list_string_san" name="fixed_modifications"/>
-    </param>
-    <param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
-      <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
-      <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
-      <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
-      <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
-      <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
-      <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
-      <option value="2-succinyl (C)">2-succinyl (C)</option>
-      <option value="2HPG (R)">2HPG (R)</option>
-      <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
-      <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
-      <option value="3sulfo (N-term)">3sulfo (N-term)</option>
-      <option value="4-ONE (C)">4-ONE (C)</option>
-      <option value="4-ONE (H)">4-ONE (H)</option>
-      <option value="4-ONE (K)">4-ONE (K)</option>
-      <option value="4-ONE+Delta:H(-2)O(-1) (C)">4-ONE+Delta:H(-2)O(-1) (C)</option>
-      <option value="4-ONE+Delta:H(-2)O(-1) (H)">4-ONE+Delta:H(-2)O(-1) (H)</option>
-      <option value="4-ONE+Delta:H(-2)O(-1) (K)">4-ONE+Delta:H(-2)O(-1) (K)</option>
-      <option value="4AcAllylGal (C)">4AcAllylGal (C)</option>
-      <option value="a-type-ion (C-term)">a-type-ion (C-term)</option>
-      <option value="AccQTag (K)">AccQTag (K)</option>
-      <option value="AccQTag (N-term)">AccQTag (N-term)</option>
-      <option value="Acetyl (C)">Acetyl (C)</option>
-      <option value="Acetyl (H)">Acetyl (H)</option>
-      <option value="Acetyl (K)">Acetyl (K)</option>
-      <option value="Acetyl (N-term)">Acetyl (N-term)</option>
-      <option value="Acetyl (Protein N-term)">Acetyl (Protein N-term)</option>
-      <option value="Acetyl (R)">Acetyl (R)</option>
-      <option value="Acetyl (S)">Acetyl (S)</option>
-      <option value="Acetyl (T)">Acetyl (T)</option>
-      <option value="Acetyl (Y)">Acetyl (Y)</option>
-      <option value="Acetyl:13C(2) (K)">Acetyl:13C(2) (K)</option>
-      <option value="Acetyl:13C(2) (Protein N-term)">Acetyl:13C(2) (Protein N-term)</option>
-      <option value="Acetyl:2H(3) (H)">Acetyl:2H(3) (H)</option>
-      <option value="Acetyl:2H(3) (K)">Acetyl:2H(3) (K)</option>
-      <option value="Acetyl:2H(3) (N-term)">Acetyl:2H(3) (N-term)</option>
-      <option value="Acetyl:2H(3) (Protein N-term)">Acetyl:2H(3) (Protein N-term)</option>
-      <option value="Acetyl:2H(3) (S)">Acetyl:2H(3) (S)</option>
-      <option value="Acetyl:2H(3) (T)">Acetyl:2H(3) (T)</option>
-      <option value="Acetyl:2H(3) (Y)">Acetyl:2H(3) (Y)</option>
-      <option value="Acetyldeoxyhypusine (K)">Acetyldeoxyhypusine (K)</option>
-      <option value="Acetylhypusine (K)">Acetylhypusine (K)</option>
-      <option value="ADP-Ribosyl (C)">ADP-Ribosyl (C)</option>
-      <option value="ADP-Ribosyl (D)">ADP-Ribosyl (D)</option>
-      <option value="ADP-Ribosyl (E)">ADP-Ribosyl (E)</option>
-      <option value="ADP-Ribosyl (K)">ADP-Ribosyl (K)</option>
-      <option value="ADP-Ribosyl (N)">ADP-Ribosyl (N)</option>
-      <option value="ADP-Ribosyl (R)">ADP-Ribosyl (R)</option>
-      <option value="ADP-Ribosyl (S)">ADP-Ribosyl (S)</option>
-      <option value="ADP-Ribosyl (T)">ADP-Ribosyl (T)</option>
-      <option value="AEBS (H)">AEBS (H)</option>
-      <option value="AEBS (K)">AEBS (K)</option>
-      <option value="AEBS (Protein N-term)">AEBS (Protein N-term)</option>
-      <option value="AEBS (S)">AEBS (S)</option>
-      <option value="AEBS (Y)">AEBS (Y)</option>
-      <option value="AEC-MAEC (S)">AEC-MAEC (S)</option>
-      <option value="AEC-MAEC (T)">AEC-MAEC (T)</option>
-      <option value="AEC-MAEC:2H(4) (S)">AEC-MAEC:2H(4) (S)</option>
-      <option value="AEC-MAEC:2H(4) (T)">AEC-MAEC:2H(4) (T)</option>
-      <option value="AFB1_Dialdehyde (K)">AFB1_Dialdehyde (K)</option>
-      <option value="AHA-Alkyne (M)">AHA-Alkyne (M)</option>
-      <option value="AHA-Alkyne-KDDDD (M)">AHA-Alkyne-KDDDD (M)</option>
-      <option value="AHA-SS (M)">AHA-SS (M)</option>
-      <option value="AHA-SS_CAM (M)">AHA-SS_CAM (M)</option>
-      <option value="Ahx2+Hsl (C-term)">Ahx2+Hsl (C-term)</option>
-      <option value="Ala-&gt;Arg (A)">Ala-&gt;Arg (A)</option>
-      <option value="Ala-&gt;Asn (A)">Ala-&gt;Asn (A)</option>
-      <option value="Ala-&gt;Asp (A)">Ala-&gt;Asp (A)</option>
-      <option value="Ala-&gt;Cys (A)">Ala-&gt;Cys (A)</option>
-      <option value="Ala-&gt;Gln (A)">Ala-&gt;Gln (A)</option>
-      <option value="Ala-&gt;Glu (A)">Ala-&gt;Glu (A)</option>
-      <option value="Ala-&gt;Gly (A)">Ala-&gt;Gly (A)</option>
-      <option value="Ala-&gt;His (A)">Ala-&gt;His (A)</option>
-      <option value="Ala-&gt;Lys (A)">Ala-&gt;Lys (A)</option>
-      <option value="Ala-&gt;Met (A)">Ala-&gt;Met (A)</option>
-      <option value="Ala-&gt;Phe (A)">Ala-&gt;Phe (A)</option>
-      <option value="Ala-&gt;Pro (A)">Ala-&gt;Pro (A)</option>
-      <option value="Ala-&gt;Ser (A)">Ala-&gt;Ser (A)</option>
-      <option value="Ala-&gt;Thr (A)">Ala-&gt;Thr (A)</option>
-      <option value="Ala-&gt;Trp (A)">Ala-&gt;Trp (A)</option>
-      <option value="Ala-&gt;Tyr (A)">Ala-&gt;Tyr (A)</option>
-      <option value="Ala-&gt;Val (A)">Ala-&gt;Val (A)</option>
-      <option value="Ala-&gt;Xle (A)">Ala-&gt;Xle (A)</option>
-      <option value="Amidated (C-term)">Amidated (C-term)</option>
-      <option value="Amidated (Protein C-term)">Amidated (Protein C-term)</option>
-      <option value="Amidine (K)">Amidine (K)</option>
-      <option value="Amidine (N-term)">Amidine (N-term)</option>
-      <option value="Amidino (C)">Amidino (C)</option>
-      <option value="Amino (Y)">Amino (Y)</option>
-      <option value="Ammonia-loss (N)">Ammonia-loss (N)</option>
-      <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
-      <option value="Ammonia-loss (Protein N-term S)">Ammonia-loss (Protein N-term S)</option>
-      <option value="Ammonia-loss (Protein N-term T)">Ammonia-loss (Protein N-term T)</option>
-      <option value="Ammonium (C-term)">Ammonium (C-term)</option>
-      <option value="Ammonium (D)">Ammonium (D)</option>
-      <option value="Ammonium (E)">Ammonium (E)</option>
-      <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
-      <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
-      <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
-      <option value="Archaeol (C)">Archaeol (C)</option>
-      <option value="Arg (N-term)">Arg (N-term)</option>
-      <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
-      <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
-      <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
-      <option value="Arg-&gt;Cys (R)">Arg-&gt;Cys (R)</option>
-      <option value="Arg-&gt;Gln (R)">Arg-&gt;Gln (R)</option>
-      <option value="Arg-&gt;Glu (R)">Arg-&gt;Glu (R)</option>
-      <option value="Arg-&gt;GluSA (R)">Arg-&gt;GluSA (R)</option>
-      <option value="Arg-&gt;Gly (R)">Arg-&gt;Gly (R)</option>
-      <option value="Arg-&gt;His (R)">Arg-&gt;His (R)</option>
-      <option value="Arg-&gt;Lys (R)">Arg-&gt;Lys (R)</option>
-      <option value="Arg-&gt;Met (R)">Arg-&gt;Met (R)</option>
-      <option value="Arg-&gt;Npo (R)">Arg-&gt;Npo (R)</option>
-      <option value="Arg-&gt;Orn (R)">Arg-&gt;Orn (R)</option>
-      <option value="Arg-&gt;Phe (R)">Arg-&gt;Phe (R)</option>
-      <option value="Arg-&gt;Pro (R)">Arg-&gt;Pro (R)</option>
-      <option value="Arg-&gt;Ser (R)">Arg-&gt;Ser (R)</option>
-      <option value="Arg-&gt;Thr (R)">Arg-&gt;Thr (R)</option>
-      <option value="Arg-&gt;Trp (R)">Arg-&gt;Trp (R)</option>
-      <option value="Arg-&gt;Tyr (R)">Arg-&gt;Tyr (R)</option>
-      <option value="Arg-&gt;Val (R)">Arg-&gt;Val (R)</option>
-      <option value="Arg-&gt;Xle (R)">Arg-&gt;Xle (R)</option>
-      <option value="Arg-loss (C-term R)">Arg-loss (C-term R)</option>
-      <option value="Arg2PG (R)">Arg2PG (R)</option>
-      <option value="Argbiotinhydrazide (R)">Argbiotinhydrazide (R)</option>
-      <option value="AROD (C)">AROD (C)</option>
-      <option value="Asn-&gt;Ala (N)">Asn-&gt;Ala (N)</option>
-      <option value="Asn-&gt;Arg (N)">Asn-&gt;Arg (N)</option>
-      <option value="Asn-&gt;Asp (N)">Asn-&gt;Asp (N)</option>
-      <option value="Asn-&gt;Cys (N)">Asn-&gt;Cys (N)</option>
-      <option value="Asn-&gt;Gln (N)">Asn-&gt;Gln (N)</option>
-      <option value="Asn-&gt;Glu (N)">Asn-&gt;Glu (N)</option>
-      <option value="Asn-&gt;Gly (N)">Asn-&gt;Gly (N)</option>
-      <option value="Asn-&gt;His (N)">Asn-&gt;His (N)</option>
-      <option value="Asn-&gt;Lys (N)">Asn-&gt;Lys (N)</option>
-      <option value="Asn-&gt;Met (N)">Asn-&gt;Met (N)</option>
-      <option value="Asn-&gt;Phe (N)">Asn-&gt;Phe (N)</option>
-      <option value="Asn-&gt;Pro (N)">Asn-&gt;Pro (N)</option>
-      <option value="Asn-&gt;Ser (N)">Asn-&gt;Ser (N)</option>
-      <option value="Asn-&gt;Thr (N)">Asn-&gt;Thr (N)</option>
-      <option value="Asn-&gt;Trp (N)">Asn-&gt;Trp (N)</option>
-      <option value="Asn-&gt;Tyr (N)">Asn-&gt;Tyr (N)</option>
-      <option value="Asn-&gt;Val (N)">Asn-&gt;Val (N)</option>
-      <option value="Asn-&gt;Xle (N)">Asn-&gt;Xle (N)</option>
-      <option value="Asp-&gt;Ala (D)">Asp-&gt;Ala (D)</option>
-      <option value="Asp-&gt;Arg (D)">Asp-&gt;Arg (D)</option>
-      <option value="Asp-&gt;Asn (D)">Asp-&gt;Asn (D)</option>
-      <option value="Asp-&gt;Cys (D)">Asp-&gt;Cys (D)</option>
-      <option value="Asp-&gt;Gln (D)">Asp-&gt;Gln (D)</option>
-      <option value="Asp-&gt;Glu (D)">Asp-&gt;Glu (D)</option>
-      <option value="Asp-&gt;Gly (D)">Asp-&gt;Gly (D)</option>
-      <option value="Asp-&gt;His (D)">Asp-&gt;His (D)</option>
-      <option value="Asp-&gt;Lys (D)">Asp-&gt;Lys (D)</option>
-      <option value="Asp-&gt;Met (D)">Asp-&gt;Met (D)</option>
-      <option value="Asp-&gt;Phe (D)">Asp-&gt;Phe (D)</option>
-      <option value="Asp-&gt;Pro (D)">Asp-&gt;Pro (D)</option>
-      <option value="Asp-&gt;Ser (D)">Asp-&gt;Ser (D)</option>
-      <option value="Asp-&gt;Thr (D)">Asp-&gt;Thr (D)</option>
-      <option value="Asp-&gt;Trp (D)">Asp-&gt;Trp (D)</option>
-      <option value="Asp-&gt;Tyr (D)">Asp-&gt;Tyr (D)</option>
-      <option value="Asp-&gt;Val (D)">Asp-&gt;Val (D)</option>
-      <option value="Asp-&gt;Xle (D)">Asp-&gt;Xle (D)</option>
-      <option value="Aspartylurea (H)">Aspartylurea (H)</option>
-      <option value="Atto495Maleimide (C)">Atto495Maleimide (C)</option>
-      <option value="AzidoF (F)">AzidoF (F)</option>
-      <option value="azole (C)">azole (C)</option>
-      <option value="azole (S)">azole (S)</option>
-      <option value="Bacillosamine (N)">Bacillosamine (N)</option>
-      <option value="BADGE (C)">BADGE (C)</option>
-      <option value="BDMAPP (H)">BDMAPP (H)</option>
-      <option value="BDMAPP (K)">BDMAPP (K)</option>
-      <option value="BDMAPP (Protein N-term)">BDMAPP (Protein N-term)</option>
-      <option value="BDMAPP (W)">BDMAPP (W)</option>
-      <option value="BDMAPP (Y)">BDMAPP (Y)</option>
-      <option value="BEMAD_C (C)">BEMAD_C (C)</option>
-      <option value="BEMAD_C:2H(6) (C)">BEMAD_C:2H(6) (C)</option>
-      <option value="BEMAD_ST (S)">BEMAD_ST (S)</option>
-      <option value="BEMAD_ST (T)">BEMAD_ST (T)</option>
-      <option value="BEMAD_ST:2H(6) (S)">BEMAD_ST:2H(6) (S)</option>
-      <option value="BEMAD_ST:2H(6) (T)">BEMAD_ST:2H(6) (T)</option>
-      <option value="Benzoyl (K)">Benzoyl (K)</option>
-      <option value="Benzoyl (N-term)">Benzoyl (N-term)</option>
-      <option value="benzylguanidine (K)">benzylguanidine (K)</option>
-      <option value="betaFNA (C)">betaFNA (C)</option>
-      <option value="betaFNA (K)">betaFNA (K)</option>
-      <option value="BHT (C)">BHT (C)</option>
-      <option value="BHT (H)">BHT (H)</option>
-      <option value="BHT (K)">BHT (K)</option>
-      <option value="BHTOH (C)">BHTOH (C)</option>
-      <option value="BHTOH (H)">BHTOH (H)</option>
-      <option value="BHTOH (K)">BHTOH (K)</option>
-      <option value="Biotin (K)">Biotin (K)</option>
-      <option value="Biotin (N-term)">Biotin (N-term)</option>
-      <option value="Biotin-HPDP (C)">Biotin-HPDP (C)</option>
-      <option value="Biotin-PEG-PRA (M)">Biotin-PEG-PRA (M)</option>
-      <option value="Biotin-PEO-Amine (D)">Biotin-PEO-Amine (D)</option>
-      <option value="Biotin-PEO-Amine (E)">Biotin-PEO-Amine (E)</option>
-      <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
-      <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
-      <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
-      <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
-      <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
-      <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
-      <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
-      <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
-      <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
-      <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
-      <option value="Biotin:Thermo-21328 (K)">Biotin:Thermo-21328 (K)</option>
-      <option value="Biotin:Thermo-21328 (N-term)">Biotin:Thermo-21328 (N-term)</option>
-      <option value="Biotin:Thermo-21330 (K)">Biotin:Thermo-21330 (K)</option>
-      <option value="Biotin:Thermo-21330 (N-term)">Biotin:Thermo-21330 (N-term)</option>
-      <option value="Biotin:Thermo-21345 (Q)">Biotin:Thermo-21345 (Q)</option>
-      <option value="Biotin:Thermo-21360 (X)">Biotin:Thermo-21360 (X)</option>
-      <option value="Biotin:Thermo-21901+2H2O (C)">Biotin:Thermo-21901+2H2O (C)</option>
-      <option value="Biotin:Thermo-21901+H2O (C)">Biotin:Thermo-21901+H2O (C)</option>
-      <option value="Biotin:Thermo-21911 (C)">Biotin:Thermo-21911 (C)</option>
-      <option value="Biotin:Thermo-33033 (X)">Biotin:Thermo-33033 (X)</option>
-      <option value="Biotin:Thermo-33033-H (X)">Biotin:Thermo-33033-H (X)</option>
-      <option value="Biotin:Thermo-88310 (K)">Biotin:Thermo-88310 (K)</option>
-      <option value="Biotin:Thermo-88317 (S)">Biotin:Thermo-88317 (S)</option>
-      <option value="Biotin:Thermo-88317 (Y)">Biotin:Thermo-88317 (Y)</option>
-      <option value="biotinAcrolein298 (C)">biotinAcrolein298 (C)</option>
-      <option value="biotinAcrolein298 (H)">biotinAcrolein298 (H)</option>
-      <option value="biotinAcrolein298 (K)">biotinAcrolein298 (K)</option>
-      <option value="biotinAcrolein298 (Protein N-term)">biotinAcrolein298 (Protein N-term)</option>
-      <option value="BisANS (K)">BisANS (K)</option>
-      <option value="bisANS-sulfonates (K)">bisANS-sulfonates (K)</option>
-      <option value="bisANS-sulfonates (S)">bisANS-sulfonates (S)</option>
-      <option value="bisANS-sulfonates (T)">bisANS-sulfonates (T)</option>
-      <option value="BITC (C)">BITC (C)</option>
-      <option value="BITC (K)">BITC (K)</option>
-      <option value="BITC (N-term)">BITC (N-term)</option>
-      <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
-      <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-      <option value="Bodipy (C)">Bodipy (C)</option>
-      <option value="Brij35 (N-term)">Brij35 (N-term)</option>
-      <option value="Brij58 (N-term)">Brij58 (N-term)</option>
-      <option value="Bromo (F)">Bromo (F)</option>
-      <option value="Bromo (H)">Bromo (H)</option>
-      <option value="Bromo (W)">Bromo (W)</option>
-      <option value="Bromo (Y)">Bromo (Y)</option>
-      <option value="Bromobimane (C)">Bromobimane (C)</option>
-      <option value="Butyryl (K)">Butyryl (K)</option>
-      <option value="C8-QAT (K)">C8-QAT (K)</option>
-      <option value="C8-QAT (N-term)">C8-QAT (N-term)</option>
-      <option value="CAF (N-term)">CAF (N-term)</option>
-      <option value="CAMthiopropanoyl (K)">CAMthiopropanoyl (K)</option>
-      <option value="CAMthiopropanoyl (Protein N-term)">CAMthiopropanoyl (Protein N-term)</option>
-      <option value="Can-FP-biotin (S)">Can-FP-biotin (S)</option>
-      <option value="Can-FP-biotin (T)">Can-FP-biotin (T)</option>
-      <option value="Can-FP-biotin (Y)">Can-FP-biotin (Y)</option>
-      <option value="Carbamidomethyl (C)">Carbamidomethyl (C)</option>
-      <option value="Carbamidomethyl (D)">Carbamidomethyl (D)</option>
-      <option value="Carbamidomethyl (E)">Carbamidomethyl (E)</option>
-      <option value="Carbamidomethyl (H)">Carbamidomethyl (H)</option>
-      <option value="Carbamidomethyl (K)">Carbamidomethyl (K)</option>
-      <option value="Carbamidomethyl (M)">Carbamidomethyl (M)</option>
-      <option value="Carbamidomethyl (N-term)">Carbamidomethyl (N-term)</option>
-      <option value="Carbamidomethyl (S)">Carbamidomethyl (S)</option>
-      <option value="Carbamidomethyl (T)">Carbamidomethyl (T)</option>
-      <option value="Carbamidomethyl (U)">Carbamidomethyl (U)</option>
-      <option value="Carbamidomethyl (Y)">Carbamidomethyl (Y)</option>
-      <option value="CarbamidomethylDTT (C)">CarbamidomethylDTT (C)</option>
-      <option value="Carbamyl (C)">Carbamyl (C)</option>
-      <option value="Carbamyl (K)">Carbamyl (K)</option>
-      <option value="Carbamyl (M)">Carbamyl (M)</option>
-      <option value="Carbamyl (N-term)">Carbamyl (N-term)</option>
-      <option value="Carbamyl (Protein N-term)">Carbamyl (Protein N-term)</option>
-      <option value="Carbamyl (R)">Carbamyl (R)</option>
-      <option value="Carbamyl (S)">Carbamyl (S)</option>
-      <option value="Carbamyl (T)">Carbamyl (T)</option>
-      <option value="Carbamyl (Y)">Carbamyl (Y)</option>
-      <option value="Carbofuran (S)">Carbofuran (S)</option>
-      <option value="Carbonyl (A)">Carbonyl (A)</option>
-      <option value="Carbonyl (E)">Carbonyl (E)</option>
-      <option value="Carbonyl (I)">Carbonyl (I)</option>
-      <option value="Carbonyl (L)">Carbonyl (L)</option>
-      <option value="Carbonyl (Q)">Carbonyl (Q)</option>
-      <option value="Carbonyl (R)">Carbonyl (R)</option>
-      <option value="Carbonyl (S)">Carbonyl (S)</option>
-      <option value="Carbonyl (V)">Carbonyl (V)</option>
-      <option value="Carboxy (D)">Carboxy (D)</option>
-      <option value="Carboxy (E)">Carboxy (E)</option>
-      <option value="Carboxy (K)">Carboxy (K)</option>
-      <option value="Carboxy (Protein N-term M)">Carboxy (Protein N-term M)</option>
-      <option value="Carboxy (W)">Carboxy (W)</option>
-      <option value="Carboxy-&gt;Thiocarboxy (Protein C-term G)">Carboxy-&gt;Thiocarboxy (Protein C-term G)</option>
-      <option value="Carboxyethyl (H)">Carboxyethyl (H)</option>
-      <option value="Carboxyethyl (K)">Carboxyethyl (K)</option>
-      <option value="Carboxyethylpyrrole (K)">Carboxyethylpyrrole (K)</option>
-      <option value="Carboxymethyl (C)">Carboxymethyl (C)</option>
-      <option value="Carboxymethyl (K)">Carboxymethyl (K)</option>
-      <option value="Carboxymethyl (N-term)">Carboxymethyl (N-term)</option>
-      <option value="Carboxymethyl (U)">Carboxymethyl (U)</option>
-      <option value="Carboxymethyl (W)">Carboxymethyl (W)</option>
-      <option value="Carboxymethyl:13C(2) (C)">Carboxymethyl:13C(2) (C)</option>
-      <option value="CarboxymethylDMAP (N-term)">CarboxymethylDMAP (N-term)</option>
-      <option value="CarboxymethylDTT (C)">CarboxymethylDTT (C)</option>
-      <option value="Cation:Ag (C-term)">Cation:Ag (C-term)</option>
-      <option value="Cation:Ag (D)">Cation:Ag (D)</option>
-      <option value="Cation:Ag (E)">Cation:Ag (E)</option>
-      <option value="Cation:Al[III] (C-term)">Cation:Al[III] (C-term)</option>
-      <option value="Cation:Al[III] (D)">Cation:Al[III] (D)</option>
-      <option value="Cation:Al[III] (E)">Cation:Al[III] (E)</option>
-      <option value="Cation:Ca[II] (C-term)">Cation:Ca[II] (C-term)</option>
-      <option value="Cation:Ca[II] (D)">Cation:Ca[II] (D)</option>
-      <option value="Cation:Ca[II] (E)">Cation:Ca[II] (E)</option>
-      <option value="Cation:Cu[I] (C-term)">Cation:Cu[I] (C-term)</option>
-      <option value="Cation:Cu[I] (D)">Cation:Cu[I] (D)</option>
-      <option value="Cation:Cu[I] (E)">Cation:Cu[I] (E)</option>
-      <option value="Cation:Cu[I] (H)">Cation:Cu[I] (H)</option>
-      <option value="Cation:Fe[II] (C-term)">Cation:Fe[II] (C-term)</option>
-      <option value="Cation:Fe[II] (D)">Cation:Fe[II] (D)</option>
-      <option value="Cation:Fe[II] (E)">Cation:Fe[II] (E)</option>
-      <option value="Cation:Fe[III] (C-term)">Cation:Fe[III] (C-term)</option>
-      <option value="Cation:Fe[III] (D)">Cation:Fe[III] (D)</option>
-      <option value="Cation:Fe[III] (E)">Cation:Fe[III] (E)</option>
-      <option value="Cation:K (C-term)">Cation:K (C-term)</option>
-      <option value="Cation:K (D)">Cation:K (D)</option>
-      <option value="Cation:K (E)">Cation:K (E)</option>
-      <option value="Cation:Li (C-term)">Cation:Li (C-term)</option>
-      <option value="Cation:Li (D)">Cation:Li (D)</option>
-      <option value="Cation:Li (E)">Cation:Li (E)</option>
-      <option value="Cation:Mg[II] (C-term)">Cation:Mg[II] (C-term)</option>
-      <option value="Cation:Mg[II] (D)">Cation:Mg[II] (D)</option>
-      <option value="Cation:Mg[II] (E)">Cation:Mg[II] (E)</option>
-      <option value="Cation:Na (C-term)">Cation:Na (C-term)</option>
-      <option value="Cation:Na (D)">Cation:Na (D)</option>
-      <option value="Cation:Na (E)">Cation:Na (E)</option>
-      <option value="Cation:Ni[II] (C-term)">Cation:Ni[II] (C-term)</option>
-      <option value="Cation:Ni[II] (D)">Cation:Ni[II] (D)</option>
-      <option value="Cation:Ni[II] (E)">Cation:Ni[II] (E)</option>
-      <option value="Cation:Zn[II] (C-term)">Cation:Zn[II] (C-term)</option>
-      <option value="Cation:Zn[II] (D)">Cation:Zn[II] (D)</option>
-      <option value="Cation:Zn[II] (E)">Cation:Zn[II] (E)</option>
-      <option value="Cation:Zn[II] (H)">Cation:Zn[II] (H)</option>
-      <option value="cGMP (C)">cGMP (C)</option>
-      <option value="cGMP (S)">cGMP (S)</option>
-      <option value="cGMP+RMP-loss (C)">cGMP+RMP-loss (C)</option>
-      <option value="cGMP+RMP-loss (S)">cGMP+RMP-loss (S)</option>
-      <option value="CHDH (D)">CHDH (D)</option>
-      <option value="Chlorination (W)">Chlorination (W)</option>
-      <option value="Chlorination (Y)">Chlorination (Y)</option>
-      <option value="Cholesterol (Protein C-term)">Cholesterol (Protein C-term)</option>
-      <option value="CIGG (K)">CIGG (K)</option>
-      <option value="CLIP_TRAQ_2 (K)">CLIP_TRAQ_2 (K)</option>
-      <option value="CLIP_TRAQ_2 (N-term)">CLIP_TRAQ_2 (N-term)</option>
-      <option value="CLIP_TRAQ_2 (Y)">CLIP_TRAQ_2 (Y)</option>
-      <option value="CLIP_TRAQ_3 (K)">CLIP_TRAQ_3 (K)</option>
-      <option value="CLIP_TRAQ_3 (N-term)">CLIP_TRAQ_3 (N-term)</option>
-      <option value="CLIP_TRAQ_3 (Y)">CLIP_TRAQ_3 (Y)</option>
-      <option value="CLIP_TRAQ_4 (K)">CLIP_TRAQ_4 (K)</option>
-      <option value="CLIP_TRAQ_4 (N-term)">CLIP_TRAQ_4 (N-term)</option>
-      <option value="CLIP_TRAQ_4 (Y)">CLIP_TRAQ_4 (Y)</option>
-      <option value="CoenzymeA (C)">CoenzymeA (C)</option>
-      <option value="Cresylphosphate (H)">Cresylphosphate (H)</option>
-      <option value="Cresylphosphate (K)">Cresylphosphate (K)</option>
-      <option value="Cresylphosphate (R)">Cresylphosphate (R)</option>
-      <option value="Cresylphosphate (S)">Cresylphosphate (S)</option>
-      <option value="Cresylphosphate (T)">Cresylphosphate (T)</option>
-      <option value="Cresylphosphate (Y)">Cresylphosphate (Y)</option>
-      <option value="CresylSaligeninPhosphate (H)">CresylSaligeninPhosphate (H)</option>
-      <option value="CresylSaligeninPhosphate (K)">CresylSaligeninPhosphate (K)</option>
-      <option value="CresylSaligeninPhosphate (R)">CresylSaligeninPhosphate (R)</option>
-      <option value="CresylSaligeninPhosphate (S)">CresylSaligeninPhosphate (S)</option>
-      <option value="CresylSaligeninPhosphate (T)">CresylSaligeninPhosphate (T)</option>
-      <option value="CresylSaligeninPhosphate (Y)">CresylSaligeninPhosphate (Y)</option>
-      <option value="Crotonaldehyde (C)">Crotonaldehyde (C)</option>
-      <option value="Crotonaldehyde (H)">Crotonaldehyde (H)</option>
-      <option value="Crotonaldehyde (K)">Crotonaldehyde (K)</option>
-      <option value="Crotonyl (K)">Crotonyl (K)</option>
-      <option value="CuSMo (C)">CuSMo (C)</option>
-      <option value="CUSTOM0 (A)">CUSTOM0 (A)</option>
-      <option value="CUSTOM0 (C)">CUSTOM0 (C)</option>
-      <option value="CUSTOM0 (C-term)">CUSTOM0 (C-term)</option>
-      <option value="CUSTOM0 (D)">CUSTOM0 (D)</option>
-      <option value="CUSTOM0 (E)">CUSTOM0 (E)</option>
-      <option value="CUSTOM0 (F)">CUSTOM0 (F)</option>
-      <option value="CUSTOM0 (G)">CUSTOM0 (G)</option>
-      <option value="CUSTOM0 (H)">CUSTOM0 (H)</option>
-      <option value="CUSTOM0 (I)">CUSTOM0 (I)</option>
-      <option value="CUSTOM0 (K)">CUSTOM0 (K)</option>
-      <option value="CUSTOM0 (L)">CUSTOM0 (L)</option>
-      <option value="CUSTOM0 (M)">CUSTOM0 (M)</option>
-      <option value="CUSTOM0 (N)">CUSTOM0 (N)</option>
-      <option value="CUSTOM0 (N-term)">CUSTOM0 (N-term)</option>
-      <option value="CUSTOM0 (P)">CUSTOM0 (P)</option>
-      <option value="CUSTOM0 (Q)">CUSTOM0 (Q)</option>
-      <option value="CUSTOM0 (R)">CUSTOM0 (R)</option>
-      <option value="CUSTOM0 (S)">CUSTOM0 (S)</option>
-      <option value="CUSTOM0 (T)">CUSTOM0 (T)</option>
-      <option value="CUSTOM0 (V)">CUSTOM0 (V)</option>
-      <option value="CUSTOM0 (W)">CUSTOM0 (W)</option>
-      <option value="CUSTOM0 (Y)">CUSTOM0 (Y)</option>
-      <option value="CUSTOM1 (A)">CUSTOM1 (A)</option>
-      <option value="CUSTOM1 (C)">CUSTOM1 (C)</option>
-      <option value="CUSTOM1 (C-term)">CUSTOM1 (C-term)</option>
-      <option value="CUSTOM1 (D)">CUSTOM1 (D)</option>
-      <option value="CUSTOM1 (E)">CUSTOM1 (E)</option>
-      <option value="CUSTOM1 (F)">CUSTOM1 (F)</option>
-      <option value="CUSTOM1 (G)">CUSTOM1 (G)</option>
-      <option value="CUSTOM1 (H)">CUSTOM1 (H)</option>
-      <option value="CUSTOM1 (I)">CUSTOM1 (I)</option>
-      <option value="CUSTOM1 (K)">CUSTOM1 (K)</option>
-      <option value="CUSTOM1 (L)">CUSTOM1 (L)</option>
-      <option value="CUSTOM1 (M)">CUSTOM1 (M)</option>
-      <option value="CUSTOM1 (N)">CUSTOM1 (N)</option>
-      <option value="CUSTOM1 (N-term)">CUSTOM1 (N-term)</option>
-      <option value="CUSTOM1 (P)">CUSTOM1 (P)</option>
-      <option value="CUSTOM1 (Q)">CUSTOM1 (Q)</option>
-      <option value="CUSTOM1 (R)">CUSTOM1 (R)</option>
-      <option value="CUSTOM1 (S)">CUSTOM1 (S)</option>
-      <option value="CUSTOM1 (T)">CUSTOM1 (T)</option>
-      <option value="CUSTOM1 (V)">CUSTOM1 (V)</option>
-      <option value="CUSTOM1 (W)">CUSTOM1 (W)</option>
-      <option value="CUSTOM1 (Y)">CUSTOM1 (Y)</option>
-      <option value="CUSTOM2 (A)">CUSTOM2 (A)</option>
-      <option value="CUSTOM2 (C)">CUSTOM2 (C)</option>
-      <option value="CUSTOM2 (C-term)">CUSTOM2 (C-term)</option>
-      <option value="CUSTOM2 (D)">CUSTOM2 (D)</option>
-      <option value="CUSTOM2 (E)">CUSTOM2 (E)</option>
-      <option value="CUSTOM2 (F)">CUSTOM2 (F)</option>
-      <option value="CUSTOM2 (G)">CUSTOM2 (G)</option>
-      <option value="CUSTOM2 (H)">CUSTOM2 (H)</option>
-      <option value="CUSTOM2 (I)">CUSTOM2 (I)</option>
-      <option value="CUSTOM2 (K)">CUSTOM2 (K)</option>
-      <option value="CUSTOM2 (L)">CUSTOM2 (L)</option>
-      <option value="CUSTOM2 (M)">CUSTOM2 (M)</option>
-      <option value="CUSTOM2 (N)">CUSTOM2 (N)</option>
-      <option value="CUSTOM2 (N-term)">CUSTOM2 (N-term)</option>
-      <option value="CUSTOM2 (P)">CUSTOM2 (P)</option>
-      <option value="CUSTOM2 (Q)">CUSTOM2 (Q)</option>
-      <option value="CUSTOM2 (R)">CUSTOM2 (R)</option>
-      <option value="CUSTOM2 (S)">CUSTOM2 (S)</option>
-      <option value="CUSTOM2 (T)">CUSTOM2 (T)</option>
-      <option value="CUSTOM2 (V)">CUSTOM2 (V)</option>
-      <option value="CUSTOM2 (W)">CUSTOM2 (W)</option>
-      <option value="CUSTOM2 (Y)">CUSTOM2 (Y)</option>
-      <option value="CUSTOM3 (A)">CUSTOM3 (A)</option>
-      <option value="CUSTOM3 (C)">CUSTOM3 (C)</option>
-      <option value="CUSTOM3 (C-term)">CUSTOM3 (C-term)</option>
-      <option value="CUSTOM3 (D)">CUSTOM3 (D)</option>
-      <option value="CUSTOM3 (E)">CUSTOM3 (E)</option>
-      <option value="CUSTOM3 (F)">CUSTOM3 (F)</option>
-      <option value="CUSTOM3 (G)">CUSTOM3 (G)</option>
-      <option value="CUSTOM3 (H)">CUSTOM3 (H)</option>
-      <option value="CUSTOM3 (I)">CUSTOM3 (I)</option>
-      <option value="CUSTOM3 (K)">CUSTOM3 (K)</option>
-      <option value="CUSTOM3 (L)">CUSTOM3 (L)</option>
-      <option value="CUSTOM3 (M)">CUSTOM3 (M)</option>
-      <option value="CUSTOM3 (N)">CUSTOM3 (N)</option>
-      <option value="CUSTOM3 (N-term)">CUSTOM3 (N-term)</option>
-      <option value="CUSTOM3 (P)">CUSTOM3 (P)</option>
-      <option value="CUSTOM3 (Q)">CUSTOM3 (Q)</option>
-      <option value="CUSTOM3 (R)">CUSTOM3 (R)</option>
-      <option value="CUSTOM3 (S)">CUSTOM3 (S)</option>
-      <option value="CUSTOM3 (T)">CUSTOM3 (T)</option>
-      <option value="CUSTOM3 (V)">CUSTOM3 (V)</option>
-      <option value="CUSTOM3 (W)">CUSTOM3 (W)</option>
-      <option value="CUSTOM3 (Y)">CUSTOM3 (Y)</option>
-      <option value="CUSTOM4 (A)">CUSTOM4 (A)</option>
-      <option value="CUSTOM4 (C)">CUSTOM4 (C)</option>
-      <option value="CUSTOM4 (C-term)">CUSTOM4 (C-term)</option>
-      <option value="CUSTOM4 (D)">CUSTOM4 (D)</option>
-      <option value="CUSTOM4 (E)">CUSTOM4 (E)</option>
-      <option value="CUSTOM4 (F)">CUSTOM4 (F)</option>
-      <option value="CUSTOM4 (G)">CUSTOM4 (G)</option>
-      <option value="CUSTOM4 (H)">CUSTOM4 (H)</option>
-      <option value="CUSTOM4 (I)">CUSTOM4 (I)</option>
-      <option value="CUSTOM4 (K)">CUSTOM4 (K)</option>
-      <option value="CUSTOM4 (L)">CUSTOM4 (L)</option>
-      <option value="CUSTOM4 (M)">CUSTOM4 (M)</option>
-      <option value="CUSTOM4 (N)">CUSTOM4 (N)</option>
-      <option value="CUSTOM4 (N-term)">CUSTOM4 (N-term)</option>
-      <option value="CUSTOM4 (P)">CUSTOM4 (P)</option>
-      <option value="CUSTOM4 (Q)">CUSTOM4 (Q)</option>
-      <option value="CUSTOM4 (R)">CUSTOM4 (R)</option>
-      <option value="CUSTOM4 (S)">CUSTOM4 (S)</option>
-      <option value="CUSTOM4 (T)">CUSTOM4 (T)</option>
-      <option value="CUSTOM4 (V)">CUSTOM4 (V)</option>
-      <option value="CUSTOM4 (W)">CUSTOM4 (W)</option>
-      <option value="CUSTOM4 (Y)">CUSTOM4 (Y)</option>
-      <option value="CUSTOM5 (A)">CUSTOM5 (A)</option>
-      <option value="CUSTOM5 (C)">CUSTOM5 (C)</option>
-      <option value="CUSTOM5 (C-term)">CUSTOM5 (C-term)</option>
-      <option value="CUSTOM5 (D)">CUSTOM5 (D)</option>
-      <option value="CUSTOM5 (E)">CUSTOM5 (E)</option>
-      <option value="CUSTOM5 (F)">CUSTOM5 (F)</option>
-      <option value="CUSTOM5 (G)">CUSTOM5 (G)</option>
-      <option value="CUSTOM5 (H)">CUSTOM5 (H)</option>
-      <option value="CUSTOM5 (I)">CUSTOM5 (I)</option>
-      <option value="CUSTOM5 (K)">CUSTOM5 (K)</option>
-      <option value="CUSTOM5 (L)">CUSTOM5 (L)</option>
-      <option value="CUSTOM5 (M)">CUSTOM5 (M)</option>
-      <option value="CUSTOM5 (N)">CUSTOM5 (N)</option>
-      <option value="CUSTOM5 (N-term)">CUSTOM5 (N-term)</option>
-      <option value="CUSTOM5 (P)">CUSTOM5 (P)</option>
-      <option value="CUSTOM5 (Q)">CUSTOM5 (Q)</option>
-      <option value="CUSTOM5 (R)">CUSTOM5 (R)</option>
-      <option value="CUSTOM5 (S)">CUSTOM5 (S)</option>
-      <option value="CUSTOM5 (T)">CUSTOM5 (T)</option>
-      <option value="CUSTOM5 (V)">CUSTOM5 (V)</option>
-      <option value="CUSTOM5 (W)">CUSTOM5 (W)</option>
-      <option value="CUSTOM5 (Y)">CUSTOM5 (Y)</option>
-      <option value="CUSTOM6 (A)">CUSTOM6 (A)</option>
-      <option value="CUSTOM6 (C)">CUSTOM6 (C)</option>
-      <option value="CUSTOM6 (C-term)">CUSTOM6 (C-term)</option>
-      <option value="CUSTOM6 (D)">CUSTOM6 (D)</option>
-      <option value="CUSTOM6 (E)">CUSTOM6 (E)</option>
-      <option value="CUSTOM6 (F)">CUSTOM6 (F)</option>
-      <option value="CUSTOM6 (G)">CUSTOM6 (G)</option>
-      <option value="CUSTOM6 (H)">CUSTOM6 (H)</option>
-      <option value="CUSTOM6 (I)">CUSTOM6 (I)</option>
-      <option value="CUSTOM6 (K)">CUSTOM6 (K)</option>
-      <option value="CUSTOM6 (L)">CUSTOM6 (L)</option>
-      <option value="CUSTOM6 (M)">CUSTOM6 (M)</option>
-      <option value="CUSTOM6 (N)">CUSTOM6 (N)</option>
-      <option value="CUSTOM6 (N-term)">CUSTOM6 (N-term)</option>
-      <option value="CUSTOM6 (P)">CUSTOM6 (P)</option>
-      <option value="CUSTOM6 (Q)">CUSTOM6 (Q)</option>
-      <option value="CUSTOM6 (R)">CUSTOM6 (R)</option>
-      <option value="CUSTOM6 (S)">CUSTOM6 (S)</option>
-      <option value="CUSTOM6 (T)">CUSTOM6 (T)</option>
-      <option value="CUSTOM6 (V)">CUSTOM6 (V)</option>
-      <option value="CUSTOM6 (W)">CUSTOM6 (W)</option>
-      <option value="CUSTOM6 (Y)">CUSTOM6 (Y)</option>
-      <option value="CUSTOM7 (A)">CUSTOM7 (A)</option>
-      <option value="CUSTOM7 (C)">CUSTOM7 (C)</option>
-      <option value="CUSTOM7 (C-term)">CUSTOM7 (C-term)</option>
-      <option value="CUSTOM7 (D)">CUSTOM7 (D)</option>
-      <option value="CUSTOM7 (E)">CUSTOM7 (E)</option>
-      <option value="CUSTOM7 (F)">CUSTOM7 (F)</option>
-      <option value="CUSTOM7 (G)">CUSTOM7 (G)</option>
-      <option value="CUSTOM7 (H)">CUSTOM7 (H)</option>
-      <option value="CUSTOM7 (I)">CUSTOM7 (I)</option>
-      <option value="CUSTOM7 (K)">CUSTOM7 (K)</option>
-      <option value="CUSTOM7 (L)">CUSTOM7 (L)</option>
-      <option value="CUSTOM7 (M)">CUSTOM7 (M)</option>
-      <option value="CUSTOM7 (N)">CUSTOM7 (N)</option>
-      <option value="CUSTOM7 (N-term)">CUSTOM7 (N-term)</option>
-      <option value="CUSTOM7 (P)">CUSTOM7 (P)</option>
-      <option value="CUSTOM7 (Q)">CUSTOM7 (Q)</option>
-      <option value="CUSTOM7 (R)">CUSTOM7 (R)</option>
-      <option value="CUSTOM7 (S)">CUSTOM7 (S)</option>
-      <option value="CUSTOM7 (T)">CUSTOM7 (T)</option>
-      <option value="CUSTOM7 (V)">CUSTOM7 (V)</option>
-      <option value="CUSTOM7 (W)">CUSTOM7 (W)</option>
-      <option value="CUSTOM7 (Y)">CUSTOM7 (Y)</option>
-      <option value="CUSTOM8 (A)">CUSTOM8 (A)</option>
-      <option value="CUSTOM8 (C)">CUSTOM8 (C)</option>
-      <option value="CUSTOM8 (C-term)">CUSTOM8 (C-term)</option>
-      <option value="CUSTOM8 (D)">CUSTOM8 (D)</option>
-      <option value="CUSTOM8 (E)">CUSTOM8 (E)</option>
-      <option value="CUSTOM8 (F)">CUSTOM8 (F)</option>
-      <option value="CUSTOM8 (G)">CUSTOM8 (G)</option>
-      <option value="CUSTOM8 (H)">CUSTOM8 (H)</option>
-      <option value="CUSTOM8 (I)">CUSTOM8 (I)</option>
-      <option value="CUSTOM8 (K)">CUSTOM8 (K)</option>
-      <option value="CUSTOM8 (L)">CUSTOM8 (L)</option>
-      <option value="CUSTOM8 (M)">CUSTOM8 (M)</option>
-      <option value="CUSTOM8 (N)">CUSTOM8 (N)</option>
-      <option value="CUSTOM8 (N-term)">CUSTOM8 (N-term)</option>
-      <option value="CUSTOM8 (P)">CUSTOM8 (P)</option>
-      <option value="CUSTOM8 (Q)">CUSTOM8 (Q)</option>
-      <option value="CUSTOM8 (R)">CUSTOM8 (R)</option>
-      <option value="CUSTOM8 (S)">CUSTOM8 (S)</option>
-      <option value="CUSTOM8 (T)">CUSTOM8 (T)</option>
-      <option value="CUSTOM8 (V)">CUSTOM8 (V)</option>
-      <option value="CUSTOM8 (W)">CUSTOM8 (W)</option>
-      <option value="CUSTOM8 (Y)">CUSTOM8 (Y)</option>
-      <option value="CUSTOM9 (A)">CUSTOM9 (A)</option>
-      <option value="CUSTOM9 (C)">CUSTOM9 (C)</option>
-      <option value="CUSTOM9 (C-term)">CUSTOM9 (C-term)</option>
-      <option value="CUSTOM9 (D)">CUSTOM9 (D)</option>
-      <option value="CUSTOM9 (E)">CUSTOM9 (E)</option>
-      <option value="CUSTOM9 (F)">CUSTOM9 (F)</option>
-      <option value="CUSTOM9 (G)">CUSTOM9 (G)</option>
-      <option value="CUSTOM9 (H)">CUSTOM9 (H)</option>
-      <option value="CUSTOM9 (I)">CUSTOM9 (I)</option>
-      <option value="CUSTOM9 (K)">CUSTOM9 (K)</option>
-      <option value="CUSTOM9 (L)">CUSTOM9 (L)</option>
-      <option value="CUSTOM9 (M)">CUSTOM9 (M)</option>
-      <option value="CUSTOM9 (N)">CUSTOM9 (N)</option>
-      <option value="CUSTOM9 (N-term)">CUSTOM9 (N-term)</option>
-      <option value="CUSTOM9 (P)">CUSTOM9 (P)</option>
-      <option value="CUSTOM9 (Q)">CUSTOM9 (Q)</option>
-      <option value="CUSTOM9 (R)">CUSTOM9 (R)</option>
-      <option value="CUSTOM9 (S)">CUSTOM9 (S)</option>
-      <option value="CUSTOM9 (T)">CUSTOM9 (T)</option>
-      <option value="CUSTOM9 (V)">CUSTOM9 (V)</option>
-      <option value="CUSTOM9 (W)">CUSTOM9 (W)</option>
-      <option value="CUSTOM9 (Y)">CUSTOM9 (Y)</option>
-      <option value="Cy3-maleimide (C)">Cy3-maleimide (C)</option>
-      <option value="Cy3b-maleimide (C)">Cy3b-maleimide (C)</option>
-      <option value="Cyano (C)">Cyano (C)</option>
-      <option value="CyDye-Cy3 (C)">CyDye-Cy3 (C)</option>
-      <option value="CyDye-Cy5 (C)">CyDye-Cy5 (C)</option>
-      <option value="Cys-&gt;Ala (C)">Cys-&gt;Ala (C)</option>
-      <option value="Cys-&gt;Arg (C)">Cys-&gt;Arg (C)</option>
-      <option value="Cys-&gt;Asn (C)">Cys-&gt;Asn (C)</option>
-      <option value="Cys-&gt;Asp (C)">Cys-&gt;Asp (C)</option>
-      <option value="Cys-&gt;CamSec (C)">Cys-&gt;CamSec (C)</option>
-      <option value="Cys-&gt;Dha (C)">Cys-&gt;Dha (C)</option>
-      <option value="Cys-&gt;ethylaminoAla (C)">Cys-&gt;ethylaminoAla (C)</option>
-      <option value="Cys-&gt;Gln (C)">Cys-&gt;Gln (C)</option>
-      <option value="Cys-&gt;Glu (C)">Cys-&gt;Glu (C)</option>
-      <option value="Cys-&gt;Gly (C)">Cys-&gt;Gly (C)</option>
-      <option value="Cys-&gt;His (C)">Cys-&gt;His (C)</option>
-      <option value="Cys-&gt;Lys (C)">Cys-&gt;Lys (C)</option>
-      <option value="Cys-&gt;Met (C)">Cys-&gt;Met (C)</option>
-      <option value="Cys-&gt;methylaminoAla (C)">Cys-&gt;methylaminoAla (C)</option>
-      <option value="Cys-&gt;Oxoalanine (C)">Cys-&gt;Oxoalanine (C)</option>
-      <option value="Cys-&gt;Phe (C)">Cys-&gt;Phe (C)</option>
-      <option value="Cys-&gt;Pro (C)">Cys-&gt;Pro (C)</option>
-      <option value="Cys-&gt;PyruvicAcid (Protein N-term C)">Cys-&gt;PyruvicAcid (Protein N-term C)</option>
-      <option value="Cys-&gt;SecNEM (C)">Cys-&gt;SecNEM (C)</option>
-      <option value="Cys-&gt;SecNEM:2H(5) (C)">Cys-&gt;SecNEM:2H(5) (C)</option>
-      <option value="Cys-&gt;Ser (C)">Cys-&gt;Ser (C)</option>
-      <option value="Cys-&gt;Thr (C)">Cys-&gt;Thr (C)</option>
-      <option value="Cys-&gt;Trp (C)">Cys-&gt;Trp (C)</option>
-      <option value="Cys-&gt;Tyr (C)">Cys-&gt;Tyr (C)</option>
-      <option value="Cys-&gt;Val (C)">Cys-&gt;Val (C)</option>
-      <option value="Cys-&gt;Xle (C)">Cys-&gt;Xle (C)</option>
-      <option value="Cysteinyl (C)">Cysteinyl (C)</option>
-      <option value="cysTMT (C)">cysTMT (C)</option>
-      <option value="cysTMT6plex (C)">cysTMT6plex (C)</option>
-      <option value="Cytopiloyne (C)">Cytopiloyne (C)</option>
-      <option value="Cytopiloyne (K)">Cytopiloyne (K)</option>
-      <option value="Cytopiloyne (N-term)">Cytopiloyne (N-term)</option>
-      <option value="Cytopiloyne (P)">Cytopiloyne (P)</option>
-      <option value="Cytopiloyne (R)">Cytopiloyne (R)</option>
-      <option value="Cytopiloyne (S)">Cytopiloyne (S)</option>
-      <option value="Cytopiloyne (Y)">Cytopiloyne (Y)</option>
-      <option value="Cytopiloyne+water (C)">Cytopiloyne+water (C)</option>
-      <option value="Cytopiloyne+water (K)">Cytopiloyne+water (K)</option>
-      <option value="Cytopiloyne+water (N-term)">Cytopiloyne+water (N-term)</option>
-      <option value="Cytopiloyne+water (R)">Cytopiloyne+water (R)</option>
-      <option value="Cytopiloyne+water (S)">Cytopiloyne+water (S)</option>
-      <option value="Cytopiloyne+water (T)">Cytopiloyne+water (T)</option>
-      <option value="Cytopiloyne+water (Y)">Cytopiloyne+water (Y)</option>
-      <option value="DAET (S)">DAET (S)</option>
-      <option value="DAET (T)">DAET (T)</option>
-      <option value="Dansyl (K)">Dansyl (K)</option>
-      <option value="Dansyl (N-term)">Dansyl (N-term)</option>
-      <option value="Dap-DSP (A)">Dap-DSP (A)</option>
-      <option value="Dap-DSP (E)">Dap-DSP (E)</option>
-      <option value="Dap-DSP (K)">Dap-DSP (K)</option>
-      <option value="Deamidated (N)">Deamidated (N)</option>
-      <option value="Deamidated (Protein N-term F)">Deamidated (Protein N-term F)</option>
-      <option value="Deamidated (Q)">Deamidated (Q)</option>
-      <option value="Deamidated (R)">Deamidated (R)</option>
-      <option value="Deamidated:18O(1) (N)">Deamidated:18O(1) (N)</option>
-      <option value="Deamidated:18O(1) (Q)">Deamidated:18O(1) (Q)</option>
-      <option value="Decanoyl (S)">Decanoyl (S)</option>
-      <option value="Decanoyl (T)">Decanoyl (T)</option>
-      <option value="Decarboxylation (D)">Decarboxylation (D)</option>
-      <option value="Decarboxylation (E)">Decarboxylation (E)</option>
-      <option value="DEDGFLYMVYASQETFG (K)">DEDGFLYMVYASQETFG (K)</option>
-      <option value="Dehydrated (D)">Dehydrated (D)</option>
-      <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
-      <option value="Dehydrated (Protein C-term N)">Dehydrated (Protein C-term N)</option>
-      <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
-      <option value="Dehydrated (S)">Dehydrated (S)</option>
-      <option value="Dehydrated (T)">Dehydrated (T)</option>
-      <option value="Dehydrated (Y)">Dehydrated (Y)</option>
-      <option value="Dehydro (C)">Dehydro (C)</option>
-      <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
-      <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-      <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
-      <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
-      <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
-      <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
-      <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
-      <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
-      <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
-      <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
-      <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
-      <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-      <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
-      <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
-      <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
-      <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
-      <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
-      <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
-      <option value="Delta:H(4)C(3) (K)">Delta:H(4)C(3) (K)</option>
-      <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
-      <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
-      <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
-      <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
-      <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
-      <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
-      <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
-      <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
-      <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
-      <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
-      <option value="Delta:H(6)C(3)O(1) (K)">Delta:H(6)C(3)O(1) (K)</option>
-      <option value="Delta:H(6)C(3)O(1) (Protein N-term)">Delta:H(6)C(3)O(1) (Protein N-term)</option>
-      <option value="Delta:H(6)C(6)O(1) (K)">Delta:H(6)C(6)O(1) (K)</option>
-      <option value="Delta:H(6)C(7)O(4) (R)">Delta:H(6)C(7)O(4) (R)</option>
-      <option value="Delta:H(8)C(6)O(1) (K)">Delta:H(8)C(6)O(1) (K)</option>
-      <option value="Delta:H(8)C(6)O(1) (Protein N-term)">Delta:H(8)C(6)O(1) (Protein N-term)</option>
-      <option value="Delta:H(8)C(6)O(2) (K)">Delta:H(8)C(6)O(2) (K)</option>
-      <option value="Delta:Hg(1) (C)">Delta:Hg(1) (C)</option>
-      <option value="Delta:O(4) (W)">Delta:O(4) (W)</option>
-      <option value="Delta:S(-1)Se(1) (C)">Delta:S(-1)Se(1) (C)</option>
-      <option value="Delta:S(-1)Se(1) (M)">Delta:S(-1)Se(1) (M)</option>
-      <option value="Delta:Se(1) (C)">Delta:Se(1) (C)</option>
-      <option value="Deoxy (D)">Deoxy (D)</option>
-      <option value="Deoxy (S)">Deoxy (S)</option>
-      <option value="Deoxy (T)">Deoxy (T)</option>
-      <option value="Deoxyhypusine (K)">Deoxyhypusine (K)</option>
-      <option value="Deoxyhypusine (Q)">Deoxyhypusine (Q)</option>
-      <option value="DeStreak (C)">DeStreak (C)</option>
-      <option value="Dethiomethyl (M)">Dethiomethyl (M)</option>
-      <option value="dHex (N)">dHex (N)</option>
-      <option value="dHex (S)">dHex (S)</option>
-      <option value="dHex (T)">dHex (T)</option>
-      <option value="dHex(1)Hex(1) (S)">dHex(1)Hex(1) (S)</option>
-      <option value="dHex(1)Hex(1) (T)">dHex(1)Hex(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexA(1)HexNAc(3) (S)">dHex(1)Hex(1)HexA(1)HexNAc(3) (S)</option>
-      <option value="dHex(1)Hex(1)HexA(1)HexNAc(3) (T)">dHex(1)Hex(1)HexA(1)HexNAc(3) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)Kdn(1) (S)">dHex(1)Hex(1)HexNAc(1)Kdn(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)Kdn(1) (T)">dHex(1)Hex(1)HexNAc(1)Kdn(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(1)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(1)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3) (S)">dHex(1)Hex(1)HexNAc(3) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3) (T)">dHex(1)Hex(1)HexNAc(3) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(4) (S)">dHex(1)Hex(1)HexNAc(4) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(4) (T)">dHex(1)Hex(1)HexNAc(4) (T)</option>
-      <option value="dHex(1)Hex(2) (S)">dHex(1)Hex(2) (S)</option>
-      <option value="dHex(1)Hex(2) (T)">dHex(1)Hex(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexA(1) (S)">dHex(1)Hex(2)HexA(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexA(1) (T)">dHex(1)Hex(2)HexA(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(1) (S)">dHex(1)Hex(2)HexA(1)HexNAc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(1) (T)">dHex(1)Hex(2)HexA(1)HexNAc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (S)">dHex(1)Hex(2)HexA(1)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (T)">dHex(1)Hex(2)HexA(1)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1) (S)">dHex(1)Hex(2)HexNAc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1) (T)">dHex(1)Hex(2)HexNAc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)Pent(1) (N)">dHex(1)Hex(2)HexNAc(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3) (N)">dHex(1)Hex(2)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3) (S)">dHex(1)Hex(2)HexNAc(3) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3) (T)">dHex(1)Hex(2)HexNAc(3) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4) (N)">dHex(1)Hex(2)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4) (S)">dHex(1)Hex(2)HexNAc(4) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4) (T)">dHex(1)Hex(2)HexNAc(4) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-      <option value="dHex(1)Hex(3) (S)">dHex(1)Hex(3) (S)</option>
-      <option value="dHex(1)Hex(3) (T)">dHex(1)Hex(3) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(2) (S)">dHex(1)Hex(3)HexA(1)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(2) (T)">dHex(1)Hex(3)HexA(1)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(2)HexNAc(2) (S)">dHex(1)Hex(3)HexA(2)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(2)HexNAc(2) (T)">dHex(1)Hex(3)HexA(2)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(1) (S)">dHex(1)Hex(3)HexNAc(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(1) (T)">dHex(1)Hex(3)HexNAc(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2) (N)">dHex(1)Hex(3)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2) (S)">dHex(1)Hex(3)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2) (T)">dHex(1)Hex(3)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)Pent(1) (N)">dHex(1)Hex(3)HexNAc(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3) (N)">dHex(1)Hex(3)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3) (S)">dHex(1)Hex(3)HexNAc(3) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3) (T)">dHex(1)Hex(3)HexNAc(3) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Pent(1) (N)">dHex(1)Hex(3)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Pent(2) (N)">dHex(1)Hex(3)HexNAc(3)Pent(2) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Pent(3) (N)">dHex(1)Hex(3)HexNAc(3)Pent(3) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4) (N)">dHex(1)Hex(3)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4) (S)">dHex(1)Hex(3)HexNAc(4) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4) (T)">dHex(1)Hex(3)HexNAc(4) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)Pent(1) (N)">dHex(1)Hex(3)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)Pent(2) (N)">dHex(1)Hex(3)HexNAc(4)Pent(2) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)Pent(3) (N)">dHex(1)Hex(3)HexNAc(4)Pent(3) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5) (N)">dHex(1)Hex(3)HexNAc(5) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5) (S)">dHex(1)Hex(3)HexNAc(5) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5) (T)">dHex(1)Hex(3)HexNAc(5) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(5)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(6) (N)">dHex(1)Hex(3)HexNAc(6) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(6) (S)">dHex(1)Hex(3)HexNAc(6) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(6) (T)">dHex(1)Hex(3)HexNAc(6) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4) (S)">dHex(1)Hex(4) (S)</option>
-      <option value="dHex(1)Hex(4) (T)">dHex(1)Hex(4) (T)</option>
-      <option value="dHex(1)Hex(4)HexA(1) (S)">dHex(1)Hex(4)HexA(1) (S)</option>
-      <option value="dHex(1)Hex(4)HexA(1) (T)">dHex(1)Hex(4)HexA(1) (T)</option>
-      <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (S)">dHex(1)Hex(4)HexA(1)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (T)">dHex(1)Hex(4)HexA(1)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(1)Pent(1) (N)">dHex(1)Hex(4)HexNAc(1)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(2) (N)">dHex(1)Hex(4)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(2) (S)">dHex(1)Hex(4)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(4)HexNAc(2) (T)">dHex(1)Hex(4)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(2)Pent(1) (N)">dHex(1)Hex(4)HexNAc(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3) (N)">dHex(1)Hex(4)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)Pent(1) (N)">dHex(1)Hex(4)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4) (N)">dHex(1)Hex(4)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4) (S)">dHex(1)Hex(4)HexNAc(4) (S)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4) (T)">dHex(1)Hex(4)HexNAc(4) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)Pent(1) (N)">dHex(1)Hex(4)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(5) (N)">dHex(1)Hex(4)HexNAc(5) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(5)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(5)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5) (S)">dHex(1)Hex(5) (S)</option>
-      <option value="dHex(1)Hex(5) (T)">dHex(1)Hex(5) (T)</option>
-      <option value="dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N)">dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(2) (N)">dHex(1)Hex(5)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(2)Pent(1) (N)">dHex(1)Hex(5)HexNAc(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3) (N)">dHex(1)Hex(5)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4) (N)">dHex(1)Hex(5)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N)">dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N)">dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)Pent(1) (N)">dHex(1)Hex(5)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)Sulf(2) (N)">dHex(1)Hex(5)HexNAc(4)Sulf(2) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(5) (N)">dHex(1)Hex(5)HexNAc(5) (N)</option>
-      <option value="dHex(1)Hex(6) (S)">dHex(1)Hex(6) (S)</option>
-      <option value="dHex(1)Hex(6) (T)">dHex(1)Hex(6) (T)</option>
-      <option value="dHex(1)Hex(6)HexNAc(2) (N)">dHex(1)Hex(6)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(6)HexNAc(3) (N)">dHex(1)Hex(6)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(6)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(6)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(6)HexNAc(4) (N)">dHex(1)Hex(6)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(2) (N)">dHex(1)Hex(7)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(3) (N)">dHex(1)Hex(7)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(3)Phos(1) (N)">dHex(1)Hex(7)HexNAc(3)Phos(1) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(4) (N)">dHex(1)Hex(7)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(8)HexNAc(2) (N)">dHex(1)Hex(8)HexNAc(2) (N)</option>
-      <option value="dHex(1)HexNAc(3) (S)">dHex(1)HexNAc(3) (S)</option>
-      <option value="dHex(1)HexNAc(3) (T)">dHex(1)HexNAc(3) (T)</option>
-      <option value="dHex(1)HexNAc(4) (S)">dHex(1)HexNAc(4) (S)</option>
-      <option value="dHex(1)HexNAc(4) (T)">dHex(1)HexNAc(4) (T)</option>
-      <option value="dHex(1)HexNAc(5) (S)">dHex(1)HexNAc(5) (S)</option>
-      <option value="dHex(1)HexNAc(5) (T)">dHex(1)HexNAc(5) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(1)Kdn(1) (S)">dHex(2)Hex(1)HexNAc(1)Kdn(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(1)Kdn(1) (T)">dHex(2)Hex(1)HexNAc(1)Kdn(1) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(2)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(2)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)NeuAc(1) (S)">dHex(2)Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)NeuAc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(3) (S)">dHex(2)Hex(1)HexNAc(3) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(3) (T)">dHex(2)Hex(1)HexNAc(3) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2) (S)">dHex(2)Hex(2) (S)</option>
-      <option value="dHex(2)Hex(2) (T)">dHex(2)Hex(2) (T)</option>
-      <option value="dHex(2)Hex(2)HexA(1) (S)">dHex(2)Hex(2)HexA(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexA(1) (T)">dHex(2)Hex(2)HexA(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexA(1)HexNAc(1) (S)">dHex(2)Hex(2)HexA(1)HexNAc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexA(1)HexNAc(1) (T)">dHex(2)Hex(2)HexA(1)HexNAc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(1) (S)">dHex(2)Hex(2)HexNAc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(1) (T)">dHex(2)Hex(2)HexNAc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2) (N)">dHex(2)Hex(2)HexNAc(2) (N)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2) (S)">dHex(2)Hex(2)HexNAc(2) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2) (T)">dHex(2)Hex(2)HexNAc(2) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(2)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(2)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(2)Sulf(2) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(2)Sulf(2) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3) (N)">dHex(2)Hex(2)HexNAc(3) (N)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3) (S)">dHex(2)Hex(2)HexNAc(3) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3) (T)">dHex(2)Hex(2)HexNAc(3) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)NeuAc(1) (S)">dHex(2)Hex(2)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(2)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)NeuGc(1) (S)">dHex(2)Hex(2)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)NeuGc(1) (T)">dHex(2)Hex(2)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(4) (S)">dHex(2)Hex(2)HexNAc(4) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(4) (T)">dHex(2)Hex(2)HexNAc(4) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(5) (S)">dHex(2)Hex(2)HexNAc(5) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(5) (T)">dHex(2)Hex(2)HexNAc(5) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3) (S)">dHex(2)Hex(3) (S)</option>
-      <option value="dHex(2)Hex(3) (T)">dHex(2)Hex(3) (T)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(1)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2) (N)">dHex(2)Hex(3)HexNAc(2) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2) (S)">dHex(2)Hex(3)HexNAc(2) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2) (T)">dHex(2)Hex(3)HexNAc(2) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(3)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(3)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3) (N)">dHex(2)Hex(3)HexNAc(3) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3) (S)">dHex(2)Hex(3)HexNAc(3) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3) (T)">dHex(2)Hex(3)HexNAc(3) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)Pent(1) (N)">dHex(2)Hex(3)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)Pent(2) (N)">dHex(2)Hex(3)HexNAc(3)Pent(2) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4) (N)">dHex(2)Hex(3)HexNAc(4) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4) (S)">dHex(2)Hex(3)HexNAc(4) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4) (T)">dHex(2)Hex(3)HexNAc(4) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4)Pent(1) (N)">dHex(2)Hex(3)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4)Pent(2) (N)">dHex(2)Hex(3)HexNAc(4)Pent(2) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(5) (N)">dHex(2)Hex(3)HexNAc(5) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(5) (S)">dHex(2)Hex(3)HexNAc(5) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(5) (T)">dHex(2)Hex(3)HexNAc(5) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(6) (N)">dHex(2)Hex(3)HexNAc(6) (N)</option>
-      <option value="dHex(2)Hex(4) (S)">dHex(2)Hex(4) (S)</option>
-      <option value="dHex(2)Hex(4) (T)">dHex(2)Hex(4) (T)</option>
-      <option value="dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(4)HexNAc(1) (S)">dHex(2)Hex(4)HexNAc(1) (S)</option>
-      <option value="dHex(2)Hex(4)HexNAc(1) (T)">dHex(2)Hex(4)HexNAc(1) (T)</option>
-      <option value="dHex(2)Hex(4)HexNAc(2) (N)">dHex(2)Hex(4)HexNAc(2) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(2) (S)">dHex(2)Hex(4)HexNAc(2) (S)</option>
-      <option value="dHex(2)Hex(4)HexNAc(2) (T)">dHex(2)Hex(4)HexNAc(2) (T)</option>
-      <option value="dHex(2)Hex(4)HexNAc(3) (N)">dHex(2)Hex(4)HexNAc(3) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(3)Pent(1) (N)">dHex(2)Hex(4)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4) (N)">dHex(2)Hex(4)HexNAc(4) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4) (S)">dHex(2)Hex(4)HexNAc(4) (S)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4) (T)">dHex(2)Hex(4)HexNAc(4) (T)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4)Pent(1) (N)">dHex(2)Hex(4)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(2)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(5) (N)">dHex(2)Hex(4)HexNAc(5) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(5) (S)">dHex(2)Hex(4)HexNAc(5) (S)</option>
-      <option value="dHex(2)Hex(4)HexNAc(5) (T)">dHex(2)Hex(4)HexNAc(5) (T)</option>
-      <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (S)">dHex(2)Hex(5)HexNAc(2)Me(1) (S)</option>
-      <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (T)">dHex(2)Hex(5)HexNAc(2)Me(1) (T)</option>
-      <option value="dHex(2)Hex(5)HexNAc(3)Pent(1) (N)">dHex(2)Hex(5)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(5)HexNAc(4) (N)">dHex(2)Hex(5)HexNAc(4) (N)</option>
-      <option value="dHex(2)HexNAc(2)Kdn(1) (S)">dHex(2)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(2)HexNAc(2)Kdn(1) (T)">dHex(2)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(2)HexNAc(5) (S)">dHex(2)HexNAc(5) (S)</option>
-      <option value="dHex(2)HexNAc(5) (T)">dHex(2)HexNAc(5) (T)</option>
-      <option value="dHex(2)HexNAc(7) (S)">dHex(2)HexNAc(7) (S)</option>
-      <option value="dHex(2)HexNAc(7) (T)">dHex(2)HexNAc(7) (T)</option>
-      <option value="dHex(3)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(3)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(3)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(3)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(3)Hex(1)HexNAc(3)Kdn(1) (S)">dHex(3)Hex(1)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(3)Hex(1)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(1)HexNAc(3)Kdn(1) (T)</option>
-      <option value="dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(2) (S)">dHex(3)Hex(2)HexNAc(2) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(2) (T)">dHex(3)Hex(2)HexNAc(2) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(3)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(3) (S)">dHex(3)Hex(2)HexNAc(3) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(3) (T)">dHex(3)Hex(2)HexNAc(3) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (S)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(4) (S)">dHex(3)Hex(2)HexNAc(4) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(4) (T)">dHex(3)Hex(2)HexNAc(4) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(1) (S)">dHex(3)Hex(3)HexNAc(1) (S)</option>
-      <option value="dHex(3)Hex(3)HexNAc(1) (T)">dHex(3)Hex(3)HexNAc(1) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(2) (S)">dHex(3)Hex(3)HexNAc(2) (S)</option>
-      <option value="dHex(3)Hex(3)HexNAc(2) (T)">dHex(3)Hex(3)HexNAc(2) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3) (S)">dHex(3)Hex(3)HexNAc(3) (S)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3) (T)">dHex(3)Hex(3)HexNAc(3) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3)Pent(1) (N)">dHex(3)Hex(3)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(3)Hex(3)HexNAc(4) (N)">dHex(3)Hex(3)HexNAc(4) (N)</option>
-      <option value="dHex(3)Hex(3)HexNAc(4)Pent(1) (N)">dHex(3)Hex(3)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(3)Hex(4)HexNAc(4) (N)">dHex(3)Hex(4)HexNAc(4) (N)</option>
-      <option value="dHex(3)Hex(4)HexNAc(4) (S)">dHex(3)Hex(4)HexNAc(4) (S)</option>
-      <option value="dHex(3)Hex(4)HexNAc(4) (T)">dHex(3)Hex(4)HexNAc(4) (T)</option>
-      <option value="dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(3)HexNAc(3)Kdn(1) (S)">dHex(3)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(3)HexNAc(3)Kdn(1) (T)">dHex(3)HexNAc(3)Kdn(1) (T)</option>
-      <option value="dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)">dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)</option>
-      <option value="dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)">dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)</option>
-      <option value="dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)">dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)">dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)</option>
-      <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(4)Hex(2)HexNAc(3) (S)">dHex(4)Hex(2)HexNAc(3) (S)</option>
-      <option value="dHex(4)Hex(2)HexNAc(3) (T)">dHex(4)Hex(2)HexNAc(3) (T)</option>
-      <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="dHex(4)Hex(3)HexNAc(3) (S)">dHex(4)Hex(3)HexNAc(3) (S)</option>
-      <option value="dHex(4)Hex(3)HexNAc(3) (T)">dHex(4)Hex(3)HexNAc(3) (T)</option>
-      <option value="dHex(4)HexNAc(3)Kdn(1) (S)">dHex(4)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(4)HexNAc(3)Kdn(1) (T)">dHex(4)HexNAc(3)Kdn(1) (T)</option>
-      <option value="DHP (C)">DHP (C)</option>
-      <option value="Diacylglycerol (C)">Diacylglycerol (C)</option>
-      <option value="DiART6plex (K)">DiART6plex (K)</option>
-      <option value="DiART6plex (N-term)">DiART6plex (N-term)</option>
-      <option value="DiART6plex (Protein N-term)">DiART6plex (Protein N-term)</option>
-      <option value="DiART6plex (Y)">DiART6plex (Y)</option>
-      <option value="DiART6plex115 (K)">DiART6plex115 (K)</option>
-      <option value="DiART6plex115 (N-term)">DiART6plex115 (N-term)</option>
-      <option value="DiART6plex115 (Protein N-term)">DiART6plex115 (Protein N-term)</option>
-      <option value="DiART6plex115 (Y)">DiART6plex115 (Y)</option>
-      <option value="DiART6plex116/119 (K)">DiART6plex116/119 (K)</option>
-      <option value="DiART6plex116/119 (N-term)">DiART6plex116/119 (N-term)</option>
-      <option value="DiART6plex116/119 (Protein N-term)">DiART6plex116/119 (Protein N-term)</option>
-      <option value="DiART6plex116/119 (Y)">DiART6plex116/119 (Y)</option>
-      <option value="DiART6plex117 (K)">DiART6plex117 (K)</option>
-      <option value="DiART6plex117 (N-term)">DiART6plex117 (N-term)</option>
-      <option value="DiART6plex117 (Protein N-term)">DiART6plex117 (Protein N-term)</option>
-      <option value="DiART6plex117 (Y)">DiART6plex117 (Y)</option>
-      <option value="DiART6plex118 (K)">DiART6plex118 (K)</option>
-      <option value="DiART6plex118 (N-term)">DiART6plex118 (N-term)</option>
-      <option value="DiART6plex118 (Protein N-term)">DiART6plex118 (Protein N-term)</option>
-      <option value="DiART6plex118 (Y)">DiART6plex118 (Y)</option>
-      <option value="Dibromo (Y)">Dibromo (Y)</option>
-      <option value="Dicarbamidomethyl (C)">Dicarbamidomethyl (C)</option>
-      <option value="Dicarbamidomethyl (H)">Dicarbamidomethyl (H)</option>
-      <option value="Dicarbamidomethyl (K)">Dicarbamidomethyl (K)</option>
-      <option value="Dicarbamidomethyl (N-term)">Dicarbamidomethyl (N-term)</option>
-      <option value="Dicarbamidomethyl (R)">Dicarbamidomethyl (R)</option>
-      <option value="dichlorination (C)">dichlorination (C)</option>
-      <option value="dichlorination (Y)">dichlorination (Y)</option>
-      <option value="Didehydro (C-term K)">Didehydro (C-term K)</option>
-      <option value="Didehydro (S)">Didehydro (S)</option>
-      <option value="Didehydro (T)">Didehydro (T)</option>
-      <option value="Didehydro (Y)">Didehydro (Y)</option>
-      <option value="Didehydroretinylidene (K)">Didehydroretinylidene (K)</option>
-      <option value="Diethyl (K)">Diethyl (K)</option>
-      <option value="Diethyl (N-term)">Diethyl (N-term)</option>
-      <option value="Diethylphosphate (C)">Diethylphosphate (C)</option>
-      <option value="Diethylphosphate (H)">Diethylphosphate (H)</option>
-      <option value="Diethylphosphate (K)">Diethylphosphate (K)</option>
-      <option value="Diethylphosphate (N-term)">Diethylphosphate (N-term)</option>
-      <option value="Diethylphosphate (S)">Diethylphosphate (S)</option>
-      <option value="Diethylphosphate (T)">Diethylphosphate (T)</option>
-      <option value="Diethylphosphate (Y)">Diethylphosphate (Y)</option>
-      <option value="Diethylphosphothione (C)">Diethylphosphothione (C)</option>
-      <option value="Diethylphosphothione (H)">Diethylphosphothione (H)</option>
-      <option value="Diethylphosphothione (K)">Diethylphosphothione (K)</option>
-      <option value="Diethylphosphothione (S)">Diethylphosphothione (S)</option>
-      <option value="Diethylphosphothione (T)">Diethylphosphothione (T)</option>
-      <option value="Diethylphosphothione (Y)">Diethylphosphothione (Y)</option>
-      <option value="Difuran (Y)">Difuran (Y)</option>
-      <option value="Dihydroxyimidazolidine (R)">Dihydroxyimidazolidine (R)</option>
-      <option value="Diiodo (H)">Diiodo (H)</option>
-      <option value="Diiodo (Y)">Diiodo (Y)</option>
-      <option value="Diironsubcluster (C)">Diironsubcluster (C)</option>
-      <option value="Diisopropylphosphate (K)">Diisopropylphosphate (K)</option>
-      <option value="Diisopropylphosphate (N-term)">Diisopropylphosphate (N-term)</option>
-      <option value="Diisopropylphosphate (S)">Diisopropylphosphate (S)</option>
-      <option value="Diisopropylphosphate (T)">Diisopropylphosphate (T)</option>
-      <option value="Diisopropylphosphate (Y)">Diisopropylphosphate (Y)</option>
-      <option value="DiLeu4plex (K)">DiLeu4plex (K)</option>
-      <option value="DiLeu4plex (N-term)">DiLeu4plex (N-term)</option>
-      <option value="DiLeu4plex (Y)">DiLeu4plex (Y)</option>
-      <option value="DiLeu4plex115 (K)">DiLeu4plex115 (K)</option>
-      <option value="DiLeu4plex115 (N-term)">DiLeu4plex115 (N-term)</option>
-      <option value="DiLeu4plex115 (Y)">DiLeu4plex115 (Y)</option>
-      <option value="DiLeu4plex117 (K)">DiLeu4plex117 (K)</option>
-      <option value="DiLeu4plex117 (N-term)">DiLeu4plex117 (N-term)</option>
-      <option value="DiLeu4plex117 (Y)">DiLeu4plex117 (Y)</option>
-      <option value="DiLeu4plex118 (K)">DiLeu4plex118 (K)</option>
-      <option value="DiLeu4plex118 (N-term)">DiLeu4plex118 (N-term)</option>
-      <option value="DiLeu4plex118 (Y)">DiLeu4plex118 (Y)</option>
-      <option value="Dimethyl (K)">Dimethyl (K)</option>
-      <option value="Dimethyl (N)">Dimethyl (N)</option>
-      <option value="Dimethyl (N-term)">Dimethyl (N-term)</option>
-      <option value="Dimethyl (Protein N-term P)">Dimethyl (Protein N-term P)</option>
-      <option value="Dimethyl (Protein N-term)">Dimethyl (Protein N-term)</option>
-      <option value="Dimethyl (R)">Dimethyl (R)</option>
-      <option value="Dimethyl:2H(2)13C (K)">Dimethyl:2H(2)13C (K)</option>
-      <option value="Dimethyl:2H(2)13C (N)">Dimethyl:2H(2)13C (N)</option>
-      <option value="Dimethyl:2H(2)13C (N-term)">Dimethyl:2H(2)13C (N-term)</option>
-      <option value="Dimethyl:2H(2)13C (Protein N-term P)">Dimethyl:2H(2)13C (Protein N-term P)</option>
-      <option value="Dimethyl:2H(2)13C (R)">Dimethyl:2H(2)13C (R)</option>
-      <option value="Dimethyl:2H(4) (K)">Dimethyl:2H(4) (K)</option>
-      <option value="Dimethyl:2H(4) (N-term)">Dimethyl:2H(4) (N-term)</option>
-      <option value="Dimethyl:2H(4) (Protein N-term)">Dimethyl:2H(4) (Protein N-term)</option>
-      <option value="Dimethyl:2H(4) (R)">Dimethyl:2H(4) (R)</option>
-      <option value="Dimethyl:2H(4)13C(2) (K)">Dimethyl:2H(4)13C(2) (K)</option>
-      <option value="Dimethyl:2H(4)13C(2) (N-term)">Dimethyl:2H(4)13C(2) (N-term)</option>
-      <option value="Dimethyl:2H(4)13C(2) (Protein N-term)">Dimethyl:2H(4)13C(2) (Protein N-term)</option>
-      <option value="Dimethyl:2H(4)13C(2) (R)">Dimethyl:2H(4)13C(2) (R)</option>
-      <option value="Dimethyl:2H(6) (K)">Dimethyl:2H(6) (K)</option>
-      <option value="Dimethyl:2H(6) (N-term)">Dimethyl:2H(6) (N-term)</option>
-      <option value="Dimethyl:2H(6) (R)">Dimethyl:2H(6) (R)</option>
-      <option value="Dimethyl:2H(6)13C(2) (K)">Dimethyl:2H(6)13C(2) (K)</option>
-      <option value="Dimethyl:2H(6)13C(2) (N-term)">Dimethyl:2H(6)13C(2) (N-term)</option>
-      <option value="Dimethyl:2H(6)13C(2) (Protein N-term)">Dimethyl:2H(6)13C(2) (Protein N-term)</option>
-      <option value="Dimethyl:2H(6)13C(2) (R)">Dimethyl:2H(6)13C(2) (R)</option>
-      <option value="DimethylamineGMBS (C)">DimethylamineGMBS (C)</option>
-      <option value="Dimethylaminoethyl (C)">Dimethylaminoethyl (C)</option>
-      <option value="DimethylArsino (C)">DimethylArsino (C)</option>
-      <option value="Dimethylphosphothione (C)">Dimethylphosphothione (C)</option>
-      <option value="Dimethylphosphothione (H)">Dimethylphosphothione (H)</option>
-      <option value="Dimethylphosphothione (K)">Dimethylphosphothione (K)</option>
-      <option value="Dimethylphosphothione (S)">Dimethylphosphothione (S)</option>
-      <option value="Dimethylphosphothione (T)">Dimethylphosphothione (T)</option>
-      <option value="Dimethylphosphothione (Y)">Dimethylphosphothione (Y)</option>
-      <option value="DimethylpyrroleAdduct (K)">DimethylpyrroleAdduct (K)</option>
-      <option value="Dioxidation (C)">Dioxidation (C)</option>
-      <option value="Dioxidation (E)">Dioxidation (E)</option>
-      <option value="Dioxidation (F)">Dioxidation (F)</option>
-      <option value="Dioxidation (I)">Dioxidation (I)</option>
-      <option value="Dioxidation (K)">Dioxidation (K)</option>
-      <option value="Dioxidation (L)">Dioxidation (L)</option>
-      <option value="Dioxidation (M)">Dioxidation (M)</option>
-      <option value="Dioxidation (P)">Dioxidation (P)</option>
-      <option value="Dioxidation (R)">Dioxidation (R)</option>
-      <option value="Dioxidation (U)">Dioxidation (U)</option>
-      <option value="Dioxidation (V)">Dioxidation (V)</option>
-      <option value="Dioxidation (W)">Dioxidation (W)</option>
-      <option value="Dioxidation (Y)">Dioxidation (Y)</option>
-      <option value="Diphthamide (H)">Diphthamide (H)</option>
-      <option value="Dipyridyl (C)">Dipyridyl (C)</option>
-      <option value="Dipyrrolylmethanemethyl (C)">Dipyrrolylmethanemethyl (C)</option>
-      <option value="DMPO (C)">DMPO (C)</option>
-      <option value="DMPO (H)">DMPO (H)</option>
-      <option value="DMPO (Y)">DMPO (Y)</option>
-      <option value="DNCB_hapten (C)">DNCB_hapten (C)</option>
-      <option value="DNCB_hapten (H)">DNCB_hapten (H)</option>
-      <option value="DNCB_hapten (K)">DNCB_hapten (K)</option>
-      <option value="DNCB_hapten (Y)">DNCB_hapten (Y)</option>
-      <option value="dNIC (K)">dNIC (K)</option>
-      <option value="dNIC (N-term)">dNIC (N-term)</option>
-      <option value="DNPS (C)">DNPS (C)</option>
-      <option value="DNPS (W)">DNPS (W)</option>
-      <option value="DTT (C)">DTT (C)</option>
-      <option value="DyLight-maleimide (C)">DyLight-maleimide (C)</option>
-      <option value="DYn-2 (C)">DYn-2 (C)</option>
-      <option value="EDEDTIDVFQQQTGG (K)">EDEDTIDVFQQQTGG (K)</option>
-      <option value="EDT-iodoacetyl-PEO-biotin (S)">EDT-iodoacetyl-PEO-biotin (S)</option>
-      <option value="EDT-iodoacetyl-PEO-biotin (T)">EDT-iodoacetyl-PEO-biotin (T)</option>
-      <option value="EDT-maleimide-PEO-biotin (S)">EDT-maleimide-PEO-biotin (S)</option>
-      <option value="EDT-maleimide-PEO-biotin (T)">EDT-maleimide-PEO-biotin (T)</option>
-      <option value="EEEDVIEVYQEQTGG (K)">EEEDVIEVYQEQTGG (K)</option>
-      <option value="EGCG1 (C)">EGCG1 (C)</option>
-      <option value="EGCG2 (C)">EGCG2 (C)</option>
-      <option value="EHD-diphenylpentanone (C)">EHD-diphenylpentanone (C)</option>
-      <option value="EHD-diphenylpentanone (M)">EHD-diphenylpentanone (M)</option>
-      <option value="EQAT (C)">EQAT (C)</option>
-      <option value="EQAT:2H(5) (C)">EQAT:2H(5) (C)</option>
-      <option value="EQIGG (K)">EQIGG (K)</option>
-      <option value="ESP (K)">ESP (K)</option>
-      <option value="ESP (N-term)">ESP (N-term)</option>
-      <option value="ESP:2H(10) (K)">ESP:2H(10) (K)</option>
-      <option value="ESP:2H(10) (N-term)">ESP:2H(10) (N-term)</option>
-      <option value="Ethanedithiol (S)">Ethanedithiol (S)</option>
-      <option value="Ethanedithiol (T)">Ethanedithiol (T)</option>
-      <option value="Ethanolamine (C)">Ethanolamine (C)</option>
-      <option value="Ethanolamine (C-term)">Ethanolamine (C-term)</option>
-      <option value="Ethanolamine (D)">Ethanolamine (D)</option>
-      <option value="Ethanolamine (E)">Ethanolamine (E)</option>
-      <option value="Ethanolyl (C)">Ethanolyl (C)</option>
-      <option value="Ethanolyl (K)">Ethanolyl (K)</option>
-      <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-      <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
-      <option value="Ethyl (C-term)">Ethyl (C-term)</option>
-      <option value="Ethyl (D)">Ethyl (D)</option>
-      <option value="Ethyl (E)">Ethyl (E)</option>
-      <option value="Ethyl (K)">Ethyl (K)</option>
-      <option value="Ethyl (N-term)">Ethyl (N-term)</option>
-      <option value="Ethyl (Protein N-term)">Ethyl (Protein N-term)</option>
-      <option value="Ethyl+Deamidated (N)">Ethyl+Deamidated (N)</option>
-      <option value="Ethyl+Deamidated (Q)">Ethyl+Deamidated (Q)</option>
-      <option value="ethylamino (S)">ethylamino (S)</option>
-      <option value="ethylamino (T)">ethylamino (T)</option>
-      <option value="Ethylphosphate (K)">Ethylphosphate (K)</option>
-      <option value="Ethylphosphate (N-term)">Ethylphosphate (N-term)</option>
-      <option value="Ethylphosphate (S)">Ethylphosphate (S)</option>
-      <option value="Ethylphosphate (T)">Ethylphosphate (T)</option>
-      <option value="Ethylphosphate (Y)">Ethylphosphate (Y)</option>
-      <option value="ethylsulfonylethyl (C)">ethylsulfonylethyl (C)</option>
-      <option value="ethylsulfonylethyl (H)">ethylsulfonylethyl (H)</option>
-      <option value="ethylsulfonylethyl (K)">ethylsulfonylethyl (K)</option>
-      <option value="ExacTagAmine (K)">ExacTagAmine (K)</option>
-      <option value="ExacTagThiol (C)">ExacTagThiol (C)</option>
-      <option value="FAD (C)">FAD (C)</option>
-      <option value="FAD (H)">FAD (H)</option>
-      <option value="FAD (Y)">FAD (Y)</option>
-      <option value="Farnesyl (C)">Farnesyl (C)</option>
-      <option value="Fluorescein (C)">Fluorescein (C)</option>
-      <option value="Fluorescein-tyramine (Y)">Fluorescein-tyramine (Y)</option>
-      <option value="Fluoro (A)">Fluoro (A)</option>
-      <option value="Fluoro (F)">Fluoro (F)</option>
-      <option value="Fluoro (W)">Fluoro (W)</option>
-      <option value="Fluoro (Y)">Fluoro (Y)</option>
-      <option value="FMN (S)">FMN (S)</option>
-      <option value="FMN (T)">FMN (T)</option>
-      <option value="FMNC (C)">FMNC (C)</option>
-      <option value="FMNH (C)">FMNH (C)</option>
-      <option value="FMNH (H)">FMNH (H)</option>
-      <option value="FNEM (C)">FNEM (C)</option>
-      <option value="Formyl (K)">Formyl (K)</option>
-      <option value="Formyl (N-term)">Formyl (N-term)</option>
-      <option value="Formyl (Protein N-term)">Formyl (Protein N-term)</option>
-      <option value="Formyl (S)">Formyl (S)</option>
-      <option value="Formyl (T)">Formyl (T)</option>
-      <option value="Formylasparagine (H)">Formylasparagine (H)</option>
-      <option value="FormylMet (Protein N-term)">FormylMet (Protein N-term)</option>
-      <option value="FP-Biotin (K)">FP-Biotin (K)</option>
-      <option value="FP-Biotin (S)">FP-Biotin (S)</option>
-      <option value="FP-Biotin (T)">FP-Biotin (T)</option>
-      <option value="FP-Biotin (Y)">FP-Biotin (Y)</option>
-      <option value="FTC (C)">FTC (C)</option>
-      <option value="FTC (K)">FTC (K)</option>
-      <option value="FTC (P)">FTC (P)</option>
-      <option value="FTC (R)">FTC (R)</option>
-      <option value="FTC (S)">FTC (S)</option>
-      <option value="Furan (Y)">Furan (Y)</option>
-      <option value="G-H1 (R)">G-H1 (R)</option>
-      <option value="Galactosyl (K)">Galactosyl (K)</option>
-      <option value="Galactosyl (N-term)">Galactosyl (N-term)</option>
-      <option value="GEE (Q)">GEE (Q)</option>
-      <option value="GeranylGeranyl (C)">GeranylGeranyl (C)</option>
-      <option value="GG (C)">GG (C)</option>
-      <option value="GG (K)">GG (K)</option>
-      <option value="GG (Protein N-term)">GG (Protein N-term)</option>
-      <option value="GG (S)">GG (S)</option>
-      <option value="GG (T)">GG (T)</option>
-      <option value="GGQ (K)">GGQ (K)</option>
-      <option value="GIST-Quat (K)">GIST-Quat (K)</option>
-      <option value="GIST-Quat (N-term)">GIST-Quat (N-term)</option>
-      <option value="GIST-Quat:2H(3) (K)">GIST-Quat:2H(3) (K)</option>
-      <option value="GIST-Quat:2H(3) (N-term)">GIST-Quat:2H(3) (N-term)</option>
-      <option value="GIST-Quat:2H(6) (K)">GIST-Quat:2H(6) (K)</option>
-      <option value="GIST-Quat:2H(6) (N-term)">GIST-Quat:2H(6) (N-term)</option>
-      <option value="GIST-Quat:2H(9) (K)">GIST-Quat:2H(9) (K)</option>
-      <option value="GIST-Quat:2H(9) (N-term)">GIST-Quat:2H(9) (N-term)</option>
-      <option value="Gln-&gt;Ala (Q)">Gln-&gt;Ala (Q)</option>
-      <option value="Gln-&gt;Arg (Q)">Gln-&gt;Arg (Q)</option>
-      <option value="Gln-&gt;Asn (Q)">Gln-&gt;Asn (Q)</option>
-      <option value="Gln-&gt;Asp (Q)">Gln-&gt;Asp (Q)</option>
-      <option value="Gln-&gt;Cys (Q)">Gln-&gt;Cys (Q)</option>
-      <option value="Gln-&gt;Glu (Q)">Gln-&gt;Glu (Q)</option>
-      <option value="Gln-&gt;Gly (Q)">Gln-&gt;Gly (Q)</option>
-      <option value="Gln-&gt;His (Q)">Gln-&gt;His (Q)</option>
-      <option value="Gln-&gt;Lys (Q)">Gln-&gt;Lys (Q)</option>
-      <option value="Gln-&gt;Met (Q)">Gln-&gt;Met (Q)</option>
-      <option value="Gln-&gt;Phe (Q)">Gln-&gt;Phe (Q)</option>
-      <option value="Gln-&gt;Pro (Q)">Gln-&gt;Pro (Q)</option>
-      <option value="Gln-&gt;pyro-Glu (N-term Q)">Gln-&gt;pyro-Glu (N-term Q)</option>
-      <option value="Gln-&gt;Ser (Q)">Gln-&gt;Ser (Q)</option>
-      <option value="Gln-&gt;Thr (Q)">Gln-&gt;Thr (Q)</option>
-      <option value="Gln-&gt;Trp (Q)">Gln-&gt;Trp (Q)</option>
-      <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
-      <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
-      <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
-      <option value="Glu (E)">Glu (E)</option>
-      <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
-      <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
-      <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
-      <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
-      <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
-      <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
-      <option value="Glu-&gt;Gln (E)">Glu-&gt;Gln (E)</option>
-      <option value="Glu-&gt;Gly (E)">Glu-&gt;Gly (E)</option>
-      <option value="Glu-&gt;His (E)">Glu-&gt;His (E)</option>
-      <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
-      <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
-      <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
-      <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
-      <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
-      <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
-      <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
-      <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
-      <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
-      <option value="Glu-&gt;Val (E)">Glu-&gt;Val (E)</option>
-      <option value="Glu-&gt;Xle (E)">Glu-&gt;Xle (E)</option>
-      <option value="glucosone (R)">glucosone (R)</option>
-      <option value="Glucosylgalactosyl (K)">Glucosylgalactosyl (K)</option>
-      <option value="Glucuronyl (Protein N-term)">Glucuronyl (Protein N-term)</option>
-      <option value="Glucuronyl (S)">Glucuronyl (S)</option>
-      <option value="Glucuronyl (T)">Glucuronyl (T)</option>
-      <option value="GluGlu (E)">GluGlu (E)</option>
-      <option value="GluGlu (Protein C-term)">GluGlu (Protein C-term)</option>
-      <option value="GluGluGlu (E)">GluGluGlu (E)</option>
-      <option value="GluGluGlu (Protein C-term)">GluGluGlu (Protein C-term)</option>
-      <option value="GluGluGluGlu (E)">GluGluGluGlu (E)</option>
-      <option value="GluGluGluGlu (Protein C-term)">GluGluGluGlu (Protein C-term)</option>
-      <option value="Gluratylation (K)">Gluratylation (K)</option>
-      <option value="Glutathione (C)">Glutathione (C)</option>
-      <option value="Gly (K)">Gly (K)</option>
-      <option value="Gly (S)">Gly (S)</option>
-      <option value="Gly (T)">Gly (T)</option>
-      <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
-      <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
-      <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
-      <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
-      <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
-      <option value="Gly-&gt;Gln (G)">Gly-&gt;Gln (G)</option>
-      <option value="Gly-&gt;Glu (G)">Gly-&gt;Glu (G)</option>
-      <option value="Gly-&gt;His (G)">Gly-&gt;His (G)</option>
-      <option value="Gly-&gt;Lys (G)">Gly-&gt;Lys (G)</option>
-      <option value="Gly-&gt;Met (G)">Gly-&gt;Met (G)</option>
-      <option value="Gly-&gt;Phe (G)">Gly-&gt;Phe (G)</option>
-      <option value="Gly-&gt;Pro (G)">Gly-&gt;Pro (G)</option>
-      <option value="Gly-&gt;Ser (G)">Gly-&gt;Ser (G)</option>
-      <option value="Gly-&gt;Thr (G)">Gly-&gt;Thr (G)</option>
-      <option value="Gly-&gt;Trp (G)">Gly-&gt;Trp (G)</option>
-      <option value="Gly-&gt;Tyr (G)">Gly-&gt;Tyr (G)</option>
-      <option value="Gly-&gt;Val (G)">Gly-&gt;Val (G)</option>
-      <option value="Gly-&gt;Xle (G)">Gly-&gt;Xle (G)</option>
-      <option value="Gly-loss+Amide (C-term G)">Gly-loss+Amide (C-term G)</option>
-      <option value="Glycerophospho (S)">Glycerophospho (S)</option>
-      <option value="GlycerylPE (E)">GlycerylPE (E)</option>
-      <option value="glycidamide (K)">glycidamide (K)</option>
-      <option value="glycidamide (N-term)">glycidamide (N-term)</option>
-      <option value="Glycosyl (P)">Glycosyl (P)</option>
-      <option value="glyoxalAGE (R)">glyoxalAGE (R)</option>
-      <option value="GNLLFLACYCIGG (K)">GNLLFLACYCIGG (K)</option>
-      <option value="GPIanchor (Protein C-term)">GPIanchor (Protein C-term)</option>
-      <option value="Guanidinyl (K)">Guanidinyl (K)</option>
-      <option value="Guanidinyl (N-term)">Guanidinyl (N-term)</option>
-      <option value="Haloxon (C)">Haloxon (C)</option>
-      <option value="Haloxon (H)">Haloxon (H)</option>
-      <option value="Haloxon (K)">Haloxon (K)</option>
-      <option value="Haloxon (S)">Haloxon (S)</option>
-      <option value="Haloxon (T)">Haloxon (T)</option>
-      <option value="Haloxon (Y)">Haloxon (Y)</option>
-      <option value="HCysteinyl (C)">HCysteinyl (C)</option>
-      <option value="HCysThiolactone (K)">HCysThiolactone (K)</option>
-      <option value="Heme (C)">Heme (C)</option>
-      <option value="Heme (H)">Heme (H)</option>
-      <option value="Hep (K)">Hep (K)</option>
-      <option value="Hep (N)">Hep (N)</option>
-      <option value="Hep (Q)">Hep (Q)</option>
-      <option value="Hep (R)">Hep (R)</option>
-      <option value="Hep (S)">Hep (S)</option>
-      <option value="Hep (T)">Hep (T)</option>
-      <option value="Hex (C)">Hex (C)</option>
-      <option value="Hex (K)">Hex (K)</option>
-      <option value="Hex (N)">Hex (N)</option>
-      <option value="Hex (N-term)">Hex (N-term)</option>
-      <option value="Hex (R)">Hex (R)</option>
-      <option value="Hex (S)">Hex (S)</option>
-      <option value="Hex (T)">Hex (T)</option>
-      <option value="Hex (W)">Hex (W)</option>
-      <option value="Hex (Y)">Hex (Y)</option>
-      <option value="Hex(1)HexA(1) (S)">Hex(1)HexA(1) (S)</option>
-      <option value="Hex(1)HexA(1) (T)">Hex(1)HexA(1) (T)</option>
-      <option value="Hex(1)HexA(1)HexNAc(1) (S)">Hex(1)HexA(1)HexNAc(1) (S)</option>
-      <option value="Hex(1)HexA(1)HexNAc(1) (T)">Hex(1)HexA(1)HexNAc(1) (T)</option>
-      <option value="Hex(1)HexA(1)HexNAc(2) (S)">Hex(1)HexA(1)HexNAc(2) (S)</option>
-      <option value="Hex(1)HexA(1)HexNAc(2) (T)">Hex(1)HexA(1)HexNAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(1) (N)">Hex(1)HexNAc(1) (N)</option>
-      <option value="Hex(1)HexNAc(1) (S)">Hex(1)HexNAc(1) (S)</option>
-      <option value="Hex(1)HexNAc(1) (T)">Hex(1)HexNAc(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1) (N)">Hex(1)HexNAc(1)dHex(1) (N)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1) (S)">Hex(1)HexNAc(1)dHex(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1) (T)">Hex(1)HexNAc(1)dHex(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1)Me(1) (S)">Hex(1)HexNAc(1)dHex(1)Me(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1)Me(1) (T)">Hex(1)HexNAc(1)dHex(1)Me(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1)Me(2) (S)">Hex(1)HexNAc(1)dHex(1)Me(2) (S)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1)Me(2) (T)">Hex(1)HexNAc(1)dHex(1)Me(2) (T)</option>
-      <option value="Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S)">Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T)">Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1) (N)">Hex(1)HexNAc(1)NeuAc(1) (N)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1) (S)">Hex(1)HexNAc(1)NeuAc(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1) (T)">Hex(1)HexNAc(1)NeuAc(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S)">Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T)">Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S)">Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T)">Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T)">Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2) (N)">Hex(1)HexNAc(1)NeuAc(2) (N)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2) (S)">Hex(1)HexNAc(1)NeuAc(2) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2) (T)">Hex(1)HexNAc(1)NeuAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S)">Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T)">Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S)">Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T)">Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(3) (S)">Hex(1)HexNAc(1)NeuAc(3) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(3) (T)">Hex(1)HexNAc(1)NeuAc(3) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(1) (S)">Hex(1)HexNAc(1)NeuGc(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(1) (T)">Hex(1)HexNAc(1)NeuGc(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(2) (S)">Hex(1)HexNAc(1)NeuGc(2) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(2) (T)">Hex(1)HexNAc(1)NeuGc(2) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(3) (S)">Hex(1)HexNAc(1)NeuGc(3) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(3) (T)">Hex(1)HexNAc(1)NeuGc(3) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(4) (S)">Hex(1)HexNAc(1)NeuGc(4) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(4) (T)">Hex(1)HexNAc(1)NeuGc(4) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(5) (S)">Hex(1)HexNAc(1)NeuGc(5) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(5) (T)">Hex(1)HexNAc(1)NeuGc(5) (T)</option>
-      <option value="Hex(1)HexNAc(1)Phos(1) (S)">Hex(1)HexNAc(1)Phos(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)Phos(1) (T)">Hex(1)HexNAc(1)Phos(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)Sulf(1) (S)">Hex(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)Sulf(1) (T)">Hex(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(2) (N)">Hex(1)HexNAc(2) (N)</option>
-      <option value="Hex(1)HexNAc(2) (S)">Hex(1)HexNAc(2) (S)</option>
-      <option value="Hex(1)HexNAc(2) (T)">Hex(1)HexNAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(2)dHex(1) (N)">Hex(1)HexNAc(2)dHex(1) (N)</option>
-      <option value="Hex(1)HexNAc(2)dHex(1) (S)">Hex(1)HexNAc(2)dHex(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)dHex(1) (T)">Hex(1)HexNAc(2)dHex(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)dHex(1)Pent(1) (N)">Hex(1)HexNAc(2)dHex(1)Pent(1) (N)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2) (N)">Hex(1)HexNAc(2)dHex(2) (N)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2) (S)">Hex(1)HexNAc(2)dHex(2) (S)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2) (T)">Hex(1)HexNAc(2)dHex(2) (T)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(1) (S)">Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(1) (T)">Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(2) (S)">Hex(1)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(2) (T)">Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T)">Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuGc(1) (S)">Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuGc(1) (T)">Hex(1)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)Pent(1) (N)">Hex(1)HexNAc(2)Pent(1) (N)</option>
-      <option value="Hex(1)HexNAc(2)Sulf(1) (S)">Hex(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)Sulf(1) (T)">Hex(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(3) (S)">Hex(1)HexNAc(3) (S)</option>
-      <option value="Hex(1)HexNAc(3) (T)">Hex(1)HexNAc(3) (T)</option>
-      <option value="Hex(1)HexNAc(3)NeuAc(1) (S)">Hex(1)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="Hex(1)HexNAc(3)NeuAc(1) (T)">Hex(1)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="Hex(1)HexNAc(3)NeuAc(2) (S)">Hex(1)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="Hex(1)HexNAc(3)NeuAc(2) (T)">Hex(1)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(3)NeuGc(1) (S)">Hex(1)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="Hex(1)HexNAc(3)NeuGc(1) (T)">Hex(1)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="Hex(1)HexNAc(3)Sulf(1) (S)">Hex(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(3)Sulf(1) (T)">Hex(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)</option>
-      <option value="Hex(1)NeuAc(1) (S)">Hex(1)NeuAc(1) (S)</option>
-      <option value="Hex(1)NeuAc(1) (T)">Hex(1)NeuAc(1) (T)</option>
-      <option value="Hex(1)NeuAc(1)Pent(1) (S)">Hex(1)NeuAc(1)Pent(1) (S)</option>
-      <option value="Hex(1)NeuAc(1)Pent(1) (T)">Hex(1)NeuAc(1)Pent(1) (T)</option>
-      <option value="Hex(1)NeuGc(1) (S)">Hex(1)NeuGc(1) (S)</option>
-      <option value="Hex(1)NeuGc(1) (T)">Hex(1)NeuGc(1) (T)</option>
-      <option value="Hex(1)Pent(1) (S)">Hex(1)Pent(1) (S)</option>
-      <option value="Hex(1)Pent(1) (T)">Hex(1)Pent(1) (T)</option>
-      <option value="Hex(1)Pent(2) (S)">Hex(1)Pent(2) (S)</option>
-      <option value="Hex(1)Pent(2) (T)">Hex(1)Pent(2) (T)</option>
-      <option value="Hex(1)Pent(2)Me(1) (S)">Hex(1)Pent(2)Me(1) (S)</option>
-      <option value="Hex(1)Pent(2)Me(1) (T)">Hex(1)Pent(2)Me(1) (T)</option>
-      <option value="Hex(1)Pent(3) (S)">Hex(1)Pent(3) (S)</option>
-      <option value="Hex(1)Pent(3) (T)">Hex(1)Pent(3) (T)</option>
-      <option value="Hex(1)Pent(3)Me(1) (S)">Hex(1)Pent(3)Me(1) (S)</option>
-      <option value="Hex(1)Pent(3)Me(1) (T)">Hex(1)Pent(3)Me(1) (T)</option>
-      <option value="Hex(10)HexNAc(1) (N)">Hex(10)HexNAc(1) (N)</option>
-      <option value="Hex(10)Phos(3) (S)">Hex(10)Phos(3) (S)</option>
-      <option value="Hex(10)Phos(3) (T)">Hex(10)Phos(3) (T)</option>
-      <option value="Hex(2) (K)">Hex(2) (K)</option>
-      <option value="Hex(2) (R)">Hex(2) (R)</option>
-      <option value="Hex(2) (S)">Hex(2) (S)</option>
-      <option value="Hex(2) (T)">Hex(2) (T)</option>
-      <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)Pent(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)Pent(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(1) (N)">Hex(2)HexNAc(1) (N)</option>
-      <option value="Hex(2)HexNAc(1) (S)">Hex(2)HexNAc(1) (S)</option>
-      <option value="Hex(2)HexNAc(1) (T)">Hex(2)HexNAc(1) (T)</option>
-      <option value="Hex(2)HexNAc(1)Me(1) (S)">Hex(2)HexNAc(1)Me(1) (S)</option>
-      <option value="Hex(2)HexNAc(1)Me(1) (T)">Hex(2)HexNAc(1)Me(1) (T)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(1) (S)">Hex(2)HexNAc(1)NeuGc(1) (S)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(1) (T)">Hex(2)HexNAc(1)NeuGc(1) (T)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(2) (S)">Hex(2)HexNAc(1)NeuGc(2) (S)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(2) (T)">Hex(2)HexNAc(1)NeuGc(2) (T)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(3) (S)">Hex(2)HexNAc(1)NeuGc(3) (S)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(3) (T)">Hex(2)HexNAc(1)NeuGc(3) (T)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(4) (S)">Hex(2)HexNAc(1)NeuGc(4) (S)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(4) (T)">Hex(2)HexNAc(1)NeuGc(4) (T)</option>
-      <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (S)">Hex(2)HexNAc(1)Pent(1)HexA(1) (S)</option>
-      <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (T)">Hex(2)HexNAc(1)Pent(1)HexA(1) (T)</option>
-      <option value="Hex(2)HexNAc(1)Sulf(1) (S)">Hex(2)HexNAc(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(1)Sulf(1) (T)">Hex(2)HexNAc(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(2) (N)">Hex(2)HexNAc(2) (N)</option>
-      <option value="Hex(2)HexNAc(2) (S)">Hex(2)HexNAc(2) (S)</option>
-      <option value="Hex(2)HexNAc(2) (T)">Hex(2)HexNAc(2) (T)</option>
-      <option value="Hex(2)HexNAc(2)dHex(1) (N)">Hex(2)HexNAc(2)dHex(1) (N)</option>
-      <option value="Hex(2)HexNAc(2)dHex(1) (S)">Hex(2)HexNAc(2)dHex(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)dHex(1) (T)">Hex(2)HexNAc(2)dHex(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1) (N)">Hex(2)HexNAc(2)NeuAc(1) (N)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1) (S)">Hex(2)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1) (T)">Hex(2)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(2) (S)">Hex(2)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(2) (T)">Hex(2)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuGc(1) (S)">Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuGc(1) (T)">Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)Pent(1) (N)">Hex(2)HexNAc(2)Pent(1) (N)</option>
-      <option value="Hex(2)HexNAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(3) (N)">Hex(2)HexNAc(3) (N)</option>
-      <option value="Hex(2)HexNAc(3) (S)">Hex(2)HexNAc(3) (S)</option>
-      <option value="Hex(2)HexNAc(3) (T)">Hex(2)HexNAc(3) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(2) (S)">Hex(2)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(2) (T)">Hex(2)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(3) (S)">Hex(2)HexNAc(3)NeuAc(3) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(3) (T)">Hex(2)HexNAc(3)NeuAc(3) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(1) (T)">Hex(2)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(2) (S)">Hex(2)HexNAc(3)NeuGc(2) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(2) (T)">Hex(2)HexNAc(3)NeuGc(2) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(3) (S)">Hex(2)HexNAc(3)NeuGc(3) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(3) (T)">Hex(2)HexNAc(3)NeuGc(3) (T)</option>
-      <option value="Hex(2)HexNAc(3)Sulf(1) (S)">Hex(2)HexNAc(3)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(3)Sulf(1) (T)">Hex(2)HexNAc(3)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(4) (N)">Hex(2)HexNAc(4) (N)</option>
-      <option value="Hex(2)HexNAc(4) (S)">Hex(2)HexNAc(4) (S)</option>
-      <option value="Hex(2)HexNAc(4) (T)">Hex(2)HexNAc(4) (T)</option>
-      <option value="Hex(2)HexNAc(4)NeuAc(1) (S)">Hex(2)HexNAc(4)NeuAc(1) (S)</option>
-      <option value="Hex(2)HexNAc(4)NeuAc(1) (T)">Hex(2)HexNAc(4)NeuAc(1) (T)</option>
-      <option value="Hex(2)HexNAc(5) (S)">Hex(2)HexNAc(5) (S)</option>
-      <option value="Hex(2)HexNAc(5) (T)">Hex(2)HexNAc(5) (T)</option>
-      <option value="Hex(2)NeuAc(1) (S)">Hex(2)NeuAc(1) (S)</option>
-      <option value="Hex(2)NeuAc(1) (T)">Hex(2)NeuAc(1) (T)</option>
-      <option value="Hex(2)Pent(2) (S)">Hex(2)Pent(2) (S)</option>
-      <option value="Hex(2)Pent(2) (T)">Hex(2)Pent(2) (T)</option>
-      <option value="Hex(2)Pent(2)Me(1) (S)">Hex(2)Pent(2)Me(1) (S)</option>
-      <option value="Hex(2)Pent(2)Me(1) (T)">Hex(2)Pent(2)Me(1) (T)</option>
-      <option value="Hex(2)Sulf(1) (S)">Hex(2)Sulf(1) (S)</option>
-      <option value="Hex(2)Sulf(1) (T)">Hex(2)Sulf(1) (T)</option>
-      <option value="Hex(3) (N)">Hex(3) (N)</option>
-      <option value="Hex(3) (S)">Hex(3) (S)</option>
-      <option value="Hex(3) (T)">Hex(3) (T)</option>
-      <option value="Hex(3)HexNAc(1) (N)">Hex(3)HexNAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(1) (S)">Hex(3)HexNAc(1) (S)</option>
-      <option value="Hex(3)HexNAc(1) (T)">Hex(3)HexNAc(1) (T)</option>
-      <option value="Hex(3)HexNAc(1)HexA(1) (S)">Hex(3)HexNAc(1)HexA(1) (S)</option>
-      <option value="Hex(3)HexNAc(1)HexA(1) (T)">Hex(3)HexNAc(1)HexA(1) (T)</option>
-      <option value="Hex(3)HexNAc(1)Me(1) (S)">Hex(3)HexNAc(1)Me(1) (S)</option>
-      <option value="Hex(3)HexNAc(1)Me(1) (T)">Hex(3)HexNAc(1)Me(1) (T)</option>
-      <option value="Hex(3)HexNAc(1)Pent(1) (N)">Hex(3)HexNAc(1)Pent(1) (N)</option>
-      <option value="Hex(3)HexNAc(2) (N)">Hex(3)HexNAc(2) (N)</option>
-      <option value="Hex(3)HexNAc(2) (S)">Hex(3)HexNAc(2) (S)</option>
-      <option value="Hex(3)HexNAc(2) (T)">Hex(3)HexNAc(2) (T)</option>
-      <option value="Hex(3)HexNAc(2)NeuAc(1) (N)">Hex(3)HexNAc(2)NeuAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(2)NeuAc(2) (S)">Hex(3)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="Hex(3)HexNAc(2)NeuAc(2) (T)">Hex(3)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="Hex(3)HexNAc(2)Pent(1) (N)">Hex(3)HexNAc(2)Pent(1) (N)</option>
-      <option value="Hex(3)HexNAc(2)Phos(1) (N)">Hex(3)HexNAc(2)Phos(1) (N)</option>
-      <option value="Hex(3)HexNAc(3) (N)">Hex(3)HexNAc(3) (N)</option>
-      <option value="Hex(3)HexNAc(3) (S)">Hex(3)HexNAc(3) (S)</option>
-      <option value="Hex(3)HexNAc(3) (T)">Hex(3)HexNAc(3) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(1) (S)">Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(1) (T)">Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(2) (S)">Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(2) (T)">Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(3) (S)">Hex(3)HexNAc(3)NeuAc(3) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(3) (T)">Hex(3)HexNAc(3)NeuAc(3) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuGc(1) (S)">Hex(3)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuGc(1) (T)">Hex(3)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)Pent(1) (N)">Hex(3)HexNAc(3)Pent(1) (N)</option>
-      <option value="Hex(3)HexNAc(3)Sulf(1) (N)">Hex(3)HexNAc(3)Sulf(1) (N)</option>
-      <option value="Hex(3)HexNAc(3)Sulf(1) (S)">Hex(3)HexNAc(3)Sulf(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)Sulf(1) (T)">Hex(3)HexNAc(3)Sulf(1) (T)</option>
-      <option value="Hex(3)HexNAc(4) (N)">Hex(3)HexNAc(4) (N)</option>
-      <option value="Hex(3)HexNAc(4) (S)">Hex(3)HexNAc(4) (S)</option>
-      <option value="Hex(3)HexNAc(4) (T)">Hex(3)HexNAc(4) (T)</option>
-      <option value="Hex(3)HexNAc(4)NeuAc(1) (N)">Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(4)NeuAc(2) (N)">Hex(3)HexNAc(4)NeuAc(2) (N)</option>
-      <option value="Hex(3)HexNAc(4)Pent(1) (N)">Hex(3)HexNAc(4)Pent(1) (N)</option>
-      <option value="Hex(3)HexNAc(4)Sulf(1) (N)">Hex(3)HexNAc(4)Sulf(1) (N)</option>
-      <option value="Hex(3)HexNAc(5) (N)">Hex(3)HexNAc(5) (N)</option>
-      <option value="Hex(3)HexNAc(5) (S)">Hex(3)HexNAc(5) (S)</option>
-      <option value="Hex(3)HexNAc(5) (T)">Hex(3)HexNAc(5) (T)</option>
-      <option value="Hex(3)HexNAc(5)NeuAc(1) (N)">Hex(3)HexNAc(5)NeuAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(5)Sulf(1) (N)">Hex(3)HexNAc(5)Sulf(1) (N)</option>
-      <option value="Hex(3)HexNAc(6) (N)">Hex(3)HexNAc(6) (N)</option>
-      <option value="Hex(3)HexNAc(6) (S)">Hex(3)HexNAc(6) (S)</option>
-      <option value="Hex(3)HexNAc(6) (T)">Hex(3)HexNAc(6) (T)</option>
-      <option value="Hex(3)HexNAc(6)NeuAc(1) (N)">Hex(3)HexNAc(6)NeuAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(6)Sulf(1) (N)">Hex(3)HexNAc(6)Sulf(1) (N)</option>
-      <option value="Hex(3)HexNAc(6)Sulf(2) (N)">Hex(3)HexNAc(6)Sulf(2) (N)</option>
-      <option value="Hex(3)HexNAc(7) (N)">Hex(3)HexNAc(7) (N)</option>
-      <option value="Hex(3)HexNAc(7)Sulf(1) (N)">Hex(3)HexNAc(7)Sulf(1) (N)</option>
-      <option value="Hex(4) (S)">Hex(4) (S)</option>
-      <option value="Hex(4) (T)">Hex(4) (T)</option>
-      <option value="Hex(4)HexA(1) (S)">Hex(4)HexA(1) (S)</option>
-      <option value="Hex(4)HexA(1) (T)">Hex(4)HexA(1) (T)</option>
-      <option value="Hex(4)HexA(1)HexNAc(1) (S)">Hex(4)HexA(1)HexNAc(1) (S)</option>
-      <option value="Hex(4)HexA(1)HexNAc(1) (T)">Hex(4)HexA(1)HexNAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(1) (N)">Hex(4)HexNAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(1) (S)">Hex(4)HexNAc(1) (S)</option>
-      <option value="Hex(4)HexNAc(1) (T)">Hex(4)HexNAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(2) (N)">Hex(4)HexNAc(2) (N)</option>
-      <option value="Hex(4)HexNAc(2)NeuAc(1) (N)">Hex(4)HexNAc(2)NeuAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(2)NeuAc(1) (S)">Hex(4)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="Hex(4)HexNAc(2)NeuAc(1) (T)">Hex(4)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(2)Pent(1) (N)">Hex(4)HexNAc(2)Pent(1) (N)</option>
-      <option value="Hex(4)HexNAc(3) (N)">Hex(4)HexNAc(3) (N)</option>
-      <option value="Hex(4)HexNAc(3) (S)">Hex(4)HexNAc(3) (S)</option>
-      <option value="Hex(4)HexNAc(3) (T)">Hex(4)HexNAc(3) (T)</option>
-      <option value="Hex(4)HexNAc(3)NeuAc(1) (N)">Hex(4)HexNAc(3)NeuAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(3)NeuAc(1) (S)">Hex(4)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="Hex(4)HexNAc(3)NeuAc(1) (T)">Hex(4)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(3)NeuAc(2) (N)">Hex(4)HexNAc(3)NeuAc(2) (N)</option>
-      <option value="Hex(4)HexNAc(3)NeuGc(1) (N)">Hex(4)HexNAc(3)NeuGc(1) (N)</option>
-      <option value="Hex(4)HexNAc(3)Pent(1) (N)">Hex(4)HexNAc(3)Pent(1) (N)</option>
-      <option value="Hex(4)HexNAc(4) (N)">Hex(4)HexNAc(4) (N)</option>
-      <option value="Hex(4)HexNAc(4) (S)">Hex(4)HexNAc(4) (S)</option>
-      <option value="Hex(4)HexNAc(4) (T)">Hex(4)HexNAc(4) (T)</option>
-      <option value="Hex(4)HexNAc(4)Me(2)Pent(1) (N)">Hex(4)HexNAc(4)Me(2)Pent(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1) (N)">Hex(4)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1) (S)">Hex(4)HexNAc(4)NeuAc(1) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1) (T)">Hex(4)HexNAc(4)NeuAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1) (N)">Hex(4)HexNAc(4)NeuGc(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1) (S)">Hex(4)HexNAc(4)NeuGc(1) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1) (T)">Hex(4)HexNAc(4)NeuGc(1) (T)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)</option>
-      <option value="Hex(4)HexNAc(4)Pent(1) (N)">Hex(4)HexNAc(4)Pent(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)Sulf(1) (N)">Hex(4)HexNAc(4)Sulf(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)Sulf(2) (S)">Hex(4)HexNAc(4)Sulf(2) (S)</option>
-      <option value="Hex(4)HexNAc(4)Sulf(2) (T)">Hex(4)HexNAc(4)Sulf(2) (T)</option>
-      <option value="Hex(4)HexNAc(5) (N)">Hex(4)HexNAc(5) (N)</option>
-      <option value="Hex(4)HexNAc(5)NeuAc(1) (N)">Hex(4)HexNAc(5)NeuAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(5)Sulf(1) (N)">Hex(4)HexNAc(5)Sulf(1) (N)</option>
-      <option value="Hex(4)HexNAc(6) (N)">Hex(4)HexNAc(6) (N)</option>
-      <option value="Hex(4)Phos(1) (S)">Hex(4)Phos(1) (S)</option>
-      <option value="Hex(4)Phos(1) (T)">Hex(4)Phos(1) (T)</option>
-      <option value="Hex(5) (S)">Hex(5) (S)</option>
-      <option value="Hex(5) (T)">Hex(5) (T)</option>
-      <option value="Hex(5)HexA(1) (S)">Hex(5)HexA(1) (S)</option>
-      <option value="Hex(5)HexA(1) (T)">Hex(5)HexA(1) (T)</option>
-      <option value="Hex(5)HexNAc(1) (N)">Hex(5)HexNAc(1) (N)</option>
-      <option value="Hex(5)HexNAc(1) (S)">Hex(5)HexNAc(1) (S)</option>
-      <option value="Hex(5)HexNAc(1) (T)">Hex(5)HexNAc(1) (T)</option>
-      <option value="Hex(5)HexNAc(2) (N)">Hex(5)HexNAc(2) (N)</option>
-      <option value="Hex(5)HexNAc(2)Phos(1) (N)">Hex(5)HexNAc(2)Phos(1) (N)</option>
-      <option value="Hex(5)HexNAc(3) (N)">Hex(5)HexNAc(3) (N)</option>
-      <option value="Hex(5)HexNAc(3)Pent(1) (N)">Hex(5)HexNAc(3)Pent(1) (N)</option>
-      <option value="Hex(5)HexNAc(4) (N)">Hex(5)HexNAc(4) (N)</option>
-      <option value="Hex(5)HexNAc(4) (S)">Hex(5)HexNAc(4) (S)</option>
-      <option value="Hex(5)HexNAc(4) (T)">Hex(5)HexNAc(4) (T)</option>
-      <option value="Hex(5)HexNAc(4)Me(2)Pent(1) (N)">Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(1) (N)">Hex(5)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(2) (N)">Hex(5)HexNAc(4)NeuAc(2) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuGc(1) (N)">Hex(5)HexNAc(4)NeuGc(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)Sulf(1) (N)">Hex(5)HexNAc(4)Sulf(1) (N)</option>
-      <option value="Hex(5)HexNAc(5) (N)">Hex(5)HexNAc(5) (N)</option>
-      <option value="Hex(5)HexNAc(5) (S)">Hex(5)HexNAc(5) (S)</option>
-      <option value="Hex(5)HexNAc(5) (T)">Hex(5)HexNAc(5) (T)</option>
-      <option value="Hex(5)Phos(1) (S)">Hex(5)Phos(1) (S)</option>
-      <option value="Hex(5)Phos(1) (T)">Hex(5)Phos(1) (T)</option>
-      <option value="Hex(5)Phos(3) (S)">Hex(5)Phos(3) (S)</option>
-      <option value="Hex(5)Phos(3) (T)">Hex(5)Phos(3) (T)</option>
-      <option value="Hex(6)HexNAc(1) (N)">Hex(6)HexNAc(1) (N)</option>
-      <option value="Hex(6)HexNAc(2) (N)">Hex(6)HexNAc(2) (N)</option>
-      <option value="Hex(6)HexNAc(2)Phos(1) (N)">Hex(6)HexNAc(2)Phos(1) (N)</option>
-      <option value="Hex(6)HexNAc(3) (N)">Hex(6)HexNAc(3) (N)</option>
-      <option value="Hex(6)HexNAc(3)Phos(1) (N)">Hex(6)HexNAc(3)Phos(1) (N)</option>
-      <option value="Hex(6)HexNAc(4) (N)">Hex(6)HexNAc(4) (N)</option>
-      <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
-      <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
-      <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
-      <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
-      <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
-      <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
-      <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
-      <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
-      <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
-      <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
-      <option value="Hex(7)HexNAc(2) (N)">Hex(7)HexNAc(2) (N)</option>
-      <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
-      <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
-      <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
-      <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
-      <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
-      <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
-      <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
-      <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
-      <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
-      <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
-      <option value="Hex(8)Phos(3) (T)">Hex(8)Phos(3) (T)</option>
-      <option value="Hex(9) (N)">Hex(9) (N)</option>
-      <option value="Hex(9)HexNAc(1) (N)">Hex(9)HexNAc(1) (N)</option>
-      <option value="Hex(9)HexNAc(2) (N)">Hex(9)HexNAc(2) (N)</option>
-      <option value="Hex(9)Phos(3) (S)">Hex(9)Phos(3) (S)</option>
-      <option value="Hex(9)Phos(3) (T)">Hex(9)Phos(3) (T)</option>
-      <option value="HexA(2)HexNAc(3) (S)">HexA(2)HexNAc(3) (S)</option>
-      <option value="HexA(2)HexNAc(3) (T)">HexA(2)HexNAc(3) (T)</option>
-      <option value="HexN (K)">HexN (K)</option>
-      <option value="HexN (N)">HexN (N)</option>
-      <option value="HexN (S)">HexN (S)</option>
-      <option value="HexN (T)">HexN (T)</option>
-      <option value="HexN (W)">HexN (W)</option>
-      <option value="HexNAc (C)">HexNAc (C)</option>
-      <option value="HexNAc (N)">HexNAc (N)</option>
-      <option value="HexNAc (S)">HexNAc (S)</option>
-      <option value="HexNAc (T)">HexNAc (T)</option>
-      <option value="HexNAc(1)dHex(1) (N)">HexNAc(1)dHex(1) (N)</option>
-      <option value="HexNAc(1)dHex(1) (S)">HexNAc(1)dHex(1) (S)</option>
-      <option value="HexNAc(1)dHex(1) (T)">HexNAc(1)dHex(1) (T)</option>
-      <option value="HexNAc(1)dHex(2) (N)">HexNAc(1)dHex(2) (N)</option>
-      <option value="HexNAc(1)Kdn(2) (S)">HexNAc(1)Kdn(2) (S)</option>
-      <option value="HexNAc(1)Kdn(2) (T)">HexNAc(1)Kdn(2) (T)</option>
-      <option value="HexNAc(1)NeuAc(1) (S)">HexNAc(1)NeuAc(1) (S)</option>
-      <option value="HexNAc(1)NeuAc(1) (T)">HexNAc(1)NeuAc(1) (T)</option>
-      <option value="HexNAc(1)NeuGc(1) (S)">HexNAc(1)NeuGc(1) (S)</option>
-      <option value="HexNAc(1)NeuGc(1) (T)">HexNAc(1)NeuGc(1) (T)</option>
-      <option value="HexNAc(1)NeuGc(2) (S)">HexNAc(1)NeuGc(2) (S)</option>
-      <option value="HexNAc(1)NeuGc(2) (T)">HexNAc(1)NeuGc(2) (T)</option>
-      <option value="HexNAc(2) (N)">HexNAc(2) (N)</option>
-      <option value="HexNAc(2) (S)">HexNAc(2) (S)</option>
-      <option value="HexNAc(2) (T)">HexNAc(2) (T)</option>
-      <option value="HexNAc(2)dHex(1) (N)">HexNAc(2)dHex(1) (N)</option>
-      <option value="HexNAc(2)dHex(2) (N)">HexNAc(2)dHex(2) (N)</option>
-      <option value="HexNAc(2)NeuAc(1) (S)">HexNAc(2)NeuAc(1) (S)</option>
-      <option value="HexNAc(2)NeuAc(1) (T)">HexNAc(2)NeuAc(1) (T)</option>
-      <option value="HexNAc(2)NeuAc(1)Sulf(1) (S)">HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="HexNAc(2)NeuAc(1)Sulf(1) (T)">HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="HexNAc(2)NeuGc(1) (S)">HexNAc(2)NeuGc(1) (S)</option>
-      <option value="HexNAc(2)NeuGc(1) (T)">HexNAc(2)NeuGc(1) (T)</option>
-      <option value="HexNAc(2)Sulf(1) (S)">HexNAc(2)Sulf(1) (S)</option>
-      <option value="HexNAc(2)Sulf(1) (T)">HexNAc(2)Sulf(1) (T)</option>
-      <option value="HexNAc(3) (S)">HexNAc(3) (S)</option>
-      <option value="HexNAc(3) (T)">HexNAc(3) (T)</option>
-      <option value="HexNAc(3)Sulf(1) (S)">HexNAc(3)Sulf(1) (S)</option>
-      <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
-      <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
-      <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
-      <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
-      <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
-      <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
-      <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
-      <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
-      <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
-      <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
-      <option value="His-&gt;Gln (H)">His-&gt;Gln (H)</option>
-      <option value="His-&gt;Glu (H)">His-&gt;Glu (H)</option>
-      <option value="His-&gt;Gly (H)">His-&gt;Gly (H)</option>
-      <option value="His-&gt;Lys (H)">His-&gt;Lys (H)</option>
-      <option value="His-&gt;Met (H)">His-&gt;Met (H)</option>
-      <option value="His-&gt;Phe (H)">His-&gt;Phe (H)</option>
-      <option value="His-&gt;Pro (H)">His-&gt;Pro (H)</option>
-      <option value="His-&gt;Ser (H)">His-&gt;Ser (H)</option>
-      <option value="His-&gt;Thr (H)">His-&gt;Thr (H)</option>
-      <option value="His-&gt;Trp (H)">His-&gt;Trp (H)</option>
-      <option value="His-&gt;Tyr (H)">His-&gt;Tyr (H)</option>
-      <option value="His-&gt;Val (H)">His-&gt;Val (H)</option>
-      <option value="His-&gt;Xle (H)">His-&gt;Xle (H)</option>
-      <option value="HMVK (C)">HMVK (C)</option>
-      <option value="HN2_mustard (C)">HN2_mustard (C)</option>
-      <option value="HN2_mustard (H)">HN2_mustard (H)</option>
-      <option value="HN2_mustard (K)">HN2_mustard (K)</option>
-      <option value="HN3_mustard (C)">HN3_mustard (C)</option>
-      <option value="HN3_mustard (H)">HN3_mustard (H)</option>
-      <option value="HN3_mustard (K)">HN3_mustard (K)</option>
-      <option value="HNE (A)">HNE (A)</option>
-      <option value="HNE (C)">HNE (C)</option>
-      <option value="HNE (H)">HNE (H)</option>
-      <option value="HNE (K)">HNE (K)</option>
-      <option value="HNE (L)">HNE (L)</option>
-      <option value="HNE+Delta:H(2) (C)">HNE+Delta:H(2) (C)</option>
-      <option value="HNE+Delta:H(2) (H)">HNE+Delta:H(2) (H)</option>
-      <option value="HNE+Delta:H(2) (K)">HNE+Delta:H(2) (K)</option>
-      <option value="HNE-BAHAH (C)">HNE-BAHAH (C)</option>
-      <option value="HNE-BAHAH (H)">HNE-BAHAH (H)</option>
-      <option value="HNE-BAHAH (K)">HNE-BAHAH (K)</option>
-      <option value="HNE-Delta:H(2)O (C)">HNE-Delta:H(2)O (C)</option>
-      <option value="HNE-Delta:H(2)O (H)">HNE-Delta:H(2)O (H)</option>
-      <option value="HNE-Delta:H(2)O (K)">HNE-Delta:H(2)O (K)</option>
-      <option value="Homocysteic_acid (M)">Homocysteic_acid (M)</option>
-      <option value="HPG (R)">HPG (R)</option>
-      <option value="Hydroxamic_acid (D)">Hydroxamic_acid (D)</option>
-      <option value="Hydroxamic_acid (E)">Hydroxamic_acid (E)</option>
-      <option value="Hydroxycinnamyl (C)">Hydroxycinnamyl (C)</option>
-      <option value="Hydroxyfarnesyl (C)">Hydroxyfarnesyl (C)</option>
-      <option value="Hydroxyheme (E)">Hydroxyheme (E)</option>
-      <option value="hydroxyisobutyryl (K)">hydroxyisobutyryl (K)</option>
-      <option value="Hydroxymethyl (N)">Hydroxymethyl (N)</option>
-      <option value="HydroxymethylOP (K)">HydroxymethylOP (K)</option>
-      <option value="Hydroxytrimethyl (K)">Hydroxytrimethyl (K)</option>
-      <option value="Hypusine (K)">Hypusine (K)</option>
-      <option value="IASD (C)">IASD (C)</option>
-      <option value="IBTP (C)">IBTP (C)</option>
-      <option value="ICAT-C (C)">ICAT-C (C)</option>
-      <option value="ICAT-C:13C(9) (C)">ICAT-C:13C(9) (C)</option>
-      <option value="ICAT-D (C)">ICAT-D (C)</option>
-      <option value="ICAT-D:2H(8) (C)">ICAT-D:2H(8) (C)</option>
-      <option value="ICAT-G (C)">ICAT-G (C)</option>
-      <option value="ICAT-G:2H(8) (C)">ICAT-G:2H(8) (C)</option>
-      <option value="ICAT-H (C)">ICAT-H (C)</option>
-      <option value="ICAT-H:13C(6) (C)">ICAT-H:13C(6) (C)</option>
-      <option value="ICDID (C)">ICDID (C)</option>
-      <option value="ICDID:2H(6) (C)">ICDID:2H(6) (C)</option>
-      <option value="ICPL (K)">ICPL (K)</option>
-      <option value="ICPL (N-term)">ICPL (N-term)</option>
-      <option value="ICPL (Protein N-term)">ICPL (Protein N-term)</option>
-      <option value="ICPL:13C(6) (K)">ICPL:13C(6) (K)</option>
-      <option value="ICPL:13C(6) (N-term)">ICPL:13C(6) (N-term)</option>
-      <option value="ICPL:13C(6) (Protein N-term)">ICPL:13C(6) (Protein N-term)</option>
-      <option value="ICPL:13C(6)2H(4) (K)">ICPL:13C(6)2H(4) (K)</option>
-      <option value="ICPL:13C(6)2H(4) (N-term)">ICPL:13C(6)2H(4) (N-term)</option>
-      <option value="ICPL:13C(6)2H(4) (Protein N-term)">ICPL:13C(6)2H(4) (Protein N-term)</option>
-      <option value="ICPL:2H(4) (K)">ICPL:2H(4) (K)</option>
-      <option value="ICPL:2H(4) (N-term)">ICPL:2H(4) (N-term)</option>
-      <option value="ICPL:2H(4) (Protein N-term)">ICPL:2H(4) (Protein N-term)</option>
-      <option value="IDEnT (C)">IDEnT (C)</option>
-      <option value="IED-Biotin (C)">IED-Biotin (C)</option>
-      <option value="IGBP (C)">IGBP (C)</option>
-      <option value="IGBP:13C(2) (C)">IGBP:13C(2) (C)</option>
-      <option value="IMEHex(2)NeuAc(1) (K)">IMEHex(2)NeuAc(1) (K)</option>
-      <option value="IMID (K)">IMID (K)</option>
-      <option value="IMID:2H(4) (K)">IMID:2H(4) (K)</option>
-      <option value="Iminobiotin (K)">Iminobiotin (K)</option>
-      <option value="Iminobiotin (N-term)">Iminobiotin (N-term)</option>
-      <option value="Iodo (H)">Iodo (H)</option>
-      <option value="Iodo (Y)">Iodo (Y)</option>
-      <option value="Iodoacetanilide (C)">Iodoacetanilide (C)</option>
-      <option value="Iodoacetanilide (K)">Iodoacetanilide (K)</option>
-      <option value="Iodoacetanilide (N-term)">Iodoacetanilide (N-term)</option>
-      <option value="Iodoacetanilide:13C(6) (C)">Iodoacetanilide:13C(6) (C)</option>
-      <option value="Iodoacetanilide:13C(6) (K)">Iodoacetanilide:13C(6) (K)</option>
-      <option value="Iodoacetanilide:13C(6) (N-term)">Iodoacetanilide:13C(6) (N-term)</option>
-      <option value="iodoTMT (C)">iodoTMT (C)</option>
-      <option value="iodoTMT (D)">iodoTMT (D)</option>
-      <option value="iodoTMT (E)">iodoTMT (E)</option>
-      <option value="iodoTMT (H)">iodoTMT (H)</option>
-      <option value="iodoTMT (K)">iodoTMT (K)</option>
-      <option value="iodoTMT6plex (C)">iodoTMT6plex (C)</option>
-      <option value="iodoTMT6plex (D)">iodoTMT6plex (D)</option>
-      <option value="iodoTMT6plex (E)">iodoTMT6plex (E)</option>
-      <option value="iodoTMT6plex (H)">iodoTMT6plex (H)</option>
-      <option value="iodoTMT6plex (K)">iodoTMT6plex (K)</option>
-      <option value="IodoU-AMP (F)">IodoU-AMP (F)</option>
-      <option value="IodoU-AMP (W)">IodoU-AMP (W)</option>
-      <option value="IodoU-AMP (Y)">IodoU-AMP (Y)</option>
-      <option value="ISD_z+2_ion (N-term)">ISD_z+2_ion (N-term)</option>
-      <option value="Isopropylphospho (S)">Isopropylphospho (S)</option>
-      <option value="Isopropylphospho (T)">Isopropylphospho (T)</option>
-      <option value="Isopropylphospho (Y)">Isopropylphospho (Y)</option>
-      <option value="iTRAQ4plex (C)">iTRAQ4plex (C)</option>
-      <option value="iTRAQ4plex (H)">iTRAQ4plex (H)</option>
-      <option value="iTRAQ4plex (K)">iTRAQ4plex (K)</option>
-      <option value="iTRAQ4plex (N-term)">iTRAQ4plex (N-term)</option>
-      <option value="iTRAQ4plex (Protein N-term)">iTRAQ4plex (Protein N-term)</option>
-      <option value="iTRAQ4plex (S)">iTRAQ4plex (S)</option>
-      <option value="iTRAQ4plex (T)">iTRAQ4plex (T)</option>
-      <option value="iTRAQ4plex (Y)">iTRAQ4plex (Y)</option>
-      <option value="iTRAQ4plex114 (C)">iTRAQ4plex114 (C)</option>
-      <option value="iTRAQ4plex114 (K)">iTRAQ4plex114 (K)</option>
-      <option value="iTRAQ4plex114 (N-term)">iTRAQ4plex114 (N-term)</option>
-      <option value="iTRAQ4plex114 (Y)">iTRAQ4plex114 (Y)</option>
-      <option value="iTRAQ4plex115 (C)">iTRAQ4plex115 (C)</option>
-      <option value="iTRAQ4plex115 (K)">iTRAQ4plex115 (K)</option>
-      <option value="iTRAQ4plex115 (N-term)">iTRAQ4plex115 (N-term)</option>
-      <option value="iTRAQ4plex115 (Y)">iTRAQ4plex115 (Y)</option>
-      <option value="iTRAQ8plex (C)">iTRAQ8plex (C)</option>
-      <option value="iTRAQ8plex (H)">iTRAQ8plex (H)</option>
-      <option value="iTRAQ8plex (K)">iTRAQ8plex (K)</option>
-      <option value="iTRAQ8plex (N-term)">iTRAQ8plex (N-term)</option>
-      <option value="iTRAQ8plex (Protein N-term)">iTRAQ8plex (Protein N-term)</option>
-      <option value="iTRAQ8plex (S)">iTRAQ8plex (S)</option>
-      <option value="iTRAQ8plex (T)">iTRAQ8plex (T)</option>
-      <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
-      <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
-      <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
-      <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
-      <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
-      <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
-      <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
-      <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
-      <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
-      <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
-      <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
-      <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
-      <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
-      <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
-      <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
-      <option value="Label:13C(5)15N(1) (E)">Label:13C(5)15N(1) (E)</option>
-      <option value="Label:13C(5)15N(1) (M)">Label:13C(5)15N(1) (M)</option>
-      <option value="Label:13C(5)15N(1) (P)">Label:13C(5)15N(1) (P)</option>
-      <option value="Label:13C(5)15N(1) (V)">Label:13C(5)15N(1) (V)</option>
-      <option value="Label:13C(6) (I)">Label:13C(6) (I)</option>
-      <option value="Label:13C(6) (K)">Label:13C(6) (K)</option>
-      <option value="Label:13C(6) (L)">Label:13C(6) (L)</option>
-      <option value="Label:13C(6) (R)">Label:13C(6) (R)</option>
-      <option value="Label:13C(6)+Acetyl (K)">Label:13C(6)+Acetyl (K)</option>
-      <option value="Label:13C(6)+Dimethyl (K)">Label:13C(6)+Dimethyl (K)</option>
-      <option value="Label:13C(6)+GG (K)">Label:13C(6)+GG (K)</option>
-      <option value="Label:13C(6)15N(1) (I)">Label:13C(6)15N(1) (I)</option>
-      <option value="Label:13C(6)15N(1) (L)">Label:13C(6)15N(1) (L)</option>
-      <option value="Label:13C(6)15N(2) (K)">Label:13C(6)15N(2) (K)</option>
-      <option value="Label:13C(6)15N(2)+Acetyl (K)">Label:13C(6)15N(2)+Acetyl (K)</option>
-      <option value="Label:13C(6)15N(2)+Dimethyl (K)">Label:13C(6)15N(2)+Dimethyl (K)</option>
-      <option value="Label:13C(6)15N(2)+GG (K)">Label:13C(6)15N(2)+GG (K)</option>
-      <option value="Label:13C(6)15N(4) (R)">Label:13C(6)15N(4) (R)</option>
-      <option value="Label:13C(6)15N(4)+Dimethyl (R)">Label:13C(6)15N(4)+Dimethyl (R)</option>
-      <option value="Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R)">Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R)</option>
-      <option value="Label:13C(6)15N(4)+Methyl (R)">Label:13C(6)15N(4)+Methyl (R)</option>
-      <option value="Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R)">Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R)</option>
-      <option value="Label:13C(9) (F)">Label:13C(9) (F)</option>
-      <option value="Label:13C(9) (Y)">Label:13C(9) (Y)</option>
-      <option value="Label:13C(9)+Phospho (Y)">Label:13C(9)+Phospho (Y)</option>
-      <option value="Label:13C(9)15N(1) (F)">Label:13C(9)15N(1) (F)</option>
-      <option value="Label:15N(1) (A)">Label:15N(1) (A)</option>
-      <option value="Label:15N(1) (C)">Label:15N(1) (C)</option>
-      <option value="Label:15N(1) (D)">Label:15N(1) (D)</option>
-      <option value="Label:15N(1) (E)">Label:15N(1) (E)</option>
-      <option value="Label:15N(1) (F)">Label:15N(1) (F)</option>
-      <option value="Label:15N(1) (G)">Label:15N(1) (G)</option>
-      <option value="Label:15N(1) (I)">Label:15N(1) (I)</option>
-      <option value="Label:15N(1) (L)">Label:15N(1) (L)</option>
-      <option value="Label:15N(1) (M)">Label:15N(1) (M)</option>
-      <option value="Label:15N(1) (P)">Label:15N(1) (P)</option>
-      <option value="Label:15N(1) (S)">Label:15N(1) (S)</option>
-      <option value="Label:15N(1) (T)">Label:15N(1) (T)</option>
-      <option value="Label:15N(1) (V)">Label:15N(1) (V)</option>
-      <option value="Label:15N(1) (Y)">Label:15N(1) (Y)</option>
-      <option value="Label:15N(2) (K)">Label:15N(2) (K)</option>
-      <option value="Label:15N(2) (N)">Label:15N(2) (N)</option>
-      <option value="Label:15N(2) (Q)">Label:15N(2) (Q)</option>
-      <option value="Label:15N(2) (W)">Label:15N(2) (W)</option>
-      <option value="Label:15N(2)2H(9) (K)">Label:15N(2)2H(9) (K)</option>
-      <option value="Label:15N(3) (H)">Label:15N(3) (H)</option>
-      <option value="Label:15N(4) (R)">Label:15N(4) (R)</option>
-      <option value="Label:18O(1) (C-term)">Label:18O(1) (C-term)</option>
-      <option value="Label:18O(1) (S)">Label:18O(1) (S)</option>
-      <option value="Label:18O(1) (T)">Label:18O(1) (T)</option>
-      <option value="Label:18O(1) (Y)">Label:18O(1) (Y)</option>
-      <option value="Label:18O(2) (C-term)">Label:18O(2) (C-term)</option>
-      <option value="Label:2H(10) (L)">Label:2H(10) (L)</option>
-      <option value="Label:2H(3) (L)">Label:2H(3) (L)</option>
-      <option value="Label:2H(3) (M)">Label:2H(3) (M)</option>
-      <option value="Label:2H(3)+Oxidation (M)">Label:2H(3)+Oxidation (M)</option>
-      <option value="Label:2H(4) (A)">Label:2H(4) (A)</option>
-      <option value="Label:2H(4) (F)">Label:2H(4) (F)</option>
-      <option value="Label:2H(4) (K)">Label:2H(4) (K)</option>
-      <option value="Label:2H(4) (U)">Label:2H(4) (U)</option>
-      <option value="Label:2H(4) (Y)">Label:2H(4) (Y)</option>
-      <option value="Label:2H(4)+Acetyl (K)">Label:2H(4)+Acetyl (K)</option>
-      <option value="Label:2H(4)+GG (K)">Label:2H(4)+GG (K)</option>
-      <option value="Label:2H(4)13C(1) (R)">Label:2H(4)13C(1) (R)</option>
-      <option value="Label:2H(6)15N(1) (P)">Label:2H(6)15N(1) (P)</option>
-      <option value="Label:2H(7)15N(4) (R)">Label:2H(7)15N(4) (R)</option>
-      <option value="Label:2H(9)13C(6)15N(2) (K)">Label:2H(9)13C(6)15N(2) (K)</option>
-      <option value="lapachenole (C)">lapachenole (C)</option>
-      <option value="Leu-&gt;MetOx (L)">Leu-&gt;MetOx (L)</option>
-      <option value="LG-anhydrolactam (K)">LG-anhydrolactam (K)</option>
-      <option value="LG-anhydrolactam (N-term)">LG-anhydrolactam (N-term)</option>
-      <option value="LG-anhyropyrrole (K)">LG-anhyropyrrole (K)</option>
-      <option value="LG-anhyropyrrole (N-term)">LG-anhyropyrrole (N-term)</option>
-      <option value="LG-Hlactam-K (K)">LG-Hlactam-K (K)</option>
-      <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
-      <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
-      <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
-      <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
-      <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
-      <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
-      <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
-      <option value="Lipoyl (K)">Lipoyl (K)</option>
-      <option value="LRGG (K)">LRGG (K)</option>
-      <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
-      <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
-      <option value="Lys (N-term)">Lys (N-term)</option>
-      <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
-      <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
-      <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
-      <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
-      <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
-      <option value="Lys-&gt;Asp (K)">Lys-&gt;Asp (K)</option>
-      <option value="Lys-&gt;CamCys (K)">Lys-&gt;CamCys (K)</option>
-      <option value="Lys-&gt;Cys (K)">Lys-&gt;Cys (K)</option>
-      <option value="Lys-&gt;Gln (K)">Lys-&gt;Gln (K)</option>
-      <option value="Lys-&gt;Glu (K)">Lys-&gt;Glu (K)</option>
-      <option value="Lys-&gt;Gly (K)">Lys-&gt;Gly (K)</option>
-      <option value="Lys-&gt;His (K)">Lys-&gt;His (K)</option>
-      <option value="Lys-&gt;Met (K)">Lys-&gt;Met (K)</option>
-      <option value="Lys-&gt;MetOx (K)">Lys-&gt;MetOx (K)</option>
-      <option value="Lys-&gt;Phe (K)">Lys-&gt;Phe (K)</option>
-      <option value="Lys-&gt;Pro (K)">Lys-&gt;Pro (K)</option>
-      <option value="Lys-&gt;Ser (K)">Lys-&gt;Ser (K)</option>
-      <option value="Lys-&gt;Thr (K)">Lys-&gt;Thr (K)</option>
-      <option value="Lys-&gt;Trp (K)">Lys-&gt;Trp (K)</option>
-      <option value="Lys-&gt;Tyr (K)">Lys-&gt;Tyr (K)</option>
-      <option value="Lys-&gt;Val (K)">Lys-&gt;Val (K)</option>
-      <option value="Lys-&gt;Xle (K)">Lys-&gt;Xle (K)</option>
-      <option value="Lys-loss (Protein C-term K)">Lys-loss (Protein C-term K)</option>
-      <option value="Lysbiotinhydrazide (K)">Lysbiotinhydrazide (K)</option>
-      <option value="maleimide (C)">maleimide (C)</option>
-      <option value="maleimide (K)">maleimide (K)</option>
-      <option value="Maleimide-PEO2-Biotin (C)">Maleimide-PEO2-Biotin (C)</option>
-      <option value="maleimide3 (C)">maleimide3 (C)</option>
-      <option value="maleimide3 (K)">maleimide3 (K)</option>
-      <option value="maleimide5 (C)">maleimide5 (C)</option>
-      <option value="maleimide5 (K)">maleimide5 (K)</option>
-      <option value="Malonyl (C)">Malonyl (C)</option>
-      <option value="Malonyl (K)">Malonyl (K)</option>
-      <option value="Malonyl (S)">Malonyl (S)</option>
-      <option value="MDCC (C)">MDCC (C)</option>
-      <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
-      <option value="Menadione (C)">Menadione (C)</option>
-      <option value="Menadione (K)">Menadione (K)</option>
-      <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
-      <option value="Menadione-HQ (K)">Menadione-HQ (K)</option>
-      <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
-      <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
-      <option value="MesitylOxide (H)">MesitylOxide (H)</option>
-      <option value="MesitylOxide (K)">MesitylOxide (K)</option>
-      <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
-      <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
-      <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
-      <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
-      <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
-      <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
-      <option value="Met-&gt;AspSA (M)">Met-&gt;AspSA (M)</option>
-      <option value="Met-&gt;Cys (M)">Met-&gt;Cys (M)</option>
-      <option value="Met-&gt;Gln (M)">Met-&gt;Gln (M)</option>
-      <option value="Met-&gt;Glu (M)">Met-&gt;Glu (M)</option>
-      <option value="Met-&gt;Gly (M)">Met-&gt;Gly (M)</option>
-      <option value="Met-&gt;His (M)">Met-&gt;His (M)</option>
-      <option value="Met-&gt;Hpg (M)">Met-&gt;Hpg (M)</option>
-      <option value="Met-&gt;Hse (C-term M)">Met-&gt;Hse (C-term M)</option>
-      <option value="Met-&gt;Hsl (C-term M)">Met-&gt;Hsl (C-term M)</option>
-      <option value="Met-&gt;Lys (M)">Met-&gt;Lys (M)</option>
-      <option value="Met-&gt;Phe (M)">Met-&gt;Phe (M)</option>
-      <option value="Met-&gt;Pro (M)">Met-&gt;Pro (M)</option>
-      <option value="Met-&gt;Ser (M)">Met-&gt;Ser (M)</option>
-      <option value="Met-&gt;Thr (M)">Met-&gt;Thr (M)</option>
-      <option value="Met-&gt;Trp (M)">Met-&gt;Trp (M)</option>
-      <option value="Met-&gt;Tyr (M)">Met-&gt;Tyr (M)</option>
-      <option value="Met-&gt;Val (M)">Met-&gt;Val (M)</option>
-      <option value="Met-&gt;Xle (M)">Met-&gt;Xle (M)</option>
-      <option value="Met-loss (Protein N-term M)">Met-loss (Protein N-term M)</option>
-      <option value="Met-loss+Acetyl (Protein N-term M)">Met-loss+Acetyl (Protein N-term M)</option>
-      <option value="Methamidophos-O (C)">Methamidophos-O (C)</option>
-      <option value="Methamidophos-O (H)">Methamidophos-O (H)</option>
-      <option value="Methamidophos-O (K)">Methamidophos-O (K)</option>
-      <option value="Methamidophos-O (S)">Methamidophos-O (S)</option>
-      <option value="Methamidophos-O (T)">Methamidophos-O (T)</option>
-      <option value="Methamidophos-O (Y)">Methamidophos-O (Y)</option>
-      <option value="Methamidophos-S (C)">Methamidophos-S (C)</option>
-      <option value="Methamidophos-S (H)">Methamidophos-S (H)</option>
-      <option value="Methamidophos-S (K)">Methamidophos-S (K)</option>
-      <option value="Methamidophos-S (S)">Methamidophos-S (S)</option>
-      <option value="Methamidophos-S (T)">Methamidophos-S (T)</option>
-      <option value="Methamidophos-S (Y)">Methamidophos-S (Y)</option>
-      <option value="Methyl (C)">Methyl (C)</option>
-      <option value="Methyl (C-term)">Methyl (C-term)</option>
-      <option value="Methyl (D)">Methyl (D)</option>
-      <option value="Methyl (E)">Methyl (E)</option>
-      <option value="Methyl (H)">Methyl (H)</option>
-      <option value="Methyl (I)">Methyl (I)</option>
-      <option value="Methyl (K)">Methyl (K)</option>
-      <option value="Methyl (L)">Methyl (L)</option>
-      <option value="Methyl (N)">Methyl (N)</option>
-      <option value="Methyl (N-term)">Methyl (N-term)</option>
-      <option value="Methyl (Protein N-term)">Methyl (Protein N-term)</option>
-      <option value="Methyl (Q)">Methyl (Q)</option>
-      <option value="Methyl (R)">Methyl (R)</option>
-      <option value="Methyl (S)">Methyl (S)</option>
-      <option value="Methyl (T)">Methyl (T)</option>
-      <option value="Methyl+Acetyl:2H(3) (K)">Methyl+Acetyl:2H(3) (K)</option>
-      <option value="Methyl+Deamidated (N)">Methyl+Deamidated (N)</option>
-      <option value="Methyl+Deamidated (Q)">Methyl+Deamidated (Q)</option>
-      <option value="Methyl-PEO12-Maleimide (C)">Methyl-PEO12-Maleimide (C)</option>
-      <option value="Methyl:2H(2) (K)">Methyl:2H(2) (K)</option>
-      <option value="Methyl:2H(2) (N-term)">Methyl:2H(2) (N-term)</option>
-      <option value="Methyl:2H(2)13C (C)">Methyl:2H(2)13C (C)</option>
-      <option value="Methyl:2H(2)13C (C-term)">Methyl:2H(2)13C (C-term)</option>
-      <option value="Methyl:2H(2)13C (D)">Methyl:2H(2)13C (D)</option>
-      <option value="Methyl:2H(2)13C (E)">Methyl:2H(2)13C (E)</option>
-      <option value="Methyl:2H(2)13C (H)">Methyl:2H(2)13C (H)</option>
-      <option value="Methyl:2H(2)13C (I)">Methyl:2H(2)13C (I)</option>
-      <option value="Methyl:2H(2)13C (K)">Methyl:2H(2)13C (K)</option>
-      <option value="Methyl:2H(2)13C (L)">Methyl:2H(2)13C (L)</option>
-      <option value="Methyl:2H(2)13C (N)">Methyl:2H(2)13C (N)</option>
-      <option value="Methyl:2H(2)13C (N-term)">Methyl:2H(2)13C (N-term)</option>
-      <option value="Methyl:2H(2)13C (Protein N-term)">Methyl:2H(2)13C (Protein N-term)</option>
-      <option value="Methyl:2H(2)13C (Q)">Methyl:2H(2)13C (Q)</option>
-      <option value="Methyl:2H(2)13C (R)">Methyl:2H(2)13C (R)</option>
-      <option value="Methyl:2H(2)13C (S)">Methyl:2H(2)13C (S)</option>
-      <option value="Methyl:2H(2)13C (T)">Methyl:2H(2)13C (T)</option>
-      <option value="Methyl:2H(3) (D)">Methyl:2H(3) (D)</option>
-      <option value="Methyl:2H(3) (E)">Methyl:2H(3) (E)</option>
-      <option value="Methyl:2H(3) (K)">Methyl:2H(3) (K)</option>
-      <option value="Methyl:2H(3) (R)">Methyl:2H(3) (R)</option>
-      <option value="Methyl:2H(3) (X)">Methyl:2H(3) (X)</option>
-      <option value="Methyl:2H(3)+Acetyl:2H(3) (K)">Methyl:2H(3)+Acetyl:2H(3) (K)</option>
-      <option value="Methyl:2H(3)13C(1) (K)">Methyl:2H(3)13C(1) (K)</option>
-      <option value="Methyl:2H(3)13C(1) (N-term)">Methyl:2H(3)13C(1) (N-term)</option>
-      <option value="Methyl:2H(3)13C(1) (R)">Methyl:2H(3)13C(1) (R)</option>
-      <option value="Methylamine (S)">Methylamine (S)</option>
-      <option value="Methylamine (T)">Methylamine (T)</option>
-      <option value="Methylmalonylation (S)">Methylmalonylation (S)</option>
-      <option value="methylol (K)">methylol (K)</option>
-      <option value="methylol (W)">methylol (W)</option>
-      <option value="methylol (Y)">methylol (Y)</option>
-      <option value="Methylphosphonate (S)">Methylphosphonate (S)</option>
-      <option value="Methylphosphonate (T)">Methylphosphonate (T)</option>
-      <option value="Methylphosphonate (Y)">Methylphosphonate (Y)</option>
-      <option value="Methylpyrroline (K)">Methylpyrroline (K)</option>
-      <option value="methylsulfonylethyl (C)">methylsulfonylethyl (C)</option>
-      <option value="methylsulfonylethyl (H)">methylsulfonylethyl (H)</option>
-      <option value="methylsulfonylethyl (K)">methylsulfonylethyl (K)</option>
-      <option value="Methylthio (C)">Methylthio (C)</option>
-      <option value="Methylthio (D)">Methylthio (D)</option>
-      <option value="Methylthio (K)">Methylthio (K)</option>
-      <option value="Methylthio (N)">Methylthio (N)</option>
-      <option value="Methylthio (N-term)">Methylthio (N-term)</option>
-      <option value="MG-H1 (R)">MG-H1 (R)</option>
-      <option value="Microcin (Protein C-term)">Microcin (Protein C-term)</option>
-      <option value="MicrocinC7 (Protein C-term)">MicrocinC7 (Protein C-term)</option>
-      <option value="MM-diphenylpentanone (C)">MM-diphenylpentanone (C)</option>
-      <option value="Molybdopterin (C)">Molybdopterin (C)</option>
-      <option value="MolybdopterinGD (C)">MolybdopterinGD (C)</option>
-      <option value="MolybdopterinGD (D)">MolybdopterinGD (D)</option>
-      <option value="MolybdopterinGD (U)">MolybdopterinGD (U)</option>
-      <option value="MolybdopterinGD+Delta:S(-1)Se(1) (C)">MolybdopterinGD+Delta:S(-1)Se(1) (C)</option>
-      <option value="monomethylphosphothione (C)">monomethylphosphothione (C)</option>
-      <option value="monomethylphosphothione (H)">monomethylphosphothione (H)</option>
-      <option value="monomethylphosphothione (K)">monomethylphosphothione (K)</option>
-      <option value="monomethylphosphothione (S)">monomethylphosphothione (S)</option>
-      <option value="monomethylphosphothione (T)">monomethylphosphothione (T)</option>
-      <option value="monomethylphosphothione (Y)">monomethylphosphothione (Y)</option>
-      <option value="mTRAQ (H)">mTRAQ (H)</option>
-      <option value="mTRAQ (K)">mTRAQ (K)</option>
-      <option value="mTRAQ (N-term)">mTRAQ (N-term)</option>
-      <option value="mTRAQ (S)">mTRAQ (S)</option>
-      <option value="mTRAQ (T)">mTRAQ (T)</option>
-      <option value="mTRAQ (Y)">mTRAQ (Y)</option>
-      <option value="mTRAQ:13C(3)15N(1) (H)">mTRAQ:13C(3)15N(1) (H)</option>
-      <option value="mTRAQ:13C(3)15N(1) (K)">mTRAQ:13C(3)15N(1) (K)</option>
-      <option value="mTRAQ:13C(3)15N(1) (N-term)">mTRAQ:13C(3)15N(1) (N-term)</option>
-      <option value="mTRAQ:13C(3)15N(1) (S)">mTRAQ:13C(3)15N(1) (S)</option>
-      <option value="mTRAQ:13C(3)15N(1) (T)">mTRAQ:13C(3)15N(1) (T)</option>
-      <option value="mTRAQ:13C(3)15N(1) (Y)">mTRAQ:13C(3)15N(1) (Y)</option>
-      <option value="mTRAQ:13C(6)15N(2) (H)">mTRAQ:13C(6)15N(2) (H)</option>
-      <option value="mTRAQ:13C(6)15N(2) (K)">mTRAQ:13C(6)15N(2) (K)</option>
-      <option value="mTRAQ:13C(6)15N(2) (N-term)">mTRAQ:13C(6)15N(2) (N-term)</option>
-      <option value="mTRAQ:13C(6)15N(2) (S)">mTRAQ:13C(6)15N(2) (S)</option>
-      <option value="mTRAQ:13C(6)15N(2) (T)">mTRAQ:13C(6)15N(2) (T)</option>
-      <option value="mTRAQ:13C(6)15N(2) (Y)">mTRAQ:13C(6)15N(2) (Y)</option>
-      <option value="MTSL (C)">MTSL (C)</option>
-      <option value="MurNAc (A)">MurNAc (A)</option>
-      <option value="Myristoleyl (Protein N-term G)">Myristoleyl (Protein N-term G)</option>
-      <option value="Myristoyl (C)">Myristoyl (C)</option>
-      <option value="Myristoyl (K)">Myristoyl (K)</option>
-      <option value="Myristoyl (N-term G)">Myristoyl (N-term G)</option>
-      <option value="Myristoyl+Delta:H(-4) (Protein N-term G)">Myristoyl+Delta:H(-4) (Protein N-term G)</option>
-      <option value="N-dimethylphosphate (S)">N-dimethylphosphate (S)</option>
-      <option value="NA-LNO2 (C)">NA-LNO2 (C)</option>
-      <option value="NA-LNO2 (H)">NA-LNO2 (H)</option>
-      <option value="NA-OA-NO2 (C)">NA-OA-NO2 (C)</option>
-      <option value="NA-OA-NO2 (H)">NA-OA-NO2 (H)</option>
-      <option value="NBS (W)">NBS (W)</option>
-      <option value="NBS:13C(6) (W)">NBS:13C(6) (W)</option>
-      <option value="NDA (K)">NDA (K)</option>
-      <option value="NDA (N-term)">NDA (N-term)</option>
-      <option value="NEIAA (C)">NEIAA (C)</option>
-      <option value="NEIAA (Y)">NEIAA (Y)</option>
-      <option value="NEIAA:2H(5) (C)">NEIAA:2H(5) (C)</option>
-      <option value="NEIAA:2H(5) (Y)">NEIAA:2H(5) (Y)</option>
-      <option value="NEM:2H(5) (C)">NEM:2H(5) (C)</option>
-      <option value="NEM:2H(5)+H2O (C)">NEM:2H(5)+H2O (C)</option>
-      <option value="NEMsulfur (C)">NEMsulfur (C)</option>
-      <option value="NEMsulfurWater (C)">NEMsulfurWater (C)</option>
-      <option value="Nethylmaleimide (C)">Nethylmaleimide (C)</option>
-      <option value="Nethylmaleimide+water (C)">Nethylmaleimide+water (C)</option>
-      <option value="Nethylmaleimide+water (K)">Nethylmaleimide+water (K)</option>
-      <option value="NeuAc (N)">NeuAc (N)</option>
-      <option value="NeuAc (S)">NeuAc (S)</option>
-      <option value="NeuAc (T)">NeuAc (T)</option>
-      <option value="NeuGc (N)">NeuGc (N)</option>
-      <option value="NeuGc (S)">NeuGc (S)</option>
-      <option value="NeuGc (T)">NeuGc (T)</option>
-      <option value="NHS-fluorescein (K)">NHS-fluorescein (K)</option>
-      <option value="NHS-LC-Biotin (K)">NHS-LC-Biotin (K)</option>
-      <option value="NHS-LC-Biotin (N-term)">NHS-LC-Biotin (N-term)</option>
-      <option value="NIC (K)">NIC (K)</option>
-      <option value="NIC (N-term)">NIC (N-term)</option>
-      <option value="NIPCAM (C)">NIPCAM (C)</option>
-      <option value="Nitrene (Y)">Nitrene (Y)</option>
-      <option value="Nitro (F)">Nitro (F)</option>
-      <option value="Nitro (W)">Nitro (W)</option>
-      <option value="Nitro (Y)">Nitro (Y)</option>
-      <option value="Nitrosyl (C)">Nitrosyl (C)</option>
-      <option value="Nitrosyl (Y)">Nitrosyl (Y)</option>
-      <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
-      <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
-      <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
-      <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
-      <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-      <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
-      <option value="NP40 (N-term)">NP40 (N-term)</option>
-      <option value="NQIGG (K)">NQIGG (K)</option>
-      <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
-      <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
-      <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
-      <option value="O-Et-N-diMePhospho (S)">O-Et-N-diMePhospho (S)</option>
-      <option value="O-Isopropylmethylphosphonate (S)">O-Isopropylmethylphosphonate (S)</option>
-      <option value="O-Isopropylmethylphosphonate (T)">O-Isopropylmethylphosphonate (T)</option>
-      <option value="O-Isopropylmethylphosphonate (Y)">O-Isopropylmethylphosphonate (Y)</option>
-      <option value="O-Methylphosphate (S)">O-Methylphosphate (S)</option>
-      <option value="O-Methylphosphate (T)">O-Methylphosphate (T)</option>
-      <option value="O-Methylphosphate (Y)">O-Methylphosphate (Y)</option>
-      <option value="O-pinacolylmethylphosphonate (H)">O-pinacolylmethylphosphonate (H)</option>
-      <option value="O-pinacolylmethylphosphonate (K)">O-pinacolylmethylphosphonate (K)</option>
-      <option value="O-pinacolylmethylphosphonate (S)">O-pinacolylmethylphosphonate (S)</option>
-      <option value="O-pinacolylmethylphosphonate (T)">O-pinacolylmethylphosphonate (T)</option>
-      <option value="O-pinacolylmethylphosphonate (Y)">O-pinacolylmethylphosphonate (Y)</option>
-      <option value="Octanoyl (C)">Octanoyl (C)</option>
-      <option value="Octanoyl (S)">Octanoyl (S)</option>
-      <option value="Octanoyl (T)">Octanoyl (T)</option>
-      <option value="OxArgBiotin (R)">OxArgBiotin (R)</option>
-      <option value="OxArgBiotinRed (R)">OxArgBiotinRed (R)</option>
-      <option value="Oxidation (C)">Oxidation (C)</option>
-      <option value="Oxidation (C-term G)">Oxidation (C-term G)</option>
-      <option value="Oxidation (D)">Oxidation (D)</option>
-      <option value="Oxidation (E)">Oxidation (E)</option>
-      <option value="Oxidation (F)">Oxidation (F)</option>
-      <option value="Oxidation (H)">Oxidation (H)</option>
-      <option value="Oxidation (I)">Oxidation (I)</option>
-      <option value="Oxidation (K)">Oxidation (K)</option>
-      <option value="Oxidation (L)">Oxidation (L)</option>
-      <option value="Oxidation (M)" selected="true">Oxidation (M)</option>
-      <option value="Oxidation (N)">Oxidation (N)</option>
-      <option value="Oxidation (P)">Oxidation (P)</option>
-      <option value="Oxidation (Q)">Oxidation (Q)</option>
-      <option value="Oxidation (R)">Oxidation (R)</option>
-      <option value="Oxidation (S)">Oxidation (S)</option>
-      <option value="Oxidation (T)">Oxidation (T)</option>
-      <option value="Oxidation (U)">Oxidation (U)</option>
-      <option value="Oxidation (V)">Oxidation (V)</option>
-      <option value="Oxidation (W)">Oxidation (W)</option>
-      <option value="Oxidation (Y)">Oxidation (Y)</option>
-      <option value="Oxidation+NEM (C)">Oxidation+NEM (C)</option>
-      <option value="OxLysBiotin (K)">OxLysBiotin (K)</option>
-      <option value="OxLysBiotinRed (K)">OxLysBiotinRed (K)</option>
-      <option value="OxProBiotin (P)">OxProBiotin (P)</option>
-      <option value="OxProBiotinRed (P)">OxProBiotinRed (P)</option>
-      <option value="Palmitoleyl (C)">Palmitoleyl (C)</option>
-      <option value="Palmitoleyl (S)">Palmitoleyl (S)</option>
-      <option value="Palmitoleyl (T)">Palmitoleyl (T)</option>
-      <option value="Palmitoyl (C)">Palmitoyl (C)</option>
-      <option value="Palmitoyl (K)">Palmitoyl (K)</option>
-      <option value="Palmitoyl (Protein N-term)">Palmitoyl (Protein N-term)</option>
-      <option value="Palmitoyl (S)">Palmitoyl (S)</option>
-      <option value="Palmitoyl (T)">Palmitoyl (T)</option>
-      <option value="PEITC (C)">PEITC (C)</option>
-      <option value="PEITC (K)">PEITC (K)</option>
-      <option value="PEITC (N-term)">PEITC (N-term)</option>
-      <option value="Pent(1)HexNAc(1) (S)">Pent(1)HexNAc(1) (S)</option>
-      <option value="Pent(1)HexNAc(1) (T)">Pent(1)HexNAc(1) (T)</option>
-      <option value="Pent(2) (S)">Pent(2) (S)</option>
-      <option value="Pent(2) (T)">Pent(2) (T)</option>
-      <option value="Pentose (S)">Pentose (S)</option>
-      <option value="Pentose (T)">Pentose (T)</option>
-      <option value="Pentylamine (Q)">Pentylamine (Q)</option>
-      <option value="PEO-Iodoacetyl-LC-Biotin (C)">PEO-Iodoacetyl-LC-Biotin (C)</option>
-      <option value="PET (S)">PET (S)</option>
-      <option value="PET (T)">PET (T)</option>
-      <option value="Phe-&gt;Ala (F)">Phe-&gt;Ala (F)</option>
-      <option value="Phe-&gt;Arg (F)">Phe-&gt;Arg (F)</option>
-      <option value="Phe-&gt;Asn (F)">Phe-&gt;Asn (F)</option>
-      <option value="Phe-&gt;Asp (F)">Phe-&gt;Asp (F)</option>
-      <option value="Phe-&gt;CamCys (F)">Phe-&gt;CamCys (F)</option>
-      <option value="Phe-&gt;Cys (F)">Phe-&gt;Cys (F)</option>
-      <option value="Phe-&gt;Gln (F)">Phe-&gt;Gln (F)</option>
-      <option value="Phe-&gt;Glu (F)">Phe-&gt;Glu (F)</option>
-      <option value="Phe-&gt;Gly (F)">Phe-&gt;Gly (F)</option>
-      <option value="Phe-&gt;His (F)">Phe-&gt;His (F)</option>
-      <option value="Phe-&gt;Lys (F)">Phe-&gt;Lys (F)</option>
-      <option value="Phe-&gt;Met (F)">Phe-&gt;Met (F)</option>
-      <option value="Phe-&gt;Pro (F)">Phe-&gt;Pro (F)</option>
-      <option value="Phe-&gt;Ser (F)">Phe-&gt;Ser (F)</option>
-      <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
-      <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
-      <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
-      <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
-      <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
-      <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
-      <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
-      <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
-      <option value="Phospho (C)">Phospho (C)</option>
-      <option value="Phospho (D)">Phospho (D)</option>
-      <option value="Phospho (E)">Phospho (E)</option>
-      <option value="Phospho (H)">Phospho (H)</option>
-      <option value="Phospho (K)">Phospho (K)</option>
-      <option value="Phospho (R)">Phospho (R)</option>
-      <option value="Phospho (S)">Phospho (S)</option>
-      <option value="Phospho (T)">Phospho (T)</option>
-      <option value="Phospho (Y)">Phospho (Y)</option>
-      <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
-      <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
-      <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
-      <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
-      <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
-      <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
-      <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
-      <option value="Phosphogluconoylation (K)">Phosphogluconoylation (K)</option>
-      <option value="Phosphogluconoylation (N-term)">Phosphogluconoylation (N-term)</option>
-      <option value="Phosphoguanosine (H)">Phosphoguanosine (H)</option>
-      <option value="Phosphoguanosine (K)">Phosphoguanosine (K)</option>
-      <option value="PhosphoHex (S)">PhosphoHex (S)</option>
-      <option value="PhosphoHex (T)">PhosphoHex (T)</option>
-      <option value="PhosphoHex(2) (N)">PhosphoHex(2) (N)</option>
-      <option value="PhosphoHex(2) (S)">PhosphoHex(2) (S)</option>
-      <option value="PhosphoHex(2) (T)">PhosphoHex(2) (T)</option>
-      <option value="PhosphoHexNAc (S)">PhosphoHexNAc (S)</option>
-      <option value="PhosphoHexNAc (T)">PhosphoHexNAc (T)</option>
-      <option value="Phosphopantetheine (S)">Phosphopantetheine (S)</option>
-      <option value="Phosphopropargyl (S)">Phosphopropargyl (S)</option>
-      <option value="Phosphopropargyl (T)">Phosphopropargyl (T)</option>
-      <option value="Phosphopropargyl (Y)">Phosphopropargyl (Y)</option>
-      <option value="phosphoRibosyl (D)">phosphoRibosyl (D)</option>
-      <option value="phosphoRibosyl (E)">phosphoRibosyl (E)</option>
-      <option value="phosphoRibosyl (R)">phosphoRibosyl (R)</option>
-      <option value="PhosphoribosyldephosphoCoA (S)">PhosphoribosyldephosphoCoA (S)</option>
-      <option value="PhosphoUridine (H)">PhosphoUridine (H)</option>
-      <option value="PhosphoUridine (Y)">PhosphoUridine (Y)</option>
-      <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
-      <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
-      <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
-      <option value="Piperidine (K)">Piperidine (K)</option>
-      <option value="Piperidine (N-term)">Piperidine (N-term)</option>
-      <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
-      <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
-      <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
-      <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
-      <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
-      <option value="Pro-&gt;Gln (P)">Pro-&gt;Gln (P)</option>
-      <option value="Pro-&gt;Glu (P)">Pro-&gt;Glu (P)</option>
-      <option value="Pro-&gt;Gly (P)">Pro-&gt;Gly (P)</option>
-      <option value="Pro-&gt;HAVA (P)">Pro-&gt;HAVA (P)</option>
-      <option value="Pro-&gt;His (P)">Pro-&gt;His (P)</option>
-      <option value="Pro-&gt;Lys (P)">Pro-&gt;Lys (P)</option>
-      <option value="Pro-&gt;Met (P)">Pro-&gt;Met (P)</option>
-      <option value="Pro-&gt;Phe (P)">Pro-&gt;Phe (P)</option>
-      <option value="Pro-&gt;pyro-Glu (P)">Pro-&gt;pyro-Glu (P)</option>
-      <option value="Pro-&gt;Pyrrolidinone (P)">Pro-&gt;Pyrrolidinone (P)</option>
-      <option value="Pro-&gt;Pyrrolidone (P)">Pro-&gt;Pyrrolidone (P)</option>
-      <option value="Pro-&gt;Ser (P)">Pro-&gt;Ser (P)</option>
-      <option value="Pro-&gt;Thr (P)">Pro-&gt;Thr (P)</option>
-      <option value="Pro-&gt;Trp (P)">Pro-&gt;Trp (P)</option>
-      <option value="Pro-&gt;Tyr (P)">Pro-&gt;Tyr (P)</option>
-      <option value="Pro-&gt;Val (P)">Pro-&gt;Val (P)</option>
-      <option value="Pro-&gt;Xle (P)">Pro-&gt;Xle (P)</option>
-      <option value="probiotinhydrazide (P)">probiotinhydrazide (P)</option>
-      <option value="Propargylamine (C-term)">Propargylamine (C-term)</option>
-      <option value="Propargylamine (D)">Propargylamine (D)</option>
-      <option value="Propargylamine (E)">Propargylamine (E)</option>
-      <option value="Propionamide (C)">Propionamide (C)</option>
-      <option value="Propionamide (K)">Propionamide (K)</option>
-      <option value="Propionamide (N-term)">Propionamide (N-term)</option>
-      <option value="Propionamide:2H(3) (C)">Propionamide:2H(3) (C)</option>
-      <option value="Propionyl (K)">Propionyl (K)</option>
-      <option value="Propionyl (N-term)">Propionyl (N-term)</option>
-      <option value="Propionyl (Protein N-term)">Propionyl (Protein N-term)</option>
-      <option value="Propionyl (S)">Propionyl (S)</option>
-      <option value="Propionyl (T)">Propionyl (T)</option>
-      <option value="Propionyl:13C(3) (K)">Propionyl:13C(3) (K)</option>
-      <option value="Propionyl:13C(3) (N-term)">Propionyl:13C(3) (N-term)</option>
-      <option value="Propiophenone (C)">Propiophenone (C)</option>
-      <option value="Propiophenone (H)">Propiophenone (H)</option>
-      <option value="Propiophenone (K)">Propiophenone (K)</option>
-      <option value="Propiophenone (R)">Propiophenone (R)</option>
-      <option value="Propiophenone (S)">Propiophenone (S)</option>
-      <option value="Propiophenone (T)">Propiophenone (T)</option>
-      <option value="Propiophenone (W)">Propiophenone (W)</option>
-      <option value="Propyl (C-term)">Propyl (C-term)</option>
-      <option value="Propyl (D)">Propyl (D)</option>
-      <option value="Propyl (E)">Propyl (E)</option>
-      <option value="Propyl (K)">Propyl (K)</option>
-      <option value="Propyl (N-term)">Propyl (N-term)</option>
-      <option value="Propyl (Protein C-term)">Propyl (Protein C-term)</option>
-      <option value="Propyl:2H(6) (K)">Propyl:2H(6) (K)</option>
-      <option value="Propyl:2H(6) (N-term)">Propyl:2H(6) (N-term)</option>
-      <option value="PropylNAGthiazoline (C)">PropylNAGthiazoline (C)</option>
-      <option value="PS_Hapten (C)">PS_Hapten (C)</option>
-      <option value="PS_Hapten (H)">PS_Hapten (H)</option>
-      <option value="PS_Hapten (K)">PS_Hapten (K)</option>
-      <option value="pupylation (K)">pupylation (K)</option>
-      <option value="Puromycin (C-term)">Puromycin (C-term)</option>
-      <option value="PyMIC (N-term)">PyMIC (N-term)</option>
-      <option value="PyridoxalPhosphate (K)">PyridoxalPhosphate (K)</option>
-      <option value="PyridoxalPhosphateH2 (K)">PyridoxalPhosphateH2 (K)</option>
-      <option value="Pyridylacetyl (K)">Pyridylacetyl (K)</option>
-      <option value="Pyridylacetyl (N-term)">Pyridylacetyl (N-term)</option>
-      <option value="Pyridylethyl (C)">Pyridylethyl (C)</option>
-      <option value="Pyro-carbamidomethyl (N-term C)">Pyro-carbamidomethyl (N-term C)</option>
-      <option value="pyrophospho (S)">pyrophospho (S)</option>
-      <option value="pyrophospho (T)">pyrophospho (T)</option>
-      <option value="PyruvicAcidIminyl (K)">PyruvicAcidIminyl (K)</option>
-      <option value="PyruvicAcidIminyl (Protein N-term C)">PyruvicAcidIminyl (Protein N-term C)</option>
-      <option value="PyruvicAcidIminyl (Protein N-term V)">PyruvicAcidIminyl (Protein N-term V)</option>
-      <option value="QAT (C)">QAT (C)</option>
-      <option value="QAT:2H(3) (C)">QAT:2H(3) (C)</option>
-      <option value="QEQTGG (K)">QEQTGG (K)</option>
-      <option value="QQQTGG (K)">QQQTGG (K)</option>
-      <option value="QTGG (K)">QTGG (K)</option>
-      <option value="Quinone (W)">Quinone (W)</option>
-      <option value="Quinone (Y)">Quinone (Y)</option>
-      <option value="Retinylidene (K)">Retinylidene (K)</option>
-      <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
-      <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
-      <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-      <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-      <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-      <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-      <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-      <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-      <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-      <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-      <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
-      <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
-      <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
-      <option value="Saligenin (H)">Saligenin (H)</option>
-      <option value="Saligenin (K)">Saligenin (K)</option>
-      <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
-      <option value="Ser-&gt;Arg (S)">Ser-&gt;Arg (S)</option>
-      <option value="Ser-&gt;Asn (S)">Ser-&gt;Asn (S)</option>
-      <option value="Ser-&gt;Asp (S)">Ser-&gt;Asp (S)</option>
-      <option value="Ser-&gt;Cys (S)">Ser-&gt;Cys (S)</option>
-      <option value="Ser-&gt;Gln (S)">Ser-&gt;Gln (S)</option>
-      <option value="Ser-&gt;Glu (S)">Ser-&gt;Glu (S)</option>
-      <option value="Ser-&gt;Gly (S)">Ser-&gt;Gly (S)</option>
-      <option value="Ser-&gt;His (S)">Ser-&gt;His (S)</option>
-      <option value="Ser-&gt;LacticAcid (Protein N-term S)">Ser-&gt;LacticAcid (Protein N-term S)</option>
-      <option value="Ser-&gt;Lys (S)">Ser-&gt;Lys (S)</option>
-      <option value="Ser-&gt;Met (S)">Ser-&gt;Met (S)</option>
-      <option value="Ser-&gt;Phe (S)">Ser-&gt;Phe (S)</option>
-      <option value="Ser-&gt;Pro (S)">Ser-&gt;Pro (S)</option>
-      <option value="Ser-&gt;Thr (S)">Ser-&gt;Thr (S)</option>
-      <option value="Ser-&gt;Trp (S)">Ser-&gt;Trp (S)</option>
-      <option value="Ser-&gt;Tyr (S)">Ser-&gt;Tyr (S)</option>
-      <option value="Ser-&gt;Val (S)">Ser-&gt;Val (S)</option>
-      <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
-      <option value="serotonylation (Q)">serotonylation (Q)</option>
-      <option value="shTMT (K)">shTMT (K)</option>
-      <option value="shTMT (N-term)">shTMT (N-term)</option>
-      <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
-      <option value="SMA (K)">SMA (K)</option>
-      <option value="SMA (N-term)">SMA (N-term)</option>
-      <option value="spermidine (Q)">spermidine (Q)</option>
-      <option value="spermine (Q)">spermine (Q)</option>
-      <option value="SPITC (K)">SPITC (K)</option>
-      <option value="SPITC (N-term)">SPITC (N-term)</option>
-      <option value="SPITC:13C(6) (K)">SPITC:13C(6) (K)</option>
-      <option value="SPITC:13C(6) (N-term)">SPITC:13C(6) (N-term)</option>
-      <option value="Succinyl (K)">Succinyl (K)</option>
-      <option value="Succinyl (N-term)">Succinyl (N-term)</option>
-      <option value="Succinyl (Protein N-term)">Succinyl (Protein N-term)</option>
-      <option value="Succinyl:13C(4) (K)">Succinyl:13C(4) (K)</option>
-      <option value="Succinyl:13C(4) (N-term)">Succinyl:13C(4) (N-term)</option>
-      <option value="Succinyl:2H(4) (K)">Succinyl:2H(4) (K)</option>
-      <option value="Succinyl:2H(4) (N-term)">Succinyl:2H(4) (N-term)</option>
-      <option value="SulfanilicAcid (C-term)">SulfanilicAcid (C-term)</option>
-      <option value="SulfanilicAcid (D)">SulfanilicAcid (D)</option>
-      <option value="SulfanilicAcid (E)">SulfanilicAcid (E)</option>
-      <option value="SulfanilicAcid:13C(6) (C-term)">SulfanilicAcid:13C(6) (C-term)</option>
-      <option value="SulfanilicAcid:13C(6) (D)">SulfanilicAcid:13C(6) (D)</option>
-      <option value="SulfanilicAcid:13C(6) (E)">SulfanilicAcid:13C(6) (E)</option>
-      <option value="Sulfide (C)">Sulfide (C)</option>
-      <option value="Sulfide (D)">Sulfide (D)</option>
-      <option value="Sulfide (W)">Sulfide (W)</option>
-      <option value="Sulfo (C)">Sulfo (C)</option>
-      <option value="Sulfo (S)">Sulfo (S)</option>
-      <option value="Sulfo (T)">Sulfo (T)</option>
-      <option value="Sulfo (Y)">Sulfo (Y)</option>
-      <option value="sulfo+amino (Y)">sulfo+amino (Y)</option>
-      <option value="Sulfo-NHS-LC-LC-Biotin (K)">Sulfo-NHS-LC-LC-Biotin (K)</option>
-      <option value="Sulfo-NHS-LC-LC-Biotin (N-term)">Sulfo-NHS-LC-LC-Biotin (N-term)</option>
-      <option value="SulfoGMBS (C)">SulfoGMBS (C)</option>
-      <option value="SulfurDioxide (C)">SulfurDioxide (C)</option>
-      <option value="SUMO2135 (K)">SUMO2135 (K)</option>
-      <option value="SUMO3549 (K)">SUMO3549 (K)</option>
-      <option value="TAMRA-FP (S)">TAMRA-FP (S)</option>
-      <option value="TAMRA-FP (Y)">TAMRA-FP (Y)</option>
-      <option value="Thiadiazole (C)">Thiadiazole (C)</option>
-      <option value="Thiazolidine (C)">Thiazolidine (C)</option>
-      <option value="Thiazolidine (F)">Thiazolidine (F)</option>
-      <option value="Thiazolidine (H)">Thiazolidine (H)</option>
-      <option value="Thiazolidine (K)">Thiazolidine (K)</option>
-      <option value="Thiazolidine (Protein N-term)">Thiazolidine (Protein N-term)</option>
-      <option value="Thiazolidine (R)">Thiazolidine (R)</option>
-      <option value="Thiazolidine (W)">Thiazolidine (W)</option>
-      <option value="Thiazolidine (Y)">Thiazolidine (Y)</option>
-      <option value="thioacylPA (K)">thioacylPA (K)</option>
-      <option value="Thiophos-S-S-biotin (S)">Thiophos-S-S-biotin (S)</option>
-      <option value="Thiophos-S-S-biotin (T)">Thiophos-S-S-biotin (T)</option>
-      <option value="Thiophos-S-S-biotin (Y)">Thiophos-S-S-biotin (Y)</option>
-      <option value="Thiophospho (S)">Thiophospho (S)</option>
-      <option value="Thiophospho (T)">Thiophospho (T)</option>
-      <option value="Thiophospho (Y)">Thiophospho (Y)</option>
-      <option value="Thr-&gt;Ala (T)">Thr-&gt;Ala (T)</option>
-      <option value="Thr-&gt;Arg (T)">Thr-&gt;Arg (T)</option>
-      <option value="Thr-&gt;Asn (T)">Thr-&gt;Asn (T)</option>
-      <option value="Thr-&gt;Asp (T)">Thr-&gt;Asp (T)</option>
-      <option value="Thr-&gt;Cys (T)">Thr-&gt;Cys (T)</option>
-      <option value="Thr-&gt;Gln (T)">Thr-&gt;Gln (T)</option>
-      <option value="Thr-&gt;Glu (T)">Thr-&gt;Glu (T)</option>
-      <option value="Thr-&gt;Gly (T)">Thr-&gt;Gly (T)</option>
-      <option value="Thr-&gt;His (T)">Thr-&gt;His (T)</option>
-      <option value="Thr-&gt;Lys (T)">Thr-&gt;Lys (T)</option>
-      <option value="Thr-&gt;Met (T)">Thr-&gt;Met (T)</option>
-      <option value="Thr-&gt;Phe (T)">Thr-&gt;Phe (T)</option>
-      <option value="Thr-&gt;Pro (T)">Thr-&gt;Pro (T)</option>
-      <option value="Thr-&gt;Ser (T)">Thr-&gt;Ser (T)</option>
-      <option value="Thr-&gt;Trp (T)">Thr-&gt;Trp (T)</option>
-      <option value="Thr-&gt;Tyr (T)">Thr-&gt;Tyr (T)</option>
-      <option value="Thr-&gt;Val (T)">Thr-&gt;Val (T)</option>
-      <option value="Thr-&gt;Xle (T)">Thr-&gt;Xle (T)</option>
-      <option value="Thrbiotinhydrazide (T)">Thrbiotinhydrazide (T)</option>
-      <option value="Thyroxine (Y)">Thyroxine (Y)</option>
-      <option value="TMAB (K)">TMAB (K)</option>
-      <option value="TMAB (N-term)">TMAB (N-term)</option>
-      <option value="TMAB:2H(9) (K)">TMAB:2H(9) (K)</option>
-      <option value="TMAB:2H(9) (N-term)">TMAB:2H(9) (N-term)</option>
-      <option value="TMPP-Ac (K)">TMPP-Ac (K)</option>
-      <option value="TMPP-Ac (N-term)">TMPP-Ac (N-term)</option>
-      <option value="TMPP-Ac (Y)">TMPP-Ac (Y)</option>
-      <option value="TMPP-Ac:13C(9) (K)">TMPP-Ac:13C(9) (K)</option>
-      <option value="TMPP-Ac:13C(9) (N-term)">TMPP-Ac:13C(9) (N-term)</option>
-      <option value="TMPP-Ac:13C(9) (Y)">TMPP-Ac:13C(9) (Y)</option>
-      <option value="TMT (H)">TMT (H)</option>
-      <option value="TMT (K)">TMT (K)</option>
-      <option value="TMT (N-term)">TMT (N-term)</option>
-      <option value="TMT (Protein N-term)">TMT (Protein N-term)</option>
-      <option value="TMT (S)">TMT (S)</option>
-      <option value="TMT (T)">TMT (T)</option>
-      <option value="TMT2plex (H)">TMT2plex (H)</option>
-      <option value="TMT2plex (K)">TMT2plex (K)</option>
-      <option value="TMT2plex (N-term)">TMT2plex (N-term)</option>
-      <option value="TMT2plex (Protein N-term)">TMT2plex (Protein N-term)</option>
-      <option value="TMT2plex (S)">TMT2plex (S)</option>
-      <option value="TMT2plex (T)">TMT2plex (T)</option>
-      <option value="TMT6plex (H)">TMT6plex (H)</option>
-      <option value="TMT6plex (K)">TMT6plex (K)</option>
-      <option value="TMT6plex (N-term)">TMT6plex (N-term)</option>
-      <option value="TMT6plex (Protein N-term)">TMT6plex (Protein N-term)</option>
-      <option value="TMT6plex (S)">TMT6plex (S)</option>
-      <option value="TMT6plex (T)">TMT6plex (T)</option>
-      <option value="TMTpro (H)">TMTpro (H)</option>
-      <option value="TMTpro (K)">TMTpro (K)</option>
-      <option value="TMTpro (N-term)">TMTpro (N-term)</option>
-      <option value="TMTpro (Protein N-term)">TMTpro (Protein N-term)</option>
-      <option value="TMTpro (S)">TMTpro (S)</option>
-      <option value="TMTpro (T)">TMTpro (T)</option>
-      <option value="TMTpro_zero (H)">TMTpro_zero (H)</option>
-      <option value="TMTpro_zero (K)">TMTpro_zero (K)</option>
-      <option value="TMTpro_zero (N-term)">TMTpro_zero (N-term)</option>
-      <option value="TMTpro_zero (Protein N-term)">TMTpro_zero (Protein N-term)</option>
-      <option value="TMTpro_zero (S)">TMTpro_zero (S)</option>
-      <option value="TMTpro_zero (T)">TMTpro_zero (T)</option>
-      <option value="TNBS (K)">TNBS (K)</option>
-      <option value="TNBS (N-term)">TNBS (N-term)</option>
-      <option value="trifluoro (L)">trifluoro (L)</option>
-      <option value="Triiodo (Y)">Triiodo (Y)</option>
-      <option value="Triiodothyronine (Y)">Triiodothyronine (Y)</option>
-      <option value="Trimethyl (K)">Trimethyl (K)</option>
-      <option value="Trimethyl (Protein N-term A)">Trimethyl (Protein N-term A)</option>
-      <option value="Trimethyl (R)">Trimethyl (R)</option>
-      <option value="Trimethyl:13C(3)2H(9) (K)">Trimethyl:13C(3)2H(9) (K)</option>
-      <option value="Trimethyl:13C(3)2H(9) (R)">Trimethyl:13C(3)2H(9) (R)</option>
-      <option value="Trimethyl:2H(9) (K)">Trimethyl:2H(9) (K)</option>
-      <option value="Trimethyl:2H(9) (R)">Trimethyl:2H(9) (R)</option>
-      <option value="Trioxidation (C)">Trioxidation (C)</option>
-      <option value="Trioxidation (F)">Trioxidation (F)</option>
-      <option value="Trioxidation (W)">Trioxidation (W)</option>
-      <option value="Trioxidation (Y)">Trioxidation (Y)</option>
-      <option value="Tripalmitate (Protein N-term C)">Tripalmitate (Protein N-term C)</option>
-      <option value="Tris (N)">Tris (N)</option>
-      <option value="Triton (C-term)">Triton (C-term)</option>
-      <option value="Triton (N-term)">Triton (N-term)</option>
-      <option value="Trp-&gt;Ala (W)">Trp-&gt;Ala (W)</option>
-      <option value="Trp-&gt;Arg (W)">Trp-&gt;Arg (W)</option>
-      <option value="Trp-&gt;Asn (W)">Trp-&gt;Asn (W)</option>
-      <option value="Trp-&gt;Asp (W)">Trp-&gt;Asp (W)</option>
-      <option value="Trp-&gt;Cys (W)">Trp-&gt;Cys (W)</option>
-      <option value="Trp-&gt;Gln (W)">Trp-&gt;Gln (W)</option>
-      <option value="Trp-&gt;Glu (W)">Trp-&gt;Glu (W)</option>
-      <option value="Trp-&gt;Gly (W)">Trp-&gt;Gly (W)</option>
-      <option value="Trp-&gt;His (W)">Trp-&gt;His (W)</option>
-      <option value="Trp-&gt;Hydroxykynurenin (W)">Trp-&gt;Hydroxykynurenin (W)</option>
-      <option value="Trp-&gt;Kynurenin (W)">Trp-&gt;Kynurenin (W)</option>
-      <option value="Trp-&gt;Lys (W)">Trp-&gt;Lys (W)</option>
-      <option value="Trp-&gt;Met (W)">Trp-&gt;Met (W)</option>
-      <option value="Trp-&gt;Oxolactone (W)">Trp-&gt;Oxolactone (W)</option>
-      <option value="Trp-&gt;Phe (W)">Trp-&gt;Phe (W)</option>
-      <option value="Trp-&gt;Pro (W)">Trp-&gt;Pro (W)</option>
-      <option value="Trp-&gt;Ser (W)">Trp-&gt;Ser (W)</option>
-      <option value="Trp-&gt;Thr (W)">Trp-&gt;Thr (W)</option>
-      <option value="Trp-&gt;Tyr (W)">Trp-&gt;Tyr (W)</option>
-      <option value="Trp-&gt;Val (W)">Trp-&gt;Val (W)</option>
-      <option value="Trp-&gt;Xle (W)">Trp-&gt;Xle (W)</option>
-      <option value="Tween20 (N-term)">Tween20 (N-term)</option>
-      <option value="Tween80 (C-term)">Tween80 (C-term)</option>
-      <option value="Tyr-&gt;Ala (Y)">Tyr-&gt;Ala (Y)</option>
-      <option value="Tyr-&gt;Arg (Y)">Tyr-&gt;Arg (Y)</option>
-      <option value="Tyr-&gt;Asn (Y)">Tyr-&gt;Asn (Y)</option>
-      <option value="Tyr-&gt;Asp (Y)">Tyr-&gt;Asp (Y)</option>
-      <option value="Tyr-&gt;Cys (Y)">Tyr-&gt;Cys (Y)</option>
-      <option value="Tyr-&gt;Dha (Y)">Tyr-&gt;Dha (Y)</option>
-      <option value="Tyr-&gt;Gln (Y)">Tyr-&gt;Gln (Y)</option>
-      <option value="Tyr-&gt;Glu (Y)">Tyr-&gt;Glu (Y)</option>
-      <option value="Tyr-&gt;Gly (Y)">Tyr-&gt;Gly (Y)</option>
-      <option value="Tyr-&gt;His (Y)">Tyr-&gt;His (Y)</option>
-      <option value="Tyr-&gt;Lys (Y)">Tyr-&gt;Lys (Y)</option>
-      <option value="Tyr-&gt;Met (Y)">Tyr-&gt;Met (Y)</option>
-      <option value="Tyr-&gt;Phe (Y)">Tyr-&gt;Phe (Y)</option>
-      <option value="Tyr-&gt;Pro (Y)">Tyr-&gt;Pro (Y)</option>
-      <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
-      <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
-      <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
-      <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
-      <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-      <option value="Ub-amide (C)">Ub-amide (C)</option>
-      <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
-      <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
-      <option value="Ub-VME (C)">Ub-VME (C)</option>
-      <option value="UgiJoullie (D)">UgiJoullie (D)</option>
-      <option value="UgiJoullie (E)">UgiJoullie (E)</option>
-      <option value="UgiJoullieProGly (D)">UgiJoullieProGly (D)</option>
-      <option value="UgiJoullieProGly (E)">UgiJoullieProGly (E)</option>
-      <option value="UgiJoullieProGlyProGly (D)">UgiJoullieProGlyProGly (D)</option>
-      <option value="UgiJoullieProGlyProGly (E)">UgiJoullieProGlyProGly (E)</option>
-      <option value="Unknown:162 (C-term)">Unknown:162 (C-term)</option>
-      <option value="Unknown:162 (D)">Unknown:162 (D)</option>
-      <option value="Unknown:162 (E)">Unknown:162 (E)</option>
-      <option value="Unknown:162 (N-term)">Unknown:162 (N-term)</option>
-      <option value="Unknown:177 (C-term)">Unknown:177 (C-term)</option>
-      <option value="Unknown:177 (D)">Unknown:177 (D)</option>
-      <option value="Unknown:177 (E)">Unknown:177 (E)</option>
-      <option value="Unknown:177 (N-term)">Unknown:177 (N-term)</option>
-      <option value="Unknown:210 (C-term)">Unknown:210 (C-term)</option>
-      <option value="Unknown:210 (D)">Unknown:210 (D)</option>
-      <option value="Unknown:210 (E)">Unknown:210 (E)</option>
-      <option value="Unknown:210 (N-term)">Unknown:210 (N-term)</option>
-      <option value="Unknown:216 (C-term)">Unknown:216 (C-term)</option>
-      <option value="Unknown:216 (D)">Unknown:216 (D)</option>
-      <option value="Unknown:216 (E)">Unknown:216 (E)</option>
-      <option value="Unknown:216 (N-term)">Unknown:216 (N-term)</option>
-      <option value="Unknown:234 (C-term)">Unknown:234 (C-term)</option>
-      <option value="Unknown:234 (D)">Unknown:234 (D)</option>
-      <option value="Unknown:234 (E)">Unknown:234 (E)</option>
-      <option value="Unknown:234 (N-term)">Unknown:234 (N-term)</option>
-      <option value="Unknown:248 (C-term)">Unknown:248 (C-term)</option>
-      <option value="Unknown:248 (D)">Unknown:248 (D)</option>
-      <option value="Unknown:248 (E)">Unknown:248 (E)</option>
-      <option value="Unknown:248 (N-term)">Unknown:248 (N-term)</option>
-      <option value="Unknown:250 (C-term)">Unknown:250 (C-term)</option>
-      <option value="Unknown:250 (D)">Unknown:250 (D)</option>
-      <option value="Unknown:250 (E)">Unknown:250 (E)</option>
-      <option value="Unknown:250 (N-term)">Unknown:250 (N-term)</option>
-      <option value="Unknown:302 (C-term)">Unknown:302 (C-term)</option>
-      <option value="Unknown:302 (D)">Unknown:302 (D)</option>
-      <option value="Unknown:302 (E)">Unknown:302 (E)</option>
-      <option value="Unknown:302 (N-term)">Unknown:302 (N-term)</option>
-      <option value="Unknown:306 (C-term)">Unknown:306 (C-term)</option>
-      <option value="Unknown:306 (D)">Unknown:306 (D)</option>
-      <option value="Unknown:306 (E)">Unknown:306 (E)</option>
-      <option value="Unknown:306 (N-term)">Unknown:306 (N-term)</option>
-      <option value="Unknown:420 (C-term)">Unknown:420 (C-term)</option>
-      <option value="Unknown:420 (N-term)">Unknown:420 (N-term)</option>
-      <option value="Val-&gt;Ala (V)">Val-&gt;Ala (V)</option>
-      <option value="Val-&gt;Arg (V)">Val-&gt;Arg (V)</option>
-      <option value="Val-&gt;Asn (V)">Val-&gt;Asn (V)</option>
-      <option value="Val-&gt;Asp (V)">Val-&gt;Asp (V)</option>
-      <option value="Val-&gt;Cys (V)">Val-&gt;Cys (V)</option>
-      <option value="Val-&gt;Gln (V)">Val-&gt;Gln (V)</option>
-      <option value="Val-&gt;Glu (V)">Val-&gt;Glu (V)</option>
-      <option value="Val-&gt;Gly (V)">Val-&gt;Gly (V)</option>
-      <option value="Val-&gt;His (V)">Val-&gt;His (V)</option>
-      <option value="Val-&gt;Lys (V)">Val-&gt;Lys (V)</option>
-      <option value="Val-&gt;Met (V)">Val-&gt;Met (V)</option>
-      <option value="Val-&gt;Phe (V)">Val-&gt;Phe (V)</option>
-      <option value="Val-&gt;Pro (V)">Val-&gt;Pro (V)</option>
-      <option value="Val-&gt;Ser (V)">Val-&gt;Ser (V)</option>
-      <option value="Val-&gt;Thr (V)">Val-&gt;Thr (V)</option>
-      <option value="Val-&gt;Trp (V)">Val-&gt;Trp (V)</option>
-      <option value="Val-&gt;Tyr (V)">Val-&gt;Tyr (V)</option>
-      <option value="Val-&gt;Xle (V)">Val-&gt;Xle (V)</option>
-      <option value="VFQQQTGG (K)">VFQQQTGG (K)</option>
-      <option value="VIEVYQEQTGG (K)">VIEVYQEQTGG (K)</option>
-      <option value="Withaferin (C)">Withaferin (C)</option>
-      <option value="Xle-&gt;Ala (I)">Xle-&gt;Ala (I)</option>
-      <option value="Xle-&gt;Ala (L)">Xle-&gt;Ala (L)</option>
-      <option value="Xle-&gt;Arg (I)">Xle-&gt;Arg (I)</option>
-      <option value="Xle-&gt;Arg (L)">Xle-&gt;Arg (L)</option>
-      <option value="Xle-&gt;Asn (I)">Xle-&gt;Asn (I)</option>
-      <option value="Xle-&gt;Asn (L)">Xle-&gt;Asn (L)</option>
-      <option value="Xle-&gt;Asp (I)">Xle-&gt;Asp (I)</option>
-      <option value="Xle-&gt;Asp (L)">Xle-&gt;Asp (L)</option>
-      <option value="Xle-&gt;Cys (I)">Xle-&gt;Cys (I)</option>
-      <option value="Xle-&gt;Cys (L)">Xle-&gt;Cys (L)</option>
-      <option value="Xle-&gt;Gln (I)">Xle-&gt;Gln (I)</option>
-      <option value="Xle-&gt;Gln (L)">Xle-&gt;Gln (L)</option>
-      <option value="Xle-&gt;Glu (I)">Xle-&gt;Glu (I)</option>
-      <option value="Xle-&gt;Glu (L)">Xle-&gt;Glu (L)</option>
-      <option value="Xle-&gt;Gly (I)">Xle-&gt;Gly (I)</option>
-      <option value="Xle-&gt;Gly (L)">Xle-&gt;Gly (L)</option>
-      <option value="Xle-&gt;His (I)">Xle-&gt;His (I)</option>
-      <option value="Xle-&gt;His (L)">Xle-&gt;His (L)</option>
-      <option value="Xle-&gt;Lys (I)">Xle-&gt;Lys (I)</option>
-      <option value="Xle-&gt;Lys (L)">Xle-&gt;Lys (L)</option>
-      <option value="Xle-&gt;Met (I)">Xle-&gt;Met (I)</option>
-      <option value="Xle-&gt;Met (L)">Xle-&gt;Met (L)</option>
-      <option value="Xle-&gt;Phe (I)">Xle-&gt;Phe (I)</option>
-      <option value="Xle-&gt;Phe (L)">Xle-&gt;Phe (L)</option>
-      <option value="Xle-&gt;Pro (I)">Xle-&gt;Pro (I)</option>
-      <option value="Xle-&gt;Pro (L)">Xle-&gt;Pro (L)</option>
-      <option value="Xle-&gt;Ser (I)">Xle-&gt;Ser (I)</option>
-      <option value="Xle-&gt;Ser (L)">Xle-&gt;Ser (L)</option>
-      <option value="Xle-&gt;Thr (I)">Xle-&gt;Thr (I)</option>
-      <option value="Xle-&gt;Thr (L)">Xle-&gt;Thr (L)</option>
-      <option value="Xle-&gt;Trp (I)">Xle-&gt;Trp (I)</option>
-      <option value="Xle-&gt;Trp (L)">Xle-&gt;Trp (L)</option>
-      <option value="Xle-&gt;Tyr (I)">Xle-&gt;Tyr (I)</option>
-      <option value="Xle-&gt;Tyr (L)">Xle-&gt;Tyr (L)</option>
-      <option value="Xle-&gt;Val (I)">Xle-&gt;Val (I)</option>
-      <option value="Xle-&gt;Val (L)">Xle-&gt;Val (L)</option>
-      <option value="Xlink:B10621 (C)">Xlink:B10621 (C)</option>
-      <option value="Xlink:BMOE (C)">Xlink:BMOE (C)</option>
-      <option value="Xlink:BS2G[113] (K)">Xlink:BS2G[113] (K)</option>
-      <option value="Xlink:BS2G[113] (Protein N-term)">Xlink:BS2G[113] (Protein N-term)</option>
-      <option value="Xlink:BS2G[114] (K)">Xlink:BS2G[114] (K)</option>
-      <option value="Xlink:BS2G[114] (Protein N-term)">Xlink:BS2G[114] (Protein N-term)</option>
-      <option value="Xlink:BS2G[217] (K)">Xlink:BS2G[217] (K)</option>
-      <option value="Xlink:BS2G[217] (Protein N-term)">Xlink:BS2G[217] (Protein N-term)</option>
-      <option value="Xlink:BS2G[96] (K)">Xlink:BS2G[96] (K)</option>
-      <option value="Xlink:BS2G[96] (Protein N-term)">Xlink:BS2G[96] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[111] (K)">Xlink:BuUrBu[111] (K)</option>
-      <option value="Xlink:BuUrBu[111] (Protein N-term)">Xlink:BuUrBu[111] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[196] (K)">Xlink:BuUrBu[196] (K)</option>
-      <option value="Xlink:BuUrBu[196] (Protein N-term)">Xlink:BuUrBu[196] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[213] (K)">Xlink:BuUrBu[213] (K)</option>
-      <option value="Xlink:BuUrBu[213] (Protein N-term)">Xlink:BuUrBu[213] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[214] (K)">Xlink:BuUrBu[214] (K)</option>
-      <option value="Xlink:BuUrBu[214] (Protein N-term)">Xlink:BuUrBu[214] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[317] (K)">Xlink:BuUrBu[317] (K)</option>
-      <option value="Xlink:BuUrBu[317] (Protein N-term)">Xlink:BuUrBu[317] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[85] (K)">Xlink:BuUrBu[85] (K)</option>
-      <option value="Xlink:BuUrBu[85] (Protein N-term)">Xlink:BuUrBu[85] (Protein N-term)</option>
-      <option value="Xlink:DFDNB (K)">Xlink:DFDNB (K)</option>
-      <option value="Xlink:DFDNB (N)">Xlink:DFDNB (N)</option>
-      <option value="Xlink:DFDNB (Q)">Xlink:DFDNB (Q)</option>
-      <option value="Xlink:DFDNB (R)">Xlink:DFDNB (R)</option>
-      <option value="Xlink:DMP[122] (K)">Xlink:DMP[122] (K)</option>
-      <option value="Xlink:DMP[122] (Protein N-term)">Xlink:DMP[122] (Protein N-term)</option>
-      <option value="Xlink:DMP[139] (K)">Xlink:DMP[139] (K)</option>
-      <option value="Xlink:DMP[139] (Protein N-term)">Xlink:DMP[139] (Protein N-term)</option>
-      <option value="Xlink:DMP[140] (K)">Xlink:DMP[140] (K)</option>
-      <option value="Xlink:DMP[140] (Protein N-term)">Xlink:DMP[140] (Protein N-term)</option>
-      <option value="Xlink:DMP[154] (K)">Xlink:DMP[154] (K)</option>
-      <option value="Xlink:DMP[154] (Protein N-term)">Xlink:DMP[154] (Protein N-term)</option>
-      <option value="Xlink:DSS[138] (K)">Xlink:DSS[138] (K)</option>
-      <option value="Xlink:DSS[138] (Protein N-term)">Xlink:DSS[138] (Protein N-term)</option>
-      <option value="Xlink:DSS[155] (K)">Xlink:DSS[155] (K)</option>
-      <option value="Xlink:DSS[155] (Protein N-term)">Xlink:DSS[155] (Protein N-term)</option>
-      <option value="Xlink:DSS[156] (K)">Xlink:DSS[156] (K)</option>
-      <option value="Xlink:DSS[156] (Protein N-term)">Xlink:DSS[156] (Protein N-term)</option>
-      <option value="Xlink:DSS[259] (K)">Xlink:DSS[259] (K)</option>
-      <option value="Xlink:DSS[259] (Protein N-term)">Xlink:DSS[259] (Protein N-term)</option>
-      <option value="Xlink:DSSO[104] (K)">Xlink:DSSO[104] (K)</option>
-      <option value="Xlink:DSSO[104] (Protein N-term)">Xlink:DSSO[104] (Protein N-term)</option>
-      <option value="Xlink:DSSO[158] (K)">Xlink:DSSO[158] (K)</option>
-      <option value="Xlink:DSSO[158] (Protein N-term)">Xlink:DSSO[158] (Protein N-term)</option>
-      <option value="Xlink:DSSO[175] (K)">Xlink:DSSO[175] (K)</option>
-      <option value="Xlink:DSSO[175] (Protein N-term)">Xlink:DSSO[175] (Protein N-term)</option>
-      <option value="Xlink:DSSO[176] (K)">Xlink:DSSO[176] (K)</option>
-      <option value="Xlink:DSSO[176] (Protein N-term)">Xlink:DSSO[176] (Protein N-term)</option>
-      <option value="Xlink:DSSO[279] (K)">Xlink:DSSO[279] (K)</option>
-      <option value="Xlink:DSSO[279] (Protein N-term)">Xlink:DSSO[279] (Protein N-term)</option>
-      <option value="Xlink:DSSO[54] (K)">Xlink:DSSO[54] (K)</option>
-      <option value="Xlink:DSSO[54] (Protein N-term)">Xlink:DSSO[54] (Protein N-term)</option>
-      <option value="Xlink:DSSO[86] (K)">Xlink:DSSO[86] (K)</option>
-      <option value="Xlink:DSSO[86] (Protein N-term)">Xlink:DSSO[86] (Protein N-term)</option>
-      <option value="Xlink:DST[114] (K)">Xlink:DST[114] (K)</option>
-      <option value="Xlink:DST[114] (Protein N-term)">Xlink:DST[114] (Protein N-term)</option>
-      <option value="Xlink:DST[132] (K)">Xlink:DST[132] (K)</option>
-      <option value="Xlink:DST[132] (Protein N-term)">Xlink:DST[132] (Protein N-term)</option>
-      <option value="Xlink:DST[56] (K)">Xlink:DST[56] (K)</option>
-      <option value="Xlink:DST[56] (Protein N-term)">Xlink:DST[56] (Protein N-term)</option>
-      <option value="Xlink:DTBP[172] (K)">Xlink:DTBP[172] (K)</option>
-      <option value="Xlink:DTBP[172] (Protein N-term)">Xlink:DTBP[172] (Protein N-term)</option>
-      <option value="Xlink:DTBP[87] (K)">Xlink:DTBP[87] (K)</option>
-      <option value="Xlink:DTBP[87] (Protein N-term)">Xlink:DTBP[87] (Protein N-term)</option>
-      <option value="Xlink:DTSSP[174] (K)">Xlink:DTSSP[174] (K)</option>
-      <option value="Xlink:DTSSP[174] (Protein N-term)">Xlink:DTSSP[174] (Protein N-term)</option>
-      <option value="Xlink:DTSSP[192] (K)">Xlink:DTSSP[192] (K)</option>
-      <option value="Xlink:DTSSP[192] (Protein N-term)">Xlink:DTSSP[192] (Protein N-term)</option>
-      <option value="Xlink:DTSSP[88] (K)">Xlink:DTSSP[88] (K)</option>
-      <option value="Xlink:DTSSP[88] (Protein N-term)">Xlink:DTSSP[88] (Protein N-term)</option>
-      <option value="Xlink:EGS[115] (K)">Xlink:EGS[115] (K)</option>
-      <option value="Xlink:EGS[115] (Protein N-term)">Xlink:EGS[115] (Protein N-term)</option>
-      <option value="Xlink:EGS[226] (K)">Xlink:EGS[226] (K)</option>
-      <option value="Xlink:EGS[226] (Protein N-term)">Xlink:EGS[226] (Protein N-term)</option>
-      <option value="Xlink:EGS[244] (K)">Xlink:EGS[244] (K)</option>
-      <option value="Xlink:EGS[244] (Protein N-term)">Xlink:EGS[244] (Protein N-term)</option>
-      <option value="Xlink:SMCC[219] (C)">Xlink:SMCC[219] (C)</option>
-      <option value="Xlink:SMCC[219] (K)">Xlink:SMCC[219] (K)</option>
-      <option value="Xlink:SMCC[219] (Protein N-term)">Xlink:SMCC[219] (Protein N-term)</option>
-      <option value="Xlink:SMCC[237] (C)">Xlink:SMCC[237] (C)</option>
-      <option value="Xlink:SMCC[237] (K)">Xlink:SMCC[237] (K)</option>
-      <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
-      <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
-      <option value="ZGB (K)">ZGB (K)</option>
-      <option value="ZGB (N-term)">ZGB (N-term)</option>
-      <option value="ZQG (K)">ZQG (K)</option>
-      <expand macro="list_string_san" name="variable_modifications"/>
-    </param>
-    <param argument="-v" type="integer" optional="true" value="1" label="number of missed cleavages allowed" help=""/>
-    <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
-      <option value="Trypsin" selected="true">Trypsin</option>
-      <option value="Formic_acid">Formic_acid</option>
-      <option value="Lys-C">Lys-C</option>
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="Chymotrypsin">Chymotrypsin</option>
-      <option value="Lys-C/P">Lys-C/P</option>
-      <option value="Asp-N">Asp-N</option>
-      <option value="CNBr">CNBr</option>
-      <option value="PepsinA">PepsinA</option>
-      <option value="TrypChymo">TrypChymo</option>
-      <option value="Trypsin/P">Trypsin/P</option>
-      <option value="Arg-C">Arg-C</option>
-      <option value="no cleavage">no cleavage</option>
-      <option value="unspecific cleavage">unspecific cleavage</option>
-      <expand macro="list_string_san" name="enzyme"/>
-    </param>
-    <param argument="-hl" type="integer" optional="true" value="30" label="maximum number of hits retained for one spectrum" help="Note: even when set to 1 OMSSA may report multiple hits with different charge states"/>
-    <param argument="-he" type="float" optional="true" value="1000.0" label="the maximum e-value allowed in the hit list" help="If you set this parameter too small (e.g., he=1), this will effectively introduce FDR filtering. Thus, allowing a less stringent FDR during post-processing will nevertheless return the (better) FDR introduced here, since mediocre hits are not even reported"/>
-    <expand macro="adv_opts_macro">
-      <param argument="-pc" type="integer" optional="true" value="1" label="The number of pseudocounts to add to each precursor mass bin" help=""/>
-      <param argument="-hs" type="integer" optional="true" value="4" label="the minimum number of m/z values a spectrum must have to be searched" help=""/>
-      <param argument="-tez" type="integer" optional="true" value="1" label="scaling of precursor mass tolerance with charge (0 = none, 1= linear)" help=""/>
-      <param argument="-tom" type="integer" optional="true" value="0" label="product ion search type, with 0 = monoisotopic, 1 = average, 2 = monoisotopic N15, 3 = exact" help=""/>
-      <param argument="-tem" type="integer" optional="true" value="0" label="precursor ion search type, with 0 = monoisotopic, 1 = average, 2 = monoisotopic N15, 3 = exact" help=""/>
-      <param argument="-tex" type="float" optional="true" value="1446.94" label="threshold in Da above which the mass of a neutron should be added in an exact mass search" help=""/>
-      <param argument="-zt" type="integer" optional="true" value="3" label="minimum precursor charge to start considering multiply charged products" help=""/>
-      <param argument="-z1" type="float" optional="true" value="0.95" label="the fraction of peaks below the precursor used to determine if the spectrum is charge +1" help=""/>
-      <param argument="-zc" type="integer" optional="true" value="1" label="should charge +1 be determined algorithmically (1=yes)" help=""/>
-      <param argument="-zcc" type="integer" optional="true" value="2" label="how should precursor charges be determined" help="(1=believe the input file,2=use the specified range)"/>
-      <param argument="-zoh" type="integer" optional="true" value="2" label="set the maximum product charge to search" help=""/>
-      <param argument="-no" type="integer" optional="true" value="4" label="minimum size of peptides for no-enzyme and semi-tryptic searches" help=""/>
-      <param argument="-nox" type="integer" optional="true" value="40" label="maximum size of peptides for no-enzyme and semi-tryptic searches" help=""/>
-      <param argument="-i" type="text" optional="true" value="1,4" label="comma delimited list of id numbers of ions to search" help="">
-        <expand macro="list_string_san" name="i"/>
-      </param>
-      <param argument="-sp" type="integer" optional="true" value="100" label="number of product ions to search" help=""/>
-      <param argument="-sb1" type="integer" optional="true" value="1" label="should first forward" help="(e.g. b1) product ions be searched (1 = no, 0 = yes)"/>
-      <param argument="-sct" type="integer" optional="true" value="0" label="should c terminus ions" help="(e.g. y1) be searched (1 = no, 0 = yes)"/>
-      <param argument="-x" type="text" optional="true" value="0" label="comma delimited list of NCBI taxonomy ids to search (0 = all" help="This is the default)">
-        <expand macro="list_string_san" name="x"/>
-      </param>
-      <param argument="-hm" type="integer" optional="true" value="2" label="the minimum number of m/z matches a sequence library peptide must have for the hit to the peptide to be recorded" help=""/>
-      <param argument="-ht" type="integer" optional="true" value="6" label="number of m/z values corresponding to the most intense peaks that must include one match to the theoretical peptide" help=""/>
-      <param argument="-mm" type="integer" optional="true" value="128" label="the maximum number of mass ladders to generate per database peptide" help=""/>
-      <param argument="-mnm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="n-term methionine should not be cleaved" help=""/>
-      <param argument="-is" type="float" optional="true" value="0.0" label="evalue threshold to include a sequence in the iterative search, 0 = all" help=""/>
-      <param argument="-ir" type="float" optional="true" value="0.0" label="evalue threshold to replace a hit, 0 = only if bette" help=""/>
-      <param argument="-ii" type="float" optional="true" value="0.0" label="evalue threshold to iteratively search a spectrum again, 0 = always" help=""/>
-      <param argument="-chunk_size" type="integer" optional="true" value="0" label="Number of spectra to submit in one chunk to OMSSA" help="Chunks with more than 30k spectra will likely cause memory allocation issues with 32bit OMSSA versions (which is usually the case on Windows). To disable chunking (i.e. submit all spectra in one big chunk), set it to '0'"/>
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><!-- TOPP_OMSSAAdapter_1 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="pc" value="1"/>
-        <param name="hs" value="4"/>
-        <param name="tez" value="1"/>
-        <param name="tom" value="0"/>
-        <param name="tem" value="0"/>
-        <param name="tex" value="1446.94"/>
-        <param name="zt" value="3"/>
-        <param name="z1" value="0.95"/>
-        <param name="zc" value="1"/>
-        <param name="zcc" value="2"/>
-        <param name="zoh" value="2"/>
-        <param name="no" value="4"/>
-        <param name="nox" value="40"/>
-        <param name="i" value="1,4"/>
-        <param name="sp" value="100"/>
-        <param name="sb1" value="1"/>
-        <param name="sct" value="0"/>
-        <param name="x" value="0"/>
-        <param name="hm" value="2"/>
-        <param name="ht" value="6"/>
-        <param name="mm" value="128"/>
-        <param name="mnm" value="false"/>
-        <param name="is" value="0.0"/>
-        <param name="ir" value="0.0"/>
-        <param name="ii" value="0.0"/>
-        <param name="chunk_size" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="spectra.mzML"/>
-      <output name="out" file="OMSSAAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <param name="precursor_mass_tolerance" value="5.0"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="fragment_mass_tolerance" value="0.3"/>
-      <param name="database" value="proteins.fasta"/>
-      <param name="min_precursor_charge" value="1"/>
-      <param name="max_precursor_charge" value="3"/>
-      <param name="fixed_modifications"/>
-      <param name="variable_modifications" value="Oxidation (M)"/>
-      <param name="v" value="1"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="hl" value="30"/>
-      <param name="he" value="1.0"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
-  <help><![CDATA[Annotates MS/MS spectra using OMSSA.
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OMSSAAdapter.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/OpenMSDatabasesInfo.xml b/tools/openms/OpenMSDatabasesInfo.xml
index f0f70e613..a451fc817 100644
--- a/tools/openms/OpenMSDatabasesInfo.xml
+++ b/tools/openms/OpenMSDatabasesInfo.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [[for Developers]]-->
 <tool id="OpenMSDatabasesInfo" name="OpenMSDatabasesInfo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Prints the content of OpenMS' enzyme and modification databases to TSV</description>
   <macros>
@@ -41,7 +40,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   <inputs>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -60,6 +59,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   <help><![CDATA[Prints the content of OpenMS' enzyme and modification databases to TSV
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenMSDatabasesInfo.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenMSDatabasesInfo.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/OpenMSInfo.xml b/tools/openms/OpenMSInfo.xml
new file mode 100644
index 000000000..81238dd1c
--- /dev/null
+++ b/tools/openms/OpenMSInfo.xml
@@ -0,0 +1,72 @@
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
+<!--Proposed Tool Section: [Misc / Helpers]-->
+<tool id="OpenMSInfo" name="OpenMSInfo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+  <description>Prints configurations details of OpenMS</description>
+  <macros>
+    <token name="@EXECUTABLE@">OpenMSInfo</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
+
+## Preprocessing
+## advanced options
+  #if $adv_opts.dummy:
+    mkdir adv_opts.dummy &&
+    cp '$adv_opts.dummy' 'adv_opts.dummy/${re.sub("[^\w\-_]", "_", $adv_opts.dummy.element_identifier)}.$gxy2omsext($adv_opts.dummy.ext)' &&
+  #end if
+
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+## advanced options
+  #if $adv_opts.dummy:
+    -dummy
+    'adv_opts.dummy/${re.sub("[^\w\-_]", "_", $adv_opts.dummy.element_identifier)}.$gxy2omsext($adv_opts.dummy.ext)'
+  #end if
+
+| tee '$stdout'
+
+## Postprocessing
+#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
+  && mv '@EXECUTABLE@.ctd' '$ctd_out'
+#end if]]></command>
+  <configfiles>
+    <inputs name="args_json" data_style="paths"/>
+    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
+  <inputs>
+    <param argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Print information (flag can also be omitted)" help=""/>
+    <expand macro="adv_opts_macro">
+      <param argument="-dummy" type="data" format="txt" optional="true" label="A fake input file, which is needed for some workflow systems to call this tool" help=" select txt data sets(s)"/>
+      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
+        <expand macro="list_string_san" name="test"/>
+      </param>
+    </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
+      <filter>OPTIONAL_OUTPUTS is None</filter>
+    </data>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+  </outputs>
+  <tests/>
+  <help><![CDATA[Prints configurations details of OpenMS.
+
+
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenMSInfo.html]]></help>
+  <expand macro="references"/>
+</tool>
diff --git a/tools/openms/OpenPepXL.xml b/tools/openms/OpenPepXL.xml
index 8a2b969aa..98653cd93 100644
--- a/tools/openms/OpenPepXL.xml
+++ b/tools/openms/OpenPepXL.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Cross-Linking]-->
 <tool id="OpenPepXL" name="OpenPepXL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Tool for protein-protein cross-linking identification using labeled linkers.</description>
+  <description>Tool for protein-protein cross-linking identification using labeled linkers</description>
   <macros>
     <token name="@EXECUTABLE@">OpenPepXL</token>
     <import>macros.xml</import>
@@ -15,11 +14,11 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir consensus &&
-ln -s '$consensus' 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)' &&
+cp '$consensus' 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)' &&
 mkdir database &&
-ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
 #if "out_idXML_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_idXML &&
 #end if
@@ -32,11 +31,13 @@ ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifi
 #if "out_xquest_specxml_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_xquest_specxml &&
 #end if
+## advanced options
   #if $adv_opts.decoy_database:
     mkdir adv_opts.decoy_database &&
-    ln -s '$adv_opts.decoy_database' 'adv_opts.decoy_database/${re.sub("[^\w\-_]", "_", $adv_opts.decoy_database.element_identifier)}.$gxy2omsext($adv_opts.decoy_database.ext)' &&
+    cp '$adv_opts.decoy_database' 'adv_opts.decoy_database/${re.sub("[^\w\-_]", "_", $adv_opts.decoy_database.element_identifier)}.$gxy2omsext($adv_opts.decoy_database.ext)' &&
   #end if
 
+
 ## Main program call
 
 set -o pipefail &&
@@ -65,10 +66,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   -out_xquest_specxml
   'out_xquest_specxml/output.${gxy2omsext("spec.xml")}'
 #end if
+## advanced options
   #if $adv_opts.decoy_database:
     -decoy_database
     'adv_opts.decoy_database/${re.sub("[^\w\-_]", "_", $adv_opts.decoy_database.element_identifier)}.$gxy2omsext($adv_opts.decoy_database.ext)'
   #end if
+
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
 #end if
@@ -94,37 +97,37 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file containing the spectra" help=" select mzml data sets(s)"/>
-    <param argument="-consensus" type="data" format="consensusxml" optional="false" label="Input file containing the linked mass peaks" help=" select consensusxml data sets(s)"/>
-    <param argument="-database" type="data" format="fasta" optional="false" label="Input file containing the protein database" help=" select fasta data sets(s)"/>
-    <param argument="-decoy_string" type="text" optional="true" value="DECOY_" label="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins" help="">
+    <param argument="-in" type="data" format="mzml" label="Input file containing the spectra" help=" select mzml data sets(s)"/>
+    <param argument="-consensus" type="data" format="consensusxml" label="Input file containing the linked mass peaks" help=" select consensusxml data sets(s)"/>
+    <param argument="-database" type="data" format="fasta" label="Input file containing the protein database" help=" select fasta data sets(s)"/>
+    <param argument="-decoy_string" type="text" value="DECOY_" label="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins" help="">
       <expand macro="list_string_san" name="decoy_string"/>
     </param>
     <param argument="-decoy_prefix" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Set to true, if the decoy_string is a prefix of accessions in the protein database" help="Otherwise it is a suffix"/>
     <section name="precursor" title="Precursor filtering settings" help="" expanded="false">
-      <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Width of precursor mass tolerance window" help=""/>
-      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
+      <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" value="10.0" label="Width of precursor mass tolerance window" help=""/>
+      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
       </param>
-      <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/>
-      <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="8" label="Maximum precursor charge to be considered" help=""/>
-      <param name="corrections" argument="-precursor:corrections" type="text" optional="true" value="4 3 2 1 0" label="Monoisotopic peak correction" help="Matches candidates for possible monoisotopic precursor peaks for experimental mass m and given numbers n at masses (m - n * (C13-C12)). These should be ordered from more extreme to less extreme corrections. Numbers later in the list will be preferred in case of ambiguities (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="min_charge" argument="-precursor:min_charge" type="integer" value="2" label="Minimum precursor charge to be considered" help=""/>
+      <param name="max_charge" argument="-precursor:max_charge" type="integer" value="8" label="Maximum precursor charge to be considered" help=""/>
+      <param name="corrections" argument="-precursor:corrections" type="text" value="4 3 2 1 0" label="Monoisotopic peak correction" help="Matches candidates for possible monoisotopic precursor peaks for experimental mass m and given numbers n at masses (m - n * (C13-C12)). These should be ordered from more extreme to less extreme corrections. Numbers later in the list will be preferred in case of ambiguities (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_integer_valsan" name="corrections"/>
       </param>
     </section>
     <section name="fragment" title="Fragment peak matching settings" help="" expanded="false">
-      <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="20.0" label="Fragment mass tolerance" help=""/>
-      <param name="mass_tolerance_xlinks" argument="-fragment:mass_tolerance_xlinks" type="float" optional="true" value="20.0" label="Fragment mass tolerance for cross-link ions" help=""/>
-      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="true" label="Unit of fragment m" help="">
+      <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" value="20.0" label="Fragment mass tolerance" help=""/>
+      <param name="mass_tolerance_xlinks" argument="-fragment:mass_tolerance_xlinks" type="float" value="20.0" label="Fragment mass tolerance for cross-link ions" help=""/>
+      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" label="Unit of fragment m" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
       </param>
     </section>
     <section name="modifications" title="Peptide modification settings" help="" expanded="false">
-      <param name="fixed" argument="-modifications:fixed" multiple="true" type="select" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
+      <param name="fixed" argument="-modifications:fixed" type="select" multiple="true" optional="false" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
         <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -134,6 +137,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="2-succinyl (C)">2-succinyl (C)</option>
         <option value="2HPG (R)">2HPG (R)</option>
         <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+        <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+        <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+        <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+        <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
         <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
         <option value="3sulfo (N-term)">3sulfo (N-term)</option>
         <option value="4-ONE (C)">4-ONE (C)</option>
@@ -223,6 +230,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
         <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
         <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+        <option value="Andro-H2O (C)">Andro-H2O (C)</option>
         <option value="Archaeol (C)">Archaeol (C)</option>
         <option value="Arg (N-term)">Arg (N-term)</option>
         <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -326,6 +334,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
         <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
         <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+        <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
         <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
         <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
         <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -358,7 +367,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="BITC (N-term)">BITC (N-term)</option>
         <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
         <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-        <option value="Bodipy (C)">Bodipy (C)</option>
         <option value="Brij35 (N-term)">Brij35 (N-term)</option>
         <option value="Brij58 (N-term)">Brij58 (N-term)</option>
         <option value="Bromo (F)">Bromo (F)</option>
@@ -790,9 +798,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Dehydrated (T)">Dehydrated (T)</option>
         <option value="Dehydrated (Y)">Dehydrated (Y)</option>
         <option value="Dehydro (C)">Dehydro (C)</option>
+        <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
         <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-        <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
         <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
         <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -802,7 +810,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
         <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
         <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-        <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
         <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
         <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -814,6 +821,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
         <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
         <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+        <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
         <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
         <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -1386,7 +1394,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Ethanolyl (C)">Ethanolyl (C)</option>
         <option value="Ethanolyl (K)">Ethanolyl (K)</option>
         <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-        <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
         <option value="Ethyl (C-term)">Ethyl (C-term)</option>
         <option value="Ethyl (D)">Ethyl (D)</option>
         <option value="Ethyl (E)">Ethyl (E)</option>
@@ -1480,6 +1487,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
         <option value="Glu (E)">Glu (E)</option>
         <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+        <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
         <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
         <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
         <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -1494,7 +1502,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
         <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
         <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
         <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -1518,6 +1525,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gly (K)">Gly (K)</option>
         <option value="Gly (S)">Gly (S)</option>
         <option value="Gly (T)">Gly (T)</option>
+        <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
         <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
         <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
         <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -1908,6 +1916,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
         <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
         <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+        <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
         <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
         <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
         <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -1919,6 +1928,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
         <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
         <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+        <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+        <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+        <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
         <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
         <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
         <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -1974,6 +1986,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
         <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
         <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+        <option value="His+O(2) (H)">His+O(2) (H)</option>
         <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
         <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
         <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -2111,11 +2124,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+        <option value="Kdo (S)">Kdo (S)</option>
+        <option value="Kdo (T)">Kdo (T)</option>
         <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
         <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
         <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
         <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
         <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+        <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
         <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
         <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
         <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -2200,13 +2216,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
         <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
         <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+        <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
         <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
         <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
         <option value="Lipoyl (K)">Lipoyl (K)</option>
         <option value="LRGG (K)">LRGG (K)</option>
         <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
         <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+        <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
         <option value="Lys (N-term)">Lys (N-term)</option>
+        <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
         <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
         <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
         <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -2241,6 +2260,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Malonyl (C)">Malonyl (C)</option>
         <option value="Malonyl (K)">Malonyl (K)</option>
         <option value="Malonyl (S)">Malonyl (S)</option>
+        <option value="MBS+peptide (C)">MBS+peptide (C)</option>
         <option value="MDCC (C)">MDCC (C)</option>
         <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
         <option value="Menadione (C)">Menadione (C)</option>
@@ -2252,6 +2272,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="MesitylOxide (H)">MesitylOxide (H)</option>
         <option value="MesitylOxide (K)">MesitylOxide (K)</option>
         <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+        <option value="Met+O(2) (H)">Met+O(2) (H)</option>
         <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
         <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
         <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -2435,7 +2456,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
         <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
         <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-        <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
         <option value="NP40 (N-term)">NP40 (N-term)</option>
         <option value="NQIGG (K)">NQIGG (K)</option>
         <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -2523,6 +2543,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
         <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
         <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+        <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+        <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+        <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+        <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
         <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
         <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
         <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -2537,6 +2561,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phospho (Y)">Phospho (Y)</option>
         <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
         <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+        <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
         <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
         <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
         <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -2568,6 +2593,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
         <option value="Piperidine (K)">Piperidine (K)</option>
         <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+        <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
         <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
         <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
         <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -2645,18 +2671,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="QTGG (K)">QTGG (K)</option>
         <option value="Quinone (W)">Quinone (W)</option>
         <option value="Quinone (Y)">Quinone (Y)</option>
+        <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+        <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+        <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+        <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+        <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+        <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+        <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+        <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+        <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+        <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+        <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+        <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+        <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+        <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+        <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+        <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+        <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+        <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+        <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+        <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
         <option value="Retinylidene (K)">Retinylidene (K)</option>
         <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
         <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
         <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-        <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-        <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-        <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-        <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-        <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-        <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-        <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-        <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
         <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
         <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
         <option value="Saligenin (H)">Saligenin (H)</option>
@@ -2684,6 +2722,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="shTMT (K)">shTMT (K)</option>
         <option value="shTMT (N-term)">shTMT (N-term)</option>
         <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+        <option value="shTMTpro (K)">shTMTpro (K)</option>
+        <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+        <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
         <option value="SMA (K)">SMA (K)</option>
         <option value="SMA (N-term)">SMA (N-term)</option>
         <option value="spermidine (Q)">spermidine (Q)</option>
@@ -2859,7 +2900,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
         <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
         <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-        <option value="Ub-amide (C)">Ub-amide (C)</option>
         <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
         <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
         <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -3054,7 +3094,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="ZQG (K)">ZQG (K)</option>
         <expand macro="list_string_san" name="fixed"/>
       </param>
-      <param name="variable" argument="-modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'">
+      <param name="variable" argument="-modifications:variable" type="select" multiple="true" optional="false" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
         <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -3064,6 +3104,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="2-succinyl (C)">2-succinyl (C)</option>
         <option value="2HPG (R)">2HPG (R)</option>
         <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+        <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+        <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+        <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+        <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
         <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
         <option value="3sulfo (N-term)">3sulfo (N-term)</option>
         <option value="4-ONE (C)">4-ONE (C)</option>
@@ -3153,6 +3197,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
         <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
         <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+        <option value="Andro-H2O (C)">Andro-H2O (C)</option>
         <option value="Archaeol (C)">Archaeol (C)</option>
         <option value="Arg (N-term)">Arg (N-term)</option>
         <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -3256,6 +3301,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
         <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
         <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+        <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
         <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
         <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
         <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -3288,7 +3334,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="BITC (N-term)">BITC (N-term)</option>
         <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
         <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-        <option value="Bodipy (C)">Bodipy (C)</option>
         <option value="Brij35 (N-term)">Brij35 (N-term)</option>
         <option value="Brij58 (N-term)">Brij58 (N-term)</option>
         <option value="Bromo (F)">Bromo (F)</option>
@@ -3720,9 +3765,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Dehydrated (T)">Dehydrated (T)</option>
         <option value="Dehydrated (Y)">Dehydrated (Y)</option>
         <option value="Dehydro (C)">Dehydro (C)</option>
+        <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
         <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-        <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
         <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
         <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -3732,7 +3777,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
         <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
         <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-        <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
         <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
         <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -3744,6 +3788,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
         <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
         <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+        <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
         <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
         <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -4316,7 +4361,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Ethanolyl (C)">Ethanolyl (C)</option>
         <option value="Ethanolyl (K)">Ethanolyl (K)</option>
         <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-        <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
         <option value="Ethyl (C-term)">Ethyl (C-term)</option>
         <option value="Ethyl (D)">Ethyl (D)</option>
         <option value="Ethyl (E)">Ethyl (E)</option>
@@ -4410,6 +4454,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
         <option value="Glu (E)">Glu (E)</option>
         <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+        <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
         <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
         <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
         <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -4424,7 +4469,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
         <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
         <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
         <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -4448,6 +4492,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gly (K)">Gly (K)</option>
         <option value="Gly (S)">Gly (S)</option>
         <option value="Gly (T)">Gly (T)</option>
+        <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
         <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
         <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
         <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -4838,6 +4883,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
         <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
         <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+        <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
         <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
         <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
         <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -4849,6 +4895,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
         <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
         <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+        <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+        <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+        <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
         <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
         <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
         <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -4904,6 +4953,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
         <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
         <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+        <option value="His+O(2) (H)">His+O(2) (H)</option>
         <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
         <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
         <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -5041,11 +5091,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+        <option value="Kdo (S)">Kdo (S)</option>
+        <option value="Kdo (T)">Kdo (T)</option>
         <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
         <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
         <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
         <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
         <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+        <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
         <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
         <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
         <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -5130,13 +5183,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
         <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
         <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+        <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
         <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
         <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
         <option value="Lipoyl (K)">Lipoyl (K)</option>
         <option value="LRGG (K)">LRGG (K)</option>
         <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
         <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+        <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
         <option value="Lys (N-term)">Lys (N-term)</option>
+        <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
         <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
         <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
         <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -5171,6 +5227,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Malonyl (C)">Malonyl (C)</option>
         <option value="Malonyl (K)">Malonyl (K)</option>
         <option value="Malonyl (S)">Malonyl (S)</option>
+        <option value="MBS+peptide (C)">MBS+peptide (C)</option>
         <option value="MDCC (C)">MDCC (C)</option>
         <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
         <option value="Menadione (C)">Menadione (C)</option>
@@ -5182,6 +5239,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="MesitylOxide (H)">MesitylOxide (H)</option>
         <option value="MesitylOxide (K)">MesitylOxide (K)</option>
         <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+        <option value="Met+O(2) (H)">Met+O(2) (H)</option>
         <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
         <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
         <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -5365,7 +5423,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
         <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
         <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-        <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
         <option value="NP40 (N-term)">NP40 (N-term)</option>
         <option value="NQIGG (K)">NQIGG (K)</option>
         <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -5453,6 +5510,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
         <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
         <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+        <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+        <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+        <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+        <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
         <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
         <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
         <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -5467,6 +5528,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phospho (Y)">Phospho (Y)</option>
         <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
         <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+        <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
         <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
         <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
         <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -5498,6 +5560,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
         <option value="Piperidine (K)">Piperidine (K)</option>
         <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+        <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
         <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
         <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
         <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -5575,18 +5638,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="QTGG (K)">QTGG (K)</option>
         <option value="Quinone (W)">Quinone (W)</option>
         <option value="Quinone (Y)">Quinone (Y)</option>
+        <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+        <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+        <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+        <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+        <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+        <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+        <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+        <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+        <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+        <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+        <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+        <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+        <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+        <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+        <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+        <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+        <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+        <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+        <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+        <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
         <option value="Retinylidene (K)">Retinylidene (K)</option>
         <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
         <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
         <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-        <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-        <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-        <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-        <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-        <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-        <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-        <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-        <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
         <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
         <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
         <option value="Saligenin (H)">Saligenin (H)</option>
@@ -5614,6 +5689,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="shTMT (K)">shTMT (K)</option>
         <option value="shTMT (N-term)">shTMT (N-term)</option>
         <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+        <option value="shTMTpro (K)">shTMTpro (K)</option>
+        <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+        <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
         <option value="SMA (K)">SMA (K)</option>
         <option value="SMA (N-term)">SMA (N-term)</option>
         <option value="spermidine (Q)">spermidine (Q)</option>
@@ -5789,7 +5867,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
         <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
         <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-        <option value="Ub-amide (C)">Ub-amide (C)</option>
         <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
         <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
         <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -5984,69 +6061,69 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="ZQG (K)">ZQG (K)</option>
         <expand macro="list_string_san" name="variable"/>
       </param>
-      <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" optional="true" value="3" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
+      <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" value="3" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
     </section>
     <section name="peptide" title="Settings for digesting proteins into peptides" help="" expanded="false">
-      <param name="min_size" argument="-peptide:min_size" type="integer" optional="true" value="5" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/>
-      <param name="missed_cleavages" argument="-peptide:missed_cleavages" type="integer" optional="true" value="3" label="Number of missed cleavages" help=""/>
-      <param name="enzyme" argument="-peptide:enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
-        <option value="Trypsin" selected="true">Trypsin</option>
-        <option value="Asp-N_ambic">Asp-N_ambic</option>
-        <option value="Chymotrypsin">Chymotrypsin</option>
-        <option value="Lys-C">Lys-C</option>
-        <option value="Lys-N">Lys-N</option>
-        <option value="2-iodobenzoate">2-iodobenzoate</option>
-        <option value="iodosobenzoate">iodosobenzoate</option>
-        <option value="staphylococcal protease/D">staphylococcal protease/D</option>
-        <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
-        <option value="Glu-C+P">Glu-C+P</option>
+      <param name="min_size" argument="-peptide:min_size" type="integer" value="5" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/>
+      <param name="missed_cleavages" argument="-peptide:missed_cleavages" type="integer" value="3" label="Number of missed cleavages" help=""/>
+      <param name="enzyme" argument="-peptide:enzyme" type="select" label="The enzyme used for peptide digestion" help="">
         <option value="PepsinA + P">PepsinA + P</option>
         <option value="cyanogen-bromide">cyanogen-bromide</option>
         <option value="Clostripain/P">Clostripain/P</option>
         <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
         <option value="no cleavage">no cleavage</option>
         <option value="unspecific cleavage">unspecific cleavage</option>
-        <option value="TrypChymo">TrypChymo</option>
-        <option value="Trypsin/P">Trypsin/P</option>
+        <option value="Asp-N/B">Asp-N/B</option>
+        <option value="Asp-N_ambic">Asp-N_ambic</option>
+        <option value="Chymotrypsin">Chymotrypsin</option>
+        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+        <option value="CNBr">CNBr</option>
         <option value="V8-DE">V8-DE</option>
         <option value="V8-E">V8-E</option>
-        <option value="Lys-C/P">Lys-C/P</option>
-        <option value="PepsinA">PepsinA</option>
         <option value="leukocyte elastase">leukocyte elastase</option>
         <option value="proline endopeptidase">proline endopeptidase</option>
         <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+        <option value="TrypChymo">TrypChymo</option>
+        <option value="Trypsin/P">Trypsin/P</option>
         <option value="Arg-C">Arg-C</option>
         <option value="Arg-C/P">Arg-C/P</option>
         <option value="Asp-N">Asp-N</option>
-        <option value="Asp-N/B">Asp-N/B</option>
-        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
-        <option value="CNBr">CNBr</option>
+        <option value="Trypsin" selected="true">Trypsin</option>
+        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+        <option value="2-iodobenzoate">2-iodobenzoate</option>
+        <option value="iodosobenzoate">iodosobenzoate</option>
+        <option value="staphylococcal protease/D">staphylococcal protease/D</option>
+        <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
+        <option value="Glu-C+P">Glu-C+P</option>
         <option value="Formic_acid">Formic_acid</option>
+        <option value="Lys-C">Lys-C</option>
+        <option value="Lys-N">Lys-N</option>
+        <option value="Lys-C/P">Lys-C/P</option>
+        <option value="PepsinA">PepsinA</option>
         <expand macro="list_string_san" name="enzyme"/>
       </param>
     </section>
     <section name="cross_linker" title="Description of the cross-linker reagent" help="" expanded="false">
-      <param name="residue1" argument="-cross_linker:residue1" type="text" optional="true" value="K N-term" label="Comma separated residues, that the first side of a bifunctional cross-linker can attach to" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="residue1" argument="-cross_linker:residue1" type="text" value="K N-term" label="Comma separated residues, that the first side of a bifunctional cross-linker can attach to" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="residue1"/>
         <expand macro="list_string_san" name="residue1"/>
       </param>
-      <param name="residue2" argument="-cross_linker:residue2" type="text" optional="true" value="K N-term" label="Comma separated residues, that the second side of a bifunctional cross-linker can attach to" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="residue2" argument="-cross_linker:residue2" type="text" value="K N-term" label="Comma separated residues, that the second side of a bifunctional cross-linker can attach to" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="residue2"/>
         <expand macro="list_string_san" name="residue2"/>
       </param>
-      <param name="mass_light" argument="-cross_linker:mass_light" type="float" optional="true" value="138.0680796" label="Mass of the light cross-linker, linking two residues on one or two peptides" help=""/>
-      <param name="mass_iso_shift" argument="-cross_linker:mass_iso_shift" type="float" optional="true" value="12.075321" label="Mass of the isotopic shift between the light and heavy linkers" help=""/>
-      <param name="mass_mono_link" argument="-cross_linker:mass_mono_link" type="text" optional="true" value="156.07864431 155.094628715" label="Possible masses of the linker, when attached to only one peptide" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="mass_light" argument="-cross_linker:mass_light" type="float" value="138.0680796" label="Mass of the light cross-linker, linking two residues on one or two peptides" help=""/>
+      <param name="mass_iso_shift" argument="-cross_linker:mass_iso_shift" type="float" value="12.075321" label="Mass of the isotopic shift between the light and heavy linkers" help=""/>
+      <param name="mass_mono_link" argument="-cross_linker:mass_mono_link" type="text" value="156.07864431 155.094628715" label="Possible masses of the linker, when attached to only one peptide" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_float_valsan" name="mass_mono_link"/>
       </param>
-      <param name="name" argument="-cross_linker:name" type="text" optional="true" value="DSS" label="Name of the searched cross-link, used to resolve ambiguity of equal masses" help="(e.g. DSS or BS3)">
+      <param name="name" argument="-cross_linker:name" type="text" value="DSS" label="Name of the searched cross-link, used to resolve ambiguity of equal masses" help="(e.g. DSS or BS3)">
         <expand macro="list_string_san" name="name"/>
       </param>
     </section>
     <section name="algorithm" title="Additional algorithm settings" help="" expanded="false">
-      <param name="number_top_hits" argument="-algorithm:number_top_hits" type="integer" optional="true" value="1" label="Number of top hits reported for each spectrum pai" help=""/>
-      <param name="deisotope" argument="-algorithm:deisotope" type="select" optional="true" label="Set to true, if the input spectra should be deisotoped before any other processing steps" help="If set to auto the spectra will be deisotoped, if the fragment mass tolerance is &lt; 0.1 Da or &lt; 100 ppm (0.1 Da at a mass of 1000)">
+      <param name="number_top_hits" argument="-algorithm:number_top_hits" type="integer" value="1" label="Number of top hits reported for each spectrum pai" help=""/>
+      <param name="deisotope" argument="-algorithm:deisotope" type="select" label="Set to true, if the input spectra should be deisotoped before any other processing steps" help="If set to auto the spectra will be deisotoped, if the fragment mass tolerance is &lt; 0.1 Da or &lt; 100 ppm (0.1 Da at a mass of 1000)">
         <option value="true">true</option>
         <option value="false">false</option>
         <option value="auto" selected="true">auto</option>
@@ -6065,7 +6142,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <expand macro="adv_opts_macro">
       <param argument="-decoy_database" type="data" format="fasta" optional="true" label="Input file containing the decoy protein database" help="Decoys can also be included in the normal database file instead (or additionally) select fasta data sets(s)"/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -6097,7 +6174,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_OpenPepXL_1 -->
+  <tests>
+    <!-- TOPP_OpenPepXL_1 -->
     <test expect_num_outputs="5">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -6108,10 +6186,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="database" value="OpenPepXL_input.fasta"/>
       <param name="decoy_string" value="decoy_"/>
       <param name="decoy_prefix" value="true"/>
-      <output name="out_idXML" file="OpenPepXL_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <output name="out_mzIdentML" file="OpenPepXL_output.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
-      <output name="out_xquestxml" file="OpenPepXL_output.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
-      <output name="out_xquest_specxml" file="OpenPepXL_output.spec.xml" compare="sim_size" delta_frac="0.7" ftype="spec.xml"/>
+      <output name="out_idXML" value="OpenPepXL_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out_mzIdentML" value="OpenPepXL_output.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
+      <output name="out_xquestxml" value="OpenPepXL_output.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
+      <output name="out_xquest_specxml" value="OpenPepXL_output.spec.xml.tmp" compare="sim_size" delta_frac="0.7" ftype="spec.xml"/>
       <section name="precursor">
         <param name="mass_tolerance" value="10.0"/>
         <param name="mass_tolerance_unit" value="ppm"/>
@@ -6161,11 +6239,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Tool for protein-protein cross-linking identification using labeled linkers.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenPepXL.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenPepXL.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/OpenPepXLLF.xml b/tools/openms/OpenPepXLLF.xml
index 3fec29b08..e95e091b0 100644
--- a/tools/openms/OpenPepXLLF.xml
+++ b/tools/openms/OpenPepXLLF.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Cross-Linking]-->
 <tool id="OpenPepXLLF" name="OpenPepXLLF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Tool for protein-protein cross linking with label-free linkers.</description>
+  <description>Tool for protein-protein cross linking with label-free linkers</description>
   <macros>
     <token name="@EXECUTABLE@">OpenPepXLLF</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir database &&
-ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
 #if "out_idXML_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_idXML &&
 #end if
@@ -30,11 +29,13 @@ ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifi
 #if "out_xquest_specxml_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_xquest_specxml &&
 #end if
+## advanced options
   #if $adv_opts.decoy_database:
     mkdir adv_opts.decoy_database &&
-    ln -s '$adv_opts.decoy_database' 'adv_opts.decoy_database/${re.sub("[^\w\-_]", "_", $adv_opts.decoy_database.element_identifier)}.$gxy2omsext($adv_opts.decoy_database.ext)' &&
+    cp '$adv_opts.decoy_database' 'adv_opts.decoy_database/${re.sub("[^\w\-_]", "_", $adv_opts.decoy_database.element_identifier)}.$gxy2omsext($adv_opts.decoy_database.ext)' &&
   #end if
 
+
 ## Main program call
 
 set -o pipefail &&
@@ -61,10 +62,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   -out_xquest_specxml
   'out_xquest_specxml/output.${gxy2omsext("spec.xml")}'
 #end if
+## advanced options
   #if $adv_opts.decoy_database:
     -decoy_database
     'adv_opts.decoy_database/${re.sub("[^\w\-_]", "_", $adv_opts.decoy_database.element_identifier)}.$gxy2omsext($adv_opts.decoy_database.ext)'
   #end if
+
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
 #end if
@@ -90,36 +93,36 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file containing the spectra" help=" select mzml data sets(s)"/>
-    <param argument="-database" type="data" format="fasta" optional="false" label="Input file containing the protein database" help=" select fasta data sets(s)"/>
-    <param argument="-decoy_string" type="text" optional="true" value="DECOY_" label="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins" help="">
+    <param argument="-in" type="data" format="mzml" label="Input file containing the spectra" help=" select mzml data sets(s)"/>
+    <param argument="-database" type="data" format="fasta" label="Input file containing the protein database" help=" select fasta data sets(s)"/>
+    <param argument="-decoy_string" type="text" value="DECOY_" label="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins" help="">
       <expand macro="list_string_san" name="decoy_string"/>
     </param>
     <param argument="-decoy_prefix" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Set to true, if the decoy_string is a prefix of accessions in the protein database" help="Otherwise it is a suffix"/>
     <section name="precursor" title="Precursor filtering settings" help="" expanded="false">
-      <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Width of precursor mass tolerance window" help=""/>
-      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
+      <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" value="10.0" label="Width of precursor mass tolerance window" help=""/>
+      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
       </param>
-      <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/>
-      <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="8" label="Maximum precursor charge to be considered" help=""/>
-      <param name="corrections" argument="-precursor:corrections" type="text" optional="true" value="4 3 2 1 0" label="Monoisotopic peak correction" help="Matches candidates for possible monoisotopic precursor peaks for experimental mass m and given numbers n at masses (m - n * (C13-C12)). These should be ordered from more extreme to less extreme corrections. Numbers later in the list will be preferred in case of ambiguities (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="min_charge" argument="-precursor:min_charge" type="integer" value="2" label="Minimum precursor charge to be considered" help=""/>
+      <param name="max_charge" argument="-precursor:max_charge" type="integer" value="8" label="Maximum precursor charge to be considered" help=""/>
+      <param name="corrections" argument="-precursor:corrections" type="text" value="4 3 2 1 0" label="Monoisotopic peak correction" help="Matches candidates for possible monoisotopic precursor peaks for experimental mass m and given numbers n at masses (m - n * (C13-C12)). These should be ordered from more extreme to less extreme corrections. Numbers later in the list will be preferred in case of ambiguities (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_integer_valsan" name="corrections"/>
       </param>
     </section>
     <section name="fragment" title="Fragment peak matching settings" help="" expanded="false">
-      <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="20.0" label="Fragment mass tolerance" help=""/>
-      <param name="mass_tolerance_xlinks" argument="-fragment:mass_tolerance_xlinks" type="float" optional="true" value="20.0" label="Fragment mass tolerance for cross-link ions" help=""/>
-      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="true" label="Unit of fragment m" help="">
+      <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" value="20.0" label="Fragment mass tolerance" help=""/>
+      <param name="mass_tolerance_xlinks" argument="-fragment:mass_tolerance_xlinks" type="float" value="20.0" label="Fragment mass tolerance for cross-link ions" help=""/>
+      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" label="Unit of fragment m" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
       </param>
     </section>
     <section name="modifications" title="Peptide modification settings" help="" expanded="false">
-      <param name="fixed" argument="-modifications:fixed" multiple="true" type="select" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
+      <param name="fixed" argument="-modifications:fixed" type="select" multiple="true" optional="false" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
         <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -129,6 +132,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="2-succinyl (C)">2-succinyl (C)</option>
         <option value="2HPG (R)">2HPG (R)</option>
         <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+        <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+        <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+        <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+        <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
         <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
         <option value="3sulfo (N-term)">3sulfo (N-term)</option>
         <option value="4-ONE (C)">4-ONE (C)</option>
@@ -218,6 +225,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
         <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
         <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+        <option value="Andro-H2O (C)">Andro-H2O (C)</option>
         <option value="Archaeol (C)">Archaeol (C)</option>
         <option value="Arg (N-term)">Arg (N-term)</option>
         <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -321,6 +329,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
         <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
         <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+        <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
         <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
         <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
         <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -353,7 +362,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="BITC (N-term)">BITC (N-term)</option>
         <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
         <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-        <option value="Bodipy (C)">Bodipy (C)</option>
         <option value="Brij35 (N-term)">Brij35 (N-term)</option>
         <option value="Brij58 (N-term)">Brij58 (N-term)</option>
         <option value="Bromo (F)">Bromo (F)</option>
@@ -785,9 +793,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Dehydrated (T)">Dehydrated (T)</option>
         <option value="Dehydrated (Y)">Dehydrated (Y)</option>
         <option value="Dehydro (C)">Dehydro (C)</option>
+        <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
         <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-        <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
         <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
         <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -797,7 +805,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
         <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
         <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-        <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
         <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
         <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -809,6 +816,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
         <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
         <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+        <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
         <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
         <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -1381,7 +1389,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Ethanolyl (C)">Ethanolyl (C)</option>
         <option value="Ethanolyl (K)">Ethanolyl (K)</option>
         <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-        <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
         <option value="Ethyl (C-term)">Ethyl (C-term)</option>
         <option value="Ethyl (D)">Ethyl (D)</option>
         <option value="Ethyl (E)">Ethyl (E)</option>
@@ -1475,6 +1482,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
         <option value="Glu (E)">Glu (E)</option>
         <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+        <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
         <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
         <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
         <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -1489,7 +1497,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
         <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
         <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
         <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -1513,6 +1520,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gly (K)">Gly (K)</option>
         <option value="Gly (S)">Gly (S)</option>
         <option value="Gly (T)">Gly (T)</option>
+        <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
         <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
         <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
         <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -1903,6 +1911,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
         <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
         <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+        <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
         <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
         <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
         <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -1914,6 +1923,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
         <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
         <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+        <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+        <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+        <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
         <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
         <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
         <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -1969,6 +1981,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
         <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
         <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+        <option value="His+O(2) (H)">His+O(2) (H)</option>
         <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
         <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
         <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -2106,11 +2119,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+        <option value="Kdo (S)">Kdo (S)</option>
+        <option value="Kdo (T)">Kdo (T)</option>
         <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
         <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
         <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
         <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
         <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+        <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
         <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
         <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
         <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -2195,13 +2211,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
         <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
         <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+        <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
         <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
         <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
         <option value="Lipoyl (K)">Lipoyl (K)</option>
         <option value="LRGG (K)">LRGG (K)</option>
         <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
         <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+        <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
         <option value="Lys (N-term)">Lys (N-term)</option>
+        <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
         <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
         <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
         <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -2236,6 +2255,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Malonyl (C)">Malonyl (C)</option>
         <option value="Malonyl (K)">Malonyl (K)</option>
         <option value="Malonyl (S)">Malonyl (S)</option>
+        <option value="MBS+peptide (C)">MBS+peptide (C)</option>
         <option value="MDCC (C)">MDCC (C)</option>
         <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
         <option value="Menadione (C)">Menadione (C)</option>
@@ -2247,6 +2267,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="MesitylOxide (H)">MesitylOxide (H)</option>
         <option value="MesitylOxide (K)">MesitylOxide (K)</option>
         <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+        <option value="Met+O(2) (H)">Met+O(2) (H)</option>
         <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
         <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
         <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -2430,7 +2451,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
         <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
         <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-        <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
         <option value="NP40 (N-term)">NP40 (N-term)</option>
         <option value="NQIGG (K)">NQIGG (K)</option>
         <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -2518,6 +2538,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
         <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
         <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+        <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+        <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+        <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+        <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
         <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
         <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
         <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -2532,6 +2556,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phospho (Y)">Phospho (Y)</option>
         <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
         <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+        <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
         <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
         <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
         <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -2563,6 +2588,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
         <option value="Piperidine (K)">Piperidine (K)</option>
         <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+        <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
         <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
         <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
         <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -2640,18 +2666,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="QTGG (K)">QTGG (K)</option>
         <option value="Quinone (W)">Quinone (W)</option>
         <option value="Quinone (Y)">Quinone (Y)</option>
+        <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+        <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+        <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+        <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+        <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+        <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+        <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+        <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+        <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+        <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+        <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+        <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+        <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+        <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+        <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+        <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+        <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+        <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+        <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+        <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
         <option value="Retinylidene (K)">Retinylidene (K)</option>
         <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
         <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
         <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-        <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-        <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-        <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-        <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-        <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-        <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-        <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-        <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
         <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
         <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
         <option value="Saligenin (H)">Saligenin (H)</option>
@@ -2679,6 +2717,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="shTMT (K)">shTMT (K)</option>
         <option value="shTMT (N-term)">shTMT (N-term)</option>
         <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+        <option value="shTMTpro (K)">shTMTpro (K)</option>
+        <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+        <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
         <option value="SMA (K)">SMA (K)</option>
         <option value="SMA (N-term)">SMA (N-term)</option>
         <option value="spermidine (Q)">spermidine (Q)</option>
@@ -2854,7 +2895,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
         <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
         <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-        <option value="Ub-amide (C)">Ub-amide (C)</option>
         <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
         <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
         <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -3049,7 +3089,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="ZQG (K)">ZQG (K)</option>
         <expand macro="list_string_san" name="fixed"/>
       </param>
-      <param name="variable" argument="-modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'">
+      <param name="variable" argument="-modifications:variable" type="select" multiple="true" optional="false" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
         <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -3059,6 +3099,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="2-succinyl (C)">2-succinyl (C)</option>
         <option value="2HPG (R)">2HPG (R)</option>
         <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+        <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+        <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+        <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+        <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
         <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
         <option value="3sulfo (N-term)">3sulfo (N-term)</option>
         <option value="4-ONE (C)">4-ONE (C)</option>
@@ -3148,6 +3192,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
         <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
         <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+        <option value="Andro-H2O (C)">Andro-H2O (C)</option>
         <option value="Archaeol (C)">Archaeol (C)</option>
         <option value="Arg (N-term)">Arg (N-term)</option>
         <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -3251,6 +3296,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
         <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
         <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+        <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
         <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
         <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
         <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -3283,7 +3329,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="BITC (N-term)">BITC (N-term)</option>
         <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
         <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-        <option value="Bodipy (C)">Bodipy (C)</option>
         <option value="Brij35 (N-term)">Brij35 (N-term)</option>
         <option value="Brij58 (N-term)">Brij58 (N-term)</option>
         <option value="Bromo (F)">Bromo (F)</option>
@@ -3715,9 +3760,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Dehydrated (T)">Dehydrated (T)</option>
         <option value="Dehydrated (Y)">Dehydrated (Y)</option>
         <option value="Dehydro (C)">Dehydro (C)</option>
+        <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
         <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-        <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
         <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
         <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -3727,7 +3772,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
         <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
         <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-        <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
         <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
         <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -3739,6 +3783,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
         <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
         <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+        <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
         <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
         <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -4311,7 +4356,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Ethanolyl (C)">Ethanolyl (C)</option>
         <option value="Ethanolyl (K)">Ethanolyl (K)</option>
         <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-        <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
         <option value="Ethyl (C-term)">Ethyl (C-term)</option>
         <option value="Ethyl (D)">Ethyl (D)</option>
         <option value="Ethyl (E)">Ethyl (E)</option>
@@ -4405,6 +4449,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
         <option value="Glu (E)">Glu (E)</option>
         <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+        <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
         <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
         <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
         <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -4419,7 +4464,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
         <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
         <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
         <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -4443,6 +4487,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gly (K)">Gly (K)</option>
         <option value="Gly (S)">Gly (S)</option>
         <option value="Gly (T)">Gly (T)</option>
+        <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
         <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
         <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
         <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -4833,6 +4878,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
         <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
         <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+        <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
         <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
         <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
         <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -4844,6 +4890,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
         <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
         <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+        <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+        <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+        <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
         <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
         <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
         <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -4899,6 +4948,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
         <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
         <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+        <option value="His+O(2) (H)">His+O(2) (H)</option>
         <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
         <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
         <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -5036,11 +5086,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+        <option value="Kdo (S)">Kdo (S)</option>
+        <option value="Kdo (T)">Kdo (T)</option>
         <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
         <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
         <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
         <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
         <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+        <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
         <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
         <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
         <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -5125,13 +5178,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
         <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
         <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+        <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
         <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
         <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
         <option value="Lipoyl (K)">Lipoyl (K)</option>
         <option value="LRGG (K)">LRGG (K)</option>
         <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
         <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+        <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
         <option value="Lys (N-term)">Lys (N-term)</option>
+        <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
         <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
         <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
         <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -5166,6 +5222,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Malonyl (C)">Malonyl (C)</option>
         <option value="Malonyl (K)">Malonyl (K)</option>
         <option value="Malonyl (S)">Malonyl (S)</option>
+        <option value="MBS+peptide (C)">MBS+peptide (C)</option>
         <option value="MDCC (C)">MDCC (C)</option>
         <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
         <option value="Menadione (C)">Menadione (C)</option>
@@ -5177,6 +5234,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="MesitylOxide (H)">MesitylOxide (H)</option>
         <option value="MesitylOxide (K)">MesitylOxide (K)</option>
         <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+        <option value="Met+O(2) (H)">Met+O(2) (H)</option>
         <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
         <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
         <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -5360,7 +5418,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
         <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
         <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-        <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
         <option value="NP40 (N-term)">NP40 (N-term)</option>
         <option value="NQIGG (K)">NQIGG (K)</option>
         <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -5448,6 +5505,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
         <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
         <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+        <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+        <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+        <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+        <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
         <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
         <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
         <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -5462,6 +5523,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phospho (Y)">Phospho (Y)</option>
         <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
         <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+        <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
         <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
         <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
         <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -5493,6 +5555,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
         <option value="Piperidine (K)">Piperidine (K)</option>
         <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+        <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
         <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
         <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
         <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -5570,18 +5633,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="QTGG (K)">QTGG (K)</option>
         <option value="Quinone (W)">Quinone (W)</option>
         <option value="Quinone (Y)">Quinone (Y)</option>
+        <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+        <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+        <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+        <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+        <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+        <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+        <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+        <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+        <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+        <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+        <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+        <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+        <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+        <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+        <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+        <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+        <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+        <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+        <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+        <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
         <option value="Retinylidene (K)">Retinylidene (K)</option>
         <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
         <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
         <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-        <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-        <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-        <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-        <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-        <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-        <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-        <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-        <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
         <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
         <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
         <option value="Saligenin (H)">Saligenin (H)</option>
@@ -5609,6 +5684,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="shTMT (K)">shTMT (K)</option>
         <option value="shTMT (N-term)">shTMT (N-term)</option>
         <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+        <option value="shTMTpro (K)">shTMTpro (K)</option>
+        <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+        <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
         <option value="SMA (K)">SMA (K)</option>
         <option value="SMA (N-term)">SMA (N-term)</option>
         <option value="spermidine (Q)">spermidine (Q)</option>
@@ -5784,7 +5862,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
         <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
         <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-        <option value="Ub-amide (C)">Ub-amide (C)</option>
         <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
         <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
         <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -5979,75 +6056,75 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="ZQG (K)">ZQG (K)</option>
         <expand macro="list_string_san" name="variable"/>
       </param>
-      <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" optional="true" value="3" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
+      <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" value="3" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
     </section>
     <section name="peptide" title="Settings for digesting proteins into peptides" help="" expanded="false">
-      <param name="min_size" argument="-peptide:min_size" type="integer" optional="true" value="5" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/>
-      <param name="missed_cleavages" argument="-peptide:missed_cleavages" type="integer" optional="true" value="3" label="Number of missed cleavages" help=""/>
-      <param name="enzyme" argument="-peptide:enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
-        <option value="Trypsin" selected="true">Trypsin</option>
+      <param name="min_size" argument="-peptide:min_size" type="integer" value="5" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/>
+      <param name="missed_cleavages" argument="-peptide:missed_cleavages" type="integer" value="3" label="Number of missed cleavages" help=""/>
+      <param name="enzyme" argument="-peptide:enzyme" type="select" label="The enzyme used for peptide digestion" help="">
+        <option value="Formic_acid">Formic_acid</option>
+        <option value="Lys-C">Lys-C</option>
+        <option value="Lys-N">Lys-N</option>
         <option value="Asp-N">Asp-N</option>
         <option value="Asp-N/B">Asp-N/B</option>
         <option value="Asp-N_ambic">Asp-N_ambic</option>
         <option value="Lys-C/P">Lys-C/P</option>
         <option value="PepsinA">PepsinA</option>
+        <option value="TrypChymo">TrypChymo</option>
+        <option value="Glu-C+P">Glu-C+P</option>
+        <option value="PepsinA + P">PepsinA + P</option>
+        <option value="cyanogen-bromide">cyanogen-bromide</option>
+        <option value="Clostripain/P">Clostripain/P</option>
+        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+        <option value="no cleavage">no cleavage</option>
+        <option value="unspecific cleavage">unspecific cleavage</option>
+        <option value="Chymotrypsin">Chymotrypsin</option>
+        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+        <option value="CNBr">CNBr</option>
+        <option value="Trypsin" selected="true">Trypsin</option>
+        <option value="proline endopeptidase">proline endopeptidase</option>
         <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
         <option value="Alpha-lytic protease">Alpha-lytic protease</option>
         <option value="2-iodobenzoate">2-iodobenzoate</option>
         <option value="iodosobenzoate">iodosobenzoate</option>
         <option value="staphylococcal protease/D">staphylococcal protease/D</option>
         <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
-        <option value="Glu-C+P">Glu-C+P</option>
-        <option value="PepsinA + P">PepsinA + P</option>
-        <option value="cyanogen-bromide">cyanogen-bromide</option>
-        <option value="Clostripain/P">Clostripain/P</option>
-        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+        <option value="Arg-C">Arg-C</option>
         <option value="Arg-C/P">Arg-C/P</option>
-        <option value="TrypChymo">TrypChymo</option>
         <option value="Trypsin/P">Trypsin/P</option>
         <option value="V8-DE">V8-DE</option>
         <option value="V8-E">V8-E</option>
         <option value="leukocyte elastase">leukocyte elastase</option>
-        <option value="proline endopeptidase">proline endopeptidase</option>
-        <option value="Arg-C">Arg-C</option>
-        <option value="Chymotrypsin">Chymotrypsin</option>
-        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
-        <option value="CNBr">CNBr</option>
-        <option value="no cleavage">no cleavage</option>
-        <option value="unspecific cleavage">unspecific cleavage</option>
-        <option value="Formic_acid">Formic_acid</option>
-        <option value="Lys-C">Lys-C</option>
-        <option value="Lys-N">Lys-N</option>
         <expand macro="list_string_san" name="enzyme"/>
       </param>
     </section>
     <section name="cross_linker" title="Description of the cross-linker reagent" help="" expanded="false">
-      <param name="residue1" argument="-cross_linker:residue1" type="text" optional="true" value="K N-term" label="Comma separated residues, that the first side of a bifunctional cross-linker can attach to" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="residue1" argument="-cross_linker:residue1" type="text" value="K N-term" label="Comma separated residues, that the first side of a bifunctional cross-linker can attach to" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="residue1"/>
         <expand macro="list_string_san" name="residue1"/>
       </param>
-      <param name="residue2" argument="-cross_linker:residue2" type="text" optional="true" value="K N-term" label="Comma separated residues, that the second side of a bifunctional cross-linker can attach to" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="residue2" argument="-cross_linker:residue2" type="text" value="K N-term" label="Comma separated residues, that the second side of a bifunctional cross-linker can attach to" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="residue2"/>
         <expand macro="list_string_san" name="residue2"/>
       </param>
-      <param name="mass" argument="-cross_linker:mass" type="float" optional="true" value="138.0680796" label="Mass of the light cross-linker, linking two residues on one or two peptides" help=""/>
-      <param name="mass_mono_link" argument="-cross_linker:mass_mono_link" type="text" optional="true" value="156.07864431 155.094628715" label="Possible masses of the linker, when attached to only one peptide" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="mass" argument="-cross_linker:mass" type="float" value="138.0680796" label="Mass of the light cross-linker, linking two residues on one or two peptides" help=""/>
+      <param name="mass_mono_link" argument="-cross_linker:mass_mono_link" type="text" value="156.07864431 155.094628715" label="Possible masses of the linker, when attached to only one peptide" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_float_valsan" name="mass_mono_link"/>
       </param>
-      <param name="name" argument="-cross_linker:name" type="text" optional="true" value="DSS" label="Name of the searched cross-link, used to resolve ambiguity of equal masses" help="(e.g. DSS or BS3)">
+      <param name="name" argument="-cross_linker:name" type="text" value="DSS" label="Name of the searched cross-link, used to resolve ambiguity of equal masses" help="(e.g. DSS or BS3)">
         <expand macro="list_string_san" name="name"/>
       </param>
     </section>
     <section name="algorithm" title="Additional algorithm settings" help="" expanded="false">
-      <param name="number_top_hits" argument="-algorithm:number_top_hits" type="integer" optional="true" value="1" label="Number of top hits reported for each spectrum pai" help=""/>
-      <param name="deisotope" argument="-algorithm:deisotope" type="select" optional="true" label="Set to true, if the input spectra should be deisotoped before any other processing steps" help="If set to auto the spectra will be deisotoped, if the fragment mass tolerance is &lt; 0.1 Da or &lt; 100 ppm (0.1 Da at a mass of 1000)">
+      <param name="number_top_hits" argument="-algorithm:number_top_hits" type="integer" value="1" label="Number of top hits reported for each spectrum pai" help=""/>
+      <param name="deisotope" argument="-algorithm:deisotope" type="select" label="Set to true, if the input spectra should be deisotoped before any other processing steps" help="If set to auto the spectra will be deisotoped, if the fragment mass tolerance is &lt; 0.1 Da or &lt; 100 ppm (0.1 Da at a mass of 1000)">
         <option value="true">true</option>
         <option value="false">false</option>
         <option value="auto" selected="true">auto</option>
         <expand macro="list_string_san" name="deisotope"/>
       </param>
       <param name="use_sequence_tags" argument="-algorithm:use_sequence_tags" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use sequence tags (de novo sequencing of short fragments) to filter out candidates before scoring" help="This will make the search faster, but can impact the sensitivity positively or negatively, depending on the dataset"/>
-      <param name="sequence_tag_min_length" argument="-algorithm:sequence_tag_min_length" type="integer" optional="true" value="2" label="Minimal length of sequence tags to use for filtering candidates" help="Longer tags will make the search faster but much less sensitive. Ignored if 'algorithm:use_sequence_tags' is false"/>
+      <param name="sequence_tag_min_length" argument="-algorithm:sequence_tag_min_length" type="integer" value="2" label="Minimal length of sequence tags to use for filtering candidates" help="Longer tags will make the search faster but much less sensitive. Ignored if 'algorithm:use_sequence_tags' is false"/>
     </section>
     <section name="ions" title="Ion types to search for in MS/MS spectra" help="" expanded="false">
       <param name="b_ions" argument="-ions:b_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Search for peaks of b-ions" help=""/>
@@ -6061,7 +6138,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <expand macro="adv_opts_macro">
       <param argument="-decoy_database" type="data" format="fasta" optional="true" label="Input file containing the decoy protein database" help="Decoys can also be included in the normal database file instead (or additionally) select fasta data sets(s)"/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -6093,7 +6170,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_OpenPepXLLF_1 -->
+  <tests>
+    <!-- TOPP_OpenPepXLLF_1 -->
     <test expect_num_outputs="5">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -6103,10 +6181,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="database" value="OpenPepXLLF_input.fasta"/>
       <param name="decoy_string" value="decoy"/>
       <param name="decoy_prefix" value="true"/>
-      <output name="out_idXML" file="OpenPepXLLF_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <output name="out_mzIdentML" file="OpenPepXLLF_output.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
-      <output name="out_xquestxml" file="OpenPepXLLF_output.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
-      <output name="out_xquest_specxml" file="OpenPepXLLF_output.spec.xml" compare="sim_size" delta_frac="0.7" ftype="spec.xml"/>
+      <output name="out_idXML" value="OpenPepXLLF_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out_mzIdentML" value="OpenPepXLLF_output.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
+      <output name="out_xquestxml" value="OpenPepXLLF_output.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
+      <output name="out_xquest_specxml" value="OpenPepXLLF_output.spec.xml.tmp" compare="sim_size" delta_frac="0.7" ftype="spec.xml"/>
       <section name="precursor">
         <param name="mass_tolerance" value="10.0"/>
         <param name="mass_tolerance_unit" value="ppm"/>
@@ -6157,6 +6235,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenPepXLLF_2 -->
     <test expect_num_outputs="2">
@@ -6168,7 +6249,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="database" value="OpenPepXLLF_input2.fasta"/>
       <param name="decoy_string" value="decoy_"/>
       <param name="decoy_prefix" value="true"/>
-      <output name="out_idXML" file="OpenPepXLLF_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out_idXML" value="OpenPepXLLF_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <section name="precursor">
         <param name="mass_tolerance" value="10.0"/>
         <param name="mass_tolerance_unit" value="ppm"/>
@@ -6195,7 +6276,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="residue1" value="&quot;D&quot; &quot;E&quot; &quot;C-term&quot;"/>
         <param name="residue2" value="&quot;K&quot; &quot;S&quot; &quot;T&quot; &quot;Y&quot; &quot;N-term&quot;"/>
         <param name="mass" value="-18.010595"/>
-        <param name="mass_mono_link" value=""/>
         <param name="name" value="DMTMM"/>
       </section>
       <section name="algorithm">
@@ -6219,11 +6299,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Tool for protein-protein cross linking with label-free linkers.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenPepXLLF.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenPepXLLF.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/OpenSwathAnalyzer.xml b/tools/openms/OpenSwathAnalyzer.xml
index 73380db68..bf4b87beb 100644
--- a/tools/openms/OpenSwathAnalyzer.xml
+++ b/tools/openms/OpenSwathAnalyzer.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Picks peaks and finds features in an SWATH-MS or SRM experiment.</description>
+  <description>Picks peaks and finds features in an SWATH-MS or SRM experiment</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathAnalyzer</token>
     <import>macros.xml</import>
@@ -15,21 +14,21 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir tr &&
-ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
+cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 #if $rt_norm:
   mkdir rt_norm &&
-  ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
+  cp '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
 #end if
 mkdir out &&
 #if $swath_files_cond.swath_files:
   mkdir swath_files_cond.swath_files &&
   #if $swath_files_cond.swath_files_select == "no"
   mkdir ${' '.join(["'swath_files_cond.swath_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} && 
-  ${' '.join(["ln -s '%s' 'swath_files_cond.swath_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])}
+  ${' '.join(["cp '%s' 'swath_files_cond.swath_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])}
   #else
-  ln -s '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' &&
+  cp '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' &&
   #end if
 #end if
 
@@ -68,10 +67,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file containing the chromatograms" help=" select mzml data sets(s)"/>
-    <param argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file containing the chromatograms" help=" select mzml data sets(s)"/>
+    <param argument="-tr" type="data" format="traml" label="transition file" help=" select traml data sets(s)"/>
     <param argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help=" select trafoxml data sets(s)"/>
-    <param name="no_strict" argument="-no-strict" type="boolean" truevalue="true" falsevalue="false" checked="false" label="run in non-strict mode and allow some chromatograms to not be mapped" help=""/>
+    <param argument="-no-strict" type="boolean" truevalue="true" falsevalue="false" checked="false" label="run in non-strict mode and allow some chromatograms to not be mapped" help=""/>
     <conditional name="swath_files_cond">
       <param name="swath_files_select" type="select" label="Run tool in batch mode for -swath_files">
         <option value="no">No: process all datasets jointly</option>
@@ -81,12 +80,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param argument="-swath_files" type="data" format="mzml" multiple="true" optional="true" label="[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be used select mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-swath_files" type="data" format="mzml" multiple="false" optional="true" label="[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be used select mzml data sets(s)"/>
+        <param argument="-swath_files" type="data" format="mzml" optional="true" label="[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be used select mzml data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="[applies only if you have full MS2 spectra maps] Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help=""/>
+    <param argument="-min_upper_edge_dist" type="float" value="0.0" label="[applies only if you have full MS2 spectra maps] Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help=""/>
     <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
-      <param name="type" argument="-model:type" type="select" optional="true" label="Type of model" help="">
+      <param name="type" argument="-model:type" type="select" label="Type of model" help="">
         <option value="linear" selected="true">linear</option>
         <option value="b_spline">b_spline</option>
         <option value="interpolated">interpolated</option>
@@ -96,37 +95,37 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="symmetric_regression" argument="-model:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
     </section>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="stop_report_after_feature" argument="-algorithm:stop_report_after_feature" type="integer" optional="true" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help=""/>
-      <param name="rt_extraction_window" argument="-algorithm:rt_extraction_window" type="float" optional="true" value="-1.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution)" help="For this to work, the TraML input file needs to contain normalized RT values"/>
-      <param name="rt_normalization_factor" argument="-algorithm:rt_normalization_factor" type="float" optional="true" value="1.0" label="The normalized RT is expected to be between 0 and 1" help="If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)"/>
-      <param name="quantification_cutoff" argument="-algorithm:quantification_cutoff" type="float" optional="true" min="0.0" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help=""/>
+      <param name="stop_report_after_feature" argument="-algorithm:stop_report_after_feature" type="integer" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help=""/>
+      <param name="rt_extraction_window" argument="-algorithm:rt_extraction_window" type="float" value="-1.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution)" help="For this to work, the TraML input file needs to contain normalized RT values"/>
+      <param name="rt_normalization_factor" argument="-algorithm:rt_normalization_factor" type="float" value="1.0" label="The normalized RT is expected to be between 0 and 1" help="If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)"/>
+      <param name="quantification_cutoff" argument="-algorithm:quantification_cutoff" type="float" min="0.0" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help=""/>
       <param name="write_convex_hull" argument="-algorithm:write_convex_hull" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write out all points of all features into the featureXML" help=""/>
-      <param name="spectrum_addition_method" argument="-algorithm:spectrum_addition_method" type="select" optional="true" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
+      <param name="spectrum_addition_method" argument="-algorithm:spectrum_addition_method" type="select" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
         <option value="simple" selected="true">simple</option>
         <option value="resample">resample</option>
         <expand macro="list_string_san" name="spectrum_addition_method"/>
       </param>
-      <param name="add_up_spectra" argument="-algorithm:add_up_spectra" type="integer" optional="true" min="1" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help=""/>
-      <param name="spacing_for_spectra_resampling" argument="-algorithm:spacing_for_spectra_resampling" type="float" optional="true" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
-      <param name="uis_threshold_sn" argument="-algorithm:uis_threshold_sn" type="integer" optional="true" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
-      <param name="uis_threshold_peak_area" argument="-algorithm:uis_threshold_peak_area" type="integer" optional="true" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
-      <param name="scoring_model" argument="-algorithm:scoring_model" type="select" optional="true" label="Scoring model to use" help="">
+      <param name="add_up_spectra" argument="-algorithm:add_up_spectra" type="integer" min="1" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help=""/>
+      <param name="spacing_for_spectra_resampling" argument="-algorithm:spacing_for_spectra_resampling" type="float" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
+      <param name="uis_threshold_sn" argument="-algorithm:uis_threshold_sn" type="integer" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
+      <param name="uis_threshold_peak_area" argument="-algorithm:uis_threshold_peak_area" type="integer" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
+      <param name="scoring_model" argument="-algorithm:scoring_model" type="select" label="Scoring model to use" help="">
         <option value="default" selected="true">default</option>
         <option value="single_transition">single_transition</option>
         <expand macro="list_string_san" name="scoring_model"/>
       </param>
-      <param name="im_extra_drift" argument="-algorithm:im_extra_drift" type="float" optional="true" min="0.0" value="0.0" label="Extra drift time to extract for IM scoring (as a fraction" help="e.g. 0.25 means 25% extra on each side)"/>
+      <param name="im_extra_drift" argument="-algorithm:im_extra_drift" type="float" min="0.0" value="0.0" label="Extra drift time to extract for IM scoring (as a fraction" help="e.g. 0.25 means 25% extra on each side)"/>
       <param name="strict" argument="-algorithm:strict" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to error (true) or skip (false) if a transition in a transition group does not have a corresponding chromatogram" help=""/>
       <section name="TransitionGroupPicker" title="" help="" expanded="false">
-        <param name="stop_after_feature" argument="-algorithm:TransitionGroupPicker:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
-        <param name="stop_after_intensity_ratio" argument="-algorithm:TransitionGroupPicker:stop_after_intensity_ratio" type="float" optional="true" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
-        <param name="min_peak_width" argument="-algorithm:TransitionGroupPicker:min_peak_width" type="float" optional="true" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
-        <param name="peak_integration" argument="-algorithm:TransitionGroupPicker:peak_integration" type="select" optional="true" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
+        <param name="stop_after_feature" argument="-algorithm:TransitionGroupPicker:stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
+        <param name="stop_after_intensity_ratio" argument="-algorithm:TransitionGroupPicker:stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
+        <param name="min_peak_width" argument="-algorithm:TransitionGroupPicker:min_peak_width" type="float" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
+        <param name="peak_integration" argument="-algorithm:TransitionGroupPicker:peak_integration" type="select" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
           <option value="original" selected="true">original</option>
           <option value="smoothed">smoothed</option>
           <expand macro="list_string_san" name="peak_integration"/>
         </param>
-        <param name="background_subtraction" argument="-algorithm:TransitionGroupPicker:background_subtraction" type="select" optional="true" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
+        <param name="background_subtraction" argument="-algorithm:TransitionGroupPicker:background_subtraction" type="select" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
           <option value="none" selected="true">none</option>
           <option value="original">original</option>
           <option value="exact">exact</option>
@@ -135,29 +134,29 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="recalculate_peaks" argument="-algorithm:TransitionGroupPicker:recalculate_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="Tries to use the consensus (median) peak border if the variation within the picked peaks is too large"/>
         <param name="use_precursors" argument="-algorithm:TransitionGroupPicker:use_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)" help=""/>
         <param name="use_consensus" argument="-algorithm:TransitionGroupPicker:use_consensus" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)" help=""/>
-        <param name="recalculate_peaks_max_z" argument="-algorithm:TransitionGroupPicker:recalculate_peaks_max_z" type="float" optional="true" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
-        <param name="minimal_quality" argument="-algorithm:TransitionGroupPicker:minimal_quality" type="float" optional="true" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
-        <param name="resample_boundary" argument="-algorithm:TransitionGroupPicker:resample_boundary" type="float" optional="true" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
+        <param name="recalculate_peaks_max_z" argument="-algorithm:TransitionGroupPicker:recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
+        <param name="minimal_quality" argument="-algorithm:TransitionGroupPicker:minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
+        <param name="resample_boundary" argument="-algorithm:TransitionGroupPicker:resample_boundary" type="float" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
         <param name="compute_peak_quality" argument="-algorithm:TransitionGroupPicker:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
         <param name="compute_peak_shape_metrics" argument="-algorithm:TransitionGroupPicker:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/>
         <param name="compute_total_mi" argument="-algorithm:TransitionGroupPicker:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/>
-        <param name="boundary_selection_method" argument="-algorithm:TransitionGroupPicker:boundary_selection_method" type="select" optional="true" label="Method to use when selecting the best boundaries for peaks" help="">
+        <param name="boundary_selection_method" argument="-algorithm:TransitionGroupPicker:boundary_selection_method" type="select" label="Method to use when selecting the best boundaries for peaks" help="">
           <option value="largest" selected="true">largest</option>
           <option value="widest">widest</option>
           <expand macro="list_string_san" name="boundary_selection_method"/>
         </param>
         <section name="PeakPickerMRM" title="" help="" expanded="false">
-          <param name="sgolay_frame_length" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length" type="integer" optional="true" value="15" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
-          <param name="sgolay_polynomial_order" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order" type="integer" optional="true" value="3" label="Order of the polynomial that is fitted" help=""/>
-          <param name="gauss_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width" type="float" optional="true" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/>
+          <param name="sgolay_frame_length" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
+          <param name="sgolay_polynomial_order" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help=""/>
+          <param name="gauss_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/>
           <param name="use_gauss" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help=""/>
-          <param name="peak_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width" type="float" optional="true" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
-          <param name="signal_to_noise" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
-          <param name="sn_win_len" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len" type="float" optional="true" value="1000.0" label="Signal to noise window length" help=""/>
-          <param name="sn_bin_count" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count" type="integer" optional="true" value="30" label="Signal to noise bin count" help=""/>
+          <param name="peak_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
+          <param name="signal_to_noise" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise" type="float" min="0.0" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
+          <param name="sn_win_len" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help=""/>
+          <param name="sn_bin_count" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help=""/>
           <param name="write_sn_log_messages" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/>
           <param name="remove_overlapping_peaks" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to remove overlapping peaks during peak picking" help=""/>
-          <param name="method" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:method" type="select" optional="true" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
+          <param name="method" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:method" type="select" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
             <option value="legacy">legacy</option>
             <option value="corrected" selected="true">corrected</option>
             <option value="crawdad">crawdad</option>
@@ -165,13 +164,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           </param>
         </section>
         <section name="PeakIntegrator" title="" help="" expanded="false">
-          <param name="integration_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" optional="true" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
+          <param name="integration_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
             <option value="intensity_sum" selected="true">intensity_sum</option>
             <option value="simpson">simpson</option>
             <option value="trapezoid">trapezoid</option>
             <expand macro="list_string_san" name="integration_type"/>
           </param>
-          <param name="baseline_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" optional="true" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
+          <param name="baseline_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
             <option value="base_to_base" selected="true">base_to_base</option>
             <option value="vertical_division">vertical_division</option>
             <option value="vertical_division_min">vertical_division_min</option>
@@ -182,27 +181,27 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         </section>
       </section>
       <section name="DIAScoring" title="" help="" expanded="false">
-        <param name="dia_extraction_window" argument="-algorithm:DIAScoring:dia_extraction_window" type="float" optional="true" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/>
-        <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" type="select" optional="true" label="DIA extraction window unit" help="">
+        <param name="dia_extraction_window" argument="-algorithm:DIAScoring:dia_extraction_window" type="float" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/>
+        <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" type="select" label="DIA extraction window unit" help="">
           <option value="Th" selected="true">Th</option>
           <option value="ppm">ppm</option>
           <expand macro="list_string_san" name="dia_extraction_unit"/>
         </param>
         <param name="dia_centroided" argument="-algorithm:DIAScoring:dia_centroided" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use centroided DIA data" help=""/>
-        <param name="dia_byseries_intensity_min" argument="-algorithm:DIAScoring:dia_byseries_intensity_min" type="float" optional="true" min="0.0" value="300.0" label="DIA b/y series minimum intensity to conside" help=""/>
-        <param name="dia_byseries_ppm_diff" argument="-algorithm:DIAScoring:dia_byseries_ppm_diff" type="float" optional="true" min="0.0" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help=""/>
-        <param name="dia_nr_isotopes" argument="-algorithm:DIAScoring:dia_nr_isotopes" type="integer" optional="true" min="0" value="4" label="DIA number of isotopes to conside" help=""/>
-        <param name="dia_nr_charges" argument="-algorithm:DIAScoring:dia_nr_charges" type="integer" optional="true" min="0" value="4" label="DIA number of charges to conside" help=""/>
-        <param name="peak_before_mono_max_ppm_diff" argument="-algorithm:DIAScoring:peak_before_mono_max_ppm_diff" type="float" optional="true" min="0.0" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help=""/>
+        <param name="dia_byseries_intensity_min" argument="-algorithm:DIAScoring:dia_byseries_intensity_min" type="float" min="0.0" value="300.0" label="DIA b/y series minimum intensity to conside" help=""/>
+        <param name="dia_byseries_ppm_diff" argument="-algorithm:DIAScoring:dia_byseries_ppm_diff" type="float" min="0.0" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help=""/>
+        <param name="dia_nr_isotopes" argument="-algorithm:DIAScoring:dia_nr_isotopes" type="integer" min="0" value="4" label="DIA number of isotopes to conside" help=""/>
+        <param name="dia_nr_charges" argument="-algorithm:DIAScoring:dia_nr_charges" type="integer" min="0" value="4" label="DIA number of charges to conside" help=""/>
+        <param name="peak_before_mono_max_ppm_diff" argument="-algorithm:DIAScoring:peak_before_mono_max_ppm_diff" type="float" min="0.0" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help=""/>
       </section>
       <section name="EMGScoring" title="" help="" expanded="false">
-        <param name="interpolation_step" argument="-algorithm:EMGScoring:interpolation_step" type="float" optional="true" value="0.2" label="Sampling rate for the interpolation of the model function" help=""/>
-        <param name="tolerance_stdev_bounding_box" argument="-algorithm:EMGScoring:tolerance_stdev_bounding_box" type="float" optional="true" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help=""/>
-        <param name="max_iteration" argument="-algorithm:EMGScoring:max_iteration" type="integer" optional="true" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help=""/>
+        <param name="interpolation_step" argument="-algorithm:EMGScoring:interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help=""/>
+        <param name="tolerance_stdev_bounding_box" argument="-algorithm:EMGScoring:tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help=""/>
+        <param name="max_iteration" argument="-algorithm:EMGScoring:max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help=""/>
         <param name="init_mom" argument="-algorithm:EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Initialize parameters using method of moments estimators" help=""/>
         <section name="statistics" title="" help="" expanded="false">
-          <param name="mean" argument="-algorithm:EMGScoring:statistics:mean" type="float" optional="true" value="1.0" label="Centroid position of the model" help=""/>
-          <param name="variance" argument="-algorithm:EMGScoring:statistics:variance" type="float" optional="true" value="1.0" label="Variance of the model" help=""/>
+          <param name="mean" argument="-algorithm:EMGScoring:statistics:mean" type="float" value="1.0" label="Centroid position of the model" help=""/>
+          <param name="variance" argument="-algorithm:EMGScoring:statistics:variance" type="float" value="1.0" label="Variance of the model" help=""/>
         </section>
       </section>
       <section name="Scores" title="" help="" expanded="false">
@@ -230,7 +229,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -244,7 +243,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_OpenSwathAnalyzer_test_1 -->
+  <tests>
+    <!-- TOPP_OpenSwathAnalyzer_test_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -253,7 +253,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
       <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
       <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-      <output name="out" file="OpenSwathAnalyzer_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="OpenSwathAnalyzer_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="no_strict" value="false"/>
       <param name="min_upper_edge_dist" value="0.0"/>
       <section name="model">
@@ -358,6 +358,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathAnalyzer_test_2 -->
     <test expect_num_outputs="2">
@@ -367,7 +370,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
       <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <output name="out" file="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="no_strict" value="false"/>
       <conditional name="swath_files_cond">
         <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
@@ -475,6 +478,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathAnalyzer_test_5_mod -->
     <test expect_num_outputs="2">
@@ -484,7 +490,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
       <param name="tr" value="OpenSwathAnalyzer_mod_input.TraML"/>
-      <output name="out" file="OpenSwathAnalyzer_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="OpenSwathAnalyzer_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="no_strict" value="false"/>
       <conditional name="swath_files_cond">
         <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
@@ -592,6 +598,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathAnalyzer_test_6_nomod -->
     <test expect_num_outputs="2">
@@ -601,7 +610,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
       <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <output name="out" file="OpenSwathAnalyzer_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="OpenSwathAnalyzer_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="no_strict" value="false"/>
       <conditional name="swath_files_cond">
         <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
@@ -709,6 +718,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathAnalyzer_test_7_backgroundSubtraction -->
     <test expect_num_outputs="2">
@@ -718,7 +730,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
       <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <output name="out" file="OpenSwathAnalyzer_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="OpenSwathAnalyzer_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="no_strict" value="false"/>
       <param name="min_upper_edge_dist" value="0.0"/>
       <section name="model">
@@ -823,6 +835,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathAnalyzer_test_8 -->
     <test expect_num_outputs="2">
@@ -833,7 +848,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
       <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
       <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-      <output name="out" file="OpenSwathAnalyzer_8_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="OpenSwathAnalyzer_8_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="no_strict" value="false"/>
       <param name="min_upper_edge_dist" value="0.0"/>
       <section name="model">
@@ -938,6 +953,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathAnalyzer_test_9 -->
     <test expect_num_outputs="2">
@@ -948,7 +966,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
       <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
       <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-      <output name="out" file="OpenSwathAnalyzer_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="OpenSwathAnalyzer_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="no_strict" value="false"/>
       <param name="min_upper_edge_dist" value="0.0"/>
       <section name="model">
@@ -1053,6 +1071,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathAnalyzer_test_10 -->
     <test expect_num_outputs="2">
@@ -1063,7 +1084,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
       <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
       <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-      <output name="out" file="OpenSwathAnalyzer_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="OpenSwathAnalyzer_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="no_strict" value="false"/>
       <param name="min_upper_edge_dist" value="0.0"/>
       <section name="model">
@@ -1168,6 +1189,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathAnalyzer_test_11 -->
     <test expect_num_outputs="2">
@@ -1178,7 +1202,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
       <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
       <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-      <output name="out" file="OpenSwathAnalyzer_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="OpenSwathAnalyzer_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="no_strict" value="false"/>
       <param name="min_upper_edge_dist" value="0.0"/>
       <section name="model">
@@ -1283,11 +1307,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Picks peaks and finds features in an SWATH-MS or SRM experiment.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathAnalyzer.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathAnalyzer.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/OpenSwathAssayGenerator.xml b/tools/openms/OpenSwathAssayGenerator.xml
index 215371522..e6a312699 100644
--- a/tools/openms/OpenSwathAssayGenerator.xml
+++ b/tools/openms/OpenSwathAssayGenerator.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Generates assays according to different models for a specific TraML</description>
   <macros>
@@ -15,15 +14,15 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if $swath_windows_file:
   mkdir swath_windows_file &&
-  ln -s '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' &&
+  cp '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' &&
 #end if
 #if $unimod_file:
   mkdir unimod_file &&
-  ln -s '$unimod_file' 'unimod_file/${re.sub("[^\w\-_]", "_", $unimod_file.element_identifier)}.$gxy2omsext($unimod_file.ext)' &&
+  cp '$unimod_file' 'unimod_file/${re.sub("[^\w\-_]", "_", $unimod_file.element_identifier)}.$gxy2omsext($unimod_file.ext)' &&
 #end if
 
 ## Main program call
@@ -55,40 +54,41 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
+    <param argument="-in" type="data" format="mrm,pqp,tabular,traml" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/>
+    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
       <option value="TraML">traml</option>
       <option value="pqp">pqp</option>
       <option value="tsv">tabular (tsv)</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param argument="-min_transitions" type="integer" optional="true" value="6" label="minimal number of transitions" help=""/>
-    <param argument="-max_transitions" type="integer" optional="true" value="6" label="maximal number of transitions" help=""/>
-    <param argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help="">
+    <param argument="-min_transitions" type="integer" value="6" label="minimal number of transitions" help=""/>
+    <param argument="-max_transitions" type="integer" value="6" label="maximal number of transitions" help=""/>
+    <param argument="-allowed_fragment_types" type="text" value="b,y" label="allowed fragment types" help="">
       <expand macro="list_string_san" name="allowed_fragment_types"/>
     </param>
-    <param argument="-allowed_fragment_charges" type="text" optional="true" value="1,2,3,4" label="allowed fragment charge states" help="">
+    <param argument="-allowed_fragment_charges" type="text" value="1,2,3,4" label="allowed fragment charge states" help="">
       <expand macro="list_string_san" name="allowed_fragment_charges"/>
     </param>
     <param argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/>
     <param argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/>
-    <param argument="-precursor_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help=""/>
-    <param argument="-precursor_lower_mz_limit" type="float" optional="true" value="400.0" label="lower MZ limit for precursor ions" help=""/>
-    <param argument="-precursor_upper_mz_limit" type="float" optional="true" value="1200.0" label="upper MZ limit for precursor ions" help=""/>
-    <param argument="-product_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/>
-    <param argument="-product_lower_mz_limit" type="float" optional="true" value="350.0" label="lower MZ limit for fragment ions" help=""/>
-    <param argument="-product_upper_mz_limit" type="float" optional="true" value="2000.0" label="upper MZ limit for fragment ions" help=""/>
+    <param argument="-precursor_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help=""/>
+    <param argument="-precursor_lower_mz_limit" type="float" value="400.0" label="lower MZ limit for precursor ions" help=""/>
+    <param argument="-precursor_upper_mz_limit" type="float" value="1200.0" label="upper MZ limit for precursor ions" help=""/>
+    <param argument="-product_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/>
+    <param argument="-product_lower_mz_limit" type="float" value="350.0" label="lower MZ limit for fragment ions" help=""/>
+    <param argument="-product_upper_mz_limit" type="float" value="2000.0" label="upper MZ limit for fragment ions" help=""/>
     <param argument="-swath_windows_file" type="data" format="txt" optional="true" label="Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline" help="Note that the first line is a header and will be skipped select txt data sets(s)"/>
     <param argument="-unimod_file" type="data" format="xml" optional="true" label="(Modified) Unimod XML file (http://www.unimod.org/xml/unimod.xml) describing residue modifiability" help=" select xml data sets(s)"/>
     <param argument="-enable_ipf" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions should be generated for IPF" help="Note: Requires setting 'unimod_file'"/>
     <expand macro="adv_opts_macro">
-      <param argument="-max_num_alternative_localizations" type="integer" optional="true" value="10000" label="IPF: maximum number of site-localization permutations" help=""/>
+      <param argument="-max_num_alternative_localizations" type="integer" value="10000" label="IPF: maximum number of site-localization permutations" help=""/>
       <param argument="-disable_identification_ms2_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if MS2-level precursor ions for identification should not be allowed for extraction of the precursor signal from the fragment ion data (MS2-level)" help=""/>
       <param argument="-disable_identification_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if specific neutral losses for identification fragment ions should not be allowed" help=""/>
       <param argument="-enable_identification_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help=""/>
       <param argument="-enable_swath_specifity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions without precursor specificity" help="(i.e. across whole precursor isolation window instead of precursor MZ) should be generated"/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -107,7 +107,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_OpenSwathAssayGenerator_test_1 -->
+  <tests>
+    <!-- TOPP_OpenSwathAssayGenerator_test_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="max_num_alternative_localizations" value="10000"/>
@@ -119,7 +120,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathAssayGenerator_input.TraML"/>
-      <output name="out" file="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <param name="min_transitions" value="6"/>
       <param name="max_transitions" value="6"/>
@@ -140,6 +141,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathAssayGenerator_test_2 -->
     <test expect_num_outputs="2">
@@ -153,7 +157,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
-      <output name="out" file="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <param name="min_transitions" value="6"/>
       <param name="max_transitions" value="6"/>
@@ -175,6 +179,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathAssayGenerator_test_3 -->
     <test expect_num_outputs="2">
@@ -188,7 +195,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
-      <output name="out" file="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <param name="min_transitions" value="6"/>
       <param name="max_transitions" value="6"/>
@@ -210,11 +217,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Generates assays according to different models for a specific TraML
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathAssayGenerator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathAssayGenerator.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/OpenSwathChromatogramExtractor.xml b/tools/openms/OpenSwathChromatogramExtractor.xml
index 9c87e55cc..be2cb249f 100644
--- a/tools/openms/OpenSwathChromatogramExtractor.xml
+++ b/tools/openms/OpenSwathChromatogramExtractor.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Extract chromatograms (XIC) from a MS2 map file.</description>
+  <description>Extract chromatograms (XIC) from a MS2 map file</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</token>
     <import>macros.xml</import>
@@ -17,15 +16,15 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir tr &&
-ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
+cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 #if $rt_norm:
   mkdir rt_norm &&
-  ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
+  cp '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
 #end if
 mkdir out &&
 
@@ -66,23 +65,23 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" multiple="true" label="Input files separated by blank" help=" select mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" label="Input files separated by blank" help=" select mzml data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-tr" type="data" format="csv,traml" optional="false" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
+    <param argument="-tr" type="data" format="csv,traml" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
     <param argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help=" select trafoxml data sets(s)"/>
-    <param argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help=""/>
-    <param argument="-rt_window" type="float" optional="true" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range)" help="This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side"/>
-    <param argument="-ion_mobility_window" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/>
-    <param argument="-mz_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag)" help="This is the full window size, e.g. 100 ppm would extract 50 ppm on either side"/>
+    <param argument="-min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help=""/>
+    <param argument="-rt_window" type="float" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range)" help="This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side"/>
+    <param argument="-ion_mobility_window" type="float" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/>
+    <param argument="-mz_window" type="float" min="0.0" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag)" help="This is the full window size, e.g. 100 ppm would extract 50 ppm on either side"/>
     <param argument="-ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="m/z extraction_window is in ppm" help=""/>
     <param argument="-is_swath" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if the data is SWATH data" help=""/>
     <param argument="-extract_MS1" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extract the MS1 transitions based on the precursor values in the TraML file (useful for extracting MS1 XIC)" help=""/>
     <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
-      <param name="type" argument="-model:type" type="select" optional="true" label="Type of model" help="">
+      <param name="type" argument="-model:type" type="select" label="Type of model" help="">
         <option value="linear" selected="true">linear</option>
         <option value="b_spline">b_spline</option>
         <option value="interpolated">interpolated</option>
@@ -92,13 +91,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <param name="symmetric_regression" argument="-model:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-extraction_function" type="select" optional="true" label="Function used to extract the signal" help="">
+      <param argument="-extraction_function" type="select" label="Function used to extract the signal" help="">
         <option value="tophat" selected="true">tophat</option>
         <option value="bartlett">bartlett</option>
         <expand macro="list_string_san" name="extraction_function"/>
       </param>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -112,7 +111,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_OpenSwathChromatogramExtractor_test_1 -->
+  <tests>
+    <!-- TOPP_OpenSwathChromatogramExtractor_test_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="extraction_function" value="tophat"/>
@@ -123,7 +123,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
       </conditional>
       <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="min_upper_edge_dist" value="0.0"/>
       <param name="rt_window" value="-1.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
@@ -141,6 +141,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathChromatogramExtractor_test_2 -->
     <test expect_num_outputs="2">
@@ -154,7 +157,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </conditional>
       <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
       <param name="rt_norm" value="OpenSwathChromatogramExtractor_input.trafoXML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_output_2.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathChromatogramExtractor_output_2.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="min_upper_edge_dist" value="0.0"/>
       <param name="rt_window" value="50.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
@@ -172,6 +175,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathChromatogramExtractor_test_3 -->
     <test expect_num_outputs="2">
@@ -184,7 +190,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
       </conditional>
       <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="min_upper_edge_dist" value="0.0"/>
       <param name="rt_window" value="-1.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
@@ -202,6 +208,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathChromatogramExtractor_test_4 -->
     <test expect_num_outputs="2">
@@ -214,7 +223,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="OpenSwathChromatogramExtractor_4_input.mzML"/>
       </conditional>
       <param name="tr" value="OpenSwathChromatogramExtractor_4_input.TraML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="min_upper_edge_dist" value="0.0"/>
       <param name="rt_window" value="-1.0"/>
       <param name="ion_mobility_window" value="0.05"/>
@@ -232,6 +241,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathChromatogramExtractor_test_5 -->
     <test expect_num_outputs="2">
@@ -244,7 +256,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
       </conditional>
       <param name="tr" value="OpenSwathChromatogramExtractor_5_input.TraML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="min_upper_edge_dist" value="0.0"/>
       <param name="rt_window" value="-1.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
@@ -262,11 +274,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Extract chromatograms (XIC) from a MS2 map file.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathChromatogramExtractor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathChromatogramExtractor.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/OpenSwathConfidenceScoring.xml b/tools/openms/OpenSwathConfidenceScoring.xml
index 00b589afe..5610f3585 100644
--- a/tools/openms/OpenSwathConfidenceScoring.xml
+++ b/tools/openms/OpenSwathConfidenceScoring.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Compute confidence scores for OpenSwath results</description>
   <macros>
@@ -15,13 +14,13 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir lib &&
-ln -s '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' &&
+cp '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' &&
 mkdir out &&
 #if $trafo:
   mkdir trafo &&
-  ln -s '$trafo' 'trafo/${re.sub("[^\w\-_]", "_", $trafo.element_identifier)}.$gxy2omsext($trafo.ext)' &&
+  cp '$trafo' 'trafo/${re.sub("[^\w\-_]", "_", $trafo.element_identifier)}.$gxy2omsext($trafo.ext)' &&
 #end if
 
 ## Main program call
@@ -51,19 +50,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="featurexml" optional="false" label="Input file (OpenSwath results)" help=" select featurexml data sets(s)"/>
-    <param argument="-lib" type="data" format="traml" optional="false" label="Assay library" help=" select traml data sets(s)"/>
+    <param argument="-in" type="data" format="featurexml" label="Input file (OpenSwath results)" help=" select featurexml data sets(s)"/>
+    <param argument="-lib" type="data" format="traml" label="Assay library" help=" select traml data sets(s)"/>
     <param argument="-trafo" type="data" format="trafoxml" optional="true" label="Retention time transformation" help=" select trafoxml data sets(s)"/>
-    <param argument="-decoys" type="integer" optional="true" min="0" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" help=""/>
-    <param argument="-transitions" type="integer" optional="true" min="0" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" help=""/>
+    <param argument="-decoys" type="integer" min="0" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" help=""/>
+    <param argument="-transitions" type="integer" min="0" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" help=""/>
     <section name="GLM" title="Parameters of the binomial GLM" help="" expanded="false">
-      <param name="intercept" argument="-GLM:intercept" type="float" optional="true" value="3.87333466" label="Intercept term" help=""/>
-      <param name="delta_rt" argument="-GLM:delta_rt" type="float" optional="true" value="-0.02898629" label="Coefficient of retention time difference" help=""/>
-      <param name="dist_int" argument="-GLM:dist_int" type="float" optional="true" value="-7.75880768" label="Coefficient of intensity distance" help=""/>
+      <param name="intercept" argument="-GLM:intercept" type="float" value="3.87333466" label="Intercept term" help=""/>
+      <param name="delta_rt" argument="-GLM:delta_rt" type="float" value="-0.02898629" label="Coefficient of retention time difference" help=""/>
+      <param name="dist_int" argument="-GLM:dist_int" type="float" value="-7.75880768" label="Coefficient of intensity distance" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -77,7 +76,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_OpenSwathConfidenceScoring_1 -->
+  <tests>
+    <!-- TOPP_OpenSwathConfidenceScoring_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -85,7 +85,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
       <param name="lib" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
-      <output name="out" file="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/>
       <param name="decoys" value="1"/>
       <param name="transitions" value="2"/>
@@ -100,11 +100,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Compute confidence scores for OpenSwath results
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathConfidenceScoring.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathConfidenceScoring.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/OpenSwathDIAPreScoring.xml b/tools/openms/OpenSwathDIAPreScoring.xml
index e836c301c..41a7edcd9 100644
--- a/tools/openms/OpenSwathDIAPreScoring.xml
+++ b/tools/openms/OpenSwathDIAPreScoring.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Scoring spectra using the DIA scores.</description>
+  <description>Scoring spectra using the DIA scores</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</token>
     <import>macros.xml</import>
@@ -15,13 +14,13 @@
 
 ## Preprocessing
 mkdir tr &&
-ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
+cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 mkdir swath_files_cond.swath_files &&
 #if $swath_files_cond.swath_files_select == "no"
 mkdir ${' '.join(["'swath_files_cond.swath_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} && 
-${' '.join(["ln -s '%s' 'swath_files_cond.swath_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])}
+${' '.join(["cp '%s' 'swath_files_cond.swath_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])}
 #else
-ln -s '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' &&
+cp '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' &&
 #end if
 mkdir output_files &&
 mkdir ${' '.join(["'output_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} && 
@@ -53,23 +52,23 @@ ${' '.join(["&& mv -n 'output_files/%(bn)s/%(id)s.%(gext)s' 'output_files/%(bn)s
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/>
+    <param argument="-tr" type="data" format="traml" label="transition file" help=" select traml data sets(s)"/>
     <conditional name="swath_files_cond">
       <param name="swath_files_select" type="select" label="Run tool in batch mode for -swath_files">
         <option value="no">No: process all datasets jointly</option>
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-swath_files" type="data" format="mzml" multiple="true" optional="false" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/>
+        <param argument="-swath_files" type="data" format="mzml" multiple="true" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-swath_files" type="data" format="mzml" multiple="false" optional="false" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/>
+        <param argument="-swath_files" type="data" format="mzml" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help=""/>
+    <param argument="-min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -85,27 +84,28 @@ ${' '.join(["&& mv -n 'output_files/%(bn)s/%(id)s.%(gext)s' 'output_files/%(bn)s
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- data from a test that included all the needed test files -->
-  <test>
-    <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-    <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
-    <output_collection name="output_files" count="1">
-      <element name="OpenSwathAnalyzer_2_swathfile_mzML" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
-    </output_collection>
-  </test>
-  <!-- test with two inputs (actually the same file .. symlinked) -->
-  <test>
-    <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-    <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/>
-    <output_collection name="output_files" count="2">
-      <element name="OpenSwathDIAPreScoring_in1_mzML" file="OpenSwathDIAPreScoring_2_1.tsv" ftype="tabular"/>
-      <element name="OpenSwathDIAPreScoring_in2_mzML" file="OpenSwathDIAPreScoring_2_2.tsv" ftype="tabular"/>
-    </output_collection>
-  </test>
-</tests>
+  <tests>
+    <!-- data from a test that included all the needed test files -->
+    <test expect_num_outputs="1">
+      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
+      <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
+      <output_collection name="output_files" count="1">
+        <element name="OpenSwathAnalyzer_2_swathfile_mzML" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
+      </output_collection>
+    </test>
+    <!-- test with two inputs (actually the same file .. symlinked) -->
+    <test expect_num_outputs="1">
+      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
+      <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/>
+      <output_collection name="output_files" count="2">
+        <element name="OpenSwathDIAPreScoring_in1_mzML" file="OpenSwathDIAPreScoring_2_1.tsv" ftype="tabular"/>
+        <element name="OpenSwathDIAPreScoring_in2_mzML" file="OpenSwathDIAPreScoring_2_2.tsv" ftype="tabular"/>
+      </output_collection>
+    </test>
+  </tests>
   <help><![CDATA[Scoring spectra using the DIA scores.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathDIAPreScoring.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathDIAPreScoring.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/OpenSwathDecoyGenerator.xml b/tools/openms/OpenSwathDecoyGenerator.xml
index 2fd025ce5..5d832dbc8 100644
--- a/tools/openms/OpenSwathDecoyGenerator.xml
+++ b/tools/openms/OpenSwathDecoyGenerator.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Generates decoys according to different models for a specific TraML</description>
   <macros>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,43 +38,44 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
+    <param argument="-in" type="data" format="mrm,pqp,tabular,traml" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/>
+    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
       <option value="TraML">traml</option>
       <option value="pqp">pqp</option>
       <option value="tsv">tabular (tsv)</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param argument="-method" type="select" optional="true" label="Decoy generation method" help="">
+    <param argument="-method" type="select" label="Decoy generation method" help="">
       <option value="shuffle" selected="true">shuffle</option>
       <option value="pseudo-reverse">pseudo-reverse</option>
       <option value="reverse">reverse</option>
       <option value="shift">shift</option>
       <expand macro="list_string_san" name="method"/>
     </param>
-    <param argument="-decoy_tag" type="text" optional="true" value="DECOY_" label="decoy tag" help="">
+    <param argument="-decoy_tag" type="text" value="DECOY_" label="decoy tag" help="">
       <expand macro="list_string_san" name="decoy_tag"/>
     </param>
     <param argument="-switchKR" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to switch terminal K and R (to achieve different precursor mass)" help=""/>
     <expand macro="adv_opts_macro">
-      <param argument="-min_decoy_fraction" type="float" optional="true" value="0.8" label="Minimum fraction of decoy / target peptides and proteins" help=""/>
-      <param argument="-aim_decoy_fraction" type="float" optional="true" value="1.0" label="Number of decoys the algorithm should generate (if unequal to 1, the algorithm will randomly select N peptides for decoy generation)" help=""/>
-      <param argument="-shuffle_max_attempts" type="integer" optional="true" value="30" label="shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm" help=""/>
-      <param argument="-shuffle_sequence_identity_threshold" type="float" optional="true" value="0.5" label="shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm" help=""/>
-      <param argument="-shift_precursor_mz_shift" type="float" optional="true" value="0.0" label="shift: precursor ion MZ shift in Thomson for shift decoy method" help=""/>
-      <param argument="-shift_product_mz_shift" type="float" optional="true" value="20.0" label="shift: fragment ion MZ shift in Thomson for shift decoy method" help=""/>
-      <param argument="-product_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/>
-      <param argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help="">
+      <param argument="-min_decoy_fraction" type="float" value="0.8" label="Minimum fraction of decoy / target peptides and proteins" help=""/>
+      <param argument="-aim_decoy_fraction" type="float" value="1.0" label="Number of decoys the algorithm should generate (if unequal to 1, the algorithm will randomly select N peptides for decoy generation)" help=""/>
+      <param argument="-shuffle_max_attempts" type="integer" value="30" label="shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm" help=""/>
+      <param argument="-shuffle_sequence_identity_threshold" type="float" value="0.5" label="shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm" help=""/>
+      <param argument="-shift_precursor_mz_shift" type="float" value="0.0" label="shift: precursor ion MZ shift in Thomson for shift decoy method" help=""/>
+      <param argument="-shift_product_mz_shift" type="float" value="20.0" label="shift: fragment ion MZ shift in Thomson for shift decoy method" help=""/>
+      <param argument="-product_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/>
+      <param argument="-allowed_fragment_types" type="text" value="b,y" label="allowed fragment types" help="">
         <expand macro="list_string_san" name="allowed_fragment_types"/>
       </param>
-      <param argument="-allowed_fragment_charges" type="text" optional="true" value="1,2,3,4" label="allowed fragment charge states" help="">
+      <param argument="-allowed_fragment_charges" type="text" value="1,2,3,4" label="allowed fragment charge states" help="">
         <expand macro="list_string_san" name="allowed_fragment_charges"/>
       </param>
       <param argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/>
       <param argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/>
       <param argument="-separate" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if decoys should not be appended to targets" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -94,7 +94,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_OpenSwathDecoyGenerator_test_1 -->
+  <tests>
+    <!-- TOPP_OpenSwathDecoyGenerator_test_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="min_decoy_fraction" value="0.8"/>
@@ -113,7 +114,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathDecoyGenerator_input.TraML"/>
-      <output name="out" file="OpenSwathDecoyGenerator_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="OpenSwathDecoyGenerator_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <param name="method" value="pseudo-reverse"/>
       <param name="decoy_tag" value="DECOY_"/>
@@ -124,6 +125,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathDecoyGenerator_test_2 -->
     <test expect_num_outputs="2">
@@ -144,7 +148,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathDecoyGenerator_input_2.TraML"/>
-      <output name="out" file="OpenSwathDecoyGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="OpenSwathDecoyGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <param name="method" value="pseudo-reverse"/>
       <param name="decoy_tag" value="DECOY_"/>
@@ -155,6 +159,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathDecoyGenerator_test_3 -->
     <test expect_num_outputs="2">
@@ -175,7 +182,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathDecoyGenerator_input_3.TraML"/>
-      <output name="out" file="OpenSwathDecoyGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="OpenSwathDecoyGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <param name="method" value="pseudo-reverse"/>
       <param name="decoy_tag" value="DECOY_"/>
@@ -186,6 +193,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathDecoyGenerator_test_4 -->
     <test expect_num_outputs="2">
@@ -206,7 +216,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathDecoyGenerator_input_4.tsv" ftype="tabular"/>
-      <output name="out" file="OpenSwathDecoyGenerator_output_4.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="OpenSwathDecoyGenerator_output_4.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <param name="method" value="pseudo-reverse"/>
       <param name="decoy_tag" value="DECOY_"/>
@@ -217,11 +227,48 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_OpenSwathDecoyGenerator_test_5 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="min_decoy_fraction" value="0.4"/>
+        <param name="aim_decoy_fraction" value="1.0"/>
+        <param name="shuffle_max_attempts" value="30"/>
+        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
+        <param name="shift_precursor_mz_shift" value="0.0"/>
+        <param name="shift_product_mz_shift" value="20.0"/>
+        <param name="product_mz_threshold" value="0.025"/>
+        <param name="allowed_fragment_types" value="b,y"/>
+        <param name="allowed_fragment_charges" value="1,2,3,4"/>
+        <param name="enable_detection_specific_losses" value="false"/>
+        <param name="enable_detection_unspecific_losses" value="false"/>
+        <param name="separate" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="OpenSwathDecoyGenerator_input_5.tsv" ftype="tabular"/>
+      <output name="out" value="OpenSwathDecoyGenerator_output_5.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <param name="out_type" value="TraML"/>
+      <param name="method" value="pseudo-reverse"/>
+      <param name="decoy_tag" value="DECOY_"/>
+      <param name="switchKR" value="false"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Generates decoys according to different models for a specific TraML
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathDecoyGenerator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathDecoyGenerator.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/OpenSwathFeatureXMLToTSV.xml b/tools/openms/OpenSwathFeatureXMLToTSV.xml
index 57d290ffb..d64c0da10 100644
--- a/tools/openms/OpenSwathFeatureXMLToTSV.xml
+++ b/tools/openms/OpenSwathFeatureXMLToTSV.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Converts a featureXML to a mProphet tsv.</description>
+  <description>Converts a featureXML to a mProphet tsv</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathFeatureXMLToTSV</token>
     <import>macros.xml</import>
@@ -17,12 +16,12 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir tr &&
-ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
+cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -58,20 +57,20 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="featurexml" multiple="true" optional="false" label="Input files separated by blank" help=" select featurexml data sets(s)"/>
+        <param argument="-in" type="data" format="featurexml" multiple="true" label="Input files separated by blank" help=" select featurexml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="featurexml" multiple="false" optional="false" label="Input files separated by blank" help=" select featurexml data sets(s)"/>
+        <param argument="-in" type="data" format="featurexml" label="Input files separated by blank" help=" select featurexml data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-tr" type="data" format="traml" optional="false" label="TraML transition file" help=" select traml data sets(s)"/>
+    <param argument="-tr" type="data" format="traml" label="TraML transition file" help=" select traml data sets(s)"/>
     <param argument="-short_format" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write short (one peptide per line) or long format (one transition per line)" help=""/>
     <param argument="-best_scoring_peptide" type="text" optional="true" value="" label="If only the best scoring feature per peptide should be printed, give the variable name" help="">
       <expand macro="list_string_san" name="best_scoring_peptide"/>
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -85,7 +84,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_OpenSwathFeatureXMLToTSV_test_1 -->
+  <tests>
+    <!-- TOPP_OpenSwathFeatureXMLToTSV_test_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -95,7 +95,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
       </conditional>
       <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
-      <output name="out" file="OpenSwathFeatureXMLToTSV_output.short.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out" value="OpenSwathFeatureXMLToTSV_output.short.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="short_format" value="true"/>
       <param name="best_scoring_peptide" value=""/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -104,6 +104,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathFeatureXMLToTSV_test_2 -->
     <test expect_num_outputs="2">
@@ -115,7 +118,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
       </conditional>
       <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
-      <output name="out" file="OpenSwathFeatureXMLToTSV_output.long.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out" value="OpenSwathFeatureXMLToTSV_output.long.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="short_format" value="false"/>
       <param name="best_scoring_peptide" value=""/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -124,6 +127,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathFeatureXMLToTSV_test_3 -->
     <test expect_num_outputs="2">
@@ -135,7 +141,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
       </conditional>
       <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
-      <output name="out" file="OpenSwathFeatureXMLToTSV_3_output.short.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out" value="OpenSwathFeatureXMLToTSV_3_output.short.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="short_format" value="true"/>
       <param name="best_scoring_peptide" value="main_var_xx_lda_prelim_score"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -144,11 +150,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Converts a featureXML to a mProphet tsv.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathFeatureXMLToTSV.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathFeatureXMLToTSV.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/OpenSwathFileSplitter.xml b/tools/openms/OpenSwathFileSplitter.xml
index 3823d3de5..2853b400f 100644
--- a/tools/openms/OpenSwathFileSplitter.xml
+++ b/tools/openms/OpenSwathFileSplitter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathFileSplitter" name="OpenSwathFileSplitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Splits SWATH files into n files, each containing one window.</description>
+  <description>Splits SWATH files into n files, each containing one window</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathFileSplitter</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir outputDirectory &&
 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_qc &&
@@ -51,10 +50,10 @@ outputDirectory/
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml,mzxml" optional="false" label="Input file (SWATH/DIA file)" help=" select mzml,mzxml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml,mzxml" label="Input file (SWATH/DIA file)" help=" select mzml,mzxml data sets(s)"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -74,28 +73,29 @@ outputDirectory/
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_OpenSwathFileSplitter_1 -->
-  <test expect_num_outputs="3">
-    <section name="adv_opts">
-      <param name="test" value="true"/>
-    </section>
-    <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
-    <output_collection name="outputDirectory" count="6">
-      <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
-      <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
-    </output_collection>
-    <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
-    <output name="ctd_out" ftype="xml">
-      <assert_contents>
-        <is_valid_xml/>
-      </assert_contents>
-    </output>
-  </test>
-</tests>
+  <tests>
+    <!-- TOPP_OpenSwathFileSplitter_1 -->
+    <test expect_num_outputs="3">
+      <section name="adv_opts">
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
+      <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
+      <output_collection name="outputDirectory" count="6">
+        <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
+        <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
+      </output_collection>
+      <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
   <help><![CDATA[Splits SWATH files into n files, each containing one window.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathFileSplitter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathFileSplitter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/OpenSwathMzMLFileCacher.xml b/tools/openms/OpenSwathMzMLFileCacher.xml
index 940bd1f80..39aeecfcb 100644
--- a/tools/openms/OpenSwathMzMLFileCacher.xml
+++ b/tools/openms/OpenSwathMzMLFileCacher.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>This tool caches the spectra and chromatogram data of an mzML to disk.</description>
+  <description>This tool caches the spectra and chromatogram data of an mzML to disk</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathMzMLFileCacher</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,20 +38,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml,sqmass" optional="false" label="Input mzML file" help=" select mzml,sqmass data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense">
+    <param argument="-in" type="data" format="mzml,sqmass" label="Input mzML file" help=" select mzml,sqmass data sets(s)"/>
+    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense">
       <option value="mzML">mzml</option>
       <option value="sqMass">sqmass</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
     <param argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data)" help=""/>
     <param argument="-full_meta" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write full meta information into sqMass file (may require large amounts of memory)" help=""/>
     <expand macro="adv_opts_macro">
-      <param argument="-lossy_mass_accuracy" type="float" optional="true" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
+      <param argument="-lossy_mass_accuracy" type="float" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
       <param argument="-process_lowmemory" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML)" help="Note: this flag will prevent conversion from spectra to chromatograms"/>
-      <param argument="-lowmem_batchsize" type="integer" optional="true" min="0" value="500" label="The batch size of the low memory conversion" help=""/>
+      <param argument="-lowmem_batchsize" type="integer" min="0" value="500" label="The batch size of the low memory conversion" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -70,7 +70,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_OpenSwathMzMLFileCacher_test_1_step1 -->
+  <tests>
+    <!-- TOPP_OpenSwathMzMLFileCacher_test_1_step1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="lossy_mass_accuracy" value="-1.0"/>
@@ -80,7 +81,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathMzMLFileCacher_1_output_1.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -90,6 +91,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathMzMLFileCacher_test_2_step1 -->
     <test expect_num_outputs="2">
@@ -101,7 +105,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathMzMLFileCacher_2_output_1.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -111,6 +115,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathMzMLFileCacher_test_3_step1 -->
     <test expect_num_outputs="2">
@@ -122,7 +129,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/>
+      <output name="out" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/>
       <param name="out_type" value="sqMass"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -132,6 +139,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathMzMLFileCacher_test_3_step2 -->
     <test expect_num_outputs="2">
@@ -143,7 +153,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_3_output.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathMzMLFileCacher_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -153,6 +163,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathMzMLFileCacher_test_4_step1 -->
     <test expect_num_outputs="2">
@@ -164,7 +177,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/>
+      <output name="out" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/>
       <param name="out_type" value="sqMass"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -174,6 +187,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathMzMLFileCacher_test_4_step2 -->
     <test expect_num_outputs="2">
@@ -185,7 +201,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_4_output.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathMzMLFileCacher_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -195,6 +211,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathMzMLFileCacher_test_5_step1 -->
     <test expect_num_outputs="2">
@@ -206,7 +225,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathMzMLFileCacher_1_output_1.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -216,6 +235,33 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_OpenSwathAnalyzer_test_3_prepare -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="lossy_mass_accuracy" value="-1.0"/>
+        <param name="process_lowmemory" value="false"/>
+        <param name="lowmem_batchsize" value="500"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
+      <output name="out" value="OpenSwathAnalyzer_3_swathfile.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/>
+      <param name="out_type" value="mzML"/>
+      <param name="lossy_compression" value="true"/>
+      <param name="full_meta" value="true"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathAnalyzer_test_4_prepare1 -->
     <test expect_num_outputs="2">
@@ -227,7 +273,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
-      <output name="out" file="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/>
+      <output name="out" value="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/>
       <param name="out_type" value="mzML"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -237,6 +283,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathAnalyzer_test_4_prepare2 -->
     <test expect_num_outputs="2">
@@ -248,7 +297,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <output name="out" file="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/>
+      <output name="out" value="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta_frac="0.7"/>
       <param name="out_type" value="mzML"/>
       <param name="lossy_compression" value="true"/>
       <param name="full_meta" value="true"/>
@@ -258,6 +307,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathWorkflow_14_step2 -->
     <test expect_num_outputs="2">
@@ -269,7 +321,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathWorkflow_14.chrom.tmp.sqMass"/>
-      <output name="out" file="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="out_type" value="mzML"/>
       <param name="lossy_compression" value="false"/>
       <param name="full_meta" value="false"/>
@@ -279,11 +331,38 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_OpenSwathWorkflow_16_prepare -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="lossy_mass_accuracy" value="0.0001"/>
+        <param name="process_lowmemory" value="false"/>
+        <param name="lowmem_batchsize" value="500"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
+      <output name="out" value="OpenSwathWorkflow_16_input.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/>
+      <param name="out_type" value="sqMass"/>
+      <param name="lossy_compression" value="true"/>
+      <param name="full_meta" value="true"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[This tool caches the spectra and chromatogram data of an mzML to disk.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathMzMLFileCacher.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathMzMLFileCacher.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/OpenSwathRTNormalizer.xml b/tools/openms/OpenSwathRTNormalizer.xml
index 908235e3f..dbbd40d74 100644
--- a/tools/openms/OpenSwathRTNormalizer.xml
+++ b/tools/openms/OpenSwathRTNormalizer.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.</description>
+  <description>This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token>
     <import>macros.xml</import>
@@ -17,16 +16,16 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir tr &&
-ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
+cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 mkdir out &&
 #if $rt_norm:
   mkdir rt_norm &&
-  ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
+  cp '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
 #end if
 
 ## Main program call
@@ -66,19 +65,19 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" multiple="true" label="Input files separated by blank" help=" select mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" label="Input files separated by blank" help=" select mzml data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-tr" type="data" format="csv,traml" optional="false" label="transition file with the RT peptides ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
+    <param argument="-tr" type="data" format="csv,traml" label="transition file with the RT peptides ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
     <param argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help=" select trafoxml data sets(s)"/>
-    <param argument="-min_rsq" type="float" optional="true" value="0.95" label="Minimum r-squared of RT peptides regression" help=""/>
-    <param argument="-min_coverage" type="float" optional="true" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/>
+    <param argument="-min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help=""/>
+    <param argument="-min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/>
     <param argument="-estimateBestPeptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether the algorithms should try to choose the best peptides based on their peak shape for normalization" help="Use this option you do not expect all your peptides to be detected in a sample and too many 'bad' peptides enter the outlier removal step (e.g. due to them being endogenous peptides or using a less curated list of peptides)"/>
     <section name="RTNormalization" title="Parameters for the RTNormalization" help="RT normalization and outlier detection can be done iteratively (by default) which removes one outlier per iteration or using the RANSAC algorithm" expanded="false">
-      <param name="outlierMethod" argument="-RTNormalization:outlierMethod" type="select" optional="true" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)">
+      <param name="outlierMethod" argument="-RTNormalization:outlierMethod" type="select" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)">
         <option value="iter_residual" selected="true">iter_residual</option>
         <option value="iter_jackknife">iter_jackknife</option>
         <option value="ransac">ransac</option>
@@ -86,42 +85,42 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <expand macro="list_string_san" name="outlierMethod"/>
       </param>
       <param name="useIterativeChauvenet" argument="-RTNormalization:useIterativeChauvenet" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to use Chauvenet's criterion when using iterative methods" help="This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained"/>
-      <param name="RANSACMaxIterations" argument="-RTNormalization:RANSACMaxIterations" type="integer" optional="true" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help=""/>
-      <param name="RANSACMaxPercentRTThreshold" argument="-RTNormalization:RANSACMaxPercentRTThreshold" type="integer" optional="true" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" help="Default is set to 3% which is around +/- 4 minutes on a 120 gradient"/>
-      <param name="RANSACSamplingSize" argument="-RTNormalization:RANSACSamplingSize" type="integer" optional="true" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help=""/>
+      <param name="RANSACMaxIterations" argument="-RTNormalization:RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help=""/>
+      <param name="RANSACMaxPercentRTThreshold" argument="-RTNormalization:RANSACMaxPercentRTThreshold" type="integer" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" help="Default is set to 3% which is around +/- 4 minutes on a 120 gradient"/>
+      <param name="RANSACSamplingSize" argument="-RTNormalization:RANSACSamplingSize" type="integer" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help=""/>
     </section>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="stop_report_after_feature" argument="-algorithm:stop_report_after_feature" type="integer" optional="true" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help=""/>
-      <param name="rt_extraction_window" argument="-algorithm:rt_extraction_window" type="float" optional="true" value="-1.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution)" help="For this to work, the TraML input file needs to contain normalized RT values"/>
-      <param name="rt_normalization_factor" argument="-algorithm:rt_normalization_factor" type="float" optional="true" value="1.0" label="The normalized RT is expected to be between 0 and 1" help="If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)"/>
-      <param name="quantification_cutoff" argument="-algorithm:quantification_cutoff" type="float" optional="true" min="0.0" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help=""/>
+      <param name="stop_report_after_feature" argument="-algorithm:stop_report_after_feature" type="integer" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help=""/>
+      <param name="rt_extraction_window" argument="-algorithm:rt_extraction_window" type="float" value="-1.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution)" help="For this to work, the TraML input file needs to contain normalized RT values"/>
+      <param name="rt_normalization_factor" argument="-algorithm:rt_normalization_factor" type="float" value="1.0" label="The normalized RT is expected to be between 0 and 1" help="If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)"/>
+      <param name="quantification_cutoff" argument="-algorithm:quantification_cutoff" type="float" min="0.0" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help=""/>
       <param name="write_convex_hull" argument="-algorithm:write_convex_hull" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write out all points of all features into the featureXML" help=""/>
-      <param name="spectrum_addition_method" argument="-algorithm:spectrum_addition_method" type="select" optional="true" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
+      <param name="spectrum_addition_method" argument="-algorithm:spectrum_addition_method" type="select" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
         <option value="simple" selected="true">simple</option>
         <option value="resample">resample</option>
         <expand macro="list_string_san" name="spectrum_addition_method"/>
       </param>
-      <param name="add_up_spectra" argument="-algorithm:add_up_spectra" type="integer" optional="true" min="1" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help=""/>
-      <param name="spacing_for_spectra_resampling" argument="-algorithm:spacing_for_spectra_resampling" type="float" optional="true" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
-      <param name="uis_threshold_sn" argument="-algorithm:uis_threshold_sn" type="integer" optional="true" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
-      <param name="uis_threshold_peak_area" argument="-algorithm:uis_threshold_peak_area" type="integer" optional="true" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
-      <param name="scoring_model" argument="-algorithm:scoring_model" type="select" optional="true" label="Scoring model to use" help="">
+      <param name="add_up_spectra" argument="-algorithm:add_up_spectra" type="integer" min="1" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help=""/>
+      <param name="spacing_for_spectra_resampling" argument="-algorithm:spacing_for_spectra_resampling" type="float" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
+      <param name="uis_threshold_sn" argument="-algorithm:uis_threshold_sn" type="integer" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
+      <param name="uis_threshold_peak_area" argument="-algorithm:uis_threshold_peak_area" type="integer" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
+      <param name="scoring_model" argument="-algorithm:scoring_model" type="select" label="Scoring model to use" help="">
         <option value="default" selected="true">default</option>
         <option value="single_transition">single_transition</option>
         <expand macro="list_string_san" name="scoring_model"/>
       </param>
-      <param name="im_extra_drift" argument="-algorithm:im_extra_drift" type="float" optional="true" min="0.0" value="0.0" label="Extra drift time to extract for IM scoring (as a fraction" help="e.g. 0.25 means 25% extra on each side)"/>
+      <param name="im_extra_drift" argument="-algorithm:im_extra_drift" type="float" min="0.0" value="0.0" label="Extra drift time to extract for IM scoring (as a fraction" help="e.g. 0.25 means 25% extra on each side)"/>
       <param name="strict" argument="-algorithm:strict" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to error (true) or skip (false) if a transition in a transition group does not have a corresponding chromatogram" help=""/>
       <section name="TransitionGroupPicker" title="" help="" expanded="false">
-        <param name="stop_after_feature" argument="-algorithm:TransitionGroupPicker:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
-        <param name="stop_after_intensity_ratio" argument="-algorithm:TransitionGroupPicker:stop_after_intensity_ratio" type="float" optional="true" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
-        <param name="min_peak_width" argument="-algorithm:TransitionGroupPicker:min_peak_width" type="float" optional="true" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
-        <param name="peak_integration" argument="-algorithm:TransitionGroupPicker:peak_integration" type="select" optional="true" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
+        <param name="stop_after_feature" argument="-algorithm:TransitionGroupPicker:stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
+        <param name="stop_after_intensity_ratio" argument="-algorithm:TransitionGroupPicker:stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
+        <param name="min_peak_width" argument="-algorithm:TransitionGroupPicker:min_peak_width" type="float" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
+        <param name="peak_integration" argument="-algorithm:TransitionGroupPicker:peak_integration" type="select" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
           <option value="original" selected="true">original</option>
           <option value="smoothed">smoothed</option>
           <expand macro="list_string_san" name="peak_integration"/>
         </param>
-        <param name="background_subtraction" argument="-algorithm:TransitionGroupPicker:background_subtraction" type="select" optional="true" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
+        <param name="background_subtraction" argument="-algorithm:TransitionGroupPicker:background_subtraction" type="select" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
           <option value="none" selected="true">none</option>
           <option value="original">original</option>
           <option value="exact">exact</option>
@@ -130,29 +129,29 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="recalculate_peaks" argument="-algorithm:TransitionGroupPicker:recalculate_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="Tries to use the consensus (median) peak border if the variation within the picked peaks is too large"/>
         <param name="use_precursors" argument="-algorithm:TransitionGroupPicker:use_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)" help=""/>
         <param name="use_consensus" argument="-algorithm:TransitionGroupPicker:use_consensus" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)" help=""/>
-        <param name="recalculate_peaks_max_z" argument="-algorithm:TransitionGroupPicker:recalculate_peaks_max_z" type="float" optional="true" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
-        <param name="minimal_quality" argument="-algorithm:TransitionGroupPicker:minimal_quality" type="float" optional="true" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
-        <param name="resample_boundary" argument="-algorithm:TransitionGroupPicker:resample_boundary" type="float" optional="true" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
+        <param name="recalculate_peaks_max_z" argument="-algorithm:TransitionGroupPicker:recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
+        <param name="minimal_quality" argument="-algorithm:TransitionGroupPicker:minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
+        <param name="resample_boundary" argument="-algorithm:TransitionGroupPicker:resample_boundary" type="float" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
         <param name="compute_peak_quality" argument="-algorithm:TransitionGroupPicker:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
         <param name="compute_peak_shape_metrics" argument="-algorithm:TransitionGroupPicker:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/>
         <param name="compute_total_mi" argument="-algorithm:TransitionGroupPicker:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/>
-        <param name="boundary_selection_method" argument="-algorithm:TransitionGroupPicker:boundary_selection_method" type="select" optional="true" label="Method to use when selecting the best boundaries for peaks" help="">
+        <param name="boundary_selection_method" argument="-algorithm:TransitionGroupPicker:boundary_selection_method" type="select" label="Method to use when selecting the best boundaries for peaks" help="">
           <option value="largest" selected="true">largest</option>
           <option value="widest">widest</option>
           <expand macro="list_string_san" name="boundary_selection_method"/>
         </param>
         <section name="PeakPickerMRM" title="" help="" expanded="false">
-          <param name="sgolay_frame_length" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length" type="integer" optional="true" value="15" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
-          <param name="sgolay_polynomial_order" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order" type="integer" optional="true" value="3" label="Order of the polynomial that is fitted" help=""/>
-          <param name="gauss_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width" type="float" optional="true" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/>
+          <param name="sgolay_frame_length" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
+          <param name="sgolay_polynomial_order" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help=""/>
+          <param name="gauss_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/>
           <param name="use_gauss" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help=""/>
-          <param name="peak_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width" type="float" optional="true" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
-          <param name="signal_to_noise" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
-          <param name="sn_win_len" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len" type="float" optional="true" value="1000.0" label="Signal to noise window length" help=""/>
-          <param name="sn_bin_count" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count" type="integer" optional="true" value="30" label="Signal to noise bin count" help=""/>
+          <param name="peak_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
+          <param name="signal_to_noise" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise" type="float" min="0.0" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
+          <param name="sn_win_len" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help=""/>
+          <param name="sn_bin_count" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help=""/>
           <param name="write_sn_log_messages" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/>
           <param name="remove_overlapping_peaks" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to remove overlapping peaks during peak picking" help=""/>
-          <param name="method" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:method" type="select" optional="true" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
+          <param name="method" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:method" type="select" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
             <option value="legacy">legacy</option>
             <option value="corrected" selected="true">corrected</option>
             <option value="crawdad">crawdad</option>
@@ -160,13 +159,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           </param>
         </section>
         <section name="PeakIntegrator" title="" help="" expanded="false">
-          <param name="integration_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" optional="true" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
+          <param name="integration_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
             <option value="intensity_sum" selected="true">intensity_sum</option>
             <option value="simpson">simpson</option>
             <option value="trapezoid">trapezoid</option>
             <expand macro="list_string_san" name="integration_type"/>
           </param>
-          <param name="baseline_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" optional="true" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
+          <param name="baseline_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
             <option value="base_to_base" selected="true">base_to_base</option>
             <option value="vertical_division">vertical_division</option>
             <option value="vertical_division_min">vertical_division_min</option>
@@ -177,27 +176,27 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         </section>
       </section>
       <section name="DIAScoring" title="" help="" expanded="false">
-        <param name="dia_extraction_window" argument="-algorithm:DIAScoring:dia_extraction_window" type="float" optional="true" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/>
-        <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" type="select" optional="true" label="DIA extraction window unit" help="">
+        <param name="dia_extraction_window" argument="-algorithm:DIAScoring:dia_extraction_window" type="float" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/>
+        <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" type="select" label="DIA extraction window unit" help="">
           <option value="Th" selected="true">Th</option>
           <option value="ppm">ppm</option>
           <expand macro="list_string_san" name="dia_extraction_unit"/>
         </param>
         <param name="dia_centroided" argument="-algorithm:DIAScoring:dia_centroided" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use centroided DIA data" help=""/>
-        <param name="dia_byseries_intensity_min" argument="-algorithm:DIAScoring:dia_byseries_intensity_min" type="float" optional="true" min="0.0" value="300.0" label="DIA b/y series minimum intensity to conside" help=""/>
-        <param name="dia_byseries_ppm_diff" argument="-algorithm:DIAScoring:dia_byseries_ppm_diff" type="float" optional="true" min="0.0" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help=""/>
-        <param name="dia_nr_isotopes" argument="-algorithm:DIAScoring:dia_nr_isotopes" type="integer" optional="true" min="0" value="4" label="DIA number of isotopes to conside" help=""/>
-        <param name="dia_nr_charges" argument="-algorithm:DIAScoring:dia_nr_charges" type="integer" optional="true" min="0" value="4" label="DIA number of charges to conside" help=""/>
-        <param name="peak_before_mono_max_ppm_diff" argument="-algorithm:DIAScoring:peak_before_mono_max_ppm_diff" type="float" optional="true" min="0.0" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help=""/>
+        <param name="dia_byseries_intensity_min" argument="-algorithm:DIAScoring:dia_byseries_intensity_min" type="float" min="0.0" value="300.0" label="DIA b/y series minimum intensity to conside" help=""/>
+        <param name="dia_byseries_ppm_diff" argument="-algorithm:DIAScoring:dia_byseries_ppm_diff" type="float" min="0.0" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help=""/>
+        <param name="dia_nr_isotopes" argument="-algorithm:DIAScoring:dia_nr_isotopes" type="integer" min="0" value="4" label="DIA number of isotopes to conside" help=""/>
+        <param name="dia_nr_charges" argument="-algorithm:DIAScoring:dia_nr_charges" type="integer" min="0" value="4" label="DIA number of charges to conside" help=""/>
+        <param name="peak_before_mono_max_ppm_diff" argument="-algorithm:DIAScoring:peak_before_mono_max_ppm_diff" type="float" min="0.0" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help=""/>
       </section>
       <section name="EMGScoring" title="" help="" expanded="false">
-        <param name="interpolation_step" argument="-algorithm:EMGScoring:interpolation_step" type="float" optional="true" value="0.2" label="Sampling rate for the interpolation of the model function" help=""/>
-        <param name="tolerance_stdev_bounding_box" argument="-algorithm:EMGScoring:tolerance_stdev_bounding_box" type="float" optional="true" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help=""/>
-        <param name="max_iteration" argument="-algorithm:EMGScoring:max_iteration" type="integer" optional="true" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help=""/>
+        <param name="interpolation_step" argument="-algorithm:EMGScoring:interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help=""/>
+        <param name="tolerance_stdev_bounding_box" argument="-algorithm:EMGScoring:tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help=""/>
+        <param name="max_iteration" argument="-algorithm:EMGScoring:max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help=""/>
         <param name="init_mom" argument="-algorithm:EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Initialize parameters using method of moments estimators" help=""/>
         <section name="statistics" title="" help="" expanded="false">
-          <param name="mean" argument="-algorithm:EMGScoring:statistics:mean" type="float" optional="true" value="1.0" label="Centroid position of the model" help=""/>
-          <param name="variance" argument="-algorithm:EMGScoring:statistics:variance" type="float" optional="true" value="1.0" label="Variance of the model" help=""/>
+          <param name="mean" argument="-algorithm:EMGScoring:statistics:mean" type="float" value="1.0" label="Centroid position of the model" help=""/>
+          <param name="variance" argument="-algorithm:EMGScoring:statistics:variance" type="float" value="1.0" label="Variance of the model" help=""/>
         </section>
       </section>
       <section name="Scores" title="" help="" expanded="false">
@@ -224,15 +223,15 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       </section>
     </section>
     <section name="peptideEstimation" title="Parameters for the peptide estimation (use -estimateBestPeptides to enable)" help="" expanded="false">
-      <param name="InitialQualityCutoff" argument="-peptideEstimation:InitialQualityCutoff" type="float" optional="true" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca" help="-2 to 2)"/>
-      <param name="OverallQualityCutoff" argument="-peptideEstimation:OverallQualityCutoff" type="float" optional="true" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="0 to 10)"/>
-      <param name="NrRTBins" argument="-peptideEstimation:NrRTBins" type="integer" optional="true" value="10" label="Number of RT bins to use to compute coverage" help="This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/>
-      <param name="MinPeptidesPerBin" argument="-peptideEstimation:MinPeptidesPerBin" type="integer" optional="true" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help=""/>
-      <param name="MinBinsFilled" argument="-peptideEstimation:MinBinsFilled" type="integer" optional="true" value="8" label="Minimal number of bins required to be covered" help=""/>
+      <param name="InitialQualityCutoff" argument="-peptideEstimation:InitialQualityCutoff" type="float" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca" help="-2 to 2)"/>
+      <param name="OverallQualityCutoff" argument="-peptideEstimation:OverallQualityCutoff" type="float" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="0 to 10)"/>
+      <param name="NrRTBins" argument="-peptideEstimation:NrRTBins" type="integer" value="10" label="Number of RT bins to use to compute coverage" help="This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/>
+      <param name="MinPeptidesPerBin" argument="-peptideEstimation:MinPeptidesPerBin" type="integer" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help=""/>
+      <param name="MinBinsFilled" argument="-peptideEstimation:MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -246,7 +245,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_OpenSwathRTNormalizer_test_1 -->
+  <tests>
+    <!-- TOPP_OpenSwathRTNormalizer_test_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -256,7 +256,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
       </conditional>
       <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
-      <output name="out" file="OpenSwathRTNormalizer_1_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
+      <output name="out" value="OpenSwathRTNormalizer_1_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
       <param name="min_rsq" value="0.95"/>
       <param name="min_coverage" value="0.6"/>
       <param name="estimateBestPeptides" value="false"/>
@@ -372,6 +372,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathRTNormalizer_test_3 -->
     <test expect_num_outputs="2">
@@ -383,7 +386,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
       </conditional>
       <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
-      <output name="out" file="OpenSwathRTNormalizer_3_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
+      <output name="out" value="OpenSwathRTNormalizer_3_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
       <param name="min_rsq" value="0.95"/>
       <param name="min_coverage" value="0.6"/>
       <param name="estimateBestPeptides" value="true"/>
@@ -499,6 +502,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathRTNormalizer_test_4 -->
     <test expect_num_outputs="2">
@@ -510,7 +516,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
       </conditional>
       <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
-      <output name="out" file="OpenSwathRTNormalizer_4_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
+      <output name="out" value="OpenSwathRTNormalizer_4_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
       <param name="min_rsq" value="0.95"/>
       <param name="min_coverage" value="0.6"/>
       <param name="estimateBestPeptides" value="false"/>
@@ -626,11 +632,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathRTNormalizer.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathRTNormalizer.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/OpenSwathRewriteToFeatureXML.xml b/tools/openms/OpenSwathRewriteToFeatureXML.xml
index d5ced6395..7e71ad5f6 100644
--- a/tools/openms/OpenSwathRewriteToFeatureXML.xml
+++ b/tools/openms/OpenSwathRewriteToFeatureXML.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
+  <description>Combines featureXML and mProphet tsv to FDR filtered featureXML</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token>
     <import>macros.xml</import>
@@ -16,10 +15,10 @@
 ## Preprocessing
 #if $csv:
   mkdir csv &&
-  ln -s '$csv' 'csv/${re.sub("[^\w\-_]", "_", $csv.element_identifier)}.$gxy2omsext($csv.ext)' &&
+  cp '$csv' 'csv/${re.sub("[^\w\-_]", "_", $csv.element_identifier)}.$gxy2omsext($csv.ext)' &&
 #end if
 mkdir featureXML &&
-ln -s '$featureXML' 'featureXML/${re.sub("[^\w\-_]", "_", $featureXML.element_identifier)}.$gxy2omsext($featureXML.ext)' &&
+cp '$featureXML' 'featureXML/${re.sub("[^\w\-_]", "_", $featureXML.element_identifier)}.$gxy2omsext($featureXML.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -48,11 +47,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-csv" type="data" format="csv" optional="true" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help=" select csv data sets(s)"/>
-    <param argument="-featureXML" type="data" format="featurexml" optional="false" label="input featureXML file" help=" select featurexml data sets(s)"/>
-    <param argument="-FDR_cutoff" type="float" optional="true" value="-1.0" label="FDR cutoff" help="(e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/>
+    <param argument="-featureXML" type="data" format="featurexml" label="input featureXML file" help=" select featurexml data sets(s)"/>
+    <param argument="-FDR_cutoff" type="float" value="-1.0" label="FDR cutoff" help="(e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -66,15 +65,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
-    <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
-    <param name="adv_opts|test" value="true"/>
-    <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- same input as used in the MSGF+Adapter -->
+      <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
+      <param name="adv_opts|test" value="true"/>
+      <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/>
+    </test>
+  </tests>
   <help><![CDATA[Combines featureXML and mProphet tsv to FDR filtered featureXML.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathRewriteToFeatureXML.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathRewriteToFeatureXML.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/OpenSwathWorkflow.xml b/tools/openms/OpenSwathWorkflow.xml
index bf58e961f..693748ae3 100644
--- a/tools/openms/OpenSwathWorkflow.xml
+++ b/tools/openms/OpenSwathWorkflow.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: []-->
 <tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Complete workflow to run OpenSWATH</description>
   <macros>
@@ -15,20 +14,20 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir tr &&
-ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
+cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 #if $tr_irt:
   mkdir tr_irt &&
-  ln -s '$tr_irt' 'tr_irt/${re.sub("[^\w\-_]", "_", $tr_irt.element_identifier)}.$gxy2omsext($tr_irt.ext)' &&
+  cp '$tr_irt' 'tr_irt/${re.sub("[^\w\-_]", "_", $tr_irt.element_identifier)}.$gxy2omsext($tr_irt.ext)' &&
 #end if
 #if $tr_irt_nonlinear:
   mkdir tr_irt_nonlinear &&
-  ln -s '$tr_irt_nonlinear' 'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)' &&
+  cp '$tr_irt_nonlinear' 'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)' &&
 #end if
 #if $swath_windows_file:
   mkdir swath_windows_file &&
-  ln -s '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' &&
+  cp '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' &&
 #end if
 #if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_features &&
@@ -51,11 +50,13 @@ ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($
 #if "irt_trafo_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir Debugging_irt_trafo &&
 #end if
+## advanced options
   #if $adv_opts.rt_norm:
     mkdir adv_opts.rt_norm &&
-    ln -s '$adv_opts.rt_norm' 'adv_opts.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts.rt_norm.element_identifier)}.$gxy2omsext($adv_opts.rt_norm.ext)' &&
+    cp '$adv_opts.rt_norm' 'adv_opts.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts.rt_norm.element_identifier)}.$gxy2omsext($adv_opts.rt_norm.ext)' &&
   #end if
 
+
 ## Main program call
 
 set -o pipefail &&
@@ -106,10 +107,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   -Debugging:irt_trafo
   'Debugging_irt_trafo/output.${gxy2omsext("trafoxml")}'
 #end if
+## advanced options
   #if $adv_opts.rt_norm:
     -rt_norm
     'adv_opts.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts.rt_norm.element_identifier)}.$gxy2omsext($adv_opts.rt_norm.ext)'
   #end if
+
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
 #end if
@@ -144,20 +147,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"tempDirectory": "\$TMP_DIR", "outer_loop_threads": "1", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml,mzxml,sqmass" optional="false" label="Input files separated by blank" help=" select mzml,mzxml,sqmass data sets(s)"/>
-    <param argument="-tr" type="data" format="pqp,tabular,traml" optional="false" label="transition file ('TraML','tsv','pqp')" help=" select pqp,tabular,traml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml,mzxml,sqmass" label="Input files separated by blank" help=" select mzml,mzxml,sqmass data sets(s)"/>
+    <param argument="-tr" type="data" format="pqp,tabular,traml" label="transition file ('TraML','tsv','pqp')" help=" select pqp,tabular,traml data sets(s)"/>
     <param argument="-tr_irt" type="data" format="pqp,tabular,traml" optional="true" label="transition file ('TraML')" help=" select pqp,tabular,traml data sets(s)"/>
     <param argument="-tr_irt_nonlinear" type="data" format="pqp,tabular,traml" optional="true" label="additional nonlinear transition file ('TraML')" help=" select pqp,tabular,traml data sets(s)"/>
     <param argument="-swath_windows_file" type="data" format="txt" optional="true" label="Optional, tab-separated file containing the SWATH windows for extraction: lower_offset upper_offset" help="Note that the first line is a header and will be skipped select txt data sets(s)"/>
     <param argument="-sonar" type="boolean" truevalue="true" falsevalue="false" checked="false" label="data is scanning SWATH data" help=""/>
-    <param argument="-rt_extraction_window" type="float" optional="true" value="600.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution)" help=""/>
-    <param argument="-ion_mobility_window" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/>
-    <param argument="-mz_extraction_window" type="float" optional="true" min="0.0" value="50.0" label="Extraction window in Thomson or ppm (see mz_extraction_window_unit)" help=""/>
-    <param argument="-mz_extraction_window_ms1" type="float" optional="true" min="0.0" value="50.0" label="Extraction window used in MS1 in Thomson or ppm (see mz_extraction_window_ms1_unit)" help=""/>
-    <param argument="-im_extraction_window_ms1" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension for MS1 (in milliseconds)" help=""/>
+    <param argument="-pasef" type="boolean" truevalue="true" falsevalue="false" checked="false" label="data is PASEF data" help=""/>
+    <param argument="-rt_extraction_window" type="float" value="600.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution)" help=""/>
+    <param argument="-ion_mobility_window" type="float" value="-1.0" label="Extraction window in ion mobility dimension (in 1/k0 or milliseconds depending on library)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side. -1 means extract over the whole range or ion mobility is not present. (Default for diaPASEF data: 0.06 1/k0)"/>
+    <param argument="-mz_extraction_window" type="float" min="0.0" value="50.0" label="Extraction window in Thomson or ppm (see mz_extraction_window_unit)" help=""/>
+    <param argument="-mz_extraction_window_ms1" type="float" min="0.0" value="50.0" label="Extraction window used in MS1 in Thomson or ppm (see mz_extraction_window_ms1_unit)" help=""/>
+    <param argument="-im_extraction_window_ms1" type="float" value="-1.0" label="Extraction window in ion mobility dimension for MS1 (in 1/k0 or milliseconds depending on library)" help="-1 means this is not ion mobility data"/>
     <section name="Calibration" title="Parameters for the m/z and ion mobility calibration" help="" expanded="false">
       <param name="ms1_im_calibration" argument="-Calibration:ms1_im_calibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to use MS1 precursor data for the ion mobility calibration (default = false, uses MS2 / fragment ions for calibration)" help=""/>
-      <param name="im_correction_function" argument="-Calibration:im_correction_function" type="select" optional="true" label="Type of normalization function for IM calibration" help="">
+      <param name="im_correction_function" argument="-Calibration:im_correction_function" type="select" label="Type of normalization function for IM calibration" help="">
         <option value="none">none</option>
         <option value="linear" selected="true">linear</option>
         <expand macro="list_string_san" name="im_correction_function"/>
@@ -170,7 +174,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </param>
     </section>
     <section name="Library" title="Library parameters section" help="" expanded="false">
-      <param name="retentionTimeInterpretation" argument="-Library:retentionTimeInterpretation" type="select" optional="true" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="">
+      <param name="retentionTimeInterpretation" argument="-Library:retentionTimeInterpretation" type="select" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="">
         <option value="iRT" selected="true">iRT</option>
         <option value="seconds">seconds</option>
         <option value="minutes">minutes</option>
@@ -180,14 +184,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="force_invalid_mods" argument="-Library:force_invalid_mods" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help=""/>
     </section>
     <section name="RTNormalization" title="Parameters for the RTNormalization for iRT petides" help="This specifies how the RT alignment is performed and how outlier detection is applied. Outlier detection can be done iteratively (by default) which removes one outlier per iteration or using the RANSAC algorithm" expanded="false">
-      <param name="alignmentMethod" argument="-RTNormalization:alignmentMethod" type="select" optional="true" label="How to perform the alignment to the normalized RT space using anchor points" help="'linear': perform linear regression (for few anchor points). 'interpolated': Interpolate between anchor points (for few, noise-free anchor points). 'lowess' Use local regression (for many, noisy anchor points). 'b_spline' use b splines for smoothing">
+      <param name="alignmentMethod" argument="-RTNormalization:alignmentMethod" type="select" label="How to perform the alignment to the normalized RT space using anchor points" help="'linear': perform linear regression (for few anchor points). 'interpolated': Interpolate between anchor points (for few, noise-free anchor points). 'lowess' Use local regression (for many, noisy anchor points). 'b_spline' use b splines for smoothing">
         <option value="linear" selected="true">linear</option>
         <option value="interpolated">interpolated</option>
         <option value="lowess">lowess</option>
         <option value="b_spline">b_spline</option>
         <expand macro="list_string_san" name="alignmentMethod"/>
       </param>
-      <param name="outlierMethod" argument="-RTNormalization:outlierMethod" type="select" optional="true" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)">
+      <param name="outlierMethod" argument="-RTNormalization:outlierMethod" type="select" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)">
         <option value="iter_residual" selected="true">iter_residual</option>
         <option value="iter_jackknife">iter_jackknife</option>
         <option value="ransac">ransac</option>
@@ -195,52 +199,52 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <expand macro="list_string_san" name="outlierMethod"/>
       </param>
       <param name="useIterativeChauvenet" argument="-RTNormalization:useIterativeChauvenet" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to use Chauvenet's criterion when using iterative methods" help="This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained"/>
-      <param name="RANSACMaxIterations" argument="-RTNormalization:RANSACMaxIterations" type="integer" optional="true" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help=""/>
-      <param name="RANSACMaxPercentRTThreshold" argument="-RTNormalization:RANSACMaxPercentRTThreshold" type="integer" optional="true" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" help="Default is set to 3% which is around +/- 4 minutes on a 120 gradient"/>
-      <param name="RANSACSamplingSize" argument="-RTNormalization:RANSACSamplingSize" type="integer" optional="true" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help=""/>
+      <param name="RANSACMaxIterations" argument="-RTNormalization:RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help=""/>
+      <param name="RANSACMaxPercentRTThreshold" argument="-RTNormalization:RANSACMaxPercentRTThreshold" type="integer" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" help="Default is set to 3% which is around +/- 4 minutes on a 120 gradient"/>
+      <param name="RANSACSamplingSize" argument="-RTNormalization:RANSACSamplingSize" type="integer" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help=""/>
       <param name="estimateBestPeptides" argument="-RTNormalization:estimateBestPeptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether the algorithms should try to choose the best peptides based on their peak shape for normalization" help="Use this option you do not expect all your peptides to be detected in a sample and too many 'bad' peptides enter the outlier removal step (e.g. due to them being endogenous peptides or using a less curated list of peptides)"/>
-      <param name="InitialQualityCutoff" argument="-RTNormalization:InitialQualityCutoff" type="float" optional="true" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca" help="-2 to 2)"/>
-      <param name="OverallQualityCutoff" argument="-RTNormalization:OverallQualityCutoff" type="float" optional="true" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="0 to 10)"/>
-      <param name="NrRTBins" argument="-RTNormalization:NrRTBins" type="integer" optional="true" value="10" label="Number of RT bins to use to compute coverage" help="This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/>
-      <param name="MinPeptidesPerBin" argument="-RTNormalization:MinPeptidesPerBin" type="integer" optional="true" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help=""/>
-      <param name="MinBinsFilled" argument="-RTNormalization:MinBinsFilled" type="integer" optional="true" value="8" label="Minimal number of bins required to be covered" help=""/>
+      <param name="InitialQualityCutoff" argument="-RTNormalization:InitialQualityCutoff" type="float" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca" help="-2 to 2)"/>
+      <param name="OverallQualityCutoff" argument="-RTNormalization:OverallQualityCutoff" type="float" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="0 to 10)"/>
+      <param name="NrRTBins" argument="-RTNormalization:NrRTBins" type="integer" value="10" label="Number of RT bins to use to compute coverage" help="This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/>
+      <param name="MinPeptidesPerBin" argument="-RTNormalization:MinPeptidesPerBin" type="integer" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help=""/>
+      <param name="MinBinsFilled" argument="-RTNormalization:MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help=""/>
       <section name="lowess" title="" help="" expanded="false">
-        <param name="span" argument="-RTNormalization:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.05" label="Span parameter for lowess" help=""/>
+        <param name="span" argument="-RTNormalization:lowess:span" type="float" min="0.0" max="1.0" value="0.05" label="Span parameter for lowess" help=""/>
       </section>
       <section name="b_spline" title="" help="" expanded="false">
-        <param name="num_nodes" argument="-RTNormalization:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for b spline" help=""/>
+        <param name="num_nodes" argument="-RTNormalization:b_spline:num_nodes" type="integer" min="0" value="5" label="Number of nodes for b spline" help=""/>
       </section>
     </section>
     <section name="Scoring" title="Scoring parameters section" help="" expanded="false">
-      <param name="stop_report_after_feature" argument="-Scoring:stop_report_after_feature" type="integer" optional="true" value="5" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help=""/>
-      <param name="rt_normalization_factor" argument="-Scoring:rt_normalization_factor" type="float" optional="true" value="100.0" label="The normalized RT is expected to be between 0 and 1" help="If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)"/>
-      <param name="quantification_cutoff" argument="-Scoring:quantification_cutoff" type="float" optional="true" min="0.0" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help=""/>
+      <param name="stop_report_after_feature" argument="-Scoring:stop_report_after_feature" type="integer" value="5" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help=""/>
+      <param name="rt_normalization_factor" argument="-Scoring:rt_normalization_factor" type="float" value="100.0" label="The normalized RT is expected to be between 0 and 1" help="If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)"/>
+      <param name="quantification_cutoff" argument="-Scoring:quantification_cutoff" type="float" min="0.0" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help=""/>
       <param name="write_convex_hull" argument="-Scoring:write_convex_hull" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write out all points of all features into the featureXML" help=""/>
-      <param name="spectrum_addition_method" argument="-Scoring:spectrum_addition_method" type="select" optional="true" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
+      <param name="spectrum_addition_method" argument="-Scoring:spectrum_addition_method" type="select" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
         <option value="simple" selected="true">simple</option>
         <option value="resample">resample</option>
         <expand macro="list_string_san" name="spectrum_addition_method"/>
       </param>
-      <param name="add_up_spectra" argument="-Scoring:add_up_spectra" type="integer" optional="true" min="1" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help=""/>
-      <param name="spacing_for_spectra_resampling" argument="-Scoring:spacing_for_spectra_resampling" type="float" optional="true" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
-      <param name="uis_threshold_sn" argument="-Scoring:uis_threshold_sn" type="integer" optional="true" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
-      <param name="uis_threshold_peak_area" argument="-Scoring:uis_threshold_peak_area" type="integer" optional="true" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
-      <param name="scoring_model" argument="-Scoring:scoring_model" type="select" optional="true" label="Scoring model to use" help="">
+      <param name="add_up_spectra" argument="-Scoring:add_up_spectra" type="integer" min="1" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help=""/>
+      <param name="spacing_for_spectra_resampling" argument="-Scoring:spacing_for_spectra_resampling" type="float" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
+      <param name="uis_threshold_sn" argument="-Scoring:uis_threshold_sn" type="integer" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
+      <param name="uis_threshold_peak_area" argument="-Scoring:uis_threshold_peak_area" type="integer" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
+      <param name="scoring_model" argument="-Scoring:scoring_model" type="select" label="Scoring model to use" help="">
         <option value="default" selected="true">default</option>
         <option value="single_transition">single_transition</option>
         <expand macro="list_string_san" name="scoring_model"/>
       </param>
-      <param name="im_extra_drift" argument="-Scoring:im_extra_drift" type="float" optional="true" min="0.0" value="0.0" label="Extra drift time to extract for IM scoring (as a fraction" help="e.g. 0.25 means 25% extra on each side)"/>
+      <param name="im_extra_drift" argument="-Scoring:im_extra_drift" type="float" min="0.0" value="0.0" label="Extra drift time to extract for IM scoring (as a fraction" help="e.g. 0.25 means 25% extra on each side)"/>
       <param name="strict" argument="-Scoring:strict" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to error (true) or skip (false) if a transition in a transition group does not have a corresponding chromatogram" help=""/>
       <section name="TransitionGroupPicker" title="" help="" expanded="false">
-        <param name="stop_after_feature" argument="-Scoring:TransitionGroupPicker:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
-        <param name="min_peak_width" argument="-Scoring:TransitionGroupPicker:min_peak_width" type="float" optional="true" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
-        <param name="peak_integration" argument="-Scoring:TransitionGroupPicker:peak_integration" type="select" optional="true" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
+        <param name="stop_after_feature" argument="-Scoring:TransitionGroupPicker:stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
+        <param name="min_peak_width" argument="-Scoring:TransitionGroupPicker:min_peak_width" type="float" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
+        <param name="peak_integration" argument="-Scoring:TransitionGroupPicker:peak_integration" type="select" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
           <option value="original" selected="true">original</option>
           <option value="smoothed">smoothed</option>
           <expand macro="list_string_san" name="peak_integration"/>
         </param>
-        <param name="background_subtraction" argument="-Scoring:TransitionGroupPicker:background_subtraction" type="select" optional="true" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
+        <param name="background_subtraction" argument="-Scoring:TransitionGroupPicker:background_subtraction" type="select" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
           <option value="none" selected="true">none</option>
           <option value="original">original</option>
           <option value="exact">exact</option>
@@ -249,27 +253,27 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="recalculate_peaks" argument="-Scoring:TransitionGroupPicker:recalculate_peaks" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="Tries to use the consensus (median) peak border if the variation within the picked peaks is too large"/>
         <param name="use_precursors" argument="-Scoring:TransitionGroupPicker:use_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)" help=""/>
         <param name="use_consensus" argument="-Scoring:TransitionGroupPicker:use_consensus" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)" help=""/>
-        <param name="recalculate_peaks_max_z" argument="-Scoring:TransitionGroupPicker:recalculate_peaks_max_z" type="float" optional="true" value="0.75" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
-        <param name="minimal_quality" argument="-Scoring:TransitionGroupPicker:minimal_quality" type="float" optional="true" value="-1.5" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
-        <param name="resample_boundary" argument="-Scoring:TransitionGroupPicker:resample_boundary" type="float" optional="true" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
+        <param name="recalculate_peaks_max_z" argument="-Scoring:TransitionGroupPicker:recalculate_peaks_max_z" type="float" value="0.75" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
+        <param name="minimal_quality" argument="-Scoring:TransitionGroupPicker:minimal_quality" type="float" value="-1.5" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
+        <param name="resample_boundary" argument="-Scoring:TransitionGroupPicker:resample_boundary" type="float" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
         <param name="compute_peak_quality" argument="-Scoring:TransitionGroupPicker:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
         <param name="compute_peak_shape_metrics" argument="-Scoring:TransitionGroupPicker:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/>
         <param name="compute_total_mi" argument="-Scoring:TransitionGroupPicker:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/>
-        <param name="boundary_selection_method" argument="-Scoring:TransitionGroupPicker:boundary_selection_method" type="select" optional="true" label="Method to use when selecting the best boundaries for peaks" help="">
+        <param name="boundary_selection_method" argument="-Scoring:TransitionGroupPicker:boundary_selection_method" type="select" label="Method to use when selecting the best boundaries for peaks" help="">
           <option value="largest" selected="true">largest</option>
           <option value="widest">widest</option>
           <expand macro="list_string_san" name="boundary_selection_method"/>
         </param>
         <section name="PeakPickerMRM" title="" help="" expanded="false">
-          <param name="sgolay_frame_length" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length" type="integer" optional="true" value="11" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
-          <param name="sgolay_polynomial_order" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order" type="integer" optional="true" value="3" label="Order of the polynomial that is fitted" help=""/>
-          <param name="gauss_width" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width" type="float" optional="true" value="30.0" label="Gaussian width in seconds, estimated peak size" help=""/>
+          <param name="sgolay_frame_length" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length" type="integer" value="11" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
+          <param name="sgolay_polynomial_order" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help=""/>
+          <param name="gauss_width" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width" type="float" value="30.0" label="Gaussian width in seconds, estimated peak size" help=""/>
           <param name="use_gauss" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help=""/>
-          <param name="peak_width" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width" type="float" optional="true" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
-          <param name="signal_to_noise" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise" type="float" optional="true" min="0.0" value="0.1" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
+          <param name="peak_width" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
+          <param name="signal_to_noise" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise" type="float" min="0.0" value="0.1" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
           <param name="write_sn_log_messages" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/>
           <param name="remove_overlapping_peaks" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Try to remove overlapping peaks during peak picking" help=""/>
-          <param name="method" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:method" type="select" optional="true" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
+          <param name="method" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:method" type="select" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
             <option value="legacy">legacy</option>
             <option value="corrected" selected="true">corrected</option>
             <option value="crawdad">crawdad</option>
@@ -277,13 +281,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           </param>
         </section>
         <section name="PeakIntegrator" title="" help="" expanded="false">
-          <param name="integration_type" argument="-Scoring:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" optional="true" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
+          <param name="integration_type" argument="-Scoring:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
             <option value="intensity_sum" selected="true">intensity_sum</option>
             <option value="simpson">simpson</option>
             <option value="trapezoid">trapezoid</option>
             <expand macro="list_string_san" name="integration_type"/>
           </param>
-          <param name="baseline_type" argument="-Scoring:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" optional="true" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
+          <param name="baseline_type" argument="-Scoring:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
             <option value="base_to_base" selected="true">base_to_base</option>
             <option value="vertical_division">vertical_division</option>
             <option value="vertical_division_min">vertical_division_min</option>
@@ -294,21 +298,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         </section>
       </section>
       <section name="DIAScoring" title="" help="" expanded="false">
-        <param name="dia_extraction_window" argument="-Scoring:DIAScoring:dia_extraction_window" type="float" optional="true" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/>
-        <param name="dia_extraction_unit" argument="-Scoring:DIAScoring:dia_extraction_unit" type="select" optional="true" label="DIA extraction window unit" help="">
+        <param name="dia_extraction_window" argument="-Scoring:DIAScoring:dia_extraction_window" type="float" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/>
+        <param name="dia_extraction_unit" argument="-Scoring:DIAScoring:dia_extraction_unit" type="select" label="DIA extraction window unit" help="">
           <option value="Th" selected="true">Th</option>
           <option value="ppm">ppm</option>
           <expand macro="list_string_san" name="dia_extraction_unit"/>
         </param>
         <param name="dia_centroided" argument="-Scoring:DIAScoring:dia_centroided" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use centroided DIA data" help=""/>
-        <param name="dia_byseries_intensity_min" argument="-Scoring:DIAScoring:dia_byseries_intensity_min" type="float" optional="true" min="0.0" value="300.0" label="DIA b/y series minimum intensity to conside" help=""/>
-        <param name="dia_byseries_ppm_diff" argument="-Scoring:DIAScoring:dia_byseries_ppm_diff" type="float" optional="true" min="0.0" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help=""/>
-        <param name="dia_nr_isotopes" argument="-Scoring:DIAScoring:dia_nr_isotopes" type="integer" optional="true" min="0" value="4" label="DIA number of isotopes to conside" help=""/>
-        <param name="dia_nr_charges" argument="-Scoring:DIAScoring:dia_nr_charges" type="integer" optional="true" min="0" value="4" label="DIA number of charges to conside" help=""/>
-        <param name="peak_before_mono_max_ppm_diff" argument="-Scoring:DIAScoring:peak_before_mono_max_ppm_diff" type="float" optional="true" min="0.0" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help=""/>
+        <param name="dia_byseries_intensity_min" argument="-Scoring:DIAScoring:dia_byseries_intensity_min" type="float" min="0.0" value="300.0" label="DIA b/y series minimum intensity to conside" help=""/>
+        <param name="dia_byseries_ppm_diff" argument="-Scoring:DIAScoring:dia_byseries_ppm_diff" type="float" min="0.0" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help=""/>
+        <param name="dia_nr_isotopes" argument="-Scoring:DIAScoring:dia_nr_isotopes" type="integer" min="0" value="4" label="DIA number of isotopes to conside" help=""/>
+        <param name="dia_nr_charges" argument="-Scoring:DIAScoring:dia_nr_charges" type="integer" min="0" value="4" label="DIA number of charges to conside" help=""/>
+        <param name="peak_before_mono_max_ppm_diff" argument="-Scoring:DIAScoring:peak_before_mono_max_ppm_diff" type="float" min="0.0" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help=""/>
       </section>
       <section name="EMGScoring" title="" help="" expanded="false">
-        <param name="max_iteration" argument="-Scoring:EMGScoring:max_iteration" type="integer" optional="true" value="10" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help=""/>
+        <param name="max_iteration" argument="-Scoring:EMGScoring:max_iteration" type="integer" value="10" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help=""/>
         <param name="init_mom" argument="-Scoring:EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Initialize parameters using method of moments estimators" help=""/>
       </section>
       <section name="Scores" title="" help="" expanded="false">
@@ -338,43 +342,43 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param argument="-sort_swath_maps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sort input SWATH files when matching to SWATH windows from swath_windows_file" help=""/>
       <param argument="-enable_ms1" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Extract the precursor ion trace(s) and use for scoring if present" help=""/>
       <param argument="-enable_ipf" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable additional scoring of identification assays using IPF (see online documentation)" help=""/>
-      <param name="out_chrom_type" type="select" optional="false" label="File type of output out_chrom (Also output all computed chromatograms output in mzML (chrom.mzML) or sqMass (SQLite format))">
+      <param name="out_chrom_type" type="select" label="File type of output out_chrom (Also output all computed chromatograms output in mzML (chrom.mzML) or sqMass (SQLite format))">
         <option value="mzML">mzml</option>
         <option value="sqMass">sqmass</option>
       </param>
-      <param argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the upper edge of a Swath window to still consider a precursor, in Thomson" help=""/>
-      <param argument="-extra_rt_extraction_window" type="float" optional="true" min="0.0" value="0.0" label="Output an XIC with a RT-window by this much large" help="(e.g. to visually inspect a larger area of the chromatogram)"/>
-      <param argument="-mz_extraction_window_unit" type="select" optional="true" label="Unit for mz extraction" help="">
+      <param argument="-min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the upper edge of a Swath window to still consider a precursor, in Thomson" help=""/>
+      <param argument="-extra_rt_extraction_window" type="float" min="0.0" value="0.0" label="Output an XIC with a RT-window by this much large" help="(e.g. to visually inspect a larger area of the chromatogram)"/>
+      <param argument="-mz_extraction_window_unit" type="select" label="Unit for mz extraction" help="">
         <option value="Th">Th</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mz_extraction_window_unit"/>
       </param>
-      <param argument="-mz_extraction_window_ms1_unit" type="select" optional="true" label="Unit of the MS1 m/z extraction window" help="">
+      <param argument="-mz_extraction_window_ms1_unit" type="select" label="Unit of the MS1 m/z extraction window" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Th">Th</option>
         <expand macro="list_string_san" name="mz_extraction_window_ms1_unit"/>
       </param>
       <param argument="-use_ms1_ion_mobility" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Also perform precursor extraction using the same ion mobility window as for fragment ion extraction" help=""/>
       <param argument="-matching_window_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assume the input data is targeted / PRM-like data with potentially overlapping DIA windows" help="Will only attempt to extract each assay from the *best* matching DIA window (instead of all matching windows)"/>
-      <param argument="-irt_mz_extraction_window" type="float" optional="true" min="0.0" value="50.0" label="Extraction window used for iRT and m/z correction in Thomson or ppm (see irt_mz_extraction_window_unit)" help=""/>
-      <param argument="-irt_mz_extraction_window_unit" type="select" optional="true" label="Unit for mz extraction" help="">
+      <param argument="-irt_mz_extraction_window" type="float" min="0.0" value="50.0" label="Extraction window used for iRT and m/z correction in Thomson or ppm (see irt_mz_extraction_window_unit)" help=""/>
+      <param argument="-irt_mz_extraction_window_unit" type="select" label="Unit for mz extraction" help="">
         <option value="Th">Th</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="irt_mz_extraction_window_unit"/>
       </param>
-      <param argument="-irt_im_extraction_window" type="float" optional="true" value="-1.0" label="Ion mobility extraction window used for iRT (in 1/K0 or milliseconds)" help=""/>
-      <param argument="-min_rsq" type="float" optional="true" value="0.95" label="Minimum r-squared of RT peptides regression" help=""/>
-      <param argument="-min_coverage" type="float" optional="true" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/>
+      <param argument="-irt_im_extraction_window" type="float" value="-1.0" label="Ion mobility extraction window used for iRT (in 1/K0 or milliseconds depending on library)" help="-1 means do not perform ion mobility calibration"/>
+      <param argument="-min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help=""/>
+      <param argument="-min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/>
       <param argument="-split_file_input" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The input files each contain one single SWATH (alternatively: all SWATH are in separate files)" help=""/>
       <param argument="-use_elution_model_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Turn on elution model score (EMG fit to peak)" help=""/>
-      <param argument="-readOptions" type="select" optional="true" label="Whether to run OpenSWATH directly on the input data, cache data to disk first or to perform a datareduction step first" help="If you choose cache, make sure to also set tempDirectory">
+      <param argument="-readOptions" type="select" label="Whether to run OpenSWATH directly on the input data, cache data to disk first or to perform a datareduction step first" help="If you choose cache, make sure to also set tempDirectory">
         <option value="normal" selected="true">normal</option>
         <option value="cache">cache</option>
         <option value="cacheWorkingInMemory">cacheWorkingInMemory</option>
         <option value="workingInMemory">workingInMemory</option>
         <expand macro="list_string_san" name="readOptions"/>
       </param>
-      <param argument="-mz_correction_function" type="select" optional="true" label="Use the retention time normalization peptide MS2 masses to perform a mass correction (linear, weighted by intensity linear or quadratic) of all spectra" help="">
+      <param argument="-mz_correction_function" type="select" label="Use the retention time normalization peptide MS2 masses to perform a mass correction (linear, weighted by intensity linear or quadratic) of all spectra" help="">
         <option value="none" selected="true">none</option>
         <option value="regression_delta_ppm">regression_delta_ppm</option>
         <option value="unweighted_regression">unweighted_regression</option>
@@ -385,15 +389,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="quadratic_regression_delta_ppm">quadratic_regression_delta_ppm</option>
         <expand macro="list_string_san" name="mz_correction_function"/>
       </param>
-      <param argument="-extraction_function" type="select" optional="true" label="Function used to extract the signal" help="">
+      <param argument="-extraction_function" type="select" label="Function used to extract the signal" help="">
         <option value="tophat" selected="true">tophat</option>
         <option value="bartlett">bartlett</option>
         <expand macro="list_string_san" name="extraction_function"/>
       </param>
-      <param argument="-batchSize" type="integer" optional="true" min="0" value="1000" label="The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 250-1000)" help=""/>
-      <param argument="-ms1_isotopes" type="integer" optional="true" min="0" value="3" label="The number of MS1 isotopes used for extraction" help=""/>
+      <param argument="-batchSize" type="integer" min="0" value="1000" label="The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 250-1000)" help=""/>
+      <param argument="-ms1_isotopes" type="integer" min="0" value="3" label="The number of MS1 isotopes used for extraction" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -440,7 +444,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_OpenSwathWorkflow_1 -->
+  <tests>
+    <!-- TOPP_OpenSwathWorkflow_1 -->
     <test expect_num_outputs="4">
       <section name="adv_opts">
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
@@ -450,7 +455,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_unit" value="Th"/>
         <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
@@ -465,19 +470,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
         <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
+        <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
-        <param name="test" value="false"/>
+        <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <output name="out_features" file="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
-      <output name="out_qc" file="OpenSwathWorkflow_1_output.json" compare="sim_size" delta_frac="0.7" ftype="json"/>
+      <output name="out_features" value="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_chrom" value="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out_qc" value="OpenSwathWorkflow_1_output.json" compare="sim_size" delta_frac="0.7" ftype="json"/>
       <param name="sonar" value="false"/>
+      <param name="pasef" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window" value="0.05"/>
       <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
@@ -536,7 +542,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
+          <param name="compute_peak_quality" value="true"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -581,13 +587,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
+          <param name="use_mi_score" value="false"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
+          <param name="use_ms1_mi" value="false"/>
           <param name="use_uis_scores" value="false"/>
           <param name="use_ionseries_scores" value="true"/>
           <param name="use_ms2_isotope_scores" value="true"/>
@@ -599,6 +605,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathWorkflow_2 -->
     <test expect_num_outputs="3">
@@ -610,7 +619,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_unit" value="Th"/>
         <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
@@ -625,18 +634,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
         <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
+        <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
-        <param name="test" value="false"/>
+        <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/>
       <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/>
-      <output name="out_features" file="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out_features" value="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_chrom" value="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="sonar" value="false"/>
+      <param name="pasef" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window" value="0.05"/>
       <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
@@ -695,7 +705,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
+          <param name="compute_peak_quality" value="true"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -740,13 +750,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
+          <param name="use_mi_score" value="false"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
+          <param name="use_ms1_mi" value="false"/>
           <param name="use_uis_scores" value="false"/>
           <param name="use_ionseries_scores" value="true"/>
           <param name="use_ms2_isotope_scores" value="true"/>
@@ -758,6 +768,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathWorkflow_3 -->
     <test expect_num_outputs="3">
@@ -769,7 +782,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_unit" value="Th"/>
         <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
@@ -784,18 +797,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
         <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
+        <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
-        <param name="test" value="false"/>
+        <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out_features" value="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_chrom" value="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="sonar" value="false"/>
+      <param name="pasef" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window" value="0.05"/>
       <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
@@ -854,7 +868,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
+          <param name="compute_peak_quality" value="true"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -899,13 +913,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
+          <param name="use_mi_score" value="false"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
+          <param name="use_ms1_mi" value="false"/>
           <param name="use_uis_scores" value="false"/>
           <param name="use_ionseries_scores" value="true"/>
           <param name="use_ms2_isotope_scores" value="true"/>
@@ -917,6 +931,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathWorkflow_4 -->
     <test expect_num_outputs="3">
@@ -928,7 +945,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_unit" value="Th"/>
         <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
@@ -943,18 +960,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
         <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
+        <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
-        <param name="test" value="false"/>
+        <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <output name="out_tsv" file="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_4.chrom.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out_tsv" value="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out_chrom" value="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="sonar" value="false"/>
+      <param name="pasef" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window" value="0.05"/>
       <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
@@ -1013,7 +1031,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
+          <param name="compute_peak_quality" value="true"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -1058,13 +1076,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
+          <param name="use_mi_score" value="false"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
+          <param name="use_ms1_mi" value="false"/>
           <param name="use_uis_scores" value="false"/>
           <param name="use_ionseries_scores" value="true"/>
           <param name="use_ms2_isotope_scores" value="true"/>
@@ -1076,6 +1094,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathWorkflow_5 -->
     <test expect_num_outputs="3">
@@ -1087,7 +1108,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_unit" value="Th"/>
         <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
@@ -1102,18 +1123,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
         <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
+        <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
-        <param name="test" value="false"/>
+        <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out_features" value="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_chrom" value="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="sonar" value="false"/>
+      <param name="pasef" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window" value="0.05"/>
       <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
@@ -1172,7 +1194,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
+          <param name="compute_peak_quality" value="true"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -1217,13 +1239,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
+          <param name="use_mi_score" value="false"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
+          <param name="use_ms1_mi" value="false"/>
           <param name="use_uis_scores" value="false"/>
           <param name="use_ionseries_scores" value="true"/>
           <param name="use_ms2_isotope_scores" value="true"/>
@@ -1235,6 +1257,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathWorkflow_6 -->
     <test expect_num_outputs="3">
@@ -1246,7 +1271,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_unit" value="Th"/>
         <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
@@ -1261,18 +1286,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
         <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
+        <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
-        <param name="test" value="false"/>
+        <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out_features" value="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_chrom" value="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="sonar" value="false"/>
+      <param name="pasef" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window" value="0.05"/>
       <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
@@ -1331,7 +1357,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
+          <param name="compute_peak_quality" value="true"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -1376,13 +1402,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
+          <param name="use_mi_score" value="false"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
+          <param name="use_ms1_mi" value="false"/>
           <param name="use_uis_scores" value="false"/>
           <param name="use_ionseries_scores" value="true"/>
           <param name="use_ms2_isotope_scores" value="true"/>
@@ -1394,6 +1420,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathWorkflow_7 -->
     <test expect_num_outputs="3">
@@ -1405,7 +1434,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_unit" value="Th"/>
         <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
@@ -1420,19 +1449,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
         <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
+        <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
-        <param name="test" value="false"/>
+        <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
       <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/>
-      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out_features" value="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_chrom" value="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="sonar" value="false"/>
+      <param name="pasef" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window" value="0.05"/>
       <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
@@ -1491,7 +1521,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
+          <param name="compute_peak_quality" value="true"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -1536,13 +1566,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
+          <param name="use_mi_score" value="false"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
+          <param name="use_ms1_mi" value="false"/>
           <param name="use_uis_scores" value="false"/>
           <param name="use_ionseries_scores" value="true"/>
           <param name="use_ms2_isotope_scores" value="true"/>
@@ -1554,6 +1584,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathWorkflow_10 -->
     <test expect_num_outputs="3">
@@ -1565,7 +1598,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_unit" value="Th"/>
         <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
@@ -1580,19 +1613,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
         <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
+        <param name="ms1_isotopes" value="0"/>
         <param name="force" value="true"/>
-        <param name="test" value="false"/>
+        <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
       <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/>
-      <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out_features" value="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_chrom" value="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="sonar" value="false"/>
+      <param name="pasef" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window" value="0.05"/>
       <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
@@ -1651,7 +1685,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
+          <param name="compute_peak_quality" value="true"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -1696,13 +1730,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
+          <param name="use_mi_score" value="false"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
+          <param name="use_ms1_mi" value="false"/>
           <param name="use_uis_scores" value="false"/>
           <param name="use_ionseries_scores" value="true"/>
           <param name="use_ms2_isotope_scores" value="true"/>
@@ -1714,21 +1748,25 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- TOPP_OpenSwathWorkflow_11 -->
+    <!-- TOPP_OpenSwathWorkflow_13 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
+        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="false"/>
+        <param name="enable_ms1" value="true"/>
         <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_unit" value="Th"/>
         <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="550.0"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
         <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
@@ -1736,22 +1774,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="split_file_input" value="false"/>
         <param name="use_elution_model_score" value="false"/>
         <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/>
+        <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
         <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
+        <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </section>
-      <param name="in" value="OpenSwathWorkflow_11_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/>
-      <param name="tr_irt" value="OpenSwathWorkflow_11_input.TraML"/>
-      <output name="out_features" file="OpenSwathWorkflow_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_11_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
-      <param name="sonar" value="true"/>
-      <param name="rt_extraction_window" value="-1.0"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
+      <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/>
+      <output name="out_osw" value="OpenSwathWorkflow_13.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
+      <output name="out_chrom" value="OpenSwathWorkflow_13_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <param name="sonar" value="false"/>
+      <param name="pasef" value="false"/>
+      <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.2"/>
+      <param name="mz_extraction_window" value="0.05"/>
       <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
@@ -1768,7 +1806,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <section name="RTNormalization">
         <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="none"/>
+        <param name="outlierMethod" value="iter_residual"/>
         <param name="useIterativeChauvenet" value="false"/>
         <param name="RANSACMaxIterations" value="1000"/>
         <param name="RANSACMaxPercentRTThreshold" value="3"/>
@@ -1810,7 +1848,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
+          <param name="compute_peak_quality" value="true"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -1855,36 +1893,39 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
+          <param name="use_mi_score" value="false"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="true"/>
+          <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
+          <param name="use_ms1_mi" value="false"/>
           <param name="use_uis_scores" value="false"/>
           <param name="use_ionseries_scores" value="true"/>
           <param name="use_ms2_isotope_scores" value="true"/>
         </section>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- TOPP_OpenSwathWorkflow_13 -->
+    <!-- TOPP_OpenSwathWorkflow_14 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
         <param name="enable_ms1" value="true"/>
         <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
+        <param name="out_chrom_type" value="sqMass"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_unit" value="Th"/>
         <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
@@ -1899,18 +1940,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
         <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
+        <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
-        <param name="test" value="false"/>
+        <param name="test" value="true"/>
       </section>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/>
-      <output name="out_osw" file="OpenSwathWorkflow_13.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_13_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/>
+      <output name="out_osw" value="OpenSwathWorkflow_14.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
+      <output name="out_chrom" value="OpenSwathWorkflow_14.chrom.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/>
       <param name="sonar" value="false"/>
+      <param name="pasef" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window" value="0.05"/>
       <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
@@ -1969,7 +2011,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
+          <param name="compute_peak_quality" value="true"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -2014,13 +2056,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
+          <param name="use_mi_score" value="false"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
+          <param name="use_ms1_mi" value="false"/>
           <param name="use_uis_scores" value="false"/>
           <param name="use_ionseries_scores" value="true"/>
           <param name="use_ms2_isotope_scores" value="true"/>
@@ -2032,18 +2074,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- TOPP_OpenSwathWorkflow_14 -->
+    <!-- TOPP_OpenSwathWorkflow_16 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
         <param name="enable_ms1" value="true"/>
         <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="sqMass"/>
+        <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_unit" value="Th"/>
         <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
@@ -2054,22 +2099,23 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="min_coverage" value="0.6"/>
         <param name="split_file_input" value="false"/>
         <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
+        <param name="readOptions" value="workingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
         <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
+        <param name="ms1_isotopes" value="2"/>
         <param name="force" value="false"/>
-        <param name="test" value="false"/>
+        <param name="test" value="true"/>
       </section>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/>
-      <output name="out_osw" file="OpenSwathWorkflow_14.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_14.chrom.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/>
+      <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/>
+      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
+      <output name="out_features" value="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_chrom" value="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="sonar" value="false"/>
+      <param name="pasef" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window" value="0.05"/>
       <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
@@ -2128,7 +2174,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
+          <param name="compute_peak_quality" value="true"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -2173,29 +2219,31 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
+          <param name="use_mi_score" value="false"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
+          <param name="use_ms1_mi" value="false"/>
           <param name="use_uis_scores" value="false"/>
           <param name="use_ionseries_scores" value="true"/>
           <param name="use_ms2_isotope_scores" value="true"/>
         </section>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- TOPP_OpenSwathWorkflow_15 -->
+    <!-- TOPP_OpenSwathWorkflow_17_cache -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
         <param name="enable_ms1" value="true"/>
         <param name="enable_ipf" value="true"/>
@@ -2204,7 +2252,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="extra_rt_extraction_window" value="0.0"/>
         <param name="mz_extraction_window_unit" value="Th"/>
         <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
+        <param name="use_ms1_ion_mobility" value="false"/>
         <param name="matching_window_only" value="false"/>
         <param name="irt_mz_extraction_window" value="50.0"/>
         <param name="irt_mz_extraction_window_unit" value="ppm"/>
@@ -2213,21 +2261,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="min_coverage" value="0.6"/>
         <param name="split_file_input" value="false"/>
         <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
+        <param name="readOptions" value="cache"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
         <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="2"/>
+        <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
-      <param name="in" value="OpenSwathWorkflow_15_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <output name="out_features" file="OpenSwathWorkflow_15_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_15_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
+      <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
+      <output name="out_features" value="OpenSwathWorkflow_17_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_chrom" value="OpenSwathWorkflow_17_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="sonar" value="false"/>
+      <param name="pasef" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
+      <param name="ion_mobility_window" value="0.05"/>
       <param name="mz_extraction_window" value="0.05"/>
       <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
@@ -2282,12 +2331,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="peak_integration" value="original"/>
           <param name="background_subtraction" value="none"/>
           <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="true"/>
+          <param name="use_precursors" value="false"/>
           <param name="use_consensus" value="true"/>
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
+          <param name="compute_peak_quality" value="true"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -2336,7 +2385,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
+          <param name="use_ion_mobility_scores" value="true"/>
           <param name="use_ms1_fullscan" value="false"/>
           <param name="use_ms1_mi" value="false"/>
           <param name="use_uis_scores" value="false"/>
@@ -2350,20 +2399,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- TOPP_OpenSwathWorkflow_16 -->
+    <!-- TOPP_OpenSwathWorkflow_17_b -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
         <param name="enable_ms1" value="true"/>
         <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_unit" value="Th"/>
         <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
+        <param name="use_ms1_ion_mobility" value="false"/>
         <param name="matching_window_only" value="false"/>
         <param name="irt_mz_extraction_window" value="50.0"/>
         <param name="irt_mz_extraction_window_unit" value="ppm"/>
@@ -2376,18 +2427,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
         <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="2"/>
+        <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
-        <param name="test" value="false"/>
+        <param name="test" value="true"/>
       </section>
-      <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <output name="out_features" file="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
+      <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/>
+      <output name="out_features" value="OpenSwathWorkflow_17_b_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_chrom" value="OpenSwathWorkflow_17_b_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="sonar" value="false"/>
+      <param name="pasef" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
+      <param name="ion_mobility_window" value="0.05"/>
+      <param name="mz_extraction_window" value="0.05"/>
       <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
@@ -2446,7 +2498,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
+          <param name="compute_peak_quality" value="true"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -2491,13 +2543,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
+          <param name="use_mi_score" value="false"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
+          <param name="use_ms1_mi" value="false"/>
           <param name="use_uis_scores" value="false"/>
           <param name="use_ionseries_scores" value="true"/>
           <param name="use_ms2_isotope_scores" value="true"/>
@@ -2509,8 +2561,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- TOPP_OpenSwathWorkflow_17 -->
+    <!-- TOPP_OpenSwathWorkflow_22 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="sort_swath_maps" value="false"/>
@@ -2519,10 +2574,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_unit" value="Th"/>
         <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="false"/>
-        <param name="matching_window_only" value="false"/>
+        <param name="use_ms1_ion_mobility" value="true"/>
+        <param name="matching_window_only" value="true"/>
         <param name="irt_mz_extraction_window" value="50.0"/>
         <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
@@ -2536,16 +2591,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="3"/>
         <param name="force" value="false"/>
-        <param name="test" value="false"/>
+        <param name="test" value="true"/>
       </section>
-      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
-      <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <param name="in" value="OpenSwathWorkflow_22_input.mzML"/>
+      <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/>
+      <output name="out_features" value="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_chrom" value="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="sonar" value="false"/>
+      <param name="pasef" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="50.0"/>
+      <param name="ion_mobility_window" value="-1.0"/>
+      <param name="mz_extraction_window" value="0.05"/>
       <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
@@ -2604,7 +2660,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
+          <param name="compute_peak_quality" value="true"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -2649,13 +2705,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
+          <param name="use_mi_score" value="false"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="true"/>
+          <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
+          <param name="use_ms1_mi" value="false"/>
           <param name="use_uis_scores" value="false"/>
           <param name="use_ionseries_scores" value="true"/>
           <param name="use_ms2_isotope_scores" value="true"/>
@@ -2667,8 +2723,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- TOPP_OpenSwathWorkflow_17_cache -->
+    <!-- TOPP_OpenSwathWorkflow_23 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="sort_swath_maps" value="false"/>
@@ -2677,7 +2736,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_unit" value="Th"/>
         <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="false"/>
         <param name="matching_window_only" value="false"/>
@@ -2688,22 +2747,23 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="min_coverage" value="0.6"/>
         <param name="split_file_input" value="false"/>
         <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="cache"/>
+        <param name="readOptions" value="workingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
         <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
+        <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
-        <param name="test" value="false"/>
+        <param name="test" value="true"/>
       </section>
-      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
-      <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <param name="in" value="OpenSwathWorkflow_23_input.mzML"/>
+      <param name="tr" value="OpenSwathWorkflow_23_input.tsv" ftype="tabular"/>
+      <output name="out_features" value="OpenSwathWorkflow_23_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_chrom" value="OpenSwathWorkflow_23_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="sonar" value="false"/>
+      <param name="pasef" value="true"/>
       <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="50.0"/>
+      <param name="ion_mobility_window" value="0.1"/>
+      <param name="mz_extraction_window" value="0.05"/>
       <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
@@ -2762,7 +2822,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
+          <param name="compute_peak_quality" value="true"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -2807,976 +2867,32 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
+          <param name="use_mi_score" value="false"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="true"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-          <param name="use_ionseries_scores" value="true"/>
-          <param name="use_ms2_isotope_scores" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_OpenSwathWorkflow_17_b -->
-    <test expect_num_outputs="3">
-      <section name="adv_opts">
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="false"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="workingInMemory"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </section>
-      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/>
-      <output name="out_features" file="OpenSwathWorkflow_17_b_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_17_b_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-          <param name="init_mom" value="false"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-          <param name="use_ionseries_scores" value="true"/>
-          <param name="use_ms2_isotope_scores" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_OpenSwathWorkflow_18 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <output name="out_features" file="OpenSwathWorkflow_18_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-          <param name="init_mom" value="false"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-          <param name="use_ionseries_scores" value="true"/>
-          <param name="use_ms2_isotope_scores" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_OpenSwathWorkflow_19 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <output name="out_features" file="OpenSwathWorkflow_19_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-          <param name="init_mom" value="false"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-          <param name="use_ionseries_scores" value="true"/>
-          <param name="use_ms2_isotope_scores" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_OpenSwathWorkflow_20 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <output name="out_features" file="OpenSwathWorkflow_20_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-          <param name="init_mom" value="false"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="true"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-          <param name="use_ionseries_scores" value="true"/>
-          <param name="use_ms2_isotope_scores" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_OpenSwathWorkflow_21 -->
-    <test expect_num_outputs="4">
-      <section name="adv_opts">
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="OpenSwathWorkflow_21_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_21_input.tsv" ftype="tabular"/>
-      <param name="tr_irt" value="OpenSwathWorkflow_21_input.irt.TraML"/>
-      <output name="out_features" file="OpenSwathWorkflow_21_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_21_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.6666666666666666"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-          <param name="init_mom" value="false"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="true"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
           <param name="use_ms1_mi" value="false"/>
           <param name="use_uis_scores" value="false"/>
           <param name="use_ionseries_scores" value="true"/>
           <param name="use_ms2_isotope_scores" value="true"/>
         </section>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,irt_trafo_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_OpenSwathWorkflow_22 -->
-    <test expect_num_outputs="3">
-      <section name="adv_opts">
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="true"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="workingInMemory"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </section>
-      <param name="in" value="OpenSwathWorkflow_22_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/>
-      <output name="out_features" file="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-          <param name="init_mom" value="false"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-          <param name="use_ionseries_scores" value="true"/>
-          <param name="use_ms2_isotope_scores" value="true"/>
-        </section>
-      </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Complete workflow to run OpenSWATH
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathWorkflow.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathWorkflow.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/PSMFeatureExtractor.xml b/tools/openms/PSMFeatureExtractor.xml
index 0d93e0a3b..b0c7e9126 100644
--- a/tools/openms/PSMFeatureExtractor.xml
+++ b/tools/openms/PSMFeatureExtractor.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Computes extra features for each input PSM.</description>
+  <description>Computes extra features for each input PSM</description>
   <macros>
     <token name="@EXECUTABLE@">PSMFeatureExtractor</token>
     <import>macros.xml</import>
@@ -17,9 +16,9 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir out &&
 
@@ -54,15 +53,16 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="idxml,mzid" multiple="true" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
+        <param argument="-in" type="data" format="idxml,mzid" multiple="true" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="idxml,mzid" multiple="false" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
+        <param argument="-in" type="data" format="idxml,mzid" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
+    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
       <option value="idXML">idxml</option>
       <option value="mzid">mzid</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
     <param argument="-extra" type="text" optional="true" value="" label="List of the MetaData parameters to be included in a feature set for precolato" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
@@ -76,7 +76,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <param argument="-impute" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed" help="Only valid together with -multiple_search_engines flag"/>
       <param argument="-limit_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score" help="Only valid together with -multiple_search_engines flag"/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -94,34 +94,89 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="adv_opts|skip_db_check" value="true"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
-    <param name="multiple_search_engines" value="true"/>
-    <param name="out_type" value="idxml"/>
-    <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="500"/>
-  </test>
-  <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="adv_opts|skip_db_check" value="true"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
-    <param name="multiple_search_engines" value="true"/>
-    <param name="out_type" value="mzid"/>
-    <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/>
-  </test>
-  <!-- test for the batch conditional crated for data parameters with multiple="true" -->
-  <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in_select" value="yes"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
-    <param name="out_type" value="idxml"/>
-    <output name="out" ftype="idxml" value="PSMFeatureExtractor_3.idXML" compare="sim_size" delta="500"/>
-  </test>
-</tests>
+  <tests>
+    <!-- TOPP_PSMFeatureExtractor_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="skip_db_check" value="true"/>
+        <param name="concat" value="false"/>
+        <param name="impute" value="false"/>
+        <param name="limit_imputation" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
+      </conditional>
+      <output name="out" value="PSMFeatureExtractor_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="out_type" value="idXML"/>
+      <param name="multiple_search_engines" value="true"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_PSMFeatureExtractor_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="skip_db_check" value="true"/>
+        <param name="concat" value="false"/>
+        <param name="impute" value="false"/>
+        <param name="limit_imputation" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
+      </conditional>
+      <output name="out" value="PSMFeatureExtractor_2_out.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
+      <param name="out_type" value="mzid"/>
+      <param name="multiple_search_engines" value="true"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_PSMFeatureExtractor_3 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="skip_db_check" value="false"/>
+        <param name="concat" value="false"/>
+        <param name="impute" value="false"/>
+        <param name="limit_imputation" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="MSGFPlusAdapter_1_out.idXML"/>
+      </conditional>
+      <output name="out" value="PSMFeatureExtractor_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="out_type" value="idXML"/>
+      <param name="multiple_search_engines" value="false"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+  </tests>
   <help><![CDATA[Computes extra features for each input PSM.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_PSMFeatureExtractor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PSMFeatureExtractor.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/PTModel.xml b/tools/openms/PTModel.xml
deleted file mode 100644
index 3d68ca633..000000000
--- a/tools/openms/PTModel.xml
+++ /dev/null
@@ -1,185 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Peptide property prediction]-->
-<tool id="PTModel" name="PTModel" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Trains a model for the prediction of proteotypic peptides from a training set.</description>
-  <macros>
-    <token name="@EXECUTABLE@">PTModel</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in_positive &&
-ln -s '$in_positive' 'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)' &&
-mkdir in_negative &&
-ln -s '$in_negative' 'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)' &&
-mkdir out &&
-#if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out_oligo_params &&
-#end if
-#if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out_oligo_trainset &&
-#end if
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in_positive
-'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)'
--in_negative
-'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)'
--out
-'out/output.${gxy2omsext("txt")}'
-#if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out_oligo_params
-  'out_oligo_params/output.${gxy2omsext("paramxml")}'
-#end if
-#if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out_oligo_trainset
-  'out_oligo_trainset/output.${gxy2omsext("txt")}'
-#end if
-#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
-  | tee '$stdout'
-#end if
-
-## Postprocessing
-&& mv 'out/output.${gxy2omsext("txt")}' '$out'
-#if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out_oligo_params/output.${gxy2omsext("paramxml")}' '$out_oligo_params'
-#end if
-#if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out_oligo_trainset/output.${gxy2omsext("txt")}' '$out_oligo_trainset'
-#end if
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
-  </configfiles>
-  <inputs>
-    <param argument="-in_positive" type="data" format="idxml" optional="false" label="input file with positive examples" help=" select idxml data sets(s)"/>
-    <param argument="-in_negative" type="data" format="idxml" optional="false" label="input file with negative examples" help=" select idxml data sets(s)"/>
-    <param argument="-c" type="float" optional="true" value="1.0" label="the penalty parameter of the svm" help=""/>
-    <param argument="-svm_type" type="select" optional="true" label="the type of the svm (NU_SVC or C_SVC)" help="">
-      <option value="NU_SVC">NU_SVC</option>
-      <option value="C_SVC" selected="true">C_SVC</option>
-      <expand macro="list_string_san" name="svm_type"/>
-    </param>
-    <param argument="-nu" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="the nu parameter [0..1] of the svm (for nu-SVR)" help=""/>
-    <param argument="-kernel_type" type="select" optional="true" label="the kernel type of the svm" help="">
-      <option value="LINEAR">LINEAR</option>
-      <option value="RBF">RBF</option>
-      <option value="POLY">POLY</option>
-      <option value="OLIGO" selected="true">OLIGO</option>
-      <expand macro="list_string_san" name="kernel_type"/>
-    </param>
-    <param argument="-degree" type="integer" optional="true" min="1" value="1" label="the degree parameter of the kernel function of the svm (POLY kernel)" help=""/>
-    <param argument="-border_length" type="integer" optional="true" min="1" value="22" label="length of the POBK" help=""/>
-    <param argument="-k_mer_length" type="integer" optional="true" min="1" value="1" label="k_mer length of the POBK" help=""/>
-    <param argument="-sigma" type="float" optional="true" value="5.0" label="sigma of the POBK" help=""/>
-    <param argument="-max_positive_count" type="integer" optional="true" min="1" value="1000" label="quantity of positive samples for training (randomly chosen if smaller than available quantity)" help=""/>
-    <param argument="-max_negative_count" type="integer" optional="true" min="1" value="1000" label="quantity of positive samples for training (randomly chosen if smaller than available quantity)" help=""/>
-    <param argument="-redundant" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if the input sets are redundant and the redundant peptides should occur more than once in the training set, this flag has to be set" help=""/>
-    <param argument="-additive_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if the step sizes should be interpreted additively (otherwise the actual value is multiplied with the step size to get the new value" help=""/>
-    <section name="cv" title="Parameters for the grid search / cross validation:" help="" expanded="false">
-      <param name="skip_cv" argument="-cv:skip_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Has to be set if the cv should be skipped and the model should just be trained with the specified parameters" help=""/>
-      <param name="number_of_runs" argument="-cv:number_of_runs" type="integer" optional="true" min="1" value="10" label="number of runs for the CV" help=""/>
-      <param name="number_of_partitions" argument="-cv:number_of_partitions" type="integer" optional="true" min="2" value="10" label="number of CV partitions" help=""/>
-      <param name="degree_start" argument="-cv:degree_start" type="integer" optional="true" min="1" value="1" label="starting point of degree" help=""/>
-      <param name="degree_step_size" argument="-cv:degree_step_size" type="integer" optional="true" value="2" label="step size point of degree" help=""/>
-      <param name="degree_stop" argument="-cv:degree_stop" type="integer" optional="true" value="4" label="stopping point of degree" help=""/>
-      <param name="c_start" argument="-cv:c_start" type="float" optional="true" value="1.0" label="starting point of c" help=""/>
-      <param name="c_step_size" argument="-cv:c_step_size" type="float" optional="true" value="100.0" label="step size of c" help=""/>
-      <param name="c_stop" argument="-cv:c_stop" type="float" optional="true" value="1000.0" label="stopping point of c" help=""/>
-      <param name="nu_start" argument="-cv:nu_start" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="starting point of nu" help=""/>
-      <param name="nu_step_size" argument="-cv:nu_step_size" type="float" optional="true" value="1.3" label="step size of nu" help=""/>
-      <param name="nu_stop" argument="-cv:nu_stop" type="float" optional="true" min="0.0" max="1.0" value="0.9" label="stopping point of nu" help=""/>
-      <param name="sigma_start" argument="-cv:sigma_start" type="float" optional="true" value="1.0" label="starting point of sigma" help=""/>
-      <param name="sigma_step_size" argument="-cv:sigma_step_size" type="float" optional="true" value="1.3" label="step size of sigma" help=""/>
-      <param name="sigma_stop" argument="-cv:sigma_stop" type="float" optional="true" value="15.0" label="stopping point of sigma" help=""/>
-    </section>
-    <expand macro="adv_opts_macro">
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="out_oligo_params_FLAG">out_oligo_params (output file with additional model parameters when using the OLIGO kernel)</option>
-      <option value="out_oligo_trainset_FLAG">out_oligo_trainset (output file with the used training dataset when using the OLIGO kernel)</option>
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
-    <data name="out_oligo_params" label="${tool.name} on ${on_string}: out_oligo_params" format="paramxml">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_oligo_params_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="out_oligo_trainset" label="${tool.name} on ${on_string}: out_oligo_trainset" format="txt">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_oligo_trainset_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><!-- TOPP_PTModel_1 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in_positive" value="PTModel_1_input_positive.idXML"/>
-      <param name="in_negative" value="PTModel_1_input_negative.idXML"/>
-      <output name="out" file="PTModel_1_output.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/>
-      <param name="c" value="0.5"/>
-      <param name="svm_type" value="C_SVC"/>
-      <param name="nu" value="0.5"/>
-      <param name="kernel_type" value="OLIGO"/>
-      <param name="degree" value="1"/>
-      <param name="border_length" value="22"/>
-      <param name="k_mer_length" value="1"/>
-      <param name="sigma" value="5.0"/>
-      <param name="max_positive_count" value="1000"/>
-      <param name="max_negative_count" value="1000"/>
-      <param name="redundant" value="false"/>
-      <param name="additive_cv" value="false"/>
-      <section name="cv">
-        <param name="skip_cv" value="true"/>
-        <param name="number_of_runs" value="10"/>
-        <param name="number_of_partitions" value="10"/>
-        <param name="degree_start" value="1"/>
-        <param name="degree_step_size" value="2"/>
-        <param name="degree_stop" value="4"/>
-        <param name="c_start" value="1.0"/>
-        <param name="c_step_size" value="100.0"/>
-        <param name="c_stop" value="1000.0"/>
-        <param name="nu_start" value="0.1"/>
-        <param name="nu_step_size" value="1.3"/>
-        <param name="nu_stop" value="0.9"/>
-        <param name="sigma_start" value="1.0"/>
-        <param name="sigma_step_size" value="1.3"/>
-        <param name="sigma_stop" value="15.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
-  <help><![CDATA[Trains a model for the prediction of proteotypic peptides from a training set.
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PTModel.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/PeakPickerHiRes.xml b/tools/openms/PeakPickerHiRes.xml
index e1553261f..4aeba9a0d 100644
--- a/tools/openms/PeakPickerHiRes.xml
+++ b/tools/openms/PeakPickerHiRes.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Spectrum processing: Centroiding]-->
 <tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Finds mass spectrometric peaks in profile mass spectra.</description>
+  <description>Finds mass spectrometric peaks in profile mass spectra</description>
   <macros>
     <token name="@EXECUTABLE@">PeakPickerHiRes</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,12 +38,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input profile data file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input profile data file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="signal_to_noise" argument="-algorithm:signal_to_noise" type="float" optional="true" min="0.0" value="0.0" label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" help=""/>
-      <param name="spacing_difference_gap" argument="-algorithm:spacing_difference_gap" type="float" optional="true" min="0.0" value="4.0" label="The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'" help="'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms"/>
-      <param name="spacing_difference" argument="-algorithm:spacing_difference" type="float" optional="true" min="0.0" value="1.5" label="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points" help="If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms"/>
-      <param name="missing" argument="-algorithm:missing" type="integer" optional="true" min="0" value="1" label="Maximum number of missing points allowed when extending a peak to the left or to the right" help="A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms"/>
+      <param name="signal_to_noise" argument="-algorithm:signal_to_noise" type="float" min="0.0" value="0.0" label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" help=""/>
+      <param name="spacing_difference_gap" argument="-algorithm:spacing_difference_gap" type="float" min="0.0" value="4.0" label="The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'" help="'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms"/>
+      <param name="spacing_difference" argument="-algorithm:spacing_difference" type="float" min="0.0" value="1.5" label="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points" help="If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms"/>
+      <param name="missing" argument="-algorithm:missing" type="integer" min="0" value="1" label="Maximum number of missing points allowed when extending a peak to the left or to the right" help="A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms"/>
       <param name="ms_levels" argument="-algorithm:ms_levels" type="text" optional="true" value="" label="List of MS levels for which the peak picking is applied" help="If empty, auto mode is enabled, all peaks which aren't picked yet will get picked. Other scans are copied to the output without changes (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_integer_valsan" name="ms_levels">
           <validator type="expression" message="a space separated list of integer values in the range 1: is required"><![CDATA[len(value.split(' ')) == len([_ for _ in value.split(' ') if  1 <= int(_)])
@@ -52,31 +51,31 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         </expand>
       </param>
       <param name="report_FWHM" argument="-algorithm:report_FWHM" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak" help=""/>
-      <param name="report_FWHM_unit" argument="-algorithm:report_FWHM_unit" type="select" optional="true" label="Unit of FWHM" help="Either absolute in the unit of input, e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms)">
+      <param name="report_FWHM_unit" argument="-algorithm:report_FWHM_unit" type="select" label="Unit of FWHM" help="Either absolute in the unit of input, e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms)">
         <option value="relative" selected="true">relative</option>
         <option value="absolute">absolute</option>
         <expand macro="list_string_san" name="report_FWHM_unit"/>
       </param>
       <section name="SignalToNoise" title="" help="" expanded="false">
-        <param name="max_intensity" argument="-algorithm:SignalToNoise:max_intensity" type="integer" optional="true" min="-1" value="-1" label="maximal intensity considered for histogram construction" help="By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well.  If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/>
-        <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoise:auto_max_stdev_factor" type="float" optional="true" min="0.0" max="999.0" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help=""/>
-        <param name="auto_max_percentile" argument="-algorithm:SignalToNoise:auto_max_percentile" type="integer" optional="true" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/>
-        <param name="auto_mode" argument="-algorithm:SignalToNoise:auto_mode" type="integer" optional="true" min="-1" max="1" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help=""/>
-        <param name="win_len" argument="-algorithm:SignalToNoise:win_len" type="float" optional="true" min="1.0" value="200.0" label="window length in Thomson" help=""/>
-        <param name="bin_count" argument="-algorithm:SignalToNoise:bin_count" type="integer" optional="true" min="3" value="30" label="number of bins for intensity values" help=""/>
-        <param name="min_required_elements" argument="-algorithm:SignalToNoise:min_required_elements" type="integer" optional="true" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/>
-        <param name="noise_for_empty_window" argument="-algorithm:SignalToNoise:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/>
+        <param name="max_intensity" argument="-algorithm:SignalToNoise:max_intensity" type="integer" min="-1" value="-1" label="maximal intensity considered for histogram construction" help="By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well.  If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/>
+        <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoise:auto_max_stdev_factor" type="float" min="0.0" max="999.0" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help=""/>
+        <param name="auto_max_percentile" argument="-algorithm:SignalToNoise:auto_max_percentile" type="integer" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/>
+        <param name="auto_mode" argument="-algorithm:SignalToNoise:auto_mode" type="integer" min="-1" max="1" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help=""/>
+        <param name="win_len" argument="-algorithm:SignalToNoise:win_len" type="float" min="1.0" value="200.0" label="window length in Thomson" help=""/>
+        <param name="bin_count" argument="-algorithm:SignalToNoise:bin_count" type="integer" min="3" value="30" label="number of bins for intensity values" help=""/>
+        <param name="min_required_elements" argument="-algorithm:SignalToNoise:min_required_elements" type="integer" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/>
+        <param name="noise_for_empty_window" argument="-algorithm:SignalToNoise:noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help=""/>
         <param name="write_log_messages" argument="-algorithm:SignalToNoise:write_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help=""/>
       </section>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-processOption" type="select" optional="true" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
+      <param argument="-processOption" type="select" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
         <option value="inmemory" selected="true">inmemory</option>
         <option value="lowmemory">lowmemory</option>
         <expand macro="list_string_san" name="processOption"/>
       </param>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -90,7 +89,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_PeakPickerHiRes_1 -->
+  <tests>
+    <!-- TOPP_PeakPickerHiRes_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="processOption" value="inmemory"/>
@@ -98,7 +98,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PeakPickerHiRes_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerHiRes_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise" value="1.0"/>
         <param name="spacing_difference_gap" value="4.0"/>
@@ -125,6 +125,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeakPickerHiRes_2 -->
     <test expect_num_outputs="2">
@@ -134,7 +137,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PeakPickerHiRes_2_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise" value="1.0"/>
         <param name="spacing_difference_gap" value="4.0"/>
@@ -161,6 +164,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeakPickerHiRes_3 -->
     <test expect_num_outputs="2">
@@ -170,7 +176,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PeakPickerHiRes_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_output_lowMem.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerHiRes_output_lowMem.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise" value="1.0"/>
         <param name="spacing_difference_gap" value="4.0"/>
@@ -197,6 +203,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeakPickerHiRes_4 -->
     <test expect_num_outputs="2">
@@ -206,7 +215,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PeakPickerHiRes_2_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise" value="1.0"/>
         <param name="spacing_difference_gap" value="4.0"/>
@@ -233,6 +242,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeakPickerHiRes_5 -->
     <test expect_num_outputs="2">
@@ -242,13 +254,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PeakPickerHiRes_5_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerHiRes_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise" value="0.0"/>
         <param name="spacing_difference_gap" value="4.0"/>
         <param name="spacing_difference" value="1.5"/>
         <param name="missing" value="1"/>
-        <param name="ms_levels" value=""/>
         <param name="report_FWHM" value="false"/>
         <param name="report_FWHM_unit" value="relative"/>
         <section name="SignalToNoise">
@@ -269,11 +280,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PeakPickerHiRes.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PeakPickerHiRes.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/PeakPickerIterative.xml b/tools/openms/PeakPickerIterative.xml
index 4262d21b2..7a25f3302 100644
--- a/tools/openms/PeakPickerIterative.xml
+++ b/tools/openms/PeakPickerIterative.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Spectrum processing: Centroiding]-->
 <tool id="PeakPickerIterative" name="PeakPickerIterative" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Finds mass spectrometric peaks in profile mass spectra.</description>
+  <description>Finds mass spectrometric peaks in profile mass spectra</description>
   <macros>
     <token name="@EXECUTABLE@">PeakPickerIterative</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,21 +38,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="signal_to_noise_" argument="-algorithm:signal_to_noise_" type="float" optional="true" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help=""/>
-      <param name="peak_width" argument="-algorithm:peak_width" type="float" optional="true" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing)" help="In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/>
-      <param name="spacing_difference" argument="-algorithm:spacing_difference" type="float" optional="true" value="1.5" label="Difference between peaks in multiples of the minimal difference to continue" help="The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak"/>
-      <param name="sn_bin_count_" argument="-algorithm:sn_bin_count_" type="integer" optional="true" value="30" label="Bin count for the Signal to Noise estimation" help=""/>
-      <param name="nr_iterations_" argument="-algorithm:nr_iterations_" type="integer" optional="true" min="1" value="5" label="Nr of iterations to perform (how many times the peaks are re-centered)" help=""/>
-      <param name="sn_win_len_" argument="-algorithm:sn_win_len_" type="float" optional="true" value="20.0" label="Window length for the Signal to Noise estimation" help=""/>
+      <param name="signal_to_noise_" argument="-algorithm:signal_to_noise_" type="float" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help=""/>
+      <param name="peak_width" argument="-algorithm:peak_width" type="float" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing)" help="In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/>
+      <param name="spacing_difference" argument="-algorithm:spacing_difference" type="float" value="1.5" label="Difference between peaks in multiples of the minimal difference to continue" help="The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak"/>
+      <param name="sn_bin_count_" argument="-algorithm:sn_bin_count_" type="integer" value="30" label="Bin count for the Signal to Noise estimation" help=""/>
+      <param name="nr_iterations_" argument="-algorithm:nr_iterations_" type="integer" min="1" value="5" label="Nr of iterations to perform (how many times the peaks are re-centered)" help=""/>
+      <param name="sn_win_len_" argument="-algorithm:sn_win_len_" type="float" value="20.0" label="Window length for the Signal to Noise estimation" help=""/>
       <param name="check_width_internally" argument="-algorithm:check_width_internally" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Delete peaks where the spacing is larger than the peak width (should be set to true to avoid artefacts)" help=""/>
       <param name="ms1_only" argument="-algorithm:ms1_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only do MS1" help=""/>
       <param name="clear_meta_data" argument="-algorithm:clear_meta_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Delete meta data about peak width" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -67,14 +66,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_PeakPickerIterative_1 -->
+  <tests>
+    <!-- TOPP_PeakPickerIterative_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PeakPickerIterative_1_input.mzML"/>
-      <output name="out" file="PeakPickerIterative_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerIterative_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise_" value="1.0"/>
         <param name="peak_width" value="0.04"/>
@@ -92,15 +92,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_PeakPickerIterative_2 -->
+    <!-- TOPP_PeakPickerIterative_2 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PeakPickerIterative_2_input.mzML"/>
-      <output name="out" file="PeakPickerIterative_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerIterative_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise_" value="0.0"/>
         <param name="peak_width" value="0.04"/>
@@ -118,11 +121,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_PeakPickerIterative.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PeakPickerIterative.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/PeakPickerWavelet.xml b/tools/openms/PeakPickerWavelet.xml
index 8f5f8334f..17d5204f0 100644
--- a/tools/openms/PeakPickerWavelet.xml
+++ b/tools/openms/PeakPickerWavelet.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Spectrum processing: Centroiding]-->
 <tool id="PeakPickerWavelet" name="PeakPickerWavelet" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Finds mass spectrometric peaks in profile mass spectra.</description>
+  <description>Finds mass spectrometric peaks in profile mass spectra</description>
   <macros>
     <token name="@EXECUTABLE@">PeakPickerWavelet</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,72 +38,72 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input profile data file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input profile data file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="signal_to_noise" argument="-algorithm:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/>
-      <param name="centroid_percentage" argument="-algorithm:centroid_percentage" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" help="If it is 1 the centroid position corresponds to the position of the highest intensity"/>
-      <param name="peak_width" argument="-algorithm:peak_width" type="float" optional="true" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/>
+      <param name="signal_to_noise" argument="-algorithm:signal_to_noise" type="float" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/>
+      <param name="centroid_percentage" argument="-algorithm:centroid_percentage" type="float" min="0.0" max="1.0" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" help="If it is 1 the centroid position corresponds to the position of the highest intensity"/>
+      <param name="peak_width" argument="-algorithm:peak_width" type="float" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/>
       <param name="estimate_peak_width" argument="-algorithm:estimate_peak_width" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag if the average peak width shall be estimated" help="Attention: when this flag is set, the peak_width is ignored"/>
-      <param name="fwhm_lower_bound_factor" argument="-algorithm:fwhm_lower_bound_factor" type="float" optional="true" min="0.0" value="0.7" label="Factor that calculates the minimal fwhm value from the peak_width" help="All peaks with width smaller than fwhm_bound_factor * peak_width are discarded"/>
-      <param name="fwhm_upper_bound_factor" argument="-algorithm:fwhm_upper_bound_factor" type="float" optional="true" min="0.0" value="20.0" label="Factor that calculates the maximal fwhm value from the peak_width" help="All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded"/>
+      <param name="fwhm_lower_bound_factor" argument="-algorithm:fwhm_lower_bound_factor" type="float" min="0.0" value="0.7" label="Factor that calculates the minimal fwhm value from the peak_width" help="All peaks with width smaller than fwhm_bound_factor * peak_width are discarded"/>
+      <param name="fwhm_upper_bound_factor" argument="-algorithm:fwhm_upper_bound_factor" type="float" min="0.0" value="20.0" label="Factor that calculates the maximal fwhm value from the peak_width" help="All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded"/>
       <section name="optimization" title="" help="" expanded="false">
-        <param name="iterations" argument="-algorithm:optimization:iterations" type="integer" optional="true" min="1" value="400" label="maximal number of iterations for the fitting step" help=""/>
+        <param name="iterations" argument="-algorithm:optimization:iterations" type="integer" min="1" value="400" label="maximal number of iterations for the fitting step" help=""/>
         <section name="penalties" title="" help="" expanded="false">
-          <param name="position" argument="-algorithm:optimization:penalties:position" type="float" optional="true" min="0.0" value="0.0" label="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized" help=""/>
-          <param name="left_width" argument="-algorithm:optimization:penalties:left_width" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized" help=""/>
-          <param name="right_width" argument="-algorithm:optimization:penalties:right_width" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized" help=""/>
-          <param name="height" argument="-algorithm:optimization:penalties:height" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized" help=""/>
+          <param name="position" argument="-algorithm:optimization:penalties:position" type="float" min="0.0" value="0.0" label="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized" help=""/>
+          <param name="left_width" argument="-algorithm:optimization:penalties:left_width" type="float" min="0.0" value="1.0" label="penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized" help=""/>
+          <param name="right_width" argument="-algorithm:optimization:penalties:right_width" type="float" min="0.0" value="1.0" label="penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized" help=""/>
+          <param name="height" argument="-algorithm:optimization:penalties:height" type="float" min="0.0" value="1.0" label="penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized" help=""/>
         </section>
         <section name="2d" title="" help="" expanded="false">
-          <param name="tolerance_mz" argument="-algorithm:optimization:2d:tolerance_mz" type="float" optional="true" min="0.0" value="2.2" label="mz tolerance for cluster construction" help=""/>
-          <param name="max_peak_distance" argument="-algorithm:optimization:2d:max_peak_distance" type="float" optional="true" min="0.0" value="1.2" label="maximal peak distance in mz in a cluste" help=""/>
+          <param name="tolerance_mz" argument="-algorithm:optimization:2d:tolerance_mz" type="float" min="0.0" value="2.2" label="mz tolerance for cluster construction" help=""/>
+          <param name="max_peak_distance" argument="-algorithm:optimization:2d:max_peak_distance" type="float" min="0.0" value="1.2" label="maximal peak distance in mz in a cluste" help=""/>
         </section>
       </section>
       <section name="thresholds" title="" help="" expanded="false">
-        <param name="peak_bound" argument="-algorithm:thresholds:peak_bound" type="float" optional="true" min="0.0" value="10.0" label="Minimal peak intensity" help=""/>
-        <param name="peak_bound_ms2_level" argument="-algorithm:thresholds:peak_bound_ms2_level" type="float" optional="true" min="0.0" value="10.0" label="Minimal peak intensity for MS/MS peaks" help=""/>
-        <param name="correlation" argument="-algorithm:thresholds:correlation" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="minimal correlation of a peak and the raw signal" help="If a peak has a lower correlation it is skipped"/>
-        <param name="noise_level" argument="-algorithm:thresholds:noise_level" type="float" optional="true" min="0.0" value="0.1" label="noise level for the search of the peak endpoints" help=""/>
-        <param name="search_radius" argument="-algorithm:thresholds:search_radius" type="integer" optional="true" min="0" value="3" label="search radius for the search of the maximum in the signal after a maximum in the cwt was found" help=""/>
+        <param name="peak_bound" argument="-algorithm:thresholds:peak_bound" type="float" min="0.0" value="10.0" label="Minimal peak intensity" help=""/>
+        <param name="peak_bound_ms2_level" argument="-algorithm:thresholds:peak_bound_ms2_level" type="float" min="0.0" value="10.0" label="Minimal peak intensity for MS/MS peaks" help=""/>
+        <param name="correlation" argument="-algorithm:thresholds:correlation" type="float" min="0.0" max="1.0" value="0.5" label="minimal correlation of a peak and the raw signal" help="If a peak has a lower correlation it is skipped"/>
+        <param name="noise_level" argument="-algorithm:thresholds:noise_level" type="float" min="0.0" value="0.1" label="noise level for the search of the peak endpoints" help=""/>
+        <param name="search_radius" argument="-algorithm:thresholds:search_radius" type="integer" min="0" value="3" label="search radius for the search of the maximum in the signal after a maximum in the cwt was found" help=""/>
       </section>
       <section name="wavelet_transform" title="" help="" expanded="false">
-        <param name="spacing" argument="-algorithm:wavelet_transform:spacing" type="float" optional="true" min="0.0" value="0.001" label="Spacing of the CWT" help="Note that the accuracy of the picked peak's centroid position depends in the Raw data spacing, i.e., 50% of raw peak distance at most"/>
+        <param name="spacing" argument="-algorithm:wavelet_transform:spacing" type="float" min="0.0" value="0.001" label="Spacing of the CWT" help="Note that the accuracy of the picked peak's centroid position depends in the Raw data spacing, i.e., 50% of raw peak distance at most"/>
       </section>
       <section name="deconvolution" title="" help="" expanded="false">
         <param name="deconvolution" argument="-algorithm:deconvolution:deconvolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If you want heavily overlapping peaks to be separated set this value to &quot;true&quot;" help=""/>
-        <param name="asym_threshold" argument="-algorithm:deconvolution:asym_threshold" type="float" optional="true" min="0.0" value="0.3" label="If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started" help=""/>
-        <param name="left_width" argument="-algorithm:deconvolution:left_width" type="float" optional="true" min="0.0" value="2.0" label="1/left_width is the initial value for the left width of the peaks found in the deconvolution step" help=""/>
-        <param name="right_width" argument="-algorithm:deconvolution:right_width" type="float" optional="true" min="0.0" value="2.0" label="1/right_width is the initial value for the right width of the peaks found in the deconvolution step" help=""/>
-        <param name="scaling" argument="-algorithm:deconvolution:scaling" type="float" optional="true" min="0.0" value="0.12" label="Initial scaling of the cwt used in the separation of heavily overlapping peaks" help="The initial value is used for charge 1, for higher charges it is adapted to scaling/charge"/>
+        <param name="asym_threshold" argument="-algorithm:deconvolution:asym_threshold" type="float" min="0.0" value="0.3" label="If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started" help=""/>
+        <param name="left_width" argument="-algorithm:deconvolution:left_width" type="float" min="0.0" value="2.0" label="1/left_width is the initial value for the left width of the peaks found in the deconvolution step" help=""/>
+        <param name="right_width" argument="-algorithm:deconvolution:right_width" type="float" min="0.0" value="2.0" label="1/right_width is the initial value for the right width of the peaks found in the deconvolution step" help=""/>
+        <param name="scaling" argument="-algorithm:deconvolution:scaling" type="float" min="0.0" value="0.12" label="Initial scaling of the cwt used in the separation of heavily overlapping peaks" help="The initial value is used for charge 1, for higher charges it is adapted to scaling/charge"/>
         <section name="fitting" title="" help="" expanded="false">
-          <param name="fwhm_threshold" argument="-algorithm:deconvolution:fitting:fwhm_threshold" type="float" optional="true" min="0.0" value="0.7" label="If the FWHM of a peak is higher than 'fwhm_thresholds' it is assumed that it consists of more than one peak and the deconvolution procedure is started" help=""/>
-          <param name="eps_abs" argument="-algorithm:deconvolution:fitting:eps_abs" type="float" optional="true" min="0.0" value="9.999999747378752e-06" label="if the absolute error gets smaller than this value the fitting is stopped" help=""/>
-          <param name="eps_rel" argument="-algorithm:deconvolution:fitting:eps_rel" type="float" optional="true" min="0.0" value="9.999999747378752e-06" label="if the relative error gets smaller than this value the fitting is stopped" help=""/>
-          <param name="max_iteration" argument="-algorithm:deconvolution:fitting:max_iteration" type="integer" optional="true" min="1" value="10" label="maximal number of iterations for the fitting step" help=""/>
+          <param name="fwhm_threshold" argument="-algorithm:deconvolution:fitting:fwhm_threshold" type="float" min="0.0" value="0.7" label="If the FWHM of a peak is higher than 'fwhm_thresholds' it is assumed that it consists of more than one peak and the deconvolution procedure is started" help=""/>
+          <param name="eps_abs" argument="-algorithm:deconvolution:fitting:eps_abs" type="float" min="0.0" value="9.999999747378752e-06" label="if the absolute error gets smaller than this value the fitting is stopped" help=""/>
+          <param name="eps_rel" argument="-algorithm:deconvolution:fitting:eps_rel" type="float" min="0.0" value="9.999999747378752e-06" label="if the relative error gets smaller than this value the fitting is stopped" help=""/>
+          <param name="max_iteration" argument="-algorithm:deconvolution:fitting:max_iteration" type="integer" min="1" value="10" label="maximal number of iterations for the fitting step" help=""/>
           <section name="penalties" title="" help="" expanded="false">
-            <param name="position" argument="-algorithm:deconvolution:fitting:penalties:position" type="float" optional="true" min="0.0" value="0.0" label="penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule" help=""/>
-            <param name="height" argument="-algorithm:deconvolution:fitting:penalties:height" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized" help=""/>
-            <param name="left_width" argument="-algorithm:deconvolution:fitting:penalties:left_width" type="float" optional="true" min="0.0" value="0.0" label="penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized" help=""/>
-            <param name="right_width" argument="-algorithm:deconvolution:fitting:penalties:right_width" type="float" optional="true" min="0.0" value="0.0" label="penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized" help=""/>
+            <param name="position" argument="-algorithm:deconvolution:fitting:penalties:position" type="float" min="0.0" value="0.0" label="penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule" help=""/>
+            <param name="height" argument="-algorithm:deconvolution:fitting:penalties:height" type="float" min="0.0" value="1.0" label="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized" help=""/>
+            <param name="left_width" argument="-algorithm:deconvolution:fitting:penalties:left_width" type="float" min="0.0" value="0.0" label="penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized" help=""/>
+            <param name="right_width" argument="-algorithm:deconvolution:fitting:penalties:right_width" type="float" min="0.0" value="0.0" label="penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized" help=""/>
           </section>
         </section>
       </section>
       <section name="SignalToNoiseEstimationParameter" title="" help="" expanded="false">
-        <param name="max_intensity" argument="-algorithm:SignalToNoiseEstimationParameter:max_intensity" type="integer" optional="true" min="-1" value="-1" label="maximal intensity considered for histogram construction" help="By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will not be added to the histogram. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime)"/>
-        <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoiseEstimationParameter:auto_max_stdev_factor" type="float" optional="true" min="0.0" max="999.0" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help=""/>
-        <param name="auto_max_percentile" argument="-algorithm:SignalToNoiseEstimationParameter:auto_max_percentile" type="integer" optional="true" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/>
-        <param name="auto_mode" argument="-algorithm:SignalToNoiseEstimationParameter:auto_mode" type="integer" optional="true" min="-1" max="1" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help=""/>
-        <param name="win_len" argument="-algorithm:SignalToNoiseEstimationParameter:win_len" type="float" optional="true" min="1.0" value="200.0" label="window length in Thomson" help=""/>
-        <param name="bin_count" argument="-algorithm:SignalToNoiseEstimationParameter:bin_count" type="integer" optional="true" min="3" value="30" label="number of bins for intensity values" help=""/>
-        <param name="stdev_mp" argument="-algorithm:SignalToNoiseEstimationParameter:stdev_mp" type="float" optional="true" min="0.01" max="999.0" value="3.0" label="multiplier for stdev" help=""/>
-        <param name="min_required_elements" argument="-algorithm:SignalToNoiseEstimationParameter:min_required_elements" type="integer" optional="true" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/>
-        <param name="noise_for_empty_window" argument="-algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/>
+        <param name="max_intensity" argument="-algorithm:SignalToNoiseEstimationParameter:max_intensity" type="integer" min="-1" value="-1" label="maximal intensity considered for histogram construction" help="By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will not be added to the histogram. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime)"/>
+        <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoiseEstimationParameter:auto_max_stdev_factor" type="float" min="0.0" max="999.0" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help=""/>
+        <param name="auto_max_percentile" argument="-algorithm:SignalToNoiseEstimationParameter:auto_max_percentile" type="integer" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/>
+        <param name="auto_mode" argument="-algorithm:SignalToNoiseEstimationParameter:auto_mode" type="integer" min="-1" max="1" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help=""/>
+        <param name="win_len" argument="-algorithm:SignalToNoiseEstimationParameter:win_len" type="float" min="1.0" value="200.0" label="window length in Thomson" help=""/>
+        <param name="bin_count" argument="-algorithm:SignalToNoiseEstimationParameter:bin_count" type="integer" min="3" value="30" label="number of bins for intensity values" help=""/>
+        <param name="stdev_mp" argument="-algorithm:SignalToNoiseEstimationParameter:stdev_mp" type="float" min="0.01" max="999.0" value="3.0" label="multiplier for stdev" help=""/>
+        <param name="min_required_elements" argument="-algorithm:SignalToNoiseEstimationParameter:min_required_elements" type="integer" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/>
+        <param name="noise_for_empty_window" argument="-algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help=""/>
       </section>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-write_peak_meta_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write additional information about the picked peaks (maximal intensity, left and right area...) into the mzML-file" help="Attention: this can blow up files, since seven arrays are stored per spectrum!"/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -118,7 +117,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_PeakPickerWavelet_1 -->
+  <tests>
+    <!-- TOPP_PeakPickerWavelet_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="write_peak_meta_data" value="true"/>
@@ -126,7 +126,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PeakPickerWavelet_input.mzML"/>
-      <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerWavelet_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise" value="3.0"/>
         <param name="centroid_percentage" value="0.6"/>
@@ -194,6 +194,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeakPickerWavelet_2 -->
     <test expect_num_outputs="2">
@@ -203,7 +206,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PeakPickerWavelet_deconv_input.mzML"/>
-      <output name="out" file="PeakPickerWavelet_deconv_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerWavelet_deconv_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise" value="2.0"/>
         <param name="centroid_percentage" value="0.8"/>
@@ -271,6 +274,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeakPickerWavelet_4 -->
     <test expect_num_outputs="2">
@@ -280,7 +286,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PeakPickerWavelet_input.mzML"/>
-      <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerWavelet_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise" value="3.0"/>
         <param name="centroid_percentage" value="0.6"/>
@@ -348,6 +354,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeakPickerWavelet_5 -->
     <test expect_num_outputs="2">
@@ -357,7 +366,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PeakPickerWavelet_input.mzML"/>
-      <output name="out" file="PeakPickerWavelet_output_noMetaData.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerWavelet_output_noMetaData.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise" value="3.0"/>
         <param name="centroid_percentage" value="0.6"/>
@@ -425,11 +434,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PeakPickerWavelet.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PeakPickerWavelet.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/PepNovoAdapter.xml b/tools/openms/PepNovoAdapter.xml
deleted file mode 100644
index 52a260524..000000000
--- a/tools/openms/PepNovoAdapter.xml
+++ /dev/null
@@ -1,5968 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
-<tool id="PepNovoAdapter" name="PepNovoAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format.</description>
-  <macros>
-    <token name="@EXECUTABLE@">PepNovoAdapter</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-mkdir out &&
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in
-'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
--out
-'out/output.${gxy2omsext("idxml")}'
-
-## Postprocessing
-&& mv 'out/output.${gxy2omsext("idxml")}' '$out'
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"pepnovo_executable": "pepnovo", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
-  </configfiles>
-  <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
-    <param name="model_directory" argument="-model_directory" type="select" optional="false" label="Name of the directory where the model files are kept" help="">
-      <options from_data_table="pepnovo_models">
-        <column name="name" index="0"/>
-        <column name="value" index="2"/>
-        <filter type="unique_value" name="unique_set" column="0"/>
-        <validator type="no_options" message="No model directory available"/>
-      </options>
-    </param>
-    <param argument="-correct_pm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find optimal precursor mass and charge values" help=""/>
-    <param argument="-use_spectrum_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct charge" help=""/>
-    <param argument="-use_spectrum_mz" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct the precursor m/z value that appears in the file" help=""/>
-    <param argument="-no_quality_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not remove low quality spectra" help=""/>
-    <param argument="-fragment_tolerance" type="float" optional="true" value="-1.0" label="The fragment tolerance (between 0 and 0.75 Da" help="Set to -1.0 to use model's default setting)"/>
-    <param argument="-pm_tolerance" type="float" optional="true" value="-1.0" label="The precursor mass tolerance (between 0 and 5.0 Da" help="Set to -1.0 to use model's default setting)"/>
-    <param name="model" argument="-model" type="select" label="Name of the model that should be used" help="">
-      <options from_data_table="pepnovo_models">
-        <column name="name" index="1"/>
-        <column name="value" index="1"/>
-        <filter type="param_value" ref="model_directory" column="2"/>
-        <filter type="unique_value" column="1"/>
-        <validator type="no_options" message="No model available"/>
-      </options>
-    </param>
-    <param argument="-digest" type="select" optional="true" label="Enzyme used for digestion (default TRYPSIN)" help="">
-      <option value="TRYPSIN" selected="true">TRYPSIN</option>
-      <option value="NON_SPECIFIC">NON_SPECIFIC</option>
-      <expand macro="list_string_san" name="digest"/>
-    </param>
-    <param argument="-tag_length" type="integer" optional="true" value="-1" label="Returns peptide sequence of the specified length (only lengths 3-6 are allowed)" help=""/>
-    <param argument="-num_solutions" type="integer" optional="true" min="1" max="2000" value="20" label="Number of solutions to be computed" help=""/>
-    <param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
-      <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
-      <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
-      <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
-      <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
-      <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
-      <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
-      <option value="2-succinyl (C)">2-succinyl (C)</option>
-      <option value="2HPG (R)">2HPG (R)</option>
-      <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
-      <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
-      <option value="3sulfo (N-term)">3sulfo (N-term)</option>
-      <option value="4-ONE (C)">4-ONE (C)</option>
-      <option value="4-ONE (H)">4-ONE (H)</option>
-      <option value="4-ONE (K)">4-ONE (K)</option>
-      <option value="4-ONE+Delta:H(-2)O(-1) (C)">4-ONE+Delta:H(-2)O(-1) (C)</option>
-      <option value="4-ONE+Delta:H(-2)O(-1) (H)">4-ONE+Delta:H(-2)O(-1) (H)</option>
-      <option value="4-ONE+Delta:H(-2)O(-1) (K)">4-ONE+Delta:H(-2)O(-1) (K)</option>
-      <option value="4AcAllylGal (C)">4AcAllylGal (C)</option>
-      <option value="a-type-ion (C-term)">a-type-ion (C-term)</option>
-      <option value="AccQTag (K)">AccQTag (K)</option>
-      <option value="AccQTag (N-term)">AccQTag (N-term)</option>
-      <option value="Acetyl (C)">Acetyl (C)</option>
-      <option value="Acetyl (H)">Acetyl (H)</option>
-      <option value="Acetyl (K)">Acetyl (K)</option>
-      <option value="Acetyl (N-term)">Acetyl (N-term)</option>
-      <option value="Acetyl (Protein N-term)">Acetyl (Protein N-term)</option>
-      <option value="Acetyl (R)">Acetyl (R)</option>
-      <option value="Acetyl (S)">Acetyl (S)</option>
-      <option value="Acetyl (T)">Acetyl (T)</option>
-      <option value="Acetyl (Y)">Acetyl (Y)</option>
-      <option value="Acetyl:13C(2) (K)">Acetyl:13C(2) (K)</option>
-      <option value="Acetyl:13C(2) (Protein N-term)">Acetyl:13C(2) (Protein N-term)</option>
-      <option value="Acetyl:2H(3) (H)">Acetyl:2H(3) (H)</option>
-      <option value="Acetyl:2H(3) (K)">Acetyl:2H(3) (K)</option>
-      <option value="Acetyl:2H(3) (N-term)">Acetyl:2H(3) (N-term)</option>
-      <option value="Acetyl:2H(3) (Protein N-term)">Acetyl:2H(3) (Protein N-term)</option>
-      <option value="Acetyl:2H(3) (S)">Acetyl:2H(3) (S)</option>
-      <option value="Acetyl:2H(3) (T)">Acetyl:2H(3) (T)</option>
-      <option value="Acetyl:2H(3) (Y)">Acetyl:2H(3) (Y)</option>
-      <option value="Acetyldeoxyhypusine (K)">Acetyldeoxyhypusine (K)</option>
-      <option value="Acetylhypusine (K)">Acetylhypusine (K)</option>
-      <option value="ADP-Ribosyl (C)">ADP-Ribosyl (C)</option>
-      <option value="ADP-Ribosyl (D)">ADP-Ribosyl (D)</option>
-      <option value="ADP-Ribosyl (E)">ADP-Ribosyl (E)</option>
-      <option value="ADP-Ribosyl (K)">ADP-Ribosyl (K)</option>
-      <option value="ADP-Ribosyl (N)">ADP-Ribosyl (N)</option>
-      <option value="ADP-Ribosyl (R)">ADP-Ribosyl (R)</option>
-      <option value="ADP-Ribosyl (S)">ADP-Ribosyl (S)</option>
-      <option value="ADP-Ribosyl (T)">ADP-Ribosyl (T)</option>
-      <option value="AEBS (H)">AEBS (H)</option>
-      <option value="AEBS (K)">AEBS (K)</option>
-      <option value="AEBS (Protein N-term)">AEBS (Protein N-term)</option>
-      <option value="AEBS (S)">AEBS (S)</option>
-      <option value="AEBS (Y)">AEBS (Y)</option>
-      <option value="AEC-MAEC (S)">AEC-MAEC (S)</option>
-      <option value="AEC-MAEC (T)">AEC-MAEC (T)</option>
-      <option value="AEC-MAEC:2H(4) (S)">AEC-MAEC:2H(4) (S)</option>
-      <option value="AEC-MAEC:2H(4) (T)">AEC-MAEC:2H(4) (T)</option>
-      <option value="AFB1_Dialdehyde (K)">AFB1_Dialdehyde (K)</option>
-      <option value="AHA-Alkyne (M)">AHA-Alkyne (M)</option>
-      <option value="AHA-Alkyne-KDDDD (M)">AHA-Alkyne-KDDDD (M)</option>
-      <option value="AHA-SS (M)">AHA-SS (M)</option>
-      <option value="AHA-SS_CAM (M)">AHA-SS_CAM (M)</option>
-      <option value="Ahx2+Hsl (C-term)">Ahx2+Hsl (C-term)</option>
-      <option value="Ala-&gt;Arg (A)">Ala-&gt;Arg (A)</option>
-      <option value="Ala-&gt;Asn (A)">Ala-&gt;Asn (A)</option>
-      <option value="Ala-&gt;Asp (A)">Ala-&gt;Asp (A)</option>
-      <option value="Ala-&gt;Cys (A)">Ala-&gt;Cys (A)</option>
-      <option value="Ala-&gt;Gln (A)">Ala-&gt;Gln (A)</option>
-      <option value="Ala-&gt;Glu (A)">Ala-&gt;Glu (A)</option>
-      <option value="Ala-&gt;Gly (A)">Ala-&gt;Gly (A)</option>
-      <option value="Ala-&gt;His (A)">Ala-&gt;His (A)</option>
-      <option value="Ala-&gt;Lys (A)">Ala-&gt;Lys (A)</option>
-      <option value="Ala-&gt;Met (A)">Ala-&gt;Met (A)</option>
-      <option value="Ala-&gt;Phe (A)">Ala-&gt;Phe (A)</option>
-      <option value="Ala-&gt;Pro (A)">Ala-&gt;Pro (A)</option>
-      <option value="Ala-&gt;Ser (A)">Ala-&gt;Ser (A)</option>
-      <option value="Ala-&gt;Thr (A)">Ala-&gt;Thr (A)</option>
-      <option value="Ala-&gt;Trp (A)">Ala-&gt;Trp (A)</option>
-      <option value="Ala-&gt;Tyr (A)">Ala-&gt;Tyr (A)</option>
-      <option value="Ala-&gt;Val (A)">Ala-&gt;Val (A)</option>
-      <option value="Ala-&gt;Xle (A)">Ala-&gt;Xle (A)</option>
-      <option value="Amidated (C-term)">Amidated (C-term)</option>
-      <option value="Amidated (Protein C-term)">Amidated (Protein C-term)</option>
-      <option value="Amidine (K)">Amidine (K)</option>
-      <option value="Amidine (N-term)">Amidine (N-term)</option>
-      <option value="Amidino (C)">Amidino (C)</option>
-      <option value="Amino (Y)">Amino (Y)</option>
-      <option value="Ammonia-loss (N)">Ammonia-loss (N)</option>
-      <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
-      <option value="Ammonia-loss (Protein N-term S)">Ammonia-loss (Protein N-term S)</option>
-      <option value="Ammonia-loss (Protein N-term T)">Ammonia-loss (Protein N-term T)</option>
-      <option value="Ammonium (C-term)">Ammonium (C-term)</option>
-      <option value="Ammonium (D)">Ammonium (D)</option>
-      <option value="Ammonium (E)">Ammonium (E)</option>
-      <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
-      <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
-      <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
-      <option value="Archaeol (C)">Archaeol (C)</option>
-      <option value="Arg (N-term)">Arg (N-term)</option>
-      <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
-      <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
-      <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
-      <option value="Arg-&gt;Cys (R)">Arg-&gt;Cys (R)</option>
-      <option value="Arg-&gt;Gln (R)">Arg-&gt;Gln (R)</option>
-      <option value="Arg-&gt;Glu (R)">Arg-&gt;Glu (R)</option>
-      <option value="Arg-&gt;GluSA (R)">Arg-&gt;GluSA (R)</option>
-      <option value="Arg-&gt;Gly (R)">Arg-&gt;Gly (R)</option>
-      <option value="Arg-&gt;His (R)">Arg-&gt;His (R)</option>
-      <option value="Arg-&gt;Lys (R)">Arg-&gt;Lys (R)</option>
-      <option value="Arg-&gt;Met (R)">Arg-&gt;Met (R)</option>
-      <option value="Arg-&gt;Npo (R)">Arg-&gt;Npo (R)</option>
-      <option value="Arg-&gt;Orn (R)">Arg-&gt;Orn (R)</option>
-      <option value="Arg-&gt;Phe (R)">Arg-&gt;Phe (R)</option>
-      <option value="Arg-&gt;Pro (R)">Arg-&gt;Pro (R)</option>
-      <option value="Arg-&gt;Ser (R)">Arg-&gt;Ser (R)</option>
-      <option value="Arg-&gt;Thr (R)">Arg-&gt;Thr (R)</option>
-      <option value="Arg-&gt;Trp (R)">Arg-&gt;Trp (R)</option>
-      <option value="Arg-&gt;Tyr (R)">Arg-&gt;Tyr (R)</option>
-      <option value="Arg-&gt;Val (R)">Arg-&gt;Val (R)</option>
-      <option value="Arg-&gt;Xle (R)">Arg-&gt;Xle (R)</option>
-      <option value="Arg-loss (C-term R)">Arg-loss (C-term R)</option>
-      <option value="Arg2PG (R)">Arg2PG (R)</option>
-      <option value="Argbiotinhydrazide (R)">Argbiotinhydrazide (R)</option>
-      <option value="AROD (C)">AROD (C)</option>
-      <option value="Asn-&gt;Ala (N)">Asn-&gt;Ala (N)</option>
-      <option value="Asn-&gt;Arg (N)">Asn-&gt;Arg (N)</option>
-      <option value="Asn-&gt;Asp (N)">Asn-&gt;Asp (N)</option>
-      <option value="Asn-&gt;Cys (N)">Asn-&gt;Cys (N)</option>
-      <option value="Asn-&gt;Gln (N)">Asn-&gt;Gln (N)</option>
-      <option value="Asn-&gt;Glu (N)">Asn-&gt;Glu (N)</option>
-      <option value="Asn-&gt;Gly (N)">Asn-&gt;Gly (N)</option>
-      <option value="Asn-&gt;His (N)">Asn-&gt;His (N)</option>
-      <option value="Asn-&gt;Lys (N)">Asn-&gt;Lys (N)</option>
-      <option value="Asn-&gt;Met (N)">Asn-&gt;Met (N)</option>
-      <option value="Asn-&gt;Phe (N)">Asn-&gt;Phe (N)</option>
-      <option value="Asn-&gt;Pro (N)">Asn-&gt;Pro (N)</option>
-      <option value="Asn-&gt;Ser (N)">Asn-&gt;Ser (N)</option>
-      <option value="Asn-&gt;Thr (N)">Asn-&gt;Thr (N)</option>
-      <option value="Asn-&gt;Trp (N)">Asn-&gt;Trp (N)</option>
-      <option value="Asn-&gt;Tyr (N)">Asn-&gt;Tyr (N)</option>
-      <option value="Asn-&gt;Val (N)">Asn-&gt;Val (N)</option>
-      <option value="Asn-&gt;Xle (N)">Asn-&gt;Xle (N)</option>
-      <option value="Asp-&gt;Ala (D)">Asp-&gt;Ala (D)</option>
-      <option value="Asp-&gt;Arg (D)">Asp-&gt;Arg (D)</option>
-      <option value="Asp-&gt;Asn (D)">Asp-&gt;Asn (D)</option>
-      <option value="Asp-&gt;Cys (D)">Asp-&gt;Cys (D)</option>
-      <option value="Asp-&gt;Gln (D)">Asp-&gt;Gln (D)</option>
-      <option value="Asp-&gt;Glu (D)">Asp-&gt;Glu (D)</option>
-      <option value="Asp-&gt;Gly (D)">Asp-&gt;Gly (D)</option>
-      <option value="Asp-&gt;His (D)">Asp-&gt;His (D)</option>
-      <option value="Asp-&gt;Lys (D)">Asp-&gt;Lys (D)</option>
-      <option value="Asp-&gt;Met (D)">Asp-&gt;Met (D)</option>
-      <option value="Asp-&gt;Phe (D)">Asp-&gt;Phe (D)</option>
-      <option value="Asp-&gt;Pro (D)">Asp-&gt;Pro (D)</option>
-      <option value="Asp-&gt;Ser (D)">Asp-&gt;Ser (D)</option>
-      <option value="Asp-&gt;Thr (D)">Asp-&gt;Thr (D)</option>
-      <option value="Asp-&gt;Trp (D)">Asp-&gt;Trp (D)</option>
-      <option value="Asp-&gt;Tyr (D)">Asp-&gt;Tyr (D)</option>
-      <option value="Asp-&gt;Val (D)">Asp-&gt;Val (D)</option>
-      <option value="Asp-&gt;Xle (D)">Asp-&gt;Xle (D)</option>
-      <option value="Aspartylurea (H)">Aspartylurea (H)</option>
-      <option value="Atto495Maleimide (C)">Atto495Maleimide (C)</option>
-      <option value="AzidoF (F)">AzidoF (F)</option>
-      <option value="azole (C)">azole (C)</option>
-      <option value="azole (S)">azole (S)</option>
-      <option value="Bacillosamine (N)">Bacillosamine (N)</option>
-      <option value="BADGE (C)">BADGE (C)</option>
-      <option value="BDMAPP (H)">BDMAPP (H)</option>
-      <option value="BDMAPP (K)">BDMAPP (K)</option>
-      <option value="BDMAPP (Protein N-term)">BDMAPP (Protein N-term)</option>
-      <option value="BDMAPP (W)">BDMAPP (W)</option>
-      <option value="BDMAPP (Y)">BDMAPP (Y)</option>
-      <option value="BEMAD_C (C)">BEMAD_C (C)</option>
-      <option value="BEMAD_C:2H(6) (C)">BEMAD_C:2H(6) (C)</option>
-      <option value="BEMAD_ST (S)">BEMAD_ST (S)</option>
-      <option value="BEMAD_ST (T)">BEMAD_ST (T)</option>
-      <option value="BEMAD_ST:2H(6) (S)">BEMAD_ST:2H(6) (S)</option>
-      <option value="BEMAD_ST:2H(6) (T)">BEMAD_ST:2H(6) (T)</option>
-      <option value="Benzoyl (K)">Benzoyl (K)</option>
-      <option value="Benzoyl (N-term)">Benzoyl (N-term)</option>
-      <option value="benzylguanidine (K)">benzylguanidine (K)</option>
-      <option value="betaFNA (C)">betaFNA (C)</option>
-      <option value="betaFNA (K)">betaFNA (K)</option>
-      <option value="BHT (C)">BHT (C)</option>
-      <option value="BHT (H)">BHT (H)</option>
-      <option value="BHT (K)">BHT (K)</option>
-      <option value="BHTOH (C)">BHTOH (C)</option>
-      <option value="BHTOH (H)">BHTOH (H)</option>
-      <option value="BHTOH (K)">BHTOH (K)</option>
-      <option value="Biotin (K)">Biotin (K)</option>
-      <option value="Biotin (N-term)">Biotin (N-term)</option>
-      <option value="Biotin-HPDP (C)">Biotin-HPDP (C)</option>
-      <option value="Biotin-PEG-PRA (M)">Biotin-PEG-PRA (M)</option>
-      <option value="Biotin-PEO-Amine (D)">Biotin-PEO-Amine (D)</option>
-      <option value="Biotin-PEO-Amine (E)">Biotin-PEO-Amine (E)</option>
-      <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
-      <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
-      <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
-      <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
-      <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
-      <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
-      <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
-      <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
-      <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
-      <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
-      <option value="Biotin:Thermo-21328 (K)">Biotin:Thermo-21328 (K)</option>
-      <option value="Biotin:Thermo-21328 (N-term)">Biotin:Thermo-21328 (N-term)</option>
-      <option value="Biotin:Thermo-21330 (K)">Biotin:Thermo-21330 (K)</option>
-      <option value="Biotin:Thermo-21330 (N-term)">Biotin:Thermo-21330 (N-term)</option>
-      <option value="Biotin:Thermo-21345 (Q)">Biotin:Thermo-21345 (Q)</option>
-      <option value="Biotin:Thermo-21360 (X)">Biotin:Thermo-21360 (X)</option>
-      <option value="Biotin:Thermo-21901+2H2O (C)">Biotin:Thermo-21901+2H2O (C)</option>
-      <option value="Biotin:Thermo-21901+H2O (C)">Biotin:Thermo-21901+H2O (C)</option>
-      <option value="Biotin:Thermo-21911 (C)">Biotin:Thermo-21911 (C)</option>
-      <option value="Biotin:Thermo-33033 (X)">Biotin:Thermo-33033 (X)</option>
-      <option value="Biotin:Thermo-33033-H (X)">Biotin:Thermo-33033-H (X)</option>
-      <option value="Biotin:Thermo-88310 (K)">Biotin:Thermo-88310 (K)</option>
-      <option value="Biotin:Thermo-88317 (S)">Biotin:Thermo-88317 (S)</option>
-      <option value="Biotin:Thermo-88317 (Y)">Biotin:Thermo-88317 (Y)</option>
-      <option value="biotinAcrolein298 (C)">biotinAcrolein298 (C)</option>
-      <option value="biotinAcrolein298 (H)">biotinAcrolein298 (H)</option>
-      <option value="biotinAcrolein298 (K)">biotinAcrolein298 (K)</option>
-      <option value="biotinAcrolein298 (Protein N-term)">biotinAcrolein298 (Protein N-term)</option>
-      <option value="BisANS (K)">BisANS (K)</option>
-      <option value="bisANS-sulfonates (K)">bisANS-sulfonates (K)</option>
-      <option value="bisANS-sulfonates (S)">bisANS-sulfonates (S)</option>
-      <option value="bisANS-sulfonates (T)">bisANS-sulfonates (T)</option>
-      <option value="BITC (C)">BITC (C)</option>
-      <option value="BITC (K)">BITC (K)</option>
-      <option value="BITC (N-term)">BITC (N-term)</option>
-      <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
-      <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-      <option value="Bodipy (C)">Bodipy (C)</option>
-      <option value="Brij35 (N-term)">Brij35 (N-term)</option>
-      <option value="Brij58 (N-term)">Brij58 (N-term)</option>
-      <option value="Bromo (F)">Bromo (F)</option>
-      <option value="Bromo (H)">Bromo (H)</option>
-      <option value="Bromo (W)">Bromo (W)</option>
-      <option value="Bromo (Y)">Bromo (Y)</option>
-      <option value="Bromobimane (C)">Bromobimane (C)</option>
-      <option value="Butyryl (K)">Butyryl (K)</option>
-      <option value="C8-QAT (K)">C8-QAT (K)</option>
-      <option value="C8-QAT (N-term)">C8-QAT (N-term)</option>
-      <option value="CAF (N-term)">CAF (N-term)</option>
-      <option value="CAMthiopropanoyl (K)">CAMthiopropanoyl (K)</option>
-      <option value="CAMthiopropanoyl (Protein N-term)">CAMthiopropanoyl (Protein N-term)</option>
-      <option value="Can-FP-biotin (S)">Can-FP-biotin (S)</option>
-      <option value="Can-FP-biotin (T)">Can-FP-biotin (T)</option>
-      <option value="Can-FP-biotin (Y)">Can-FP-biotin (Y)</option>
-      <option value="Carbamidomethyl (C)" selected="true">Carbamidomethyl (C)</option>
-      <option value="Carbamidomethyl (D)">Carbamidomethyl (D)</option>
-      <option value="Carbamidomethyl (E)">Carbamidomethyl (E)</option>
-      <option value="Carbamidomethyl (H)">Carbamidomethyl (H)</option>
-      <option value="Carbamidomethyl (K)">Carbamidomethyl (K)</option>
-      <option value="Carbamidomethyl (M)">Carbamidomethyl (M)</option>
-      <option value="Carbamidomethyl (N-term)">Carbamidomethyl (N-term)</option>
-      <option value="Carbamidomethyl (S)">Carbamidomethyl (S)</option>
-      <option value="Carbamidomethyl (T)">Carbamidomethyl (T)</option>
-      <option value="Carbamidomethyl (U)">Carbamidomethyl (U)</option>
-      <option value="Carbamidomethyl (Y)">Carbamidomethyl (Y)</option>
-      <option value="CarbamidomethylDTT (C)">CarbamidomethylDTT (C)</option>
-      <option value="Carbamyl (C)">Carbamyl (C)</option>
-      <option value="Carbamyl (K)">Carbamyl (K)</option>
-      <option value="Carbamyl (M)">Carbamyl (M)</option>
-      <option value="Carbamyl (N-term)">Carbamyl (N-term)</option>
-      <option value="Carbamyl (Protein N-term)">Carbamyl (Protein N-term)</option>
-      <option value="Carbamyl (R)">Carbamyl (R)</option>
-      <option value="Carbamyl (S)">Carbamyl (S)</option>
-      <option value="Carbamyl (T)">Carbamyl (T)</option>
-      <option value="Carbamyl (Y)">Carbamyl (Y)</option>
-      <option value="Carbofuran (S)">Carbofuran (S)</option>
-      <option value="Carbonyl (A)">Carbonyl (A)</option>
-      <option value="Carbonyl (E)">Carbonyl (E)</option>
-      <option value="Carbonyl (I)">Carbonyl (I)</option>
-      <option value="Carbonyl (L)">Carbonyl (L)</option>
-      <option value="Carbonyl (Q)">Carbonyl (Q)</option>
-      <option value="Carbonyl (R)">Carbonyl (R)</option>
-      <option value="Carbonyl (S)">Carbonyl (S)</option>
-      <option value="Carbonyl (V)">Carbonyl (V)</option>
-      <option value="Carboxy (D)">Carboxy (D)</option>
-      <option value="Carboxy (E)">Carboxy (E)</option>
-      <option value="Carboxy (K)">Carboxy (K)</option>
-      <option value="Carboxy (Protein N-term M)">Carboxy (Protein N-term M)</option>
-      <option value="Carboxy (W)">Carboxy (W)</option>
-      <option value="Carboxy-&gt;Thiocarboxy (Protein C-term G)">Carboxy-&gt;Thiocarboxy (Protein C-term G)</option>
-      <option value="Carboxyethyl (H)">Carboxyethyl (H)</option>
-      <option value="Carboxyethyl (K)">Carboxyethyl (K)</option>
-      <option value="Carboxyethylpyrrole (K)">Carboxyethylpyrrole (K)</option>
-      <option value="Carboxymethyl (C)">Carboxymethyl (C)</option>
-      <option value="Carboxymethyl (K)">Carboxymethyl (K)</option>
-      <option value="Carboxymethyl (N-term)">Carboxymethyl (N-term)</option>
-      <option value="Carboxymethyl (U)">Carboxymethyl (U)</option>
-      <option value="Carboxymethyl (W)">Carboxymethyl (W)</option>
-      <option value="Carboxymethyl:13C(2) (C)">Carboxymethyl:13C(2) (C)</option>
-      <option value="CarboxymethylDMAP (N-term)">CarboxymethylDMAP (N-term)</option>
-      <option value="CarboxymethylDTT (C)">CarboxymethylDTT (C)</option>
-      <option value="Cation:Ag (C-term)">Cation:Ag (C-term)</option>
-      <option value="Cation:Ag (D)">Cation:Ag (D)</option>
-      <option value="Cation:Ag (E)">Cation:Ag (E)</option>
-      <option value="Cation:Al[III] (C-term)">Cation:Al[III] (C-term)</option>
-      <option value="Cation:Al[III] (D)">Cation:Al[III] (D)</option>
-      <option value="Cation:Al[III] (E)">Cation:Al[III] (E)</option>
-      <option value="Cation:Ca[II] (C-term)">Cation:Ca[II] (C-term)</option>
-      <option value="Cation:Ca[II] (D)">Cation:Ca[II] (D)</option>
-      <option value="Cation:Ca[II] (E)">Cation:Ca[II] (E)</option>
-      <option value="Cation:Cu[I] (C-term)">Cation:Cu[I] (C-term)</option>
-      <option value="Cation:Cu[I] (D)">Cation:Cu[I] (D)</option>
-      <option value="Cation:Cu[I] (E)">Cation:Cu[I] (E)</option>
-      <option value="Cation:Cu[I] (H)">Cation:Cu[I] (H)</option>
-      <option value="Cation:Fe[II] (C-term)">Cation:Fe[II] (C-term)</option>
-      <option value="Cation:Fe[II] (D)">Cation:Fe[II] (D)</option>
-      <option value="Cation:Fe[II] (E)">Cation:Fe[II] (E)</option>
-      <option value="Cation:Fe[III] (C-term)">Cation:Fe[III] (C-term)</option>
-      <option value="Cation:Fe[III] (D)">Cation:Fe[III] (D)</option>
-      <option value="Cation:Fe[III] (E)">Cation:Fe[III] (E)</option>
-      <option value="Cation:K (C-term)">Cation:K (C-term)</option>
-      <option value="Cation:K (D)">Cation:K (D)</option>
-      <option value="Cation:K (E)">Cation:K (E)</option>
-      <option value="Cation:Li (C-term)">Cation:Li (C-term)</option>
-      <option value="Cation:Li (D)">Cation:Li (D)</option>
-      <option value="Cation:Li (E)">Cation:Li (E)</option>
-      <option value="Cation:Mg[II] (C-term)">Cation:Mg[II] (C-term)</option>
-      <option value="Cation:Mg[II] (D)">Cation:Mg[II] (D)</option>
-      <option value="Cation:Mg[II] (E)">Cation:Mg[II] (E)</option>
-      <option value="Cation:Na (C-term)">Cation:Na (C-term)</option>
-      <option value="Cation:Na (D)">Cation:Na (D)</option>
-      <option value="Cation:Na (E)">Cation:Na (E)</option>
-      <option value="Cation:Ni[II] (C-term)">Cation:Ni[II] (C-term)</option>
-      <option value="Cation:Ni[II] (D)">Cation:Ni[II] (D)</option>
-      <option value="Cation:Ni[II] (E)">Cation:Ni[II] (E)</option>
-      <option value="Cation:Zn[II] (C-term)">Cation:Zn[II] (C-term)</option>
-      <option value="Cation:Zn[II] (D)">Cation:Zn[II] (D)</option>
-      <option value="Cation:Zn[II] (E)">Cation:Zn[II] (E)</option>
-      <option value="Cation:Zn[II] (H)">Cation:Zn[II] (H)</option>
-      <option value="cGMP (C)">cGMP (C)</option>
-      <option value="cGMP (S)">cGMP (S)</option>
-      <option value="cGMP+RMP-loss (C)">cGMP+RMP-loss (C)</option>
-      <option value="cGMP+RMP-loss (S)">cGMP+RMP-loss (S)</option>
-      <option value="CHDH (D)">CHDH (D)</option>
-      <option value="Chlorination (W)">Chlorination (W)</option>
-      <option value="Chlorination (Y)">Chlorination (Y)</option>
-      <option value="Cholesterol (Protein C-term)">Cholesterol (Protein C-term)</option>
-      <option value="CIGG (K)">CIGG (K)</option>
-      <option value="CLIP_TRAQ_2 (K)">CLIP_TRAQ_2 (K)</option>
-      <option value="CLIP_TRAQ_2 (N-term)">CLIP_TRAQ_2 (N-term)</option>
-      <option value="CLIP_TRAQ_2 (Y)">CLIP_TRAQ_2 (Y)</option>
-      <option value="CLIP_TRAQ_3 (K)">CLIP_TRAQ_3 (K)</option>
-      <option value="CLIP_TRAQ_3 (N-term)">CLIP_TRAQ_3 (N-term)</option>
-      <option value="CLIP_TRAQ_3 (Y)">CLIP_TRAQ_3 (Y)</option>
-      <option value="CLIP_TRAQ_4 (K)">CLIP_TRAQ_4 (K)</option>
-      <option value="CLIP_TRAQ_4 (N-term)">CLIP_TRAQ_4 (N-term)</option>
-      <option value="CLIP_TRAQ_4 (Y)">CLIP_TRAQ_4 (Y)</option>
-      <option value="CoenzymeA (C)">CoenzymeA (C)</option>
-      <option value="Cresylphosphate (H)">Cresylphosphate (H)</option>
-      <option value="Cresylphosphate (K)">Cresylphosphate (K)</option>
-      <option value="Cresylphosphate (R)">Cresylphosphate (R)</option>
-      <option value="Cresylphosphate (S)">Cresylphosphate (S)</option>
-      <option value="Cresylphosphate (T)">Cresylphosphate (T)</option>
-      <option value="Cresylphosphate (Y)">Cresylphosphate (Y)</option>
-      <option value="CresylSaligeninPhosphate (H)">CresylSaligeninPhosphate (H)</option>
-      <option value="CresylSaligeninPhosphate (K)">CresylSaligeninPhosphate (K)</option>
-      <option value="CresylSaligeninPhosphate (R)">CresylSaligeninPhosphate (R)</option>
-      <option value="CresylSaligeninPhosphate (S)">CresylSaligeninPhosphate (S)</option>
-      <option value="CresylSaligeninPhosphate (T)">CresylSaligeninPhosphate (T)</option>
-      <option value="CresylSaligeninPhosphate (Y)">CresylSaligeninPhosphate (Y)</option>
-      <option value="Crotonaldehyde (C)">Crotonaldehyde (C)</option>
-      <option value="Crotonaldehyde (H)">Crotonaldehyde (H)</option>
-      <option value="Crotonaldehyde (K)">Crotonaldehyde (K)</option>
-      <option value="Crotonyl (K)">Crotonyl (K)</option>
-      <option value="CuSMo (C)">CuSMo (C)</option>
-      <option value="CUSTOM0 (A)">CUSTOM0 (A)</option>
-      <option value="CUSTOM0 (C)">CUSTOM0 (C)</option>
-      <option value="CUSTOM0 (C-term)">CUSTOM0 (C-term)</option>
-      <option value="CUSTOM0 (D)">CUSTOM0 (D)</option>
-      <option value="CUSTOM0 (E)">CUSTOM0 (E)</option>
-      <option value="CUSTOM0 (F)">CUSTOM0 (F)</option>
-      <option value="CUSTOM0 (G)">CUSTOM0 (G)</option>
-      <option value="CUSTOM0 (H)">CUSTOM0 (H)</option>
-      <option value="CUSTOM0 (I)">CUSTOM0 (I)</option>
-      <option value="CUSTOM0 (K)">CUSTOM0 (K)</option>
-      <option value="CUSTOM0 (L)">CUSTOM0 (L)</option>
-      <option value="CUSTOM0 (M)">CUSTOM0 (M)</option>
-      <option value="CUSTOM0 (N)">CUSTOM0 (N)</option>
-      <option value="CUSTOM0 (N-term)">CUSTOM0 (N-term)</option>
-      <option value="CUSTOM0 (P)">CUSTOM0 (P)</option>
-      <option value="CUSTOM0 (Q)">CUSTOM0 (Q)</option>
-      <option value="CUSTOM0 (R)">CUSTOM0 (R)</option>
-      <option value="CUSTOM0 (S)">CUSTOM0 (S)</option>
-      <option value="CUSTOM0 (T)">CUSTOM0 (T)</option>
-      <option value="CUSTOM0 (V)">CUSTOM0 (V)</option>
-      <option value="CUSTOM0 (W)">CUSTOM0 (W)</option>
-      <option value="CUSTOM0 (Y)">CUSTOM0 (Y)</option>
-      <option value="CUSTOM1 (A)">CUSTOM1 (A)</option>
-      <option value="CUSTOM1 (C)">CUSTOM1 (C)</option>
-      <option value="CUSTOM1 (C-term)">CUSTOM1 (C-term)</option>
-      <option value="CUSTOM1 (D)">CUSTOM1 (D)</option>
-      <option value="CUSTOM1 (E)">CUSTOM1 (E)</option>
-      <option value="CUSTOM1 (F)">CUSTOM1 (F)</option>
-      <option value="CUSTOM1 (G)">CUSTOM1 (G)</option>
-      <option value="CUSTOM1 (H)">CUSTOM1 (H)</option>
-      <option value="CUSTOM1 (I)">CUSTOM1 (I)</option>
-      <option value="CUSTOM1 (K)">CUSTOM1 (K)</option>
-      <option value="CUSTOM1 (L)">CUSTOM1 (L)</option>
-      <option value="CUSTOM1 (M)">CUSTOM1 (M)</option>
-      <option value="CUSTOM1 (N)">CUSTOM1 (N)</option>
-      <option value="CUSTOM1 (N-term)">CUSTOM1 (N-term)</option>
-      <option value="CUSTOM1 (P)">CUSTOM1 (P)</option>
-      <option value="CUSTOM1 (Q)">CUSTOM1 (Q)</option>
-      <option value="CUSTOM1 (R)">CUSTOM1 (R)</option>
-      <option value="CUSTOM1 (S)">CUSTOM1 (S)</option>
-      <option value="CUSTOM1 (T)">CUSTOM1 (T)</option>
-      <option value="CUSTOM1 (V)">CUSTOM1 (V)</option>
-      <option value="CUSTOM1 (W)">CUSTOM1 (W)</option>
-      <option value="CUSTOM1 (Y)">CUSTOM1 (Y)</option>
-      <option value="CUSTOM2 (A)">CUSTOM2 (A)</option>
-      <option value="CUSTOM2 (C)">CUSTOM2 (C)</option>
-      <option value="CUSTOM2 (C-term)">CUSTOM2 (C-term)</option>
-      <option value="CUSTOM2 (D)">CUSTOM2 (D)</option>
-      <option value="CUSTOM2 (E)">CUSTOM2 (E)</option>
-      <option value="CUSTOM2 (F)">CUSTOM2 (F)</option>
-      <option value="CUSTOM2 (G)">CUSTOM2 (G)</option>
-      <option value="CUSTOM2 (H)">CUSTOM2 (H)</option>
-      <option value="CUSTOM2 (I)">CUSTOM2 (I)</option>
-      <option value="CUSTOM2 (K)">CUSTOM2 (K)</option>
-      <option value="CUSTOM2 (L)">CUSTOM2 (L)</option>
-      <option value="CUSTOM2 (M)">CUSTOM2 (M)</option>
-      <option value="CUSTOM2 (N)">CUSTOM2 (N)</option>
-      <option value="CUSTOM2 (N-term)">CUSTOM2 (N-term)</option>
-      <option value="CUSTOM2 (P)">CUSTOM2 (P)</option>
-      <option value="CUSTOM2 (Q)">CUSTOM2 (Q)</option>
-      <option value="CUSTOM2 (R)">CUSTOM2 (R)</option>
-      <option value="CUSTOM2 (S)">CUSTOM2 (S)</option>
-      <option value="CUSTOM2 (T)">CUSTOM2 (T)</option>
-      <option value="CUSTOM2 (V)">CUSTOM2 (V)</option>
-      <option value="CUSTOM2 (W)">CUSTOM2 (W)</option>
-      <option value="CUSTOM2 (Y)">CUSTOM2 (Y)</option>
-      <option value="CUSTOM3 (A)">CUSTOM3 (A)</option>
-      <option value="CUSTOM3 (C)">CUSTOM3 (C)</option>
-      <option value="CUSTOM3 (C-term)">CUSTOM3 (C-term)</option>
-      <option value="CUSTOM3 (D)">CUSTOM3 (D)</option>
-      <option value="CUSTOM3 (E)">CUSTOM3 (E)</option>
-      <option value="CUSTOM3 (F)">CUSTOM3 (F)</option>
-      <option value="CUSTOM3 (G)">CUSTOM3 (G)</option>
-      <option value="CUSTOM3 (H)">CUSTOM3 (H)</option>
-      <option value="CUSTOM3 (I)">CUSTOM3 (I)</option>
-      <option value="CUSTOM3 (K)">CUSTOM3 (K)</option>
-      <option value="CUSTOM3 (L)">CUSTOM3 (L)</option>
-      <option value="CUSTOM3 (M)">CUSTOM3 (M)</option>
-      <option value="CUSTOM3 (N)">CUSTOM3 (N)</option>
-      <option value="CUSTOM3 (N-term)">CUSTOM3 (N-term)</option>
-      <option value="CUSTOM3 (P)">CUSTOM3 (P)</option>
-      <option value="CUSTOM3 (Q)">CUSTOM3 (Q)</option>
-      <option value="CUSTOM3 (R)">CUSTOM3 (R)</option>
-      <option value="CUSTOM3 (S)">CUSTOM3 (S)</option>
-      <option value="CUSTOM3 (T)">CUSTOM3 (T)</option>
-      <option value="CUSTOM3 (V)">CUSTOM3 (V)</option>
-      <option value="CUSTOM3 (W)">CUSTOM3 (W)</option>
-      <option value="CUSTOM3 (Y)">CUSTOM3 (Y)</option>
-      <option value="CUSTOM4 (A)">CUSTOM4 (A)</option>
-      <option value="CUSTOM4 (C)">CUSTOM4 (C)</option>
-      <option value="CUSTOM4 (C-term)">CUSTOM4 (C-term)</option>
-      <option value="CUSTOM4 (D)">CUSTOM4 (D)</option>
-      <option value="CUSTOM4 (E)">CUSTOM4 (E)</option>
-      <option value="CUSTOM4 (F)">CUSTOM4 (F)</option>
-      <option value="CUSTOM4 (G)">CUSTOM4 (G)</option>
-      <option value="CUSTOM4 (H)">CUSTOM4 (H)</option>
-      <option value="CUSTOM4 (I)">CUSTOM4 (I)</option>
-      <option value="CUSTOM4 (K)">CUSTOM4 (K)</option>
-      <option value="CUSTOM4 (L)">CUSTOM4 (L)</option>
-      <option value="CUSTOM4 (M)">CUSTOM4 (M)</option>
-      <option value="CUSTOM4 (N)">CUSTOM4 (N)</option>
-      <option value="CUSTOM4 (N-term)">CUSTOM4 (N-term)</option>
-      <option value="CUSTOM4 (P)">CUSTOM4 (P)</option>
-      <option value="CUSTOM4 (Q)">CUSTOM4 (Q)</option>
-      <option value="CUSTOM4 (R)">CUSTOM4 (R)</option>
-      <option value="CUSTOM4 (S)">CUSTOM4 (S)</option>
-      <option value="CUSTOM4 (T)">CUSTOM4 (T)</option>
-      <option value="CUSTOM4 (V)">CUSTOM4 (V)</option>
-      <option value="CUSTOM4 (W)">CUSTOM4 (W)</option>
-      <option value="CUSTOM4 (Y)">CUSTOM4 (Y)</option>
-      <option value="CUSTOM5 (A)">CUSTOM5 (A)</option>
-      <option value="CUSTOM5 (C)">CUSTOM5 (C)</option>
-      <option value="CUSTOM5 (C-term)">CUSTOM5 (C-term)</option>
-      <option value="CUSTOM5 (D)">CUSTOM5 (D)</option>
-      <option value="CUSTOM5 (E)">CUSTOM5 (E)</option>
-      <option value="CUSTOM5 (F)">CUSTOM5 (F)</option>
-      <option value="CUSTOM5 (G)">CUSTOM5 (G)</option>
-      <option value="CUSTOM5 (H)">CUSTOM5 (H)</option>
-      <option value="CUSTOM5 (I)">CUSTOM5 (I)</option>
-      <option value="CUSTOM5 (K)">CUSTOM5 (K)</option>
-      <option value="CUSTOM5 (L)">CUSTOM5 (L)</option>
-      <option value="CUSTOM5 (M)">CUSTOM5 (M)</option>
-      <option value="CUSTOM5 (N)">CUSTOM5 (N)</option>
-      <option value="CUSTOM5 (N-term)">CUSTOM5 (N-term)</option>
-      <option value="CUSTOM5 (P)">CUSTOM5 (P)</option>
-      <option value="CUSTOM5 (Q)">CUSTOM5 (Q)</option>
-      <option value="CUSTOM5 (R)">CUSTOM5 (R)</option>
-      <option value="CUSTOM5 (S)">CUSTOM5 (S)</option>
-      <option value="CUSTOM5 (T)">CUSTOM5 (T)</option>
-      <option value="CUSTOM5 (V)">CUSTOM5 (V)</option>
-      <option value="CUSTOM5 (W)">CUSTOM5 (W)</option>
-      <option value="CUSTOM5 (Y)">CUSTOM5 (Y)</option>
-      <option value="CUSTOM6 (A)">CUSTOM6 (A)</option>
-      <option value="CUSTOM6 (C)">CUSTOM6 (C)</option>
-      <option value="CUSTOM6 (C-term)">CUSTOM6 (C-term)</option>
-      <option value="CUSTOM6 (D)">CUSTOM6 (D)</option>
-      <option value="CUSTOM6 (E)">CUSTOM6 (E)</option>
-      <option value="CUSTOM6 (F)">CUSTOM6 (F)</option>
-      <option value="CUSTOM6 (G)">CUSTOM6 (G)</option>
-      <option value="CUSTOM6 (H)">CUSTOM6 (H)</option>
-      <option value="CUSTOM6 (I)">CUSTOM6 (I)</option>
-      <option value="CUSTOM6 (K)">CUSTOM6 (K)</option>
-      <option value="CUSTOM6 (L)">CUSTOM6 (L)</option>
-      <option value="CUSTOM6 (M)">CUSTOM6 (M)</option>
-      <option value="CUSTOM6 (N)">CUSTOM6 (N)</option>
-      <option value="CUSTOM6 (N-term)">CUSTOM6 (N-term)</option>
-      <option value="CUSTOM6 (P)">CUSTOM6 (P)</option>
-      <option value="CUSTOM6 (Q)">CUSTOM6 (Q)</option>
-      <option value="CUSTOM6 (R)">CUSTOM6 (R)</option>
-      <option value="CUSTOM6 (S)">CUSTOM6 (S)</option>
-      <option value="CUSTOM6 (T)">CUSTOM6 (T)</option>
-      <option value="CUSTOM6 (V)">CUSTOM6 (V)</option>
-      <option value="CUSTOM6 (W)">CUSTOM6 (W)</option>
-      <option value="CUSTOM6 (Y)">CUSTOM6 (Y)</option>
-      <option value="CUSTOM7 (A)">CUSTOM7 (A)</option>
-      <option value="CUSTOM7 (C)">CUSTOM7 (C)</option>
-      <option value="CUSTOM7 (C-term)">CUSTOM7 (C-term)</option>
-      <option value="CUSTOM7 (D)">CUSTOM7 (D)</option>
-      <option value="CUSTOM7 (E)">CUSTOM7 (E)</option>
-      <option value="CUSTOM7 (F)">CUSTOM7 (F)</option>
-      <option value="CUSTOM7 (G)">CUSTOM7 (G)</option>
-      <option value="CUSTOM7 (H)">CUSTOM7 (H)</option>
-      <option value="CUSTOM7 (I)">CUSTOM7 (I)</option>
-      <option value="CUSTOM7 (K)">CUSTOM7 (K)</option>
-      <option value="CUSTOM7 (L)">CUSTOM7 (L)</option>
-      <option value="CUSTOM7 (M)">CUSTOM7 (M)</option>
-      <option value="CUSTOM7 (N)">CUSTOM7 (N)</option>
-      <option value="CUSTOM7 (N-term)">CUSTOM7 (N-term)</option>
-      <option value="CUSTOM7 (P)">CUSTOM7 (P)</option>
-      <option value="CUSTOM7 (Q)">CUSTOM7 (Q)</option>
-      <option value="CUSTOM7 (R)">CUSTOM7 (R)</option>
-      <option value="CUSTOM7 (S)">CUSTOM7 (S)</option>
-      <option value="CUSTOM7 (T)">CUSTOM7 (T)</option>
-      <option value="CUSTOM7 (V)">CUSTOM7 (V)</option>
-      <option value="CUSTOM7 (W)">CUSTOM7 (W)</option>
-      <option value="CUSTOM7 (Y)">CUSTOM7 (Y)</option>
-      <option value="CUSTOM8 (A)">CUSTOM8 (A)</option>
-      <option value="CUSTOM8 (C)">CUSTOM8 (C)</option>
-      <option value="CUSTOM8 (C-term)">CUSTOM8 (C-term)</option>
-      <option value="CUSTOM8 (D)">CUSTOM8 (D)</option>
-      <option value="CUSTOM8 (E)">CUSTOM8 (E)</option>
-      <option value="CUSTOM8 (F)">CUSTOM8 (F)</option>
-      <option value="CUSTOM8 (G)">CUSTOM8 (G)</option>
-      <option value="CUSTOM8 (H)">CUSTOM8 (H)</option>
-      <option value="CUSTOM8 (I)">CUSTOM8 (I)</option>
-      <option value="CUSTOM8 (K)">CUSTOM8 (K)</option>
-      <option value="CUSTOM8 (L)">CUSTOM8 (L)</option>
-      <option value="CUSTOM8 (M)">CUSTOM8 (M)</option>
-      <option value="CUSTOM8 (N)">CUSTOM8 (N)</option>
-      <option value="CUSTOM8 (N-term)">CUSTOM8 (N-term)</option>
-      <option value="CUSTOM8 (P)">CUSTOM8 (P)</option>
-      <option value="CUSTOM8 (Q)">CUSTOM8 (Q)</option>
-      <option value="CUSTOM8 (R)">CUSTOM8 (R)</option>
-      <option value="CUSTOM8 (S)">CUSTOM8 (S)</option>
-      <option value="CUSTOM8 (T)">CUSTOM8 (T)</option>
-      <option value="CUSTOM8 (V)">CUSTOM8 (V)</option>
-      <option value="CUSTOM8 (W)">CUSTOM8 (W)</option>
-      <option value="CUSTOM8 (Y)">CUSTOM8 (Y)</option>
-      <option value="CUSTOM9 (A)">CUSTOM9 (A)</option>
-      <option value="CUSTOM9 (C)">CUSTOM9 (C)</option>
-      <option value="CUSTOM9 (C-term)">CUSTOM9 (C-term)</option>
-      <option value="CUSTOM9 (D)">CUSTOM9 (D)</option>
-      <option value="CUSTOM9 (E)">CUSTOM9 (E)</option>
-      <option value="CUSTOM9 (F)">CUSTOM9 (F)</option>
-      <option value="CUSTOM9 (G)">CUSTOM9 (G)</option>
-      <option value="CUSTOM9 (H)">CUSTOM9 (H)</option>
-      <option value="CUSTOM9 (I)">CUSTOM9 (I)</option>
-      <option value="CUSTOM9 (K)">CUSTOM9 (K)</option>
-      <option value="CUSTOM9 (L)">CUSTOM9 (L)</option>
-      <option value="CUSTOM9 (M)">CUSTOM9 (M)</option>
-      <option value="CUSTOM9 (N)">CUSTOM9 (N)</option>
-      <option value="CUSTOM9 (N-term)">CUSTOM9 (N-term)</option>
-      <option value="CUSTOM9 (P)">CUSTOM9 (P)</option>
-      <option value="CUSTOM9 (Q)">CUSTOM9 (Q)</option>
-      <option value="CUSTOM9 (R)">CUSTOM9 (R)</option>
-      <option value="CUSTOM9 (S)">CUSTOM9 (S)</option>
-      <option value="CUSTOM9 (T)">CUSTOM9 (T)</option>
-      <option value="CUSTOM9 (V)">CUSTOM9 (V)</option>
-      <option value="CUSTOM9 (W)">CUSTOM9 (W)</option>
-      <option value="CUSTOM9 (Y)">CUSTOM9 (Y)</option>
-      <option value="Cy3-maleimide (C)">Cy3-maleimide (C)</option>
-      <option value="Cy3b-maleimide (C)">Cy3b-maleimide (C)</option>
-      <option value="Cyano (C)">Cyano (C)</option>
-      <option value="CyDye-Cy3 (C)">CyDye-Cy3 (C)</option>
-      <option value="CyDye-Cy5 (C)">CyDye-Cy5 (C)</option>
-      <option value="Cys-&gt;Ala (C)">Cys-&gt;Ala (C)</option>
-      <option value="Cys-&gt;Arg (C)">Cys-&gt;Arg (C)</option>
-      <option value="Cys-&gt;Asn (C)">Cys-&gt;Asn (C)</option>
-      <option value="Cys-&gt;Asp (C)">Cys-&gt;Asp (C)</option>
-      <option value="Cys-&gt;CamSec (C)">Cys-&gt;CamSec (C)</option>
-      <option value="Cys-&gt;Dha (C)">Cys-&gt;Dha (C)</option>
-      <option value="Cys-&gt;ethylaminoAla (C)">Cys-&gt;ethylaminoAla (C)</option>
-      <option value="Cys-&gt;Gln (C)">Cys-&gt;Gln (C)</option>
-      <option value="Cys-&gt;Glu (C)">Cys-&gt;Glu (C)</option>
-      <option value="Cys-&gt;Gly (C)">Cys-&gt;Gly (C)</option>
-      <option value="Cys-&gt;His (C)">Cys-&gt;His (C)</option>
-      <option value="Cys-&gt;Lys (C)">Cys-&gt;Lys (C)</option>
-      <option value="Cys-&gt;Met (C)">Cys-&gt;Met (C)</option>
-      <option value="Cys-&gt;methylaminoAla (C)">Cys-&gt;methylaminoAla (C)</option>
-      <option value="Cys-&gt;Oxoalanine (C)">Cys-&gt;Oxoalanine (C)</option>
-      <option value="Cys-&gt;Phe (C)">Cys-&gt;Phe (C)</option>
-      <option value="Cys-&gt;Pro (C)">Cys-&gt;Pro (C)</option>
-      <option value="Cys-&gt;PyruvicAcid (Protein N-term C)">Cys-&gt;PyruvicAcid (Protein N-term C)</option>
-      <option value="Cys-&gt;SecNEM (C)">Cys-&gt;SecNEM (C)</option>
-      <option value="Cys-&gt;SecNEM:2H(5) (C)">Cys-&gt;SecNEM:2H(5) (C)</option>
-      <option value="Cys-&gt;Ser (C)">Cys-&gt;Ser (C)</option>
-      <option value="Cys-&gt;Thr (C)">Cys-&gt;Thr (C)</option>
-      <option value="Cys-&gt;Trp (C)">Cys-&gt;Trp (C)</option>
-      <option value="Cys-&gt;Tyr (C)">Cys-&gt;Tyr (C)</option>
-      <option value="Cys-&gt;Val (C)">Cys-&gt;Val (C)</option>
-      <option value="Cys-&gt;Xle (C)">Cys-&gt;Xle (C)</option>
-      <option value="Cysteinyl (C)">Cysteinyl (C)</option>
-      <option value="cysTMT (C)">cysTMT (C)</option>
-      <option value="cysTMT6plex (C)">cysTMT6plex (C)</option>
-      <option value="Cytopiloyne (C)">Cytopiloyne (C)</option>
-      <option value="Cytopiloyne (K)">Cytopiloyne (K)</option>
-      <option value="Cytopiloyne (N-term)">Cytopiloyne (N-term)</option>
-      <option value="Cytopiloyne (P)">Cytopiloyne (P)</option>
-      <option value="Cytopiloyne (R)">Cytopiloyne (R)</option>
-      <option value="Cytopiloyne (S)">Cytopiloyne (S)</option>
-      <option value="Cytopiloyne (Y)">Cytopiloyne (Y)</option>
-      <option value="Cytopiloyne+water (C)">Cytopiloyne+water (C)</option>
-      <option value="Cytopiloyne+water (K)">Cytopiloyne+water (K)</option>
-      <option value="Cytopiloyne+water (N-term)">Cytopiloyne+water (N-term)</option>
-      <option value="Cytopiloyne+water (R)">Cytopiloyne+water (R)</option>
-      <option value="Cytopiloyne+water (S)">Cytopiloyne+water (S)</option>
-      <option value="Cytopiloyne+water (T)">Cytopiloyne+water (T)</option>
-      <option value="Cytopiloyne+water (Y)">Cytopiloyne+water (Y)</option>
-      <option value="DAET (S)">DAET (S)</option>
-      <option value="DAET (T)">DAET (T)</option>
-      <option value="Dansyl (K)">Dansyl (K)</option>
-      <option value="Dansyl (N-term)">Dansyl (N-term)</option>
-      <option value="Dap-DSP (A)">Dap-DSP (A)</option>
-      <option value="Dap-DSP (E)">Dap-DSP (E)</option>
-      <option value="Dap-DSP (K)">Dap-DSP (K)</option>
-      <option value="Deamidated (N)">Deamidated (N)</option>
-      <option value="Deamidated (Protein N-term F)">Deamidated (Protein N-term F)</option>
-      <option value="Deamidated (Q)">Deamidated (Q)</option>
-      <option value="Deamidated (R)">Deamidated (R)</option>
-      <option value="Deamidated:18O(1) (N)">Deamidated:18O(1) (N)</option>
-      <option value="Deamidated:18O(1) (Q)">Deamidated:18O(1) (Q)</option>
-      <option value="Decanoyl (S)">Decanoyl (S)</option>
-      <option value="Decanoyl (T)">Decanoyl (T)</option>
-      <option value="Decarboxylation (D)">Decarboxylation (D)</option>
-      <option value="Decarboxylation (E)">Decarboxylation (E)</option>
-      <option value="DEDGFLYMVYASQETFG (K)">DEDGFLYMVYASQETFG (K)</option>
-      <option value="Dehydrated (D)">Dehydrated (D)</option>
-      <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
-      <option value="Dehydrated (Protein C-term N)">Dehydrated (Protein C-term N)</option>
-      <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
-      <option value="Dehydrated (S)">Dehydrated (S)</option>
-      <option value="Dehydrated (T)">Dehydrated (T)</option>
-      <option value="Dehydrated (Y)">Dehydrated (Y)</option>
-      <option value="Dehydro (C)">Dehydro (C)</option>
-      <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
-      <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-      <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
-      <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
-      <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
-      <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
-      <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
-      <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
-      <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
-      <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
-      <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
-      <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-      <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
-      <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
-      <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
-      <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
-      <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
-      <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
-      <option value="Delta:H(4)C(3) (K)">Delta:H(4)C(3) (K)</option>
-      <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
-      <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
-      <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
-      <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
-      <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
-      <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
-      <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
-      <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
-      <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
-      <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
-      <option value="Delta:H(6)C(3)O(1) (K)">Delta:H(6)C(3)O(1) (K)</option>
-      <option value="Delta:H(6)C(3)O(1) (Protein N-term)">Delta:H(6)C(3)O(1) (Protein N-term)</option>
-      <option value="Delta:H(6)C(6)O(1) (K)">Delta:H(6)C(6)O(1) (K)</option>
-      <option value="Delta:H(6)C(7)O(4) (R)">Delta:H(6)C(7)O(4) (R)</option>
-      <option value="Delta:H(8)C(6)O(1) (K)">Delta:H(8)C(6)O(1) (K)</option>
-      <option value="Delta:H(8)C(6)O(1) (Protein N-term)">Delta:H(8)C(6)O(1) (Protein N-term)</option>
-      <option value="Delta:H(8)C(6)O(2) (K)">Delta:H(8)C(6)O(2) (K)</option>
-      <option value="Delta:Hg(1) (C)">Delta:Hg(1) (C)</option>
-      <option value="Delta:O(4) (W)">Delta:O(4) (W)</option>
-      <option value="Delta:S(-1)Se(1) (C)">Delta:S(-1)Se(1) (C)</option>
-      <option value="Delta:S(-1)Se(1) (M)">Delta:S(-1)Se(1) (M)</option>
-      <option value="Delta:Se(1) (C)">Delta:Se(1) (C)</option>
-      <option value="Deoxy (D)">Deoxy (D)</option>
-      <option value="Deoxy (S)">Deoxy (S)</option>
-      <option value="Deoxy (T)">Deoxy (T)</option>
-      <option value="Deoxyhypusine (K)">Deoxyhypusine (K)</option>
-      <option value="Deoxyhypusine (Q)">Deoxyhypusine (Q)</option>
-      <option value="DeStreak (C)">DeStreak (C)</option>
-      <option value="Dethiomethyl (M)">Dethiomethyl (M)</option>
-      <option value="dHex (N)">dHex (N)</option>
-      <option value="dHex (S)">dHex (S)</option>
-      <option value="dHex (T)">dHex (T)</option>
-      <option value="dHex(1)Hex(1) (S)">dHex(1)Hex(1) (S)</option>
-      <option value="dHex(1)Hex(1) (T)">dHex(1)Hex(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexA(1)HexNAc(3) (S)">dHex(1)Hex(1)HexA(1)HexNAc(3) (S)</option>
-      <option value="dHex(1)Hex(1)HexA(1)HexNAc(3) (T)">dHex(1)Hex(1)HexA(1)HexNAc(3) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)Kdn(1) (S)">dHex(1)Hex(1)HexNAc(1)Kdn(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)Kdn(1) (T)">dHex(1)Hex(1)HexNAc(1)Kdn(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(1)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(1)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3) (S)">dHex(1)Hex(1)HexNAc(3) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3) (T)">dHex(1)Hex(1)HexNAc(3) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(4) (S)">dHex(1)Hex(1)HexNAc(4) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(4) (T)">dHex(1)Hex(1)HexNAc(4) (T)</option>
-      <option value="dHex(1)Hex(2) (S)">dHex(1)Hex(2) (S)</option>
-      <option value="dHex(1)Hex(2) (T)">dHex(1)Hex(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexA(1) (S)">dHex(1)Hex(2)HexA(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexA(1) (T)">dHex(1)Hex(2)HexA(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(1) (S)">dHex(1)Hex(2)HexA(1)HexNAc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(1) (T)">dHex(1)Hex(2)HexA(1)HexNAc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (S)">dHex(1)Hex(2)HexA(1)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (T)">dHex(1)Hex(2)HexA(1)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1) (S)">dHex(1)Hex(2)HexNAc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1) (T)">dHex(1)Hex(2)HexNAc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)Pent(1) (N)">dHex(1)Hex(2)HexNAc(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3) (N)">dHex(1)Hex(2)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3) (S)">dHex(1)Hex(2)HexNAc(3) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3) (T)">dHex(1)Hex(2)HexNAc(3) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4) (N)">dHex(1)Hex(2)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4) (S)">dHex(1)Hex(2)HexNAc(4) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4) (T)">dHex(1)Hex(2)HexNAc(4) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-      <option value="dHex(1)Hex(3) (S)">dHex(1)Hex(3) (S)</option>
-      <option value="dHex(1)Hex(3) (T)">dHex(1)Hex(3) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(2) (S)">dHex(1)Hex(3)HexA(1)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(2) (T)">dHex(1)Hex(3)HexA(1)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(2)HexNAc(2) (S)">dHex(1)Hex(3)HexA(2)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(2)HexNAc(2) (T)">dHex(1)Hex(3)HexA(2)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(1) (S)">dHex(1)Hex(3)HexNAc(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(1) (T)">dHex(1)Hex(3)HexNAc(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2) (N)">dHex(1)Hex(3)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2) (S)">dHex(1)Hex(3)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2) (T)">dHex(1)Hex(3)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)Pent(1) (N)">dHex(1)Hex(3)HexNAc(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3) (N)">dHex(1)Hex(3)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3) (S)">dHex(1)Hex(3)HexNAc(3) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3) (T)">dHex(1)Hex(3)HexNAc(3) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Pent(1) (N)">dHex(1)Hex(3)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Pent(2) (N)">dHex(1)Hex(3)HexNAc(3)Pent(2) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Pent(3) (N)">dHex(1)Hex(3)HexNAc(3)Pent(3) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4) (N)">dHex(1)Hex(3)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4) (S)">dHex(1)Hex(3)HexNAc(4) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4) (T)">dHex(1)Hex(3)HexNAc(4) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)Pent(1) (N)">dHex(1)Hex(3)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)Pent(2) (N)">dHex(1)Hex(3)HexNAc(4)Pent(2) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)Pent(3) (N)">dHex(1)Hex(3)HexNAc(4)Pent(3) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5) (N)">dHex(1)Hex(3)HexNAc(5) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5) (S)">dHex(1)Hex(3)HexNAc(5) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5) (T)">dHex(1)Hex(3)HexNAc(5) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(5)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(6) (N)">dHex(1)Hex(3)HexNAc(6) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(6) (S)">dHex(1)Hex(3)HexNAc(6) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(6) (T)">dHex(1)Hex(3)HexNAc(6) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4) (S)">dHex(1)Hex(4) (S)</option>
-      <option value="dHex(1)Hex(4) (T)">dHex(1)Hex(4) (T)</option>
-      <option value="dHex(1)Hex(4)HexA(1) (S)">dHex(1)Hex(4)HexA(1) (S)</option>
-      <option value="dHex(1)Hex(4)HexA(1) (T)">dHex(1)Hex(4)HexA(1) (T)</option>
-      <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (S)">dHex(1)Hex(4)HexA(1)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (T)">dHex(1)Hex(4)HexA(1)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(1)Pent(1) (N)">dHex(1)Hex(4)HexNAc(1)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(2) (N)">dHex(1)Hex(4)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(2) (S)">dHex(1)Hex(4)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(4)HexNAc(2) (T)">dHex(1)Hex(4)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(2)Pent(1) (N)">dHex(1)Hex(4)HexNAc(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3) (N)">dHex(1)Hex(4)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)Pent(1) (N)">dHex(1)Hex(4)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4) (N)">dHex(1)Hex(4)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4) (S)">dHex(1)Hex(4)HexNAc(4) (S)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4) (T)">dHex(1)Hex(4)HexNAc(4) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)Pent(1) (N)">dHex(1)Hex(4)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(5) (N)">dHex(1)Hex(4)HexNAc(5) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(5)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(5)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5) (S)">dHex(1)Hex(5) (S)</option>
-      <option value="dHex(1)Hex(5) (T)">dHex(1)Hex(5) (T)</option>
-      <option value="dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N)">dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(2) (N)">dHex(1)Hex(5)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(2)Pent(1) (N)">dHex(1)Hex(5)HexNAc(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3) (N)">dHex(1)Hex(5)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4) (N)">dHex(1)Hex(5)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N)">dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N)">dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)Pent(1) (N)">dHex(1)Hex(5)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)Sulf(2) (N)">dHex(1)Hex(5)HexNAc(4)Sulf(2) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(5) (N)">dHex(1)Hex(5)HexNAc(5) (N)</option>
-      <option value="dHex(1)Hex(6) (S)">dHex(1)Hex(6) (S)</option>
-      <option value="dHex(1)Hex(6) (T)">dHex(1)Hex(6) (T)</option>
-      <option value="dHex(1)Hex(6)HexNAc(2) (N)">dHex(1)Hex(6)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(6)HexNAc(3) (N)">dHex(1)Hex(6)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(6)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(6)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(6)HexNAc(4) (N)">dHex(1)Hex(6)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(2) (N)">dHex(1)Hex(7)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(3) (N)">dHex(1)Hex(7)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(3)Phos(1) (N)">dHex(1)Hex(7)HexNAc(3)Phos(1) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(4) (N)">dHex(1)Hex(7)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(8)HexNAc(2) (N)">dHex(1)Hex(8)HexNAc(2) (N)</option>
-      <option value="dHex(1)HexNAc(3) (S)">dHex(1)HexNAc(3) (S)</option>
-      <option value="dHex(1)HexNAc(3) (T)">dHex(1)HexNAc(3) (T)</option>
-      <option value="dHex(1)HexNAc(4) (S)">dHex(1)HexNAc(4) (S)</option>
-      <option value="dHex(1)HexNAc(4) (T)">dHex(1)HexNAc(4) (T)</option>
-      <option value="dHex(1)HexNAc(5) (S)">dHex(1)HexNAc(5) (S)</option>
-      <option value="dHex(1)HexNAc(5) (T)">dHex(1)HexNAc(5) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(1)Kdn(1) (S)">dHex(2)Hex(1)HexNAc(1)Kdn(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(1)Kdn(1) (T)">dHex(2)Hex(1)HexNAc(1)Kdn(1) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(2)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(2)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)NeuAc(1) (S)">dHex(2)Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)NeuAc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(3) (S)">dHex(2)Hex(1)HexNAc(3) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(3) (T)">dHex(2)Hex(1)HexNAc(3) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2) (S)">dHex(2)Hex(2) (S)</option>
-      <option value="dHex(2)Hex(2) (T)">dHex(2)Hex(2) (T)</option>
-      <option value="dHex(2)Hex(2)HexA(1) (S)">dHex(2)Hex(2)HexA(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexA(1) (T)">dHex(2)Hex(2)HexA(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexA(1)HexNAc(1) (S)">dHex(2)Hex(2)HexA(1)HexNAc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexA(1)HexNAc(1) (T)">dHex(2)Hex(2)HexA(1)HexNAc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(1) (S)">dHex(2)Hex(2)HexNAc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(1) (T)">dHex(2)Hex(2)HexNAc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2) (N)">dHex(2)Hex(2)HexNAc(2) (N)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2) (S)">dHex(2)Hex(2)HexNAc(2) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2) (T)">dHex(2)Hex(2)HexNAc(2) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(2)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(2)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(2)Sulf(2) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(2)Sulf(2) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3) (N)">dHex(2)Hex(2)HexNAc(3) (N)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3) (S)">dHex(2)Hex(2)HexNAc(3) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3) (T)">dHex(2)Hex(2)HexNAc(3) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)NeuAc(1) (S)">dHex(2)Hex(2)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(2)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)NeuGc(1) (S)">dHex(2)Hex(2)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)NeuGc(1) (T)">dHex(2)Hex(2)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(4) (S)">dHex(2)Hex(2)HexNAc(4) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(4) (T)">dHex(2)Hex(2)HexNAc(4) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(5) (S)">dHex(2)Hex(2)HexNAc(5) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(5) (T)">dHex(2)Hex(2)HexNAc(5) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3) (S)">dHex(2)Hex(3) (S)</option>
-      <option value="dHex(2)Hex(3) (T)">dHex(2)Hex(3) (T)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(1)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2) (N)">dHex(2)Hex(3)HexNAc(2) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2) (S)">dHex(2)Hex(3)HexNAc(2) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2) (T)">dHex(2)Hex(3)HexNAc(2) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(3)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(3)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3) (N)">dHex(2)Hex(3)HexNAc(3) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3) (S)">dHex(2)Hex(3)HexNAc(3) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3) (T)">dHex(2)Hex(3)HexNAc(3) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)Pent(1) (N)">dHex(2)Hex(3)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)Pent(2) (N)">dHex(2)Hex(3)HexNAc(3)Pent(2) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4) (N)">dHex(2)Hex(3)HexNAc(4) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4) (S)">dHex(2)Hex(3)HexNAc(4) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4) (T)">dHex(2)Hex(3)HexNAc(4) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4)Pent(1) (N)">dHex(2)Hex(3)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4)Pent(2) (N)">dHex(2)Hex(3)HexNAc(4)Pent(2) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(5) (N)">dHex(2)Hex(3)HexNAc(5) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(5) (S)">dHex(2)Hex(3)HexNAc(5) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(5) (T)">dHex(2)Hex(3)HexNAc(5) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(6) (N)">dHex(2)Hex(3)HexNAc(6) (N)</option>
-      <option value="dHex(2)Hex(4) (S)">dHex(2)Hex(4) (S)</option>
-      <option value="dHex(2)Hex(4) (T)">dHex(2)Hex(4) (T)</option>
-      <option value="dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(4)HexNAc(1) (S)">dHex(2)Hex(4)HexNAc(1) (S)</option>
-      <option value="dHex(2)Hex(4)HexNAc(1) (T)">dHex(2)Hex(4)HexNAc(1) (T)</option>
-      <option value="dHex(2)Hex(4)HexNAc(2) (N)">dHex(2)Hex(4)HexNAc(2) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(2) (S)">dHex(2)Hex(4)HexNAc(2) (S)</option>
-      <option value="dHex(2)Hex(4)HexNAc(2) (T)">dHex(2)Hex(4)HexNAc(2) (T)</option>
-      <option value="dHex(2)Hex(4)HexNAc(3) (N)">dHex(2)Hex(4)HexNAc(3) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(3)Pent(1) (N)">dHex(2)Hex(4)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4) (N)">dHex(2)Hex(4)HexNAc(4) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4) (S)">dHex(2)Hex(4)HexNAc(4) (S)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4) (T)">dHex(2)Hex(4)HexNAc(4) (T)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4)Pent(1) (N)">dHex(2)Hex(4)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(2)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(5) (N)">dHex(2)Hex(4)HexNAc(5) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(5) (S)">dHex(2)Hex(4)HexNAc(5) (S)</option>
-      <option value="dHex(2)Hex(4)HexNAc(5) (T)">dHex(2)Hex(4)HexNAc(5) (T)</option>
-      <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (S)">dHex(2)Hex(5)HexNAc(2)Me(1) (S)</option>
-      <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (T)">dHex(2)Hex(5)HexNAc(2)Me(1) (T)</option>
-      <option value="dHex(2)Hex(5)HexNAc(3)Pent(1) (N)">dHex(2)Hex(5)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(5)HexNAc(4) (N)">dHex(2)Hex(5)HexNAc(4) (N)</option>
-      <option value="dHex(2)HexNAc(2)Kdn(1) (S)">dHex(2)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(2)HexNAc(2)Kdn(1) (T)">dHex(2)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(2)HexNAc(5) (S)">dHex(2)HexNAc(5) (S)</option>
-      <option value="dHex(2)HexNAc(5) (T)">dHex(2)HexNAc(5) (T)</option>
-      <option value="dHex(2)HexNAc(7) (S)">dHex(2)HexNAc(7) (S)</option>
-      <option value="dHex(2)HexNAc(7) (T)">dHex(2)HexNAc(7) (T)</option>
-      <option value="dHex(3)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(3)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(3)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(3)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(3)Hex(1)HexNAc(3)Kdn(1) (S)">dHex(3)Hex(1)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(3)Hex(1)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(1)HexNAc(3)Kdn(1) (T)</option>
-      <option value="dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(2) (S)">dHex(3)Hex(2)HexNAc(2) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(2) (T)">dHex(3)Hex(2)HexNAc(2) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(3)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(3) (S)">dHex(3)Hex(2)HexNAc(3) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(3) (T)">dHex(3)Hex(2)HexNAc(3) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (S)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(4) (S)">dHex(3)Hex(2)HexNAc(4) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(4) (T)">dHex(3)Hex(2)HexNAc(4) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(1) (S)">dHex(3)Hex(3)HexNAc(1) (S)</option>
-      <option value="dHex(3)Hex(3)HexNAc(1) (T)">dHex(3)Hex(3)HexNAc(1) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(2) (S)">dHex(3)Hex(3)HexNAc(2) (S)</option>
-      <option value="dHex(3)Hex(3)HexNAc(2) (T)">dHex(3)Hex(3)HexNAc(2) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3) (S)">dHex(3)Hex(3)HexNAc(3) (S)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3) (T)">dHex(3)Hex(3)HexNAc(3) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3)Pent(1) (N)">dHex(3)Hex(3)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(3)Hex(3)HexNAc(4) (N)">dHex(3)Hex(3)HexNAc(4) (N)</option>
-      <option value="dHex(3)Hex(3)HexNAc(4)Pent(1) (N)">dHex(3)Hex(3)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(3)Hex(4)HexNAc(4) (N)">dHex(3)Hex(4)HexNAc(4) (N)</option>
-      <option value="dHex(3)Hex(4)HexNAc(4) (S)">dHex(3)Hex(4)HexNAc(4) (S)</option>
-      <option value="dHex(3)Hex(4)HexNAc(4) (T)">dHex(3)Hex(4)HexNAc(4) (T)</option>
-      <option value="dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(3)HexNAc(3)Kdn(1) (S)">dHex(3)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(3)HexNAc(3)Kdn(1) (T)">dHex(3)HexNAc(3)Kdn(1) (T)</option>
-      <option value="dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)">dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)</option>
-      <option value="dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)">dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)</option>
-      <option value="dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)">dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)">dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)</option>
-      <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(4)Hex(2)HexNAc(3) (S)">dHex(4)Hex(2)HexNAc(3) (S)</option>
-      <option value="dHex(4)Hex(2)HexNAc(3) (T)">dHex(4)Hex(2)HexNAc(3) (T)</option>
-      <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="dHex(4)Hex(3)HexNAc(3) (S)">dHex(4)Hex(3)HexNAc(3) (S)</option>
-      <option value="dHex(4)Hex(3)HexNAc(3) (T)">dHex(4)Hex(3)HexNAc(3) (T)</option>
-      <option value="dHex(4)HexNAc(3)Kdn(1) (S)">dHex(4)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(4)HexNAc(3)Kdn(1) (T)">dHex(4)HexNAc(3)Kdn(1) (T)</option>
-      <option value="DHP (C)">DHP (C)</option>
-      <option value="Diacylglycerol (C)">Diacylglycerol (C)</option>
-      <option value="DiART6plex (K)">DiART6plex (K)</option>
-      <option value="DiART6plex (N-term)">DiART6plex (N-term)</option>
-      <option value="DiART6plex (Protein N-term)">DiART6plex (Protein N-term)</option>
-      <option value="DiART6plex (Y)">DiART6plex (Y)</option>
-      <option value="DiART6plex115 (K)">DiART6plex115 (K)</option>
-      <option value="DiART6plex115 (N-term)">DiART6plex115 (N-term)</option>
-      <option value="DiART6plex115 (Protein N-term)">DiART6plex115 (Protein N-term)</option>
-      <option value="DiART6plex115 (Y)">DiART6plex115 (Y)</option>
-      <option value="DiART6plex116/119 (K)">DiART6plex116/119 (K)</option>
-      <option value="DiART6plex116/119 (N-term)">DiART6plex116/119 (N-term)</option>
-      <option value="DiART6plex116/119 (Protein N-term)">DiART6plex116/119 (Protein N-term)</option>
-      <option value="DiART6plex116/119 (Y)">DiART6plex116/119 (Y)</option>
-      <option value="DiART6plex117 (K)">DiART6plex117 (K)</option>
-      <option value="DiART6plex117 (N-term)">DiART6plex117 (N-term)</option>
-      <option value="DiART6plex117 (Protein N-term)">DiART6plex117 (Protein N-term)</option>
-      <option value="DiART6plex117 (Y)">DiART6plex117 (Y)</option>
-      <option value="DiART6plex118 (K)">DiART6plex118 (K)</option>
-      <option value="DiART6plex118 (N-term)">DiART6plex118 (N-term)</option>
-      <option value="DiART6plex118 (Protein N-term)">DiART6plex118 (Protein N-term)</option>
-      <option value="DiART6plex118 (Y)">DiART6plex118 (Y)</option>
-      <option value="Dibromo (Y)">Dibromo (Y)</option>
-      <option value="Dicarbamidomethyl (C)">Dicarbamidomethyl (C)</option>
-      <option value="Dicarbamidomethyl (H)">Dicarbamidomethyl (H)</option>
-      <option value="Dicarbamidomethyl (K)">Dicarbamidomethyl (K)</option>
-      <option value="Dicarbamidomethyl (N-term)">Dicarbamidomethyl (N-term)</option>
-      <option value="Dicarbamidomethyl (R)">Dicarbamidomethyl (R)</option>
-      <option value="dichlorination (C)">dichlorination (C)</option>
-      <option value="dichlorination (Y)">dichlorination (Y)</option>
-      <option value="Didehydro (C-term K)">Didehydro (C-term K)</option>
-      <option value="Didehydro (S)">Didehydro (S)</option>
-      <option value="Didehydro (T)">Didehydro (T)</option>
-      <option value="Didehydro (Y)">Didehydro (Y)</option>
-      <option value="Didehydroretinylidene (K)">Didehydroretinylidene (K)</option>
-      <option value="Diethyl (K)">Diethyl (K)</option>
-      <option value="Diethyl (N-term)">Diethyl (N-term)</option>
-      <option value="Diethylphosphate (C)">Diethylphosphate (C)</option>
-      <option value="Diethylphosphate (H)">Diethylphosphate (H)</option>
-      <option value="Diethylphosphate (K)">Diethylphosphate (K)</option>
-      <option value="Diethylphosphate (N-term)">Diethylphosphate (N-term)</option>
-      <option value="Diethylphosphate (S)">Diethylphosphate (S)</option>
-      <option value="Diethylphosphate (T)">Diethylphosphate (T)</option>
-      <option value="Diethylphosphate (Y)">Diethylphosphate (Y)</option>
-      <option value="Diethylphosphothione (C)">Diethylphosphothione (C)</option>
-      <option value="Diethylphosphothione (H)">Diethylphosphothione (H)</option>
-      <option value="Diethylphosphothione (K)">Diethylphosphothione (K)</option>
-      <option value="Diethylphosphothione (S)">Diethylphosphothione (S)</option>
-      <option value="Diethylphosphothione (T)">Diethylphosphothione (T)</option>
-      <option value="Diethylphosphothione (Y)">Diethylphosphothione (Y)</option>
-      <option value="Difuran (Y)">Difuran (Y)</option>
-      <option value="Dihydroxyimidazolidine (R)">Dihydroxyimidazolidine (R)</option>
-      <option value="Diiodo (H)">Diiodo (H)</option>
-      <option value="Diiodo (Y)">Diiodo (Y)</option>
-      <option value="Diironsubcluster (C)">Diironsubcluster (C)</option>
-      <option value="Diisopropylphosphate (K)">Diisopropylphosphate (K)</option>
-      <option value="Diisopropylphosphate (N-term)">Diisopropylphosphate (N-term)</option>
-      <option value="Diisopropylphosphate (S)">Diisopropylphosphate (S)</option>
-      <option value="Diisopropylphosphate (T)">Diisopropylphosphate (T)</option>
-      <option value="Diisopropylphosphate (Y)">Diisopropylphosphate (Y)</option>
-      <option value="DiLeu4plex (K)">DiLeu4plex (K)</option>
-      <option value="DiLeu4plex (N-term)">DiLeu4plex (N-term)</option>
-      <option value="DiLeu4plex (Y)">DiLeu4plex (Y)</option>
-      <option value="DiLeu4plex115 (K)">DiLeu4plex115 (K)</option>
-      <option value="DiLeu4plex115 (N-term)">DiLeu4plex115 (N-term)</option>
-      <option value="DiLeu4plex115 (Y)">DiLeu4plex115 (Y)</option>
-      <option value="DiLeu4plex117 (K)">DiLeu4plex117 (K)</option>
-      <option value="DiLeu4plex117 (N-term)">DiLeu4plex117 (N-term)</option>
-      <option value="DiLeu4plex117 (Y)">DiLeu4plex117 (Y)</option>
-      <option value="DiLeu4plex118 (K)">DiLeu4plex118 (K)</option>
-      <option value="DiLeu4plex118 (N-term)">DiLeu4plex118 (N-term)</option>
-      <option value="DiLeu4plex118 (Y)">DiLeu4plex118 (Y)</option>
-      <option value="Dimethyl (K)">Dimethyl (K)</option>
-      <option value="Dimethyl (N)">Dimethyl (N)</option>
-      <option value="Dimethyl (N-term)">Dimethyl (N-term)</option>
-      <option value="Dimethyl (Protein N-term P)">Dimethyl (Protein N-term P)</option>
-      <option value="Dimethyl (Protein N-term)">Dimethyl (Protein N-term)</option>
-      <option value="Dimethyl (R)">Dimethyl (R)</option>
-      <option value="Dimethyl:2H(2)13C (K)">Dimethyl:2H(2)13C (K)</option>
-      <option value="Dimethyl:2H(2)13C (N)">Dimethyl:2H(2)13C (N)</option>
-      <option value="Dimethyl:2H(2)13C (N-term)">Dimethyl:2H(2)13C (N-term)</option>
-      <option value="Dimethyl:2H(2)13C (Protein N-term P)">Dimethyl:2H(2)13C (Protein N-term P)</option>
-      <option value="Dimethyl:2H(2)13C (R)">Dimethyl:2H(2)13C (R)</option>
-      <option value="Dimethyl:2H(4) (K)">Dimethyl:2H(4) (K)</option>
-      <option value="Dimethyl:2H(4) (N-term)">Dimethyl:2H(4) (N-term)</option>
-      <option value="Dimethyl:2H(4) (Protein N-term)">Dimethyl:2H(4) (Protein N-term)</option>
-      <option value="Dimethyl:2H(4) (R)">Dimethyl:2H(4) (R)</option>
-      <option value="Dimethyl:2H(4)13C(2) (K)">Dimethyl:2H(4)13C(2) (K)</option>
-      <option value="Dimethyl:2H(4)13C(2) (N-term)">Dimethyl:2H(4)13C(2) (N-term)</option>
-      <option value="Dimethyl:2H(4)13C(2) (Protein N-term)">Dimethyl:2H(4)13C(2) (Protein N-term)</option>
-      <option value="Dimethyl:2H(4)13C(2) (R)">Dimethyl:2H(4)13C(2) (R)</option>
-      <option value="Dimethyl:2H(6) (K)">Dimethyl:2H(6) (K)</option>
-      <option value="Dimethyl:2H(6) (N-term)">Dimethyl:2H(6) (N-term)</option>
-      <option value="Dimethyl:2H(6) (R)">Dimethyl:2H(6) (R)</option>
-      <option value="Dimethyl:2H(6)13C(2) (K)">Dimethyl:2H(6)13C(2) (K)</option>
-      <option value="Dimethyl:2H(6)13C(2) (N-term)">Dimethyl:2H(6)13C(2) (N-term)</option>
-      <option value="Dimethyl:2H(6)13C(2) (Protein N-term)">Dimethyl:2H(6)13C(2) (Protein N-term)</option>
-      <option value="Dimethyl:2H(6)13C(2) (R)">Dimethyl:2H(6)13C(2) (R)</option>
-      <option value="DimethylamineGMBS (C)">DimethylamineGMBS (C)</option>
-      <option value="Dimethylaminoethyl (C)">Dimethylaminoethyl (C)</option>
-      <option value="DimethylArsino (C)">DimethylArsino (C)</option>
-      <option value="Dimethylphosphothione (C)">Dimethylphosphothione (C)</option>
-      <option value="Dimethylphosphothione (H)">Dimethylphosphothione (H)</option>
-      <option value="Dimethylphosphothione (K)">Dimethylphosphothione (K)</option>
-      <option value="Dimethylphosphothione (S)">Dimethylphosphothione (S)</option>
-      <option value="Dimethylphosphothione (T)">Dimethylphosphothione (T)</option>
-      <option value="Dimethylphosphothione (Y)">Dimethylphosphothione (Y)</option>
-      <option value="DimethylpyrroleAdduct (K)">DimethylpyrroleAdduct (K)</option>
-      <option value="Dioxidation (C)">Dioxidation (C)</option>
-      <option value="Dioxidation (E)">Dioxidation (E)</option>
-      <option value="Dioxidation (F)">Dioxidation (F)</option>
-      <option value="Dioxidation (I)">Dioxidation (I)</option>
-      <option value="Dioxidation (K)">Dioxidation (K)</option>
-      <option value="Dioxidation (L)">Dioxidation (L)</option>
-      <option value="Dioxidation (M)">Dioxidation (M)</option>
-      <option value="Dioxidation (P)">Dioxidation (P)</option>
-      <option value="Dioxidation (R)">Dioxidation (R)</option>
-      <option value="Dioxidation (U)">Dioxidation (U)</option>
-      <option value="Dioxidation (V)">Dioxidation (V)</option>
-      <option value="Dioxidation (W)">Dioxidation (W)</option>
-      <option value="Dioxidation (Y)">Dioxidation (Y)</option>
-      <option value="Diphthamide (H)">Diphthamide (H)</option>
-      <option value="Dipyridyl (C)">Dipyridyl (C)</option>
-      <option value="Dipyrrolylmethanemethyl (C)">Dipyrrolylmethanemethyl (C)</option>
-      <option value="DMPO (C)">DMPO (C)</option>
-      <option value="DMPO (H)">DMPO (H)</option>
-      <option value="DMPO (Y)">DMPO (Y)</option>
-      <option value="DNCB_hapten (C)">DNCB_hapten (C)</option>
-      <option value="DNCB_hapten (H)">DNCB_hapten (H)</option>
-      <option value="DNCB_hapten (K)">DNCB_hapten (K)</option>
-      <option value="DNCB_hapten (Y)">DNCB_hapten (Y)</option>
-      <option value="dNIC (K)">dNIC (K)</option>
-      <option value="dNIC (N-term)">dNIC (N-term)</option>
-      <option value="DNPS (C)">DNPS (C)</option>
-      <option value="DNPS (W)">DNPS (W)</option>
-      <option value="DTT (C)">DTT (C)</option>
-      <option value="DyLight-maleimide (C)">DyLight-maleimide (C)</option>
-      <option value="DYn-2 (C)">DYn-2 (C)</option>
-      <option value="EDEDTIDVFQQQTGG (K)">EDEDTIDVFQQQTGG (K)</option>
-      <option value="EDT-iodoacetyl-PEO-biotin (S)">EDT-iodoacetyl-PEO-biotin (S)</option>
-      <option value="EDT-iodoacetyl-PEO-biotin (T)">EDT-iodoacetyl-PEO-biotin (T)</option>
-      <option value="EDT-maleimide-PEO-biotin (S)">EDT-maleimide-PEO-biotin (S)</option>
-      <option value="EDT-maleimide-PEO-biotin (T)">EDT-maleimide-PEO-biotin (T)</option>
-      <option value="EEEDVIEVYQEQTGG (K)">EEEDVIEVYQEQTGG (K)</option>
-      <option value="EGCG1 (C)">EGCG1 (C)</option>
-      <option value="EGCG2 (C)">EGCG2 (C)</option>
-      <option value="EHD-diphenylpentanone (C)">EHD-diphenylpentanone (C)</option>
-      <option value="EHD-diphenylpentanone (M)">EHD-diphenylpentanone (M)</option>
-      <option value="EQAT (C)">EQAT (C)</option>
-      <option value="EQAT:2H(5) (C)">EQAT:2H(5) (C)</option>
-      <option value="EQIGG (K)">EQIGG (K)</option>
-      <option value="ESP (K)">ESP (K)</option>
-      <option value="ESP (N-term)">ESP (N-term)</option>
-      <option value="ESP:2H(10) (K)">ESP:2H(10) (K)</option>
-      <option value="ESP:2H(10) (N-term)">ESP:2H(10) (N-term)</option>
-      <option value="Ethanedithiol (S)">Ethanedithiol (S)</option>
-      <option value="Ethanedithiol (T)">Ethanedithiol (T)</option>
-      <option value="Ethanolamine (C)">Ethanolamine (C)</option>
-      <option value="Ethanolamine (C-term)">Ethanolamine (C-term)</option>
-      <option value="Ethanolamine (D)">Ethanolamine (D)</option>
-      <option value="Ethanolamine (E)">Ethanolamine (E)</option>
-      <option value="Ethanolyl (C)">Ethanolyl (C)</option>
-      <option value="Ethanolyl (K)">Ethanolyl (K)</option>
-      <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-      <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
-      <option value="Ethyl (C-term)">Ethyl (C-term)</option>
-      <option value="Ethyl (D)">Ethyl (D)</option>
-      <option value="Ethyl (E)">Ethyl (E)</option>
-      <option value="Ethyl (K)">Ethyl (K)</option>
-      <option value="Ethyl (N-term)">Ethyl (N-term)</option>
-      <option value="Ethyl (Protein N-term)">Ethyl (Protein N-term)</option>
-      <option value="Ethyl+Deamidated (N)">Ethyl+Deamidated (N)</option>
-      <option value="Ethyl+Deamidated (Q)">Ethyl+Deamidated (Q)</option>
-      <option value="ethylamino (S)">ethylamino (S)</option>
-      <option value="ethylamino (T)">ethylamino (T)</option>
-      <option value="Ethylphosphate (K)">Ethylphosphate (K)</option>
-      <option value="Ethylphosphate (N-term)">Ethylphosphate (N-term)</option>
-      <option value="Ethylphosphate (S)">Ethylphosphate (S)</option>
-      <option value="Ethylphosphate (T)">Ethylphosphate (T)</option>
-      <option value="Ethylphosphate (Y)">Ethylphosphate (Y)</option>
-      <option value="ethylsulfonylethyl (C)">ethylsulfonylethyl (C)</option>
-      <option value="ethylsulfonylethyl (H)">ethylsulfonylethyl (H)</option>
-      <option value="ethylsulfonylethyl (K)">ethylsulfonylethyl (K)</option>
-      <option value="ExacTagAmine (K)">ExacTagAmine (K)</option>
-      <option value="ExacTagThiol (C)">ExacTagThiol (C)</option>
-      <option value="FAD (C)">FAD (C)</option>
-      <option value="FAD (H)">FAD (H)</option>
-      <option value="FAD (Y)">FAD (Y)</option>
-      <option value="Farnesyl (C)">Farnesyl (C)</option>
-      <option value="Fluorescein (C)">Fluorescein (C)</option>
-      <option value="Fluorescein-tyramine (Y)">Fluorescein-tyramine (Y)</option>
-      <option value="Fluoro (A)">Fluoro (A)</option>
-      <option value="Fluoro (F)">Fluoro (F)</option>
-      <option value="Fluoro (W)">Fluoro (W)</option>
-      <option value="Fluoro (Y)">Fluoro (Y)</option>
-      <option value="FMN (S)">FMN (S)</option>
-      <option value="FMN (T)">FMN (T)</option>
-      <option value="FMNC (C)">FMNC (C)</option>
-      <option value="FMNH (C)">FMNH (C)</option>
-      <option value="FMNH (H)">FMNH (H)</option>
-      <option value="FNEM (C)">FNEM (C)</option>
-      <option value="Formyl (K)">Formyl (K)</option>
-      <option value="Formyl (N-term)">Formyl (N-term)</option>
-      <option value="Formyl (Protein N-term)">Formyl (Protein N-term)</option>
-      <option value="Formyl (S)">Formyl (S)</option>
-      <option value="Formyl (T)">Formyl (T)</option>
-      <option value="Formylasparagine (H)">Formylasparagine (H)</option>
-      <option value="FormylMet (Protein N-term)">FormylMet (Protein N-term)</option>
-      <option value="FP-Biotin (K)">FP-Biotin (K)</option>
-      <option value="FP-Biotin (S)">FP-Biotin (S)</option>
-      <option value="FP-Biotin (T)">FP-Biotin (T)</option>
-      <option value="FP-Biotin (Y)">FP-Biotin (Y)</option>
-      <option value="FTC (C)">FTC (C)</option>
-      <option value="FTC (K)">FTC (K)</option>
-      <option value="FTC (P)">FTC (P)</option>
-      <option value="FTC (R)">FTC (R)</option>
-      <option value="FTC (S)">FTC (S)</option>
-      <option value="Furan (Y)">Furan (Y)</option>
-      <option value="G-H1 (R)">G-H1 (R)</option>
-      <option value="Galactosyl (K)">Galactosyl (K)</option>
-      <option value="Galactosyl (N-term)">Galactosyl (N-term)</option>
-      <option value="GEE (Q)">GEE (Q)</option>
-      <option value="GeranylGeranyl (C)">GeranylGeranyl (C)</option>
-      <option value="GG (C)">GG (C)</option>
-      <option value="GG (K)">GG (K)</option>
-      <option value="GG (Protein N-term)">GG (Protein N-term)</option>
-      <option value="GG (S)">GG (S)</option>
-      <option value="GG (T)">GG (T)</option>
-      <option value="GGQ (K)">GGQ (K)</option>
-      <option value="GIST-Quat (K)">GIST-Quat (K)</option>
-      <option value="GIST-Quat (N-term)">GIST-Quat (N-term)</option>
-      <option value="GIST-Quat:2H(3) (K)">GIST-Quat:2H(3) (K)</option>
-      <option value="GIST-Quat:2H(3) (N-term)">GIST-Quat:2H(3) (N-term)</option>
-      <option value="GIST-Quat:2H(6) (K)">GIST-Quat:2H(6) (K)</option>
-      <option value="GIST-Quat:2H(6) (N-term)">GIST-Quat:2H(6) (N-term)</option>
-      <option value="GIST-Quat:2H(9) (K)">GIST-Quat:2H(9) (K)</option>
-      <option value="GIST-Quat:2H(9) (N-term)">GIST-Quat:2H(9) (N-term)</option>
-      <option value="Gln-&gt;Ala (Q)">Gln-&gt;Ala (Q)</option>
-      <option value="Gln-&gt;Arg (Q)">Gln-&gt;Arg (Q)</option>
-      <option value="Gln-&gt;Asn (Q)">Gln-&gt;Asn (Q)</option>
-      <option value="Gln-&gt;Asp (Q)">Gln-&gt;Asp (Q)</option>
-      <option value="Gln-&gt;Cys (Q)">Gln-&gt;Cys (Q)</option>
-      <option value="Gln-&gt;Glu (Q)">Gln-&gt;Glu (Q)</option>
-      <option value="Gln-&gt;Gly (Q)">Gln-&gt;Gly (Q)</option>
-      <option value="Gln-&gt;His (Q)">Gln-&gt;His (Q)</option>
-      <option value="Gln-&gt;Lys (Q)">Gln-&gt;Lys (Q)</option>
-      <option value="Gln-&gt;Met (Q)">Gln-&gt;Met (Q)</option>
-      <option value="Gln-&gt;Phe (Q)">Gln-&gt;Phe (Q)</option>
-      <option value="Gln-&gt;Pro (Q)">Gln-&gt;Pro (Q)</option>
-      <option value="Gln-&gt;pyro-Glu (N-term Q)">Gln-&gt;pyro-Glu (N-term Q)</option>
-      <option value="Gln-&gt;Ser (Q)">Gln-&gt;Ser (Q)</option>
-      <option value="Gln-&gt;Thr (Q)">Gln-&gt;Thr (Q)</option>
-      <option value="Gln-&gt;Trp (Q)">Gln-&gt;Trp (Q)</option>
-      <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
-      <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
-      <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
-      <option value="Glu (E)">Glu (E)</option>
-      <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
-      <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
-      <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
-      <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
-      <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
-      <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
-      <option value="Glu-&gt;Gln (E)">Glu-&gt;Gln (E)</option>
-      <option value="Glu-&gt;Gly (E)">Glu-&gt;Gly (E)</option>
-      <option value="Glu-&gt;His (E)">Glu-&gt;His (E)</option>
-      <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
-      <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
-      <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
-      <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
-      <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
-      <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
-      <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
-      <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
-      <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
-      <option value="Glu-&gt;Val (E)">Glu-&gt;Val (E)</option>
-      <option value="Glu-&gt;Xle (E)">Glu-&gt;Xle (E)</option>
-      <option value="glucosone (R)">glucosone (R)</option>
-      <option value="Glucosylgalactosyl (K)">Glucosylgalactosyl (K)</option>
-      <option value="Glucuronyl (Protein N-term)">Glucuronyl (Protein N-term)</option>
-      <option value="Glucuronyl (S)">Glucuronyl (S)</option>
-      <option value="Glucuronyl (T)">Glucuronyl (T)</option>
-      <option value="GluGlu (E)">GluGlu (E)</option>
-      <option value="GluGlu (Protein C-term)">GluGlu (Protein C-term)</option>
-      <option value="GluGluGlu (E)">GluGluGlu (E)</option>
-      <option value="GluGluGlu (Protein C-term)">GluGluGlu (Protein C-term)</option>
-      <option value="GluGluGluGlu (E)">GluGluGluGlu (E)</option>
-      <option value="GluGluGluGlu (Protein C-term)">GluGluGluGlu (Protein C-term)</option>
-      <option value="Gluratylation (K)">Gluratylation (K)</option>
-      <option value="Glutathione (C)">Glutathione (C)</option>
-      <option value="Gly (K)">Gly (K)</option>
-      <option value="Gly (S)">Gly (S)</option>
-      <option value="Gly (T)">Gly (T)</option>
-      <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
-      <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
-      <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
-      <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
-      <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
-      <option value="Gly-&gt;Gln (G)">Gly-&gt;Gln (G)</option>
-      <option value="Gly-&gt;Glu (G)">Gly-&gt;Glu (G)</option>
-      <option value="Gly-&gt;His (G)">Gly-&gt;His (G)</option>
-      <option value="Gly-&gt;Lys (G)">Gly-&gt;Lys (G)</option>
-      <option value="Gly-&gt;Met (G)">Gly-&gt;Met (G)</option>
-      <option value="Gly-&gt;Phe (G)">Gly-&gt;Phe (G)</option>
-      <option value="Gly-&gt;Pro (G)">Gly-&gt;Pro (G)</option>
-      <option value="Gly-&gt;Ser (G)">Gly-&gt;Ser (G)</option>
-      <option value="Gly-&gt;Thr (G)">Gly-&gt;Thr (G)</option>
-      <option value="Gly-&gt;Trp (G)">Gly-&gt;Trp (G)</option>
-      <option value="Gly-&gt;Tyr (G)">Gly-&gt;Tyr (G)</option>
-      <option value="Gly-&gt;Val (G)">Gly-&gt;Val (G)</option>
-      <option value="Gly-&gt;Xle (G)">Gly-&gt;Xle (G)</option>
-      <option value="Gly-loss+Amide (C-term G)">Gly-loss+Amide (C-term G)</option>
-      <option value="Glycerophospho (S)">Glycerophospho (S)</option>
-      <option value="GlycerylPE (E)">GlycerylPE (E)</option>
-      <option value="glycidamide (K)">glycidamide (K)</option>
-      <option value="glycidamide (N-term)">glycidamide (N-term)</option>
-      <option value="Glycosyl (P)">Glycosyl (P)</option>
-      <option value="glyoxalAGE (R)">glyoxalAGE (R)</option>
-      <option value="GNLLFLACYCIGG (K)">GNLLFLACYCIGG (K)</option>
-      <option value="GPIanchor (Protein C-term)">GPIanchor (Protein C-term)</option>
-      <option value="Guanidinyl (K)">Guanidinyl (K)</option>
-      <option value="Guanidinyl (N-term)">Guanidinyl (N-term)</option>
-      <option value="Haloxon (C)">Haloxon (C)</option>
-      <option value="Haloxon (H)">Haloxon (H)</option>
-      <option value="Haloxon (K)">Haloxon (K)</option>
-      <option value="Haloxon (S)">Haloxon (S)</option>
-      <option value="Haloxon (T)">Haloxon (T)</option>
-      <option value="Haloxon (Y)">Haloxon (Y)</option>
-      <option value="HCysteinyl (C)">HCysteinyl (C)</option>
-      <option value="HCysThiolactone (K)">HCysThiolactone (K)</option>
-      <option value="Heme (C)">Heme (C)</option>
-      <option value="Heme (H)">Heme (H)</option>
-      <option value="Hep (K)">Hep (K)</option>
-      <option value="Hep (N)">Hep (N)</option>
-      <option value="Hep (Q)">Hep (Q)</option>
-      <option value="Hep (R)">Hep (R)</option>
-      <option value="Hep (S)">Hep (S)</option>
-      <option value="Hep (T)">Hep (T)</option>
-      <option value="Hex (C)">Hex (C)</option>
-      <option value="Hex (K)">Hex (K)</option>
-      <option value="Hex (N)">Hex (N)</option>
-      <option value="Hex (N-term)">Hex (N-term)</option>
-      <option value="Hex (R)">Hex (R)</option>
-      <option value="Hex (S)">Hex (S)</option>
-      <option value="Hex (T)">Hex (T)</option>
-      <option value="Hex (W)">Hex (W)</option>
-      <option value="Hex (Y)">Hex (Y)</option>
-      <option value="Hex(1)HexA(1) (S)">Hex(1)HexA(1) (S)</option>
-      <option value="Hex(1)HexA(1) (T)">Hex(1)HexA(1) (T)</option>
-      <option value="Hex(1)HexA(1)HexNAc(1) (S)">Hex(1)HexA(1)HexNAc(1) (S)</option>
-      <option value="Hex(1)HexA(1)HexNAc(1) (T)">Hex(1)HexA(1)HexNAc(1) (T)</option>
-      <option value="Hex(1)HexA(1)HexNAc(2) (S)">Hex(1)HexA(1)HexNAc(2) (S)</option>
-      <option value="Hex(1)HexA(1)HexNAc(2) (T)">Hex(1)HexA(1)HexNAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(1) (N)">Hex(1)HexNAc(1) (N)</option>
-      <option value="Hex(1)HexNAc(1) (S)">Hex(1)HexNAc(1) (S)</option>
-      <option value="Hex(1)HexNAc(1) (T)">Hex(1)HexNAc(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1) (N)">Hex(1)HexNAc(1)dHex(1) (N)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1) (S)">Hex(1)HexNAc(1)dHex(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1) (T)">Hex(1)HexNAc(1)dHex(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1)Me(1) (S)">Hex(1)HexNAc(1)dHex(1)Me(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1)Me(1) (T)">Hex(1)HexNAc(1)dHex(1)Me(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1)Me(2) (S)">Hex(1)HexNAc(1)dHex(1)Me(2) (S)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1)Me(2) (T)">Hex(1)HexNAc(1)dHex(1)Me(2) (T)</option>
-      <option value="Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S)">Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T)">Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1) (N)">Hex(1)HexNAc(1)NeuAc(1) (N)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1) (S)">Hex(1)HexNAc(1)NeuAc(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1) (T)">Hex(1)HexNAc(1)NeuAc(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S)">Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T)">Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S)">Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T)">Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T)">Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2) (N)">Hex(1)HexNAc(1)NeuAc(2) (N)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2) (S)">Hex(1)HexNAc(1)NeuAc(2) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2) (T)">Hex(1)HexNAc(1)NeuAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S)">Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T)">Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S)">Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T)">Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(3) (S)">Hex(1)HexNAc(1)NeuAc(3) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(3) (T)">Hex(1)HexNAc(1)NeuAc(3) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(1) (S)">Hex(1)HexNAc(1)NeuGc(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(1) (T)">Hex(1)HexNAc(1)NeuGc(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(2) (S)">Hex(1)HexNAc(1)NeuGc(2) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(2) (T)">Hex(1)HexNAc(1)NeuGc(2) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(3) (S)">Hex(1)HexNAc(1)NeuGc(3) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(3) (T)">Hex(1)HexNAc(1)NeuGc(3) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(4) (S)">Hex(1)HexNAc(1)NeuGc(4) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(4) (T)">Hex(1)HexNAc(1)NeuGc(4) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(5) (S)">Hex(1)HexNAc(1)NeuGc(5) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(5) (T)">Hex(1)HexNAc(1)NeuGc(5) (T)</option>
-      <option value="Hex(1)HexNAc(1)Phos(1) (S)">Hex(1)HexNAc(1)Phos(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)Phos(1) (T)">Hex(1)HexNAc(1)Phos(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)Sulf(1) (S)">Hex(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)Sulf(1) (T)">Hex(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(2) (N)">Hex(1)HexNAc(2) (N)</option>
-      <option value="Hex(1)HexNAc(2) (S)">Hex(1)HexNAc(2) (S)</option>
-      <option value="Hex(1)HexNAc(2) (T)">Hex(1)HexNAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(2)dHex(1) (N)">Hex(1)HexNAc(2)dHex(1) (N)</option>
-      <option value="Hex(1)HexNAc(2)dHex(1) (S)">Hex(1)HexNAc(2)dHex(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)dHex(1) (T)">Hex(1)HexNAc(2)dHex(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)dHex(1)Pent(1) (N)">Hex(1)HexNAc(2)dHex(1)Pent(1) (N)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2) (N)">Hex(1)HexNAc(2)dHex(2) (N)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2) (S)">Hex(1)HexNAc(2)dHex(2) (S)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2) (T)">Hex(1)HexNAc(2)dHex(2) (T)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(1) (S)">Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(1) (T)">Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(2) (S)">Hex(1)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(2) (T)">Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T)">Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuGc(1) (S)">Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuGc(1) (T)">Hex(1)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)Pent(1) (N)">Hex(1)HexNAc(2)Pent(1) (N)</option>
-      <option value="Hex(1)HexNAc(2)Sulf(1) (S)">Hex(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)Sulf(1) (T)">Hex(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(3) (S)">Hex(1)HexNAc(3) (S)</option>
-      <option value="Hex(1)HexNAc(3) (T)">Hex(1)HexNAc(3) (T)</option>
-      <option value="Hex(1)HexNAc(3)NeuAc(1) (S)">Hex(1)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="Hex(1)HexNAc(3)NeuAc(1) (T)">Hex(1)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="Hex(1)HexNAc(3)NeuAc(2) (S)">Hex(1)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="Hex(1)HexNAc(3)NeuAc(2) (T)">Hex(1)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(3)NeuGc(1) (S)">Hex(1)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="Hex(1)HexNAc(3)NeuGc(1) (T)">Hex(1)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="Hex(1)HexNAc(3)Sulf(1) (S)">Hex(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(3)Sulf(1) (T)">Hex(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)</option>
-      <option value="Hex(1)NeuAc(1) (S)">Hex(1)NeuAc(1) (S)</option>
-      <option value="Hex(1)NeuAc(1) (T)">Hex(1)NeuAc(1) (T)</option>
-      <option value="Hex(1)NeuAc(1)Pent(1) (S)">Hex(1)NeuAc(1)Pent(1) (S)</option>
-      <option value="Hex(1)NeuAc(1)Pent(1) (T)">Hex(1)NeuAc(1)Pent(1) (T)</option>
-      <option value="Hex(1)NeuGc(1) (S)">Hex(1)NeuGc(1) (S)</option>
-      <option value="Hex(1)NeuGc(1) (T)">Hex(1)NeuGc(1) (T)</option>
-      <option value="Hex(1)Pent(1) (S)">Hex(1)Pent(1) (S)</option>
-      <option value="Hex(1)Pent(1) (T)">Hex(1)Pent(1) (T)</option>
-      <option value="Hex(1)Pent(2) (S)">Hex(1)Pent(2) (S)</option>
-      <option value="Hex(1)Pent(2) (T)">Hex(1)Pent(2) (T)</option>
-      <option value="Hex(1)Pent(2)Me(1) (S)">Hex(1)Pent(2)Me(1) (S)</option>
-      <option value="Hex(1)Pent(2)Me(1) (T)">Hex(1)Pent(2)Me(1) (T)</option>
-      <option value="Hex(1)Pent(3) (S)">Hex(1)Pent(3) (S)</option>
-      <option value="Hex(1)Pent(3) (T)">Hex(1)Pent(3) (T)</option>
-      <option value="Hex(1)Pent(3)Me(1) (S)">Hex(1)Pent(3)Me(1) (S)</option>
-      <option value="Hex(1)Pent(3)Me(1) (T)">Hex(1)Pent(3)Me(1) (T)</option>
-      <option value="Hex(10)HexNAc(1) (N)">Hex(10)HexNAc(1) (N)</option>
-      <option value="Hex(10)Phos(3) (S)">Hex(10)Phos(3) (S)</option>
-      <option value="Hex(10)Phos(3) (T)">Hex(10)Phos(3) (T)</option>
-      <option value="Hex(2) (K)">Hex(2) (K)</option>
-      <option value="Hex(2) (R)">Hex(2) (R)</option>
-      <option value="Hex(2) (S)">Hex(2) (S)</option>
-      <option value="Hex(2) (T)">Hex(2) (T)</option>
-      <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)Pent(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)Pent(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(1) (N)">Hex(2)HexNAc(1) (N)</option>
-      <option value="Hex(2)HexNAc(1) (S)">Hex(2)HexNAc(1) (S)</option>
-      <option value="Hex(2)HexNAc(1) (T)">Hex(2)HexNAc(1) (T)</option>
-      <option value="Hex(2)HexNAc(1)Me(1) (S)">Hex(2)HexNAc(1)Me(1) (S)</option>
-      <option value="Hex(2)HexNAc(1)Me(1) (T)">Hex(2)HexNAc(1)Me(1) (T)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(1) (S)">Hex(2)HexNAc(1)NeuGc(1) (S)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(1) (T)">Hex(2)HexNAc(1)NeuGc(1) (T)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(2) (S)">Hex(2)HexNAc(1)NeuGc(2) (S)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(2) (T)">Hex(2)HexNAc(1)NeuGc(2) (T)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(3) (S)">Hex(2)HexNAc(1)NeuGc(3) (S)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(3) (T)">Hex(2)HexNAc(1)NeuGc(3) (T)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(4) (S)">Hex(2)HexNAc(1)NeuGc(4) (S)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(4) (T)">Hex(2)HexNAc(1)NeuGc(4) (T)</option>
-      <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (S)">Hex(2)HexNAc(1)Pent(1)HexA(1) (S)</option>
-      <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (T)">Hex(2)HexNAc(1)Pent(1)HexA(1) (T)</option>
-      <option value="Hex(2)HexNAc(1)Sulf(1) (S)">Hex(2)HexNAc(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(1)Sulf(1) (T)">Hex(2)HexNAc(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(2) (N)">Hex(2)HexNAc(2) (N)</option>
-      <option value="Hex(2)HexNAc(2) (S)">Hex(2)HexNAc(2) (S)</option>
-      <option value="Hex(2)HexNAc(2) (T)">Hex(2)HexNAc(2) (T)</option>
-      <option value="Hex(2)HexNAc(2)dHex(1) (N)">Hex(2)HexNAc(2)dHex(1) (N)</option>
-      <option value="Hex(2)HexNAc(2)dHex(1) (S)">Hex(2)HexNAc(2)dHex(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)dHex(1) (T)">Hex(2)HexNAc(2)dHex(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1) (N)">Hex(2)HexNAc(2)NeuAc(1) (N)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1) (S)">Hex(2)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1) (T)">Hex(2)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(2) (S)">Hex(2)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(2) (T)">Hex(2)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuGc(1) (S)">Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuGc(1) (T)">Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)Pent(1) (N)">Hex(2)HexNAc(2)Pent(1) (N)</option>
-      <option value="Hex(2)HexNAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(3) (N)">Hex(2)HexNAc(3) (N)</option>
-      <option value="Hex(2)HexNAc(3) (S)">Hex(2)HexNAc(3) (S)</option>
-      <option value="Hex(2)HexNAc(3) (T)">Hex(2)HexNAc(3) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(2) (S)">Hex(2)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(2) (T)">Hex(2)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(3) (S)">Hex(2)HexNAc(3)NeuAc(3) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(3) (T)">Hex(2)HexNAc(3)NeuAc(3) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(1) (T)">Hex(2)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(2) (S)">Hex(2)HexNAc(3)NeuGc(2) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(2) (T)">Hex(2)HexNAc(3)NeuGc(2) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(3) (S)">Hex(2)HexNAc(3)NeuGc(3) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(3) (T)">Hex(2)HexNAc(3)NeuGc(3) (T)</option>
-      <option value="Hex(2)HexNAc(3)Sulf(1) (S)">Hex(2)HexNAc(3)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(3)Sulf(1) (T)">Hex(2)HexNAc(3)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(4) (N)">Hex(2)HexNAc(4) (N)</option>
-      <option value="Hex(2)HexNAc(4) (S)">Hex(2)HexNAc(4) (S)</option>
-      <option value="Hex(2)HexNAc(4) (T)">Hex(2)HexNAc(4) (T)</option>
-      <option value="Hex(2)HexNAc(4)NeuAc(1) (S)">Hex(2)HexNAc(4)NeuAc(1) (S)</option>
-      <option value="Hex(2)HexNAc(4)NeuAc(1) (T)">Hex(2)HexNAc(4)NeuAc(1) (T)</option>
-      <option value="Hex(2)HexNAc(5) (S)">Hex(2)HexNAc(5) (S)</option>
-      <option value="Hex(2)HexNAc(5) (T)">Hex(2)HexNAc(5) (T)</option>
-      <option value="Hex(2)NeuAc(1) (S)">Hex(2)NeuAc(1) (S)</option>
-      <option value="Hex(2)NeuAc(1) (T)">Hex(2)NeuAc(1) (T)</option>
-      <option value="Hex(2)Pent(2) (S)">Hex(2)Pent(2) (S)</option>
-      <option value="Hex(2)Pent(2) (T)">Hex(2)Pent(2) (T)</option>
-      <option value="Hex(2)Pent(2)Me(1) (S)">Hex(2)Pent(2)Me(1) (S)</option>
-      <option value="Hex(2)Pent(2)Me(1) (T)">Hex(2)Pent(2)Me(1) (T)</option>
-      <option value="Hex(2)Sulf(1) (S)">Hex(2)Sulf(1) (S)</option>
-      <option value="Hex(2)Sulf(1) (T)">Hex(2)Sulf(1) (T)</option>
-      <option value="Hex(3) (N)">Hex(3) (N)</option>
-      <option value="Hex(3) (S)">Hex(3) (S)</option>
-      <option value="Hex(3) (T)">Hex(3) (T)</option>
-      <option value="Hex(3)HexNAc(1) (N)">Hex(3)HexNAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(1) (S)">Hex(3)HexNAc(1) (S)</option>
-      <option value="Hex(3)HexNAc(1) (T)">Hex(3)HexNAc(1) (T)</option>
-      <option value="Hex(3)HexNAc(1)HexA(1) (S)">Hex(3)HexNAc(1)HexA(1) (S)</option>
-      <option value="Hex(3)HexNAc(1)HexA(1) (T)">Hex(3)HexNAc(1)HexA(1) (T)</option>
-      <option value="Hex(3)HexNAc(1)Me(1) (S)">Hex(3)HexNAc(1)Me(1) (S)</option>
-      <option value="Hex(3)HexNAc(1)Me(1) (T)">Hex(3)HexNAc(1)Me(1) (T)</option>
-      <option value="Hex(3)HexNAc(1)Pent(1) (N)">Hex(3)HexNAc(1)Pent(1) (N)</option>
-      <option value="Hex(3)HexNAc(2) (N)">Hex(3)HexNAc(2) (N)</option>
-      <option value="Hex(3)HexNAc(2) (S)">Hex(3)HexNAc(2) (S)</option>
-      <option value="Hex(3)HexNAc(2) (T)">Hex(3)HexNAc(2) (T)</option>
-      <option value="Hex(3)HexNAc(2)NeuAc(1) (N)">Hex(3)HexNAc(2)NeuAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(2)NeuAc(2) (S)">Hex(3)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="Hex(3)HexNAc(2)NeuAc(2) (T)">Hex(3)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="Hex(3)HexNAc(2)Pent(1) (N)">Hex(3)HexNAc(2)Pent(1) (N)</option>
-      <option value="Hex(3)HexNAc(2)Phos(1) (N)">Hex(3)HexNAc(2)Phos(1) (N)</option>
-      <option value="Hex(3)HexNAc(3) (N)">Hex(3)HexNAc(3) (N)</option>
-      <option value="Hex(3)HexNAc(3) (S)">Hex(3)HexNAc(3) (S)</option>
-      <option value="Hex(3)HexNAc(3) (T)">Hex(3)HexNAc(3) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(1) (S)">Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(1) (T)">Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(2) (S)">Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(2) (T)">Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(3) (S)">Hex(3)HexNAc(3)NeuAc(3) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(3) (T)">Hex(3)HexNAc(3)NeuAc(3) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuGc(1) (S)">Hex(3)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuGc(1) (T)">Hex(3)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)Pent(1) (N)">Hex(3)HexNAc(3)Pent(1) (N)</option>
-      <option value="Hex(3)HexNAc(3)Sulf(1) (N)">Hex(3)HexNAc(3)Sulf(1) (N)</option>
-      <option value="Hex(3)HexNAc(3)Sulf(1) (S)">Hex(3)HexNAc(3)Sulf(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)Sulf(1) (T)">Hex(3)HexNAc(3)Sulf(1) (T)</option>
-      <option value="Hex(3)HexNAc(4) (N)">Hex(3)HexNAc(4) (N)</option>
-      <option value="Hex(3)HexNAc(4) (S)">Hex(3)HexNAc(4) (S)</option>
-      <option value="Hex(3)HexNAc(4) (T)">Hex(3)HexNAc(4) (T)</option>
-      <option value="Hex(3)HexNAc(4)NeuAc(1) (N)">Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(4)NeuAc(2) (N)">Hex(3)HexNAc(4)NeuAc(2) (N)</option>
-      <option value="Hex(3)HexNAc(4)Pent(1) (N)">Hex(3)HexNAc(4)Pent(1) (N)</option>
-      <option value="Hex(3)HexNAc(4)Sulf(1) (N)">Hex(3)HexNAc(4)Sulf(1) (N)</option>
-      <option value="Hex(3)HexNAc(5) (N)">Hex(3)HexNAc(5) (N)</option>
-      <option value="Hex(3)HexNAc(5) (S)">Hex(3)HexNAc(5) (S)</option>
-      <option value="Hex(3)HexNAc(5) (T)">Hex(3)HexNAc(5) (T)</option>
-      <option value="Hex(3)HexNAc(5)NeuAc(1) (N)">Hex(3)HexNAc(5)NeuAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(5)Sulf(1) (N)">Hex(3)HexNAc(5)Sulf(1) (N)</option>
-      <option value="Hex(3)HexNAc(6) (N)">Hex(3)HexNAc(6) (N)</option>
-      <option value="Hex(3)HexNAc(6) (S)">Hex(3)HexNAc(6) (S)</option>
-      <option value="Hex(3)HexNAc(6) (T)">Hex(3)HexNAc(6) (T)</option>
-      <option value="Hex(3)HexNAc(6)NeuAc(1) (N)">Hex(3)HexNAc(6)NeuAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(6)Sulf(1) (N)">Hex(3)HexNAc(6)Sulf(1) (N)</option>
-      <option value="Hex(3)HexNAc(6)Sulf(2) (N)">Hex(3)HexNAc(6)Sulf(2) (N)</option>
-      <option value="Hex(3)HexNAc(7) (N)">Hex(3)HexNAc(7) (N)</option>
-      <option value="Hex(3)HexNAc(7)Sulf(1) (N)">Hex(3)HexNAc(7)Sulf(1) (N)</option>
-      <option value="Hex(4) (S)">Hex(4) (S)</option>
-      <option value="Hex(4) (T)">Hex(4) (T)</option>
-      <option value="Hex(4)HexA(1) (S)">Hex(4)HexA(1) (S)</option>
-      <option value="Hex(4)HexA(1) (T)">Hex(4)HexA(1) (T)</option>
-      <option value="Hex(4)HexA(1)HexNAc(1) (S)">Hex(4)HexA(1)HexNAc(1) (S)</option>
-      <option value="Hex(4)HexA(1)HexNAc(1) (T)">Hex(4)HexA(1)HexNAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(1) (N)">Hex(4)HexNAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(1) (S)">Hex(4)HexNAc(1) (S)</option>
-      <option value="Hex(4)HexNAc(1) (T)">Hex(4)HexNAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(2) (N)">Hex(4)HexNAc(2) (N)</option>
-      <option value="Hex(4)HexNAc(2)NeuAc(1) (N)">Hex(4)HexNAc(2)NeuAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(2)NeuAc(1) (S)">Hex(4)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="Hex(4)HexNAc(2)NeuAc(1) (T)">Hex(4)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(2)Pent(1) (N)">Hex(4)HexNAc(2)Pent(1) (N)</option>
-      <option value="Hex(4)HexNAc(3) (N)">Hex(4)HexNAc(3) (N)</option>
-      <option value="Hex(4)HexNAc(3) (S)">Hex(4)HexNAc(3) (S)</option>
-      <option value="Hex(4)HexNAc(3) (T)">Hex(4)HexNAc(3) (T)</option>
-      <option value="Hex(4)HexNAc(3)NeuAc(1) (N)">Hex(4)HexNAc(3)NeuAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(3)NeuAc(1) (S)">Hex(4)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="Hex(4)HexNAc(3)NeuAc(1) (T)">Hex(4)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(3)NeuAc(2) (N)">Hex(4)HexNAc(3)NeuAc(2) (N)</option>
-      <option value="Hex(4)HexNAc(3)NeuGc(1) (N)">Hex(4)HexNAc(3)NeuGc(1) (N)</option>
-      <option value="Hex(4)HexNAc(3)Pent(1) (N)">Hex(4)HexNAc(3)Pent(1) (N)</option>
-      <option value="Hex(4)HexNAc(4) (N)">Hex(4)HexNAc(4) (N)</option>
-      <option value="Hex(4)HexNAc(4) (S)">Hex(4)HexNAc(4) (S)</option>
-      <option value="Hex(4)HexNAc(4) (T)">Hex(4)HexNAc(4) (T)</option>
-      <option value="Hex(4)HexNAc(4)Me(2)Pent(1) (N)">Hex(4)HexNAc(4)Me(2)Pent(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1) (N)">Hex(4)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1) (S)">Hex(4)HexNAc(4)NeuAc(1) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1) (T)">Hex(4)HexNAc(4)NeuAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1) (N)">Hex(4)HexNAc(4)NeuGc(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1) (S)">Hex(4)HexNAc(4)NeuGc(1) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1) (T)">Hex(4)HexNAc(4)NeuGc(1) (T)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)</option>
-      <option value="Hex(4)HexNAc(4)Pent(1) (N)">Hex(4)HexNAc(4)Pent(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)Sulf(1) (N)">Hex(4)HexNAc(4)Sulf(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)Sulf(2) (S)">Hex(4)HexNAc(4)Sulf(2) (S)</option>
-      <option value="Hex(4)HexNAc(4)Sulf(2) (T)">Hex(4)HexNAc(4)Sulf(2) (T)</option>
-      <option value="Hex(4)HexNAc(5) (N)">Hex(4)HexNAc(5) (N)</option>
-      <option value="Hex(4)HexNAc(5)NeuAc(1) (N)">Hex(4)HexNAc(5)NeuAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(5)Sulf(1) (N)">Hex(4)HexNAc(5)Sulf(1) (N)</option>
-      <option value="Hex(4)HexNAc(6) (N)">Hex(4)HexNAc(6) (N)</option>
-      <option value="Hex(4)Phos(1) (S)">Hex(4)Phos(1) (S)</option>
-      <option value="Hex(4)Phos(1) (T)">Hex(4)Phos(1) (T)</option>
-      <option value="Hex(5) (S)">Hex(5) (S)</option>
-      <option value="Hex(5) (T)">Hex(5) (T)</option>
-      <option value="Hex(5)HexA(1) (S)">Hex(5)HexA(1) (S)</option>
-      <option value="Hex(5)HexA(1) (T)">Hex(5)HexA(1) (T)</option>
-      <option value="Hex(5)HexNAc(1) (N)">Hex(5)HexNAc(1) (N)</option>
-      <option value="Hex(5)HexNAc(1) (S)">Hex(5)HexNAc(1) (S)</option>
-      <option value="Hex(5)HexNAc(1) (T)">Hex(5)HexNAc(1) (T)</option>
-      <option value="Hex(5)HexNAc(2) (N)">Hex(5)HexNAc(2) (N)</option>
-      <option value="Hex(5)HexNAc(2)Phos(1) (N)">Hex(5)HexNAc(2)Phos(1) (N)</option>
-      <option value="Hex(5)HexNAc(3) (N)">Hex(5)HexNAc(3) (N)</option>
-      <option value="Hex(5)HexNAc(3)Pent(1) (N)">Hex(5)HexNAc(3)Pent(1) (N)</option>
-      <option value="Hex(5)HexNAc(4) (N)">Hex(5)HexNAc(4) (N)</option>
-      <option value="Hex(5)HexNAc(4) (S)">Hex(5)HexNAc(4) (S)</option>
-      <option value="Hex(5)HexNAc(4) (T)">Hex(5)HexNAc(4) (T)</option>
-      <option value="Hex(5)HexNAc(4)Me(2)Pent(1) (N)">Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(1) (N)">Hex(5)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(2) (N)">Hex(5)HexNAc(4)NeuAc(2) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuGc(1) (N)">Hex(5)HexNAc(4)NeuGc(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)Sulf(1) (N)">Hex(5)HexNAc(4)Sulf(1) (N)</option>
-      <option value="Hex(5)HexNAc(5) (N)">Hex(5)HexNAc(5) (N)</option>
-      <option value="Hex(5)HexNAc(5) (S)">Hex(5)HexNAc(5) (S)</option>
-      <option value="Hex(5)HexNAc(5) (T)">Hex(5)HexNAc(5) (T)</option>
-      <option value="Hex(5)Phos(1) (S)">Hex(5)Phos(1) (S)</option>
-      <option value="Hex(5)Phos(1) (T)">Hex(5)Phos(1) (T)</option>
-      <option value="Hex(5)Phos(3) (S)">Hex(5)Phos(3) (S)</option>
-      <option value="Hex(5)Phos(3) (T)">Hex(5)Phos(3) (T)</option>
-      <option value="Hex(6)HexNAc(1) (N)">Hex(6)HexNAc(1) (N)</option>
-      <option value="Hex(6)HexNAc(2) (N)">Hex(6)HexNAc(2) (N)</option>
-      <option value="Hex(6)HexNAc(2)Phos(1) (N)">Hex(6)HexNAc(2)Phos(1) (N)</option>
-      <option value="Hex(6)HexNAc(3) (N)">Hex(6)HexNAc(3) (N)</option>
-      <option value="Hex(6)HexNAc(3)Phos(1) (N)">Hex(6)HexNAc(3)Phos(1) (N)</option>
-      <option value="Hex(6)HexNAc(4) (N)">Hex(6)HexNAc(4) (N)</option>
-      <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
-      <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
-      <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
-      <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
-      <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
-      <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
-      <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
-      <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
-      <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
-      <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
-      <option value="Hex(7)HexNAc(2) (N)">Hex(7)HexNAc(2) (N)</option>
-      <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
-      <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
-      <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
-      <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
-      <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
-      <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
-      <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
-      <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
-      <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
-      <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
-      <option value="Hex(8)Phos(3) (T)">Hex(8)Phos(3) (T)</option>
-      <option value="Hex(9) (N)">Hex(9) (N)</option>
-      <option value="Hex(9)HexNAc(1) (N)">Hex(9)HexNAc(1) (N)</option>
-      <option value="Hex(9)HexNAc(2) (N)">Hex(9)HexNAc(2) (N)</option>
-      <option value="Hex(9)Phos(3) (S)">Hex(9)Phos(3) (S)</option>
-      <option value="Hex(9)Phos(3) (T)">Hex(9)Phos(3) (T)</option>
-      <option value="HexA(2)HexNAc(3) (S)">HexA(2)HexNAc(3) (S)</option>
-      <option value="HexA(2)HexNAc(3) (T)">HexA(2)HexNAc(3) (T)</option>
-      <option value="HexN (K)">HexN (K)</option>
-      <option value="HexN (N)">HexN (N)</option>
-      <option value="HexN (S)">HexN (S)</option>
-      <option value="HexN (T)">HexN (T)</option>
-      <option value="HexN (W)">HexN (W)</option>
-      <option value="HexNAc (C)">HexNAc (C)</option>
-      <option value="HexNAc (N)">HexNAc (N)</option>
-      <option value="HexNAc (S)">HexNAc (S)</option>
-      <option value="HexNAc (T)">HexNAc (T)</option>
-      <option value="HexNAc(1)dHex(1) (N)">HexNAc(1)dHex(1) (N)</option>
-      <option value="HexNAc(1)dHex(1) (S)">HexNAc(1)dHex(1) (S)</option>
-      <option value="HexNAc(1)dHex(1) (T)">HexNAc(1)dHex(1) (T)</option>
-      <option value="HexNAc(1)dHex(2) (N)">HexNAc(1)dHex(2) (N)</option>
-      <option value="HexNAc(1)Kdn(2) (S)">HexNAc(1)Kdn(2) (S)</option>
-      <option value="HexNAc(1)Kdn(2) (T)">HexNAc(1)Kdn(2) (T)</option>
-      <option value="HexNAc(1)NeuAc(1) (S)">HexNAc(1)NeuAc(1) (S)</option>
-      <option value="HexNAc(1)NeuAc(1) (T)">HexNAc(1)NeuAc(1) (T)</option>
-      <option value="HexNAc(1)NeuGc(1) (S)">HexNAc(1)NeuGc(1) (S)</option>
-      <option value="HexNAc(1)NeuGc(1) (T)">HexNAc(1)NeuGc(1) (T)</option>
-      <option value="HexNAc(1)NeuGc(2) (S)">HexNAc(1)NeuGc(2) (S)</option>
-      <option value="HexNAc(1)NeuGc(2) (T)">HexNAc(1)NeuGc(2) (T)</option>
-      <option value="HexNAc(2) (N)">HexNAc(2) (N)</option>
-      <option value="HexNAc(2) (S)">HexNAc(2) (S)</option>
-      <option value="HexNAc(2) (T)">HexNAc(2) (T)</option>
-      <option value="HexNAc(2)dHex(1) (N)">HexNAc(2)dHex(1) (N)</option>
-      <option value="HexNAc(2)dHex(2) (N)">HexNAc(2)dHex(2) (N)</option>
-      <option value="HexNAc(2)NeuAc(1) (S)">HexNAc(2)NeuAc(1) (S)</option>
-      <option value="HexNAc(2)NeuAc(1) (T)">HexNAc(2)NeuAc(1) (T)</option>
-      <option value="HexNAc(2)NeuAc(1)Sulf(1) (S)">HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="HexNAc(2)NeuAc(1)Sulf(1) (T)">HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="HexNAc(2)NeuGc(1) (S)">HexNAc(2)NeuGc(1) (S)</option>
-      <option value="HexNAc(2)NeuGc(1) (T)">HexNAc(2)NeuGc(1) (T)</option>
-      <option value="HexNAc(2)Sulf(1) (S)">HexNAc(2)Sulf(1) (S)</option>
-      <option value="HexNAc(2)Sulf(1) (T)">HexNAc(2)Sulf(1) (T)</option>
-      <option value="HexNAc(3) (S)">HexNAc(3) (S)</option>
-      <option value="HexNAc(3) (T)">HexNAc(3) (T)</option>
-      <option value="HexNAc(3)Sulf(1) (S)">HexNAc(3)Sulf(1) (S)</option>
-      <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
-      <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
-      <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
-      <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
-      <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
-      <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
-      <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
-      <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
-      <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
-      <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
-      <option value="His-&gt;Gln (H)">His-&gt;Gln (H)</option>
-      <option value="His-&gt;Glu (H)">His-&gt;Glu (H)</option>
-      <option value="His-&gt;Gly (H)">His-&gt;Gly (H)</option>
-      <option value="His-&gt;Lys (H)">His-&gt;Lys (H)</option>
-      <option value="His-&gt;Met (H)">His-&gt;Met (H)</option>
-      <option value="His-&gt;Phe (H)">His-&gt;Phe (H)</option>
-      <option value="His-&gt;Pro (H)">His-&gt;Pro (H)</option>
-      <option value="His-&gt;Ser (H)">His-&gt;Ser (H)</option>
-      <option value="His-&gt;Thr (H)">His-&gt;Thr (H)</option>
-      <option value="His-&gt;Trp (H)">His-&gt;Trp (H)</option>
-      <option value="His-&gt;Tyr (H)">His-&gt;Tyr (H)</option>
-      <option value="His-&gt;Val (H)">His-&gt;Val (H)</option>
-      <option value="His-&gt;Xle (H)">His-&gt;Xle (H)</option>
-      <option value="HMVK (C)">HMVK (C)</option>
-      <option value="HN2_mustard (C)">HN2_mustard (C)</option>
-      <option value="HN2_mustard (H)">HN2_mustard (H)</option>
-      <option value="HN2_mustard (K)">HN2_mustard (K)</option>
-      <option value="HN3_mustard (C)">HN3_mustard (C)</option>
-      <option value="HN3_mustard (H)">HN3_mustard (H)</option>
-      <option value="HN3_mustard (K)">HN3_mustard (K)</option>
-      <option value="HNE (A)">HNE (A)</option>
-      <option value="HNE (C)">HNE (C)</option>
-      <option value="HNE (H)">HNE (H)</option>
-      <option value="HNE (K)">HNE (K)</option>
-      <option value="HNE (L)">HNE (L)</option>
-      <option value="HNE+Delta:H(2) (C)">HNE+Delta:H(2) (C)</option>
-      <option value="HNE+Delta:H(2) (H)">HNE+Delta:H(2) (H)</option>
-      <option value="HNE+Delta:H(2) (K)">HNE+Delta:H(2) (K)</option>
-      <option value="HNE-BAHAH (C)">HNE-BAHAH (C)</option>
-      <option value="HNE-BAHAH (H)">HNE-BAHAH (H)</option>
-      <option value="HNE-BAHAH (K)">HNE-BAHAH (K)</option>
-      <option value="HNE-Delta:H(2)O (C)">HNE-Delta:H(2)O (C)</option>
-      <option value="HNE-Delta:H(2)O (H)">HNE-Delta:H(2)O (H)</option>
-      <option value="HNE-Delta:H(2)O (K)">HNE-Delta:H(2)O (K)</option>
-      <option value="Homocysteic_acid (M)">Homocysteic_acid (M)</option>
-      <option value="HPG (R)">HPG (R)</option>
-      <option value="Hydroxamic_acid (D)">Hydroxamic_acid (D)</option>
-      <option value="Hydroxamic_acid (E)">Hydroxamic_acid (E)</option>
-      <option value="Hydroxycinnamyl (C)">Hydroxycinnamyl (C)</option>
-      <option value="Hydroxyfarnesyl (C)">Hydroxyfarnesyl (C)</option>
-      <option value="Hydroxyheme (E)">Hydroxyheme (E)</option>
-      <option value="hydroxyisobutyryl (K)">hydroxyisobutyryl (K)</option>
-      <option value="Hydroxymethyl (N)">Hydroxymethyl (N)</option>
-      <option value="HydroxymethylOP (K)">HydroxymethylOP (K)</option>
-      <option value="Hydroxytrimethyl (K)">Hydroxytrimethyl (K)</option>
-      <option value="Hypusine (K)">Hypusine (K)</option>
-      <option value="IASD (C)">IASD (C)</option>
-      <option value="IBTP (C)">IBTP (C)</option>
-      <option value="ICAT-C (C)">ICAT-C (C)</option>
-      <option value="ICAT-C:13C(9) (C)">ICAT-C:13C(9) (C)</option>
-      <option value="ICAT-D (C)">ICAT-D (C)</option>
-      <option value="ICAT-D:2H(8) (C)">ICAT-D:2H(8) (C)</option>
-      <option value="ICAT-G (C)">ICAT-G (C)</option>
-      <option value="ICAT-G:2H(8) (C)">ICAT-G:2H(8) (C)</option>
-      <option value="ICAT-H (C)">ICAT-H (C)</option>
-      <option value="ICAT-H:13C(6) (C)">ICAT-H:13C(6) (C)</option>
-      <option value="ICDID (C)">ICDID (C)</option>
-      <option value="ICDID:2H(6) (C)">ICDID:2H(6) (C)</option>
-      <option value="ICPL (K)">ICPL (K)</option>
-      <option value="ICPL (N-term)">ICPL (N-term)</option>
-      <option value="ICPL (Protein N-term)">ICPL (Protein N-term)</option>
-      <option value="ICPL:13C(6) (K)">ICPL:13C(6) (K)</option>
-      <option value="ICPL:13C(6) (N-term)">ICPL:13C(6) (N-term)</option>
-      <option value="ICPL:13C(6) (Protein N-term)">ICPL:13C(6) (Protein N-term)</option>
-      <option value="ICPL:13C(6)2H(4) (K)">ICPL:13C(6)2H(4) (K)</option>
-      <option value="ICPL:13C(6)2H(4) (N-term)">ICPL:13C(6)2H(4) (N-term)</option>
-      <option value="ICPL:13C(6)2H(4) (Protein N-term)">ICPL:13C(6)2H(4) (Protein N-term)</option>
-      <option value="ICPL:2H(4) (K)">ICPL:2H(4) (K)</option>
-      <option value="ICPL:2H(4) (N-term)">ICPL:2H(4) (N-term)</option>
-      <option value="ICPL:2H(4) (Protein N-term)">ICPL:2H(4) (Protein N-term)</option>
-      <option value="IDEnT (C)">IDEnT (C)</option>
-      <option value="IED-Biotin (C)">IED-Biotin (C)</option>
-      <option value="IGBP (C)">IGBP (C)</option>
-      <option value="IGBP:13C(2) (C)">IGBP:13C(2) (C)</option>
-      <option value="IMEHex(2)NeuAc(1) (K)">IMEHex(2)NeuAc(1) (K)</option>
-      <option value="IMID (K)">IMID (K)</option>
-      <option value="IMID:2H(4) (K)">IMID:2H(4) (K)</option>
-      <option value="Iminobiotin (K)">Iminobiotin (K)</option>
-      <option value="Iminobiotin (N-term)">Iminobiotin (N-term)</option>
-      <option value="Iodo (H)">Iodo (H)</option>
-      <option value="Iodo (Y)">Iodo (Y)</option>
-      <option value="Iodoacetanilide (C)">Iodoacetanilide (C)</option>
-      <option value="Iodoacetanilide (K)">Iodoacetanilide (K)</option>
-      <option value="Iodoacetanilide (N-term)">Iodoacetanilide (N-term)</option>
-      <option value="Iodoacetanilide:13C(6) (C)">Iodoacetanilide:13C(6) (C)</option>
-      <option value="Iodoacetanilide:13C(6) (K)">Iodoacetanilide:13C(6) (K)</option>
-      <option value="Iodoacetanilide:13C(6) (N-term)">Iodoacetanilide:13C(6) (N-term)</option>
-      <option value="iodoTMT (C)">iodoTMT (C)</option>
-      <option value="iodoTMT (D)">iodoTMT (D)</option>
-      <option value="iodoTMT (E)">iodoTMT (E)</option>
-      <option value="iodoTMT (H)">iodoTMT (H)</option>
-      <option value="iodoTMT (K)">iodoTMT (K)</option>
-      <option value="iodoTMT6plex (C)">iodoTMT6plex (C)</option>
-      <option value="iodoTMT6plex (D)">iodoTMT6plex (D)</option>
-      <option value="iodoTMT6plex (E)">iodoTMT6plex (E)</option>
-      <option value="iodoTMT6plex (H)">iodoTMT6plex (H)</option>
-      <option value="iodoTMT6plex (K)">iodoTMT6plex (K)</option>
-      <option value="IodoU-AMP (F)">IodoU-AMP (F)</option>
-      <option value="IodoU-AMP (W)">IodoU-AMP (W)</option>
-      <option value="IodoU-AMP (Y)">IodoU-AMP (Y)</option>
-      <option value="ISD_z+2_ion (N-term)">ISD_z+2_ion (N-term)</option>
-      <option value="Isopropylphospho (S)">Isopropylphospho (S)</option>
-      <option value="Isopropylphospho (T)">Isopropylphospho (T)</option>
-      <option value="Isopropylphospho (Y)">Isopropylphospho (Y)</option>
-      <option value="iTRAQ4plex (C)">iTRAQ4plex (C)</option>
-      <option value="iTRAQ4plex (H)">iTRAQ4plex (H)</option>
-      <option value="iTRAQ4plex (K)">iTRAQ4plex (K)</option>
-      <option value="iTRAQ4plex (N-term)">iTRAQ4plex (N-term)</option>
-      <option value="iTRAQ4plex (Protein N-term)">iTRAQ4plex (Protein N-term)</option>
-      <option value="iTRAQ4plex (S)">iTRAQ4plex (S)</option>
-      <option value="iTRAQ4plex (T)">iTRAQ4plex (T)</option>
-      <option value="iTRAQ4plex (Y)">iTRAQ4plex (Y)</option>
-      <option value="iTRAQ4plex114 (C)">iTRAQ4plex114 (C)</option>
-      <option value="iTRAQ4plex114 (K)">iTRAQ4plex114 (K)</option>
-      <option value="iTRAQ4plex114 (N-term)">iTRAQ4plex114 (N-term)</option>
-      <option value="iTRAQ4plex114 (Y)">iTRAQ4plex114 (Y)</option>
-      <option value="iTRAQ4plex115 (C)">iTRAQ4plex115 (C)</option>
-      <option value="iTRAQ4plex115 (K)">iTRAQ4plex115 (K)</option>
-      <option value="iTRAQ4plex115 (N-term)">iTRAQ4plex115 (N-term)</option>
-      <option value="iTRAQ4plex115 (Y)">iTRAQ4plex115 (Y)</option>
-      <option value="iTRAQ8plex (C)">iTRAQ8plex (C)</option>
-      <option value="iTRAQ8plex (H)">iTRAQ8plex (H)</option>
-      <option value="iTRAQ8plex (K)">iTRAQ8plex (K)</option>
-      <option value="iTRAQ8plex (N-term)">iTRAQ8plex (N-term)</option>
-      <option value="iTRAQ8plex (Protein N-term)">iTRAQ8plex (Protein N-term)</option>
-      <option value="iTRAQ8plex (S)">iTRAQ8plex (S)</option>
-      <option value="iTRAQ8plex (T)">iTRAQ8plex (T)</option>
-      <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
-      <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
-      <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
-      <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
-      <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
-      <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
-      <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
-      <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
-      <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
-      <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
-      <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
-      <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
-      <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
-      <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
-      <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
-      <option value="Label:13C(5)15N(1) (E)">Label:13C(5)15N(1) (E)</option>
-      <option value="Label:13C(5)15N(1) (M)">Label:13C(5)15N(1) (M)</option>
-      <option value="Label:13C(5)15N(1) (P)">Label:13C(5)15N(1) (P)</option>
-      <option value="Label:13C(5)15N(1) (V)">Label:13C(5)15N(1) (V)</option>
-      <option value="Label:13C(6) (I)">Label:13C(6) (I)</option>
-      <option value="Label:13C(6) (K)">Label:13C(6) (K)</option>
-      <option value="Label:13C(6) (L)">Label:13C(6) (L)</option>
-      <option value="Label:13C(6) (R)">Label:13C(6) (R)</option>
-      <option value="Label:13C(6)+Acetyl (K)">Label:13C(6)+Acetyl (K)</option>
-      <option value="Label:13C(6)+Dimethyl (K)">Label:13C(6)+Dimethyl (K)</option>
-      <option value="Label:13C(6)+GG (K)">Label:13C(6)+GG (K)</option>
-      <option value="Label:13C(6)15N(1) (I)">Label:13C(6)15N(1) (I)</option>
-      <option value="Label:13C(6)15N(1) (L)">Label:13C(6)15N(1) (L)</option>
-      <option value="Label:13C(6)15N(2) (K)">Label:13C(6)15N(2) (K)</option>
-      <option value="Label:13C(6)15N(2)+Acetyl (K)">Label:13C(6)15N(2)+Acetyl (K)</option>
-      <option value="Label:13C(6)15N(2)+Dimethyl (K)">Label:13C(6)15N(2)+Dimethyl (K)</option>
-      <option value="Label:13C(6)15N(2)+GG (K)">Label:13C(6)15N(2)+GG (K)</option>
-      <option value="Label:13C(6)15N(4) (R)">Label:13C(6)15N(4) (R)</option>
-      <option value="Label:13C(6)15N(4)+Dimethyl (R)">Label:13C(6)15N(4)+Dimethyl (R)</option>
-      <option value="Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R)">Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R)</option>
-      <option value="Label:13C(6)15N(4)+Methyl (R)">Label:13C(6)15N(4)+Methyl (R)</option>
-      <option value="Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R)">Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R)</option>
-      <option value="Label:13C(9) (F)">Label:13C(9) (F)</option>
-      <option value="Label:13C(9) (Y)">Label:13C(9) (Y)</option>
-      <option value="Label:13C(9)+Phospho (Y)">Label:13C(9)+Phospho (Y)</option>
-      <option value="Label:13C(9)15N(1) (F)">Label:13C(9)15N(1) (F)</option>
-      <option value="Label:15N(1) (A)">Label:15N(1) (A)</option>
-      <option value="Label:15N(1) (C)">Label:15N(1) (C)</option>
-      <option value="Label:15N(1) (D)">Label:15N(1) (D)</option>
-      <option value="Label:15N(1) (E)">Label:15N(1) (E)</option>
-      <option value="Label:15N(1) (F)">Label:15N(1) (F)</option>
-      <option value="Label:15N(1) (G)">Label:15N(1) (G)</option>
-      <option value="Label:15N(1) (I)">Label:15N(1) (I)</option>
-      <option value="Label:15N(1) (L)">Label:15N(1) (L)</option>
-      <option value="Label:15N(1) (M)">Label:15N(1) (M)</option>
-      <option value="Label:15N(1) (P)">Label:15N(1) (P)</option>
-      <option value="Label:15N(1) (S)">Label:15N(1) (S)</option>
-      <option value="Label:15N(1) (T)">Label:15N(1) (T)</option>
-      <option value="Label:15N(1) (V)">Label:15N(1) (V)</option>
-      <option value="Label:15N(1) (Y)">Label:15N(1) (Y)</option>
-      <option value="Label:15N(2) (K)">Label:15N(2) (K)</option>
-      <option value="Label:15N(2) (N)">Label:15N(2) (N)</option>
-      <option value="Label:15N(2) (Q)">Label:15N(2) (Q)</option>
-      <option value="Label:15N(2) (W)">Label:15N(2) (W)</option>
-      <option value="Label:15N(2)2H(9) (K)">Label:15N(2)2H(9) (K)</option>
-      <option value="Label:15N(3) (H)">Label:15N(3) (H)</option>
-      <option value="Label:15N(4) (R)">Label:15N(4) (R)</option>
-      <option value="Label:18O(1) (C-term)">Label:18O(1) (C-term)</option>
-      <option value="Label:18O(1) (S)">Label:18O(1) (S)</option>
-      <option value="Label:18O(1) (T)">Label:18O(1) (T)</option>
-      <option value="Label:18O(1) (Y)">Label:18O(1) (Y)</option>
-      <option value="Label:18O(2) (C-term)">Label:18O(2) (C-term)</option>
-      <option value="Label:2H(10) (L)">Label:2H(10) (L)</option>
-      <option value="Label:2H(3) (L)">Label:2H(3) (L)</option>
-      <option value="Label:2H(3) (M)">Label:2H(3) (M)</option>
-      <option value="Label:2H(3)+Oxidation (M)">Label:2H(3)+Oxidation (M)</option>
-      <option value="Label:2H(4) (A)">Label:2H(4) (A)</option>
-      <option value="Label:2H(4) (F)">Label:2H(4) (F)</option>
-      <option value="Label:2H(4) (K)">Label:2H(4) (K)</option>
-      <option value="Label:2H(4) (U)">Label:2H(4) (U)</option>
-      <option value="Label:2H(4) (Y)">Label:2H(4) (Y)</option>
-      <option value="Label:2H(4)+Acetyl (K)">Label:2H(4)+Acetyl (K)</option>
-      <option value="Label:2H(4)+GG (K)">Label:2H(4)+GG (K)</option>
-      <option value="Label:2H(4)13C(1) (R)">Label:2H(4)13C(1) (R)</option>
-      <option value="Label:2H(6)15N(1) (P)">Label:2H(6)15N(1) (P)</option>
-      <option value="Label:2H(7)15N(4) (R)">Label:2H(7)15N(4) (R)</option>
-      <option value="Label:2H(9)13C(6)15N(2) (K)">Label:2H(9)13C(6)15N(2) (K)</option>
-      <option value="lapachenole (C)">lapachenole (C)</option>
-      <option value="Leu-&gt;MetOx (L)">Leu-&gt;MetOx (L)</option>
-      <option value="LG-anhydrolactam (K)">LG-anhydrolactam (K)</option>
-      <option value="LG-anhydrolactam (N-term)">LG-anhydrolactam (N-term)</option>
-      <option value="LG-anhyropyrrole (K)">LG-anhyropyrrole (K)</option>
-      <option value="LG-anhyropyrrole (N-term)">LG-anhyropyrrole (N-term)</option>
-      <option value="LG-Hlactam-K (K)">LG-Hlactam-K (K)</option>
-      <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
-      <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
-      <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
-      <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
-      <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
-      <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
-      <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
-      <option value="Lipoyl (K)">Lipoyl (K)</option>
-      <option value="LRGG (K)">LRGG (K)</option>
-      <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
-      <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
-      <option value="Lys (N-term)">Lys (N-term)</option>
-      <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
-      <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
-      <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
-      <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
-      <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
-      <option value="Lys-&gt;Asp (K)">Lys-&gt;Asp (K)</option>
-      <option value="Lys-&gt;CamCys (K)">Lys-&gt;CamCys (K)</option>
-      <option value="Lys-&gt;Cys (K)">Lys-&gt;Cys (K)</option>
-      <option value="Lys-&gt;Gln (K)">Lys-&gt;Gln (K)</option>
-      <option value="Lys-&gt;Glu (K)">Lys-&gt;Glu (K)</option>
-      <option value="Lys-&gt;Gly (K)">Lys-&gt;Gly (K)</option>
-      <option value="Lys-&gt;His (K)">Lys-&gt;His (K)</option>
-      <option value="Lys-&gt;Met (K)">Lys-&gt;Met (K)</option>
-      <option value="Lys-&gt;MetOx (K)">Lys-&gt;MetOx (K)</option>
-      <option value="Lys-&gt;Phe (K)">Lys-&gt;Phe (K)</option>
-      <option value="Lys-&gt;Pro (K)">Lys-&gt;Pro (K)</option>
-      <option value="Lys-&gt;Ser (K)">Lys-&gt;Ser (K)</option>
-      <option value="Lys-&gt;Thr (K)">Lys-&gt;Thr (K)</option>
-      <option value="Lys-&gt;Trp (K)">Lys-&gt;Trp (K)</option>
-      <option value="Lys-&gt;Tyr (K)">Lys-&gt;Tyr (K)</option>
-      <option value="Lys-&gt;Val (K)">Lys-&gt;Val (K)</option>
-      <option value="Lys-&gt;Xle (K)">Lys-&gt;Xle (K)</option>
-      <option value="Lys-loss (Protein C-term K)">Lys-loss (Protein C-term K)</option>
-      <option value="Lysbiotinhydrazide (K)">Lysbiotinhydrazide (K)</option>
-      <option value="maleimide (C)">maleimide (C)</option>
-      <option value="maleimide (K)">maleimide (K)</option>
-      <option value="Maleimide-PEO2-Biotin (C)">Maleimide-PEO2-Biotin (C)</option>
-      <option value="maleimide3 (C)">maleimide3 (C)</option>
-      <option value="maleimide3 (K)">maleimide3 (K)</option>
-      <option value="maleimide5 (C)">maleimide5 (C)</option>
-      <option value="maleimide5 (K)">maleimide5 (K)</option>
-      <option value="Malonyl (C)">Malonyl (C)</option>
-      <option value="Malonyl (K)">Malonyl (K)</option>
-      <option value="Malonyl (S)">Malonyl (S)</option>
-      <option value="MDCC (C)">MDCC (C)</option>
-      <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
-      <option value="Menadione (C)">Menadione (C)</option>
-      <option value="Menadione (K)">Menadione (K)</option>
-      <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
-      <option value="Menadione-HQ (K)">Menadione-HQ (K)</option>
-      <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
-      <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
-      <option value="MesitylOxide (H)">MesitylOxide (H)</option>
-      <option value="MesitylOxide (K)">MesitylOxide (K)</option>
-      <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
-      <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
-      <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
-      <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
-      <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
-      <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
-      <option value="Met-&gt;AspSA (M)">Met-&gt;AspSA (M)</option>
-      <option value="Met-&gt;Cys (M)">Met-&gt;Cys (M)</option>
-      <option value="Met-&gt;Gln (M)">Met-&gt;Gln (M)</option>
-      <option value="Met-&gt;Glu (M)">Met-&gt;Glu (M)</option>
-      <option value="Met-&gt;Gly (M)">Met-&gt;Gly (M)</option>
-      <option value="Met-&gt;His (M)">Met-&gt;His (M)</option>
-      <option value="Met-&gt;Hpg (M)">Met-&gt;Hpg (M)</option>
-      <option value="Met-&gt;Hse (C-term M)">Met-&gt;Hse (C-term M)</option>
-      <option value="Met-&gt;Hsl (C-term M)">Met-&gt;Hsl (C-term M)</option>
-      <option value="Met-&gt;Lys (M)">Met-&gt;Lys (M)</option>
-      <option value="Met-&gt;Phe (M)">Met-&gt;Phe (M)</option>
-      <option value="Met-&gt;Pro (M)">Met-&gt;Pro (M)</option>
-      <option value="Met-&gt;Ser (M)">Met-&gt;Ser (M)</option>
-      <option value="Met-&gt;Thr (M)">Met-&gt;Thr (M)</option>
-      <option value="Met-&gt;Trp (M)">Met-&gt;Trp (M)</option>
-      <option value="Met-&gt;Tyr (M)">Met-&gt;Tyr (M)</option>
-      <option value="Met-&gt;Val (M)">Met-&gt;Val (M)</option>
-      <option value="Met-&gt;Xle (M)">Met-&gt;Xle (M)</option>
-      <option value="Met-loss (Protein N-term M)">Met-loss (Protein N-term M)</option>
-      <option value="Met-loss+Acetyl (Protein N-term M)">Met-loss+Acetyl (Protein N-term M)</option>
-      <option value="Methamidophos-O (C)">Methamidophos-O (C)</option>
-      <option value="Methamidophos-O (H)">Methamidophos-O (H)</option>
-      <option value="Methamidophos-O (K)">Methamidophos-O (K)</option>
-      <option value="Methamidophos-O (S)">Methamidophos-O (S)</option>
-      <option value="Methamidophos-O (T)">Methamidophos-O (T)</option>
-      <option value="Methamidophos-O (Y)">Methamidophos-O (Y)</option>
-      <option value="Methamidophos-S (C)">Methamidophos-S (C)</option>
-      <option value="Methamidophos-S (H)">Methamidophos-S (H)</option>
-      <option value="Methamidophos-S (K)">Methamidophos-S (K)</option>
-      <option value="Methamidophos-S (S)">Methamidophos-S (S)</option>
-      <option value="Methamidophos-S (T)">Methamidophos-S (T)</option>
-      <option value="Methamidophos-S (Y)">Methamidophos-S (Y)</option>
-      <option value="Methyl (C)">Methyl (C)</option>
-      <option value="Methyl (C-term)">Methyl (C-term)</option>
-      <option value="Methyl (D)">Methyl (D)</option>
-      <option value="Methyl (E)">Methyl (E)</option>
-      <option value="Methyl (H)">Methyl (H)</option>
-      <option value="Methyl (I)">Methyl (I)</option>
-      <option value="Methyl (K)">Methyl (K)</option>
-      <option value="Methyl (L)">Methyl (L)</option>
-      <option value="Methyl (N)">Methyl (N)</option>
-      <option value="Methyl (N-term)">Methyl (N-term)</option>
-      <option value="Methyl (Protein N-term)">Methyl (Protein N-term)</option>
-      <option value="Methyl (Q)">Methyl (Q)</option>
-      <option value="Methyl (R)">Methyl (R)</option>
-      <option value="Methyl (S)">Methyl (S)</option>
-      <option value="Methyl (T)">Methyl (T)</option>
-      <option value="Methyl+Acetyl:2H(3) (K)">Methyl+Acetyl:2H(3) (K)</option>
-      <option value="Methyl+Deamidated (N)">Methyl+Deamidated (N)</option>
-      <option value="Methyl+Deamidated (Q)">Methyl+Deamidated (Q)</option>
-      <option value="Methyl-PEO12-Maleimide (C)">Methyl-PEO12-Maleimide (C)</option>
-      <option value="Methyl:2H(2) (K)">Methyl:2H(2) (K)</option>
-      <option value="Methyl:2H(2) (N-term)">Methyl:2H(2) (N-term)</option>
-      <option value="Methyl:2H(2)13C (C)">Methyl:2H(2)13C (C)</option>
-      <option value="Methyl:2H(2)13C (C-term)">Methyl:2H(2)13C (C-term)</option>
-      <option value="Methyl:2H(2)13C (D)">Methyl:2H(2)13C (D)</option>
-      <option value="Methyl:2H(2)13C (E)">Methyl:2H(2)13C (E)</option>
-      <option value="Methyl:2H(2)13C (H)">Methyl:2H(2)13C (H)</option>
-      <option value="Methyl:2H(2)13C (I)">Methyl:2H(2)13C (I)</option>
-      <option value="Methyl:2H(2)13C (K)">Methyl:2H(2)13C (K)</option>
-      <option value="Methyl:2H(2)13C (L)">Methyl:2H(2)13C (L)</option>
-      <option value="Methyl:2H(2)13C (N)">Methyl:2H(2)13C (N)</option>
-      <option value="Methyl:2H(2)13C (N-term)">Methyl:2H(2)13C (N-term)</option>
-      <option value="Methyl:2H(2)13C (Protein N-term)">Methyl:2H(2)13C (Protein N-term)</option>
-      <option value="Methyl:2H(2)13C (Q)">Methyl:2H(2)13C (Q)</option>
-      <option value="Methyl:2H(2)13C (R)">Methyl:2H(2)13C (R)</option>
-      <option value="Methyl:2H(2)13C (S)">Methyl:2H(2)13C (S)</option>
-      <option value="Methyl:2H(2)13C (T)">Methyl:2H(2)13C (T)</option>
-      <option value="Methyl:2H(3) (D)">Methyl:2H(3) (D)</option>
-      <option value="Methyl:2H(3) (E)">Methyl:2H(3) (E)</option>
-      <option value="Methyl:2H(3) (K)">Methyl:2H(3) (K)</option>
-      <option value="Methyl:2H(3) (R)">Methyl:2H(3) (R)</option>
-      <option value="Methyl:2H(3) (X)">Methyl:2H(3) (X)</option>
-      <option value="Methyl:2H(3)+Acetyl:2H(3) (K)">Methyl:2H(3)+Acetyl:2H(3) (K)</option>
-      <option value="Methyl:2H(3)13C(1) (K)">Methyl:2H(3)13C(1) (K)</option>
-      <option value="Methyl:2H(3)13C(1) (N-term)">Methyl:2H(3)13C(1) (N-term)</option>
-      <option value="Methyl:2H(3)13C(1) (R)">Methyl:2H(3)13C(1) (R)</option>
-      <option value="Methylamine (S)">Methylamine (S)</option>
-      <option value="Methylamine (T)">Methylamine (T)</option>
-      <option value="Methylmalonylation (S)">Methylmalonylation (S)</option>
-      <option value="methylol (K)">methylol (K)</option>
-      <option value="methylol (W)">methylol (W)</option>
-      <option value="methylol (Y)">methylol (Y)</option>
-      <option value="Methylphosphonate (S)">Methylphosphonate (S)</option>
-      <option value="Methylphosphonate (T)">Methylphosphonate (T)</option>
-      <option value="Methylphosphonate (Y)">Methylphosphonate (Y)</option>
-      <option value="Methylpyrroline (K)">Methylpyrroline (K)</option>
-      <option value="methylsulfonylethyl (C)">methylsulfonylethyl (C)</option>
-      <option value="methylsulfonylethyl (H)">methylsulfonylethyl (H)</option>
-      <option value="methylsulfonylethyl (K)">methylsulfonylethyl (K)</option>
-      <option value="Methylthio (C)">Methylthio (C)</option>
-      <option value="Methylthio (D)">Methylthio (D)</option>
-      <option value="Methylthio (K)">Methylthio (K)</option>
-      <option value="Methylthio (N)">Methylthio (N)</option>
-      <option value="Methylthio (N-term)">Methylthio (N-term)</option>
-      <option value="MG-H1 (R)">MG-H1 (R)</option>
-      <option value="Microcin (Protein C-term)">Microcin (Protein C-term)</option>
-      <option value="MicrocinC7 (Protein C-term)">MicrocinC7 (Protein C-term)</option>
-      <option value="MM-diphenylpentanone (C)">MM-diphenylpentanone (C)</option>
-      <option value="Molybdopterin (C)">Molybdopterin (C)</option>
-      <option value="MolybdopterinGD (C)">MolybdopterinGD (C)</option>
-      <option value="MolybdopterinGD (D)">MolybdopterinGD (D)</option>
-      <option value="MolybdopterinGD (U)">MolybdopterinGD (U)</option>
-      <option value="MolybdopterinGD+Delta:S(-1)Se(1) (C)">MolybdopterinGD+Delta:S(-1)Se(1) (C)</option>
-      <option value="monomethylphosphothione (C)">monomethylphosphothione (C)</option>
-      <option value="monomethylphosphothione (H)">monomethylphosphothione (H)</option>
-      <option value="monomethylphosphothione (K)">monomethylphosphothione (K)</option>
-      <option value="monomethylphosphothione (S)">monomethylphosphothione (S)</option>
-      <option value="monomethylphosphothione (T)">monomethylphosphothione (T)</option>
-      <option value="monomethylphosphothione (Y)">monomethylphosphothione (Y)</option>
-      <option value="mTRAQ (H)">mTRAQ (H)</option>
-      <option value="mTRAQ (K)">mTRAQ (K)</option>
-      <option value="mTRAQ (N-term)">mTRAQ (N-term)</option>
-      <option value="mTRAQ (S)">mTRAQ (S)</option>
-      <option value="mTRAQ (T)">mTRAQ (T)</option>
-      <option value="mTRAQ (Y)">mTRAQ (Y)</option>
-      <option value="mTRAQ:13C(3)15N(1) (H)">mTRAQ:13C(3)15N(1) (H)</option>
-      <option value="mTRAQ:13C(3)15N(1) (K)">mTRAQ:13C(3)15N(1) (K)</option>
-      <option value="mTRAQ:13C(3)15N(1) (N-term)">mTRAQ:13C(3)15N(1) (N-term)</option>
-      <option value="mTRAQ:13C(3)15N(1) (S)">mTRAQ:13C(3)15N(1) (S)</option>
-      <option value="mTRAQ:13C(3)15N(1) (T)">mTRAQ:13C(3)15N(1) (T)</option>
-      <option value="mTRAQ:13C(3)15N(1) (Y)">mTRAQ:13C(3)15N(1) (Y)</option>
-      <option value="mTRAQ:13C(6)15N(2) (H)">mTRAQ:13C(6)15N(2) (H)</option>
-      <option value="mTRAQ:13C(6)15N(2) (K)">mTRAQ:13C(6)15N(2) (K)</option>
-      <option value="mTRAQ:13C(6)15N(2) (N-term)">mTRAQ:13C(6)15N(2) (N-term)</option>
-      <option value="mTRAQ:13C(6)15N(2) (S)">mTRAQ:13C(6)15N(2) (S)</option>
-      <option value="mTRAQ:13C(6)15N(2) (T)">mTRAQ:13C(6)15N(2) (T)</option>
-      <option value="mTRAQ:13C(6)15N(2) (Y)">mTRAQ:13C(6)15N(2) (Y)</option>
-      <option value="MTSL (C)">MTSL (C)</option>
-      <option value="MurNAc (A)">MurNAc (A)</option>
-      <option value="Myristoleyl (Protein N-term G)">Myristoleyl (Protein N-term G)</option>
-      <option value="Myristoyl (C)">Myristoyl (C)</option>
-      <option value="Myristoyl (K)">Myristoyl (K)</option>
-      <option value="Myristoyl (N-term G)">Myristoyl (N-term G)</option>
-      <option value="Myristoyl+Delta:H(-4) (Protein N-term G)">Myristoyl+Delta:H(-4) (Protein N-term G)</option>
-      <option value="N-dimethylphosphate (S)">N-dimethylphosphate (S)</option>
-      <option value="NA-LNO2 (C)">NA-LNO2 (C)</option>
-      <option value="NA-LNO2 (H)">NA-LNO2 (H)</option>
-      <option value="NA-OA-NO2 (C)">NA-OA-NO2 (C)</option>
-      <option value="NA-OA-NO2 (H)">NA-OA-NO2 (H)</option>
-      <option value="NBS (W)">NBS (W)</option>
-      <option value="NBS:13C(6) (W)">NBS:13C(6) (W)</option>
-      <option value="NDA (K)">NDA (K)</option>
-      <option value="NDA (N-term)">NDA (N-term)</option>
-      <option value="NEIAA (C)">NEIAA (C)</option>
-      <option value="NEIAA (Y)">NEIAA (Y)</option>
-      <option value="NEIAA:2H(5) (C)">NEIAA:2H(5) (C)</option>
-      <option value="NEIAA:2H(5) (Y)">NEIAA:2H(5) (Y)</option>
-      <option value="NEM:2H(5) (C)">NEM:2H(5) (C)</option>
-      <option value="NEM:2H(5)+H2O (C)">NEM:2H(5)+H2O (C)</option>
-      <option value="NEMsulfur (C)">NEMsulfur (C)</option>
-      <option value="NEMsulfurWater (C)">NEMsulfurWater (C)</option>
-      <option value="Nethylmaleimide (C)">Nethylmaleimide (C)</option>
-      <option value="Nethylmaleimide+water (C)">Nethylmaleimide+water (C)</option>
-      <option value="Nethylmaleimide+water (K)">Nethylmaleimide+water (K)</option>
-      <option value="NeuAc (N)">NeuAc (N)</option>
-      <option value="NeuAc (S)">NeuAc (S)</option>
-      <option value="NeuAc (T)">NeuAc (T)</option>
-      <option value="NeuGc (N)">NeuGc (N)</option>
-      <option value="NeuGc (S)">NeuGc (S)</option>
-      <option value="NeuGc (T)">NeuGc (T)</option>
-      <option value="NHS-fluorescein (K)">NHS-fluorescein (K)</option>
-      <option value="NHS-LC-Biotin (K)">NHS-LC-Biotin (K)</option>
-      <option value="NHS-LC-Biotin (N-term)">NHS-LC-Biotin (N-term)</option>
-      <option value="NIC (K)">NIC (K)</option>
-      <option value="NIC (N-term)">NIC (N-term)</option>
-      <option value="NIPCAM (C)">NIPCAM (C)</option>
-      <option value="Nitrene (Y)">Nitrene (Y)</option>
-      <option value="Nitro (F)">Nitro (F)</option>
-      <option value="Nitro (W)">Nitro (W)</option>
-      <option value="Nitro (Y)">Nitro (Y)</option>
-      <option value="Nitrosyl (C)">Nitrosyl (C)</option>
-      <option value="Nitrosyl (Y)">Nitrosyl (Y)</option>
-      <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
-      <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
-      <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
-      <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
-      <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-      <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
-      <option value="NP40 (N-term)">NP40 (N-term)</option>
-      <option value="NQIGG (K)">NQIGG (K)</option>
-      <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
-      <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
-      <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
-      <option value="O-Et-N-diMePhospho (S)">O-Et-N-diMePhospho (S)</option>
-      <option value="O-Isopropylmethylphosphonate (S)">O-Isopropylmethylphosphonate (S)</option>
-      <option value="O-Isopropylmethylphosphonate (T)">O-Isopropylmethylphosphonate (T)</option>
-      <option value="O-Isopropylmethylphosphonate (Y)">O-Isopropylmethylphosphonate (Y)</option>
-      <option value="O-Methylphosphate (S)">O-Methylphosphate (S)</option>
-      <option value="O-Methylphosphate (T)">O-Methylphosphate (T)</option>
-      <option value="O-Methylphosphate (Y)">O-Methylphosphate (Y)</option>
-      <option value="O-pinacolylmethylphosphonate (H)">O-pinacolylmethylphosphonate (H)</option>
-      <option value="O-pinacolylmethylphosphonate (K)">O-pinacolylmethylphosphonate (K)</option>
-      <option value="O-pinacolylmethylphosphonate (S)">O-pinacolylmethylphosphonate (S)</option>
-      <option value="O-pinacolylmethylphosphonate (T)">O-pinacolylmethylphosphonate (T)</option>
-      <option value="O-pinacolylmethylphosphonate (Y)">O-pinacolylmethylphosphonate (Y)</option>
-      <option value="Octanoyl (C)">Octanoyl (C)</option>
-      <option value="Octanoyl (S)">Octanoyl (S)</option>
-      <option value="Octanoyl (T)">Octanoyl (T)</option>
-      <option value="OxArgBiotin (R)">OxArgBiotin (R)</option>
-      <option value="OxArgBiotinRed (R)">OxArgBiotinRed (R)</option>
-      <option value="Oxidation (C)">Oxidation (C)</option>
-      <option value="Oxidation (C-term G)">Oxidation (C-term G)</option>
-      <option value="Oxidation (D)">Oxidation (D)</option>
-      <option value="Oxidation (E)">Oxidation (E)</option>
-      <option value="Oxidation (F)">Oxidation (F)</option>
-      <option value="Oxidation (H)">Oxidation (H)</option>
-      <option value="Oxidation (I)">Oxidation (I)</option>
-      <option value="Oxidation (K)">Oxidation (K)</option>
-      <option value="Oxidation (L)">Oxidation (L)</option>
-      <option value="Oxidation (M)">Oxidation (M)</option>
-      <option value="Oxidation (N)">Oxidation (N)</option>
-      <option value="Oxidation (P)">Oxidation (P)</option>
-      <option value="Oxidation (Q)">Oxidation (Q)</option>
-      <option value="Oxidation (R)">Oxidation (R)</option>
-      <option value="Oxidation (S)">Oxidation (S)</option>
-      <option value="Oxidation (T)">Oxidation (T)</option>
-      <option value="Oxidation (U)">Oxidation (U)</option>
-      <option value="Oxidation (V)">Oxidation (V)</option>
-      <option value="Oxidation (W)">Oxidation (W)</option>
-      <option value="Oxidation (Y)">Oxidation (Y)</option>
-      <option value="Oxidation+NEM (C)">Oxidation+NEM (C)</option>
-      <option value="OxLysBiotin (K)">OxLysBiotin (K)</option>
-      <option value="OxLysBiotinRed (K)">OxLysBiotinRed (K)</option>
-      <option value="OxProBiotin (P)">OxProBiotin (P)</option>
-      <option value="OxProBiotinRed (P)">OxProBiotinRed (P)</option>
-      <option value="Palmitoleyl (C)">Palmitoleyl (C)</option>
-      <option value="Palmitoleyl (S)">Palmitoleyl (S)</option>
-      <option value="Palmitoleyl (T)">Palmitoleyl (T)</option>
-      <option value="Palmitoyl (C)">Palmitoyl (C)</option>
-      <option value="Palmitoyl (K)">Palmitoyl (K)</option>
-      <option value="Palmitoyl (Protein N-term)">Palmitoyl (Protein N-term)</option>
-      <option value="Palmitoyl (S)">Palmitoyl (S)</option>
-      <option value="Palmitoyl (T)">Palmitoyl (T)</option>
-      <option value="PEITC (C)">PEITC (C)</option>
-      <option value="PEITC (K)">PEITC (K)</option>
-      <option value="PEITC (N-term)">PEITC (N-term)</option>
-      <option value="Pent(1)HexNAc(1) (S)">Pent(1)HexNAc(1) (S)</option>
-      <option value="Pent(1)HexNAc(1) (T)">Pent(1)HexNAc(1) (T)</option>
-      <option value="Pent(2) (S)">Pent(2) (S)</option>
-      <option value="Pent(2) (T)">Pent(2) (T)</option>
-      <option value="Pentose (S)">Pentose (S)</option>
-      <option value="Pentose (T)">Pentose (T)</option>
-      <option value="Pentylamine (Q)">Pentylamine (Q)</option>
-      <option value="PEO-Iodoacetyl-LC-Biotin (C)">PEO-Iodoacetyl-LC-Biotin (C)</option>
-      <option value="PET (S)">PET (S)</option>
-      <option value="PET (T)">PET (T)</option>
-      <option value="Phe-&gt;Ala (F)">Phe-&gt;Ala (F)</option>
-      <option value="Phe-&gt;Arg (F)">Phe-&gt;Arg (F)</option>
-      <option value="Phe-&gt;Asn (F)">Phe-&gt;Asn (F)</option>
-      <option value="Phe-&gt;Asp (F)">Phe-&gt;Asp (F)</option>
-      <option value="Phe-&gt;CamCys (F)">Phe-&gt;CamCys (F)</option>
-      <option value="Phe-&gt;Cys (F)">Phe-&gt;Cys (F)</option>
-      <option value="Phe-&gt;Gln (F)">Phe-&gt;Gln (F)</option>
-      <option value="Phe-&gt;Glu (F)">Phe-&gt;Glu (F)</option>
-      <option value="Phe-&gt;Gly (F)">Phe-&gt;Gly (F)</option>
-      <option value="Phe-&gt;His (F)">Phe-&gt;His (F)</option>
-      <option value="Phe-&gt;Lys (F)">Phe-&gt;Lys (F)</option>
-      <option value="Phe-&gt;Met (F)">Phe-&gt;Met (F)</option>
-      <option value="Phe-&gt;Pro (F)">Phe-&gt;Pro (F)</option>
-      <option value="Phe-&gt;Ser (F)">Phe-&gt;Ser (F)</option>
-      <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
-      <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
-      <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
-      <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
-      <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
-      <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
-      <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
-      <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
-      <option value="Phospho (C)">Phospho (C)</option>
-      <option value="Phospho (D)">Phospho (D)</option>
-      <option value="Phospho (E)">Phospho (E)</option>
-      <option value="Phospho (H)">Phospho (H)</option>
-      <option value="Phospho (K)">Phospho (K)</option>
-      <option value="Phospho (R)">Phospho (R)</option>
-      <option value="Phospho (S)">Phospho (S)</option>
-      <option value="Phospho (T)">Phospho (T)</option>
-      <option value="Phospho (Y)">Phospho (Y)</option>
-      <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
-      <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
-      <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
-      <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
-      <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
-      <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
-      <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
-      <option value="Phosphogluconoylation (K)">Phosphogluconoylation (K)</option>
-      <option value="Phosphogluconoylation (N-term)">Phosphogluconoylation (N-term)</option>
-      <option value="Phosphoguanosine (H)">Phosphoguanosine (H)</option>
-      <option value="Phosphoguanosine (K)">Phosphoguanosine (K)</option>
-      <option value="PhosphoHex (S)">PhosphoHex (S)</option>
-      <option value="PhosphoHex (T)">PhosphoHex (T)</option>
-      <option value="PhosphoHex(2) (N)">PhosphoHex(2) (N)</option>
-      <option value="PhosphoHex(2) (S)">PhosphoHex(2) (S)</option>
-      <option value="PhosphoHex(2) (T)">PhosphoHex(2) (T)</option>
-      <option value="PhosphoHexNAc (S)">PhosphoHexNAc (S)</option>
-      <option value="PhosphoHexNAc (T)">PhosphoHexNAc (T)</option>
-      <option value="Phosphopantetheine (S)">Phosphopantetheine (S)</option>
-      <option value="Phosphopropargyl (S)">Phosphopropargyl (S)</option>
-      <option value="Phosphopropargyl (T)">Phosphopropargyl (T)</option>
-      <option value="Phosphopropargyl (Y)">Phosphopropargyl (Y)</option>
-      <option value="phosphoRibosyl (D)">phosphoRibosyl (D)</option>
-      <option value="phosphoRibosyl (E)">phosphoRibosyl (E)</option>
-      <option value="phosphoRibosyl (R)">phosphoRibosyl (R)</option>
-      <option value="PhosphoribosyldephosphoCoA (S)">PhosphoribosyldephosphoCoA (S)</option>
-      <option value="PhosphoUridine (H)">PhosphoUridine (H)</option>
-      <option value="PhosphoUridine (Y)">PhosphoUridine (Y)</option>
-      <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
-      <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
-      <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
-      <option value="Piperidine (K)">Piperidine (K)</option>
-      <option value="Piperidine (N-term)">Piperidine (N-term)</option>
-      <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
-      <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
-      <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
-      <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
-      <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
-      <option value="Pro-&gt;Gln (P)">Pro-&gt;Gln (P)</option>
-      <option value="Pro-&gt;Glu (P)">Pro-&gt;Glu (P)</option>
-      <option value="Pro-&gt;Gly (P)">Pro-&gt;Gly (P)</option>
-      <option value="Pro-&gt;HAVA (P)">Pro-&gt;HAVA (P)</option>
-      <option value="Pro-&gt;His (P)">Pro-&gt;His (P)</option>
-      <option value="Pro-&gt;Lys (P)">Pro-&gt;Lys (P)</option>
-      <option value="Pro-&gt;Met (P)">Pro-&gt;Met (P)</option>
-      <option value="Pro-&gt;Phe (P)">Pro-&gt;Phe (P)</option>
-      <option value="Pro-&gt;pyro-Glu (P)">Pro-&gt;pyro-Glu (P)</option>
-      <option value="Pro-&gt;Pyrrolidinone (P)">Pro-&gt;Pyrrolidinone (P)</option>
-      <option value="Pro-&gt;Pyrrolidone (P)">Pro-&gt;Pyrrolidone (P)</option>
-      <option value="Pro-&gt;Ser (P)">Pro-&gt;Ser (P)</option>
-      <option value="Pro-&gt;Thr (P)">Pro-&gt;Thr (P)</option>
-      <option value="Pro-&gt;Trp (P)">Pro-&gt;Trp (P)</option>
-      <option value="Pro-&gt;Tyr (P)">Pro-&gt;Tyr (P)</option>
-      <option value="Pro-&gt;Val (P)">Pro-&gt;Val (P)</option>
-      <option value="Pro-&gt;Xle (P)">Pro-&gt;Xle (P)</option>
-      <option value="probiotinhydrazide (P)">probiotinhydrazide (P)</option>
-      <option value="Propargylamine (C-term)">Propargylamine (C-term)</option>
-      <option value="Propargylamine (D)">Propargylamine (D)</option>
-      <option value="Propargylamine (E)">Propargylamine (E)</option>
-      <option value="Propionamide (C)">Propionamide (C)</option>
-      <option value="Propionamide (K)">Propionamide (K)</option>
-      <option value="Propionamide (N-term)">Propionamide (N-term)</option>
-      <option value="Propionamide:2H(3) (C)">Propionamide:2H(3) (C)</option>
-      <option value="Propionyl (K)">Propionyl (K)</option>
-      <option value="Propionyl (N-term)">Propionyl (N-term)</option>
-      <option value="Propionyl (Protein N-term)">Propionyl (Protein N-term)</option>
-      <option value="Propionyl (S)">Propionyl (S)</option>
-      <option value="Propionyl (T)">Propionyl (T)</option>
-      <option value="Propionyl:13C(3) (K)">Propionyl:13C(3) (K)</option>
-      <option value="Propionyl:13C(3) (N-term)">Propionyl:13C(3) (N-term)</option>
-      <option value="Propiophenone (C)">Propiophenone (C)</option>
-      <option value="Propiophenone (H)">Propiophenone (H)</option>
-      <option value="Propiophenone (K)">Propiophenone (K)</option>
-      <option value="Propiophenone (R)">Propiophenone (R)</option>
-      <option value="Propiophenone (S)">Propiophenone (S)</option>
-      <option value="Propiophenone (T)">Propiophenone (T)</option>
-      <option value="Propiophenone (W)">Propiophenone (W)</option>
-      <option value="Propyl (C-term)">Propyl (C-term)</option>
-      <option value="Propyl (D)">Propyl (D)</option>
-      <option value="Propyl (E)">Propyl (E)</option>
-      <option value="Propyl (K)">Propyl (K)</option>
-      <option value="Propyl (N-term)">Propyl (N-term)</option>
-      <option value="Propyl (Protein C-term)">Propyl (Protein C-term)</option>
-      <option value="Propyl:2H(6) (K)">Propyl:2H(6) (K)</option>
-      <option value="Propyl:2H(6) (N-term)">Propyl:2H(6) (N-term)</option>
-      <option value="PropylNAGthiazoline (C)">PropylNAGthiazoline (C)</option>
-      <option value="PS_Hapten (C)">PS_Hapten (C)</option>
-      <option value="PS_Hapten (H)">PS_Hapten (H)</option>
-      <option value="PS_Hapten (K)">PS_Hapten (K)</option>
-      <option value="pupylation (K)">pupylation (K)</option>
-      <option value="Puromycin (C-term)">Puromycin (C-term)</option>
-      <option value="PyMIC (N-term)">PyMIC (N-term)</option>
-      <option value="PyridoxalPhosphate (K)">PyridoxalPhosphate (K)</option>
-      <option value="PyridoxalPhosphateH2 (K)">PyridoxalPhosphateH2 (K)</option>
-      <option value="Pyridylacetyl (K)">Pyridylacetyl (K)</option>
-      <option value="Pyridylacetyl (N-term)">Pyridylacetyl (N-term)</option>
-      <option value="Pyridylethyl (C)">Pyridylethyl (C)</option>
-      <option value="Pyro-carbamidomethyl (N-term C)">Pyro-carbamidomethyl (N-term C)</option>
-      <option value="pyrophospho (S)">pyrophospho (S)</option>
-      <option value="pyrophospho (T)">pyrophospho (T)</option>
-      <option value="PyruvicAcidIminyl (K)">PyruvicAcidIminyl (K)</option>
-      <option value="PyruvicAcidIminyl (Protein N-term C)">PyruvicAcidIminyl (Protein N-term C)</option>
-      <option value="PyruvicAcidIminyl (Protein N-term V)">PyruvicAcidIminyl (Protein N-term V)</option>
-      <option value="QAT (C)">QAT (C)</option>
-      <option value="QAT:2H(3) (C)">QAT:2H(3) (C)</option>
-      <option value="QEQTGG (K)">QEQTGG (K)</option>
-      <option value="QQQTGG (K)">QQQTGG (K)</option>
-      <option value="QTGG (K)">QTGG (K)</option>
-      <option value="Quinone (W)">Quinone (W)</option>
-      <option value="Quinone (Y)">Quinone (Y)</option>
-      <option value="Retinylidene (K)">Retinylidene (K)</option>
-      <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
-      <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
-      <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-      <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-      <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-      <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-      <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-      <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-      <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-      <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-      <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
-      <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
-      <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
-      <option value="Saligenin (H)">Saligenin (H)</option>
-      <option value="Saligenin (K)">Saligenin (K)</option>
-      <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
-      <option value="Ser-&gt;Arg (S)">Ser-&gt;Arg (S)</option>
-      <option value="Ser-&gt;Asn (S)">Ser-&gt;Asn (S)</option>
-      <option value="Ser-&gt;Asp (S)">Ser-&gt;Asp (S)</option>
-      <option value="Ser-&gt;Cys (S)">Ser-&gt;Cys (S)</option>
-      <option value="Ser-&gt;Gln (S)">Ser-&gt;Gln (S)</option>
-      <option value="Ser-&gt;Glu (S)">Ser-&gt;Glu (S)</option>
-      <option value="Ser-&gt;Gly (S)">Ser-&gt;Gly (S)</option>
-      <option value="Ser-&gt;His (S)">Ser-&gt;His (S)</option>
-      <option value="Ser-&gt;LacticAcid (Protein N-term S)">Ser-&gt;LacticAcid (Protein N-term S)</option>
-      <option value="Ser-&gt;Lys (S)">Ser-&gt;Lys (S)</option>
-      <option value="Ser-&gt;Met (S)">Ser-&gt;Met (S)</option>
-      <option value="Ser-&gt;Phe (S)">Ser-&gt;Phe (S)</option>
-      <option value="Ser-&gt;Pro (S)">Ser-&gt;Pro (S)</option>
-      <option value="Ser-&gt;Thr (S)">Ser-&gt;Thr (S)</option>
-      <option value="Ser-&gt;Trp (S)">Ser-&gt;Trp (S)</option>
-      <option value="Ser-&gt;Tyr (S)">Ser-&gt;Tyr (S)</option>
-      <option value="Ser-&gt;Val (S)">Ser-&gt;Val (S)</option>
-      <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
-      <option value="serotonylation (Q)">serotonylation (Q)</option>
-      <option value="shTMT (K)">shTMT (K)</option>
-      <option value="shTMT (N-term)">shTMT (N-term)</option>
-      <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
-      <option value="SMA (K)">SMA (K)</option>
-      <option value="SMA (N-term)">SMA (N-term)</option>
-      <option value="spermidine (Q)">spermidine (Q)</option>
-      <option value="spermine (Q)">spermine (Q)</option>
-      <option value="SPITC (K)">SPITC (K)</option>
-      <option value="SPITC (N-term)">SPITC (N-term)</option>
-      <option value="SPITC:13C(6) (K)">SPITC:13C(6) (K)</option>
-      <option value="SPITC:13C(6) (N-term)">SPITC:13C(6) (N-term)</option>
-      <option value="Succinyl (K)">Succinyl (K)</option>
-      <option value="Succinyl (N-term)">Succinyl (N-term)</option>
-      <option value="Succinyl (Protein N-term)">Succinyl (Protein N-term)</option>
-      <option value="Succinyl:13C(4) (K)">Succinyl:13C(4) (K)</option>
-      <option value="Succinyl:13C(4) (N-term)">Succinyl:13C(4) (N-term)</option>
-      <option value="Succinyl:2H(4) (K)">Succinyl:2H(4) (K)</option>
-      <option value="Succinyl:2H(4) (N-term)">Succinyl:2H(4) (N-term)</option>
-      <option value="SulfanilicAcid (C-term)">SulfanilicAcid (C-term)</option>
-      <option value="SulfanilicAcid (D)">SulfanilicAcid (D)</option>
-      <option value="SulfanilicAcid (E)">SulfanilicAcid (E)</option>
-      <option value="SulfanilicAcid:13C(6) (C-term)">SulfanilicAcid:13C(6) (C-term)</option>
-      <option value="SulfanilicAcid:13C(6) (D)">SulfanilicAcid:13C(6) (D)</option>
-      <option value="SulfanilicAcid:13C(6) (E)">SulfanilicAcid:13C(6) (E)</option>
-      <option value="Sulfide (C)">Sulfide (C)</option>
-      <option value="Sulfide (D)">Sulfide (D)</option>
-      <option value="Sulfide (W)">Sulfide (W)</option>
-      <option value="Sulfo (C)">Sulfo (C)</option>
-      <option value="Sulfo (S)">Sulfo (S)</option>
-      <option value="Sulfo (T)">Sulfo (T)</option>
-      <option value="Sulfo (Y)">Sulfo (Y)</option>
-      <option value="sulfo+amino (Y)">sulfo+amino (Y)</option>
-      <option value="Sulfo-NHS-LC-LC-Biotin (K)">Sulfo-NHS-LC-LC-Biotin (K)</option>
-      <option value="Sulfo-NHS-LC-LC-Biotin (N-term)">Sulfo-NHS-LC-LC-Biotin (N-term)</option>
-      <option value="SulfoGMBS (C)">SulfoGMBS (C)</option>
-      <option value="SulfurDioxide (C)">SulfurDioxide (C)</option>
-      <option value="SUMO2135 (K)">SUMO2135 (K)</option>
-      <option value="SUMO3549 (K)">SUMO3549 (K)</option>
-      <option value="TAMRA-FP (S)">TAMRA-FP (S)</option>
-      <option value="TAMRA-FP (Y)">TAMRA-FP (Y)</option>
-      <option value="Thiadiazole (C)">Thiadiazole (C)</option>
-      <option value="Thiazolidine (C)">Thiazolidine (C)</option>
-      <option value="Thiazolidine (F)">Thiazolidine (F)</option>
-      <option value="Thiazolidine (H)">Thiazolidine (H)</option>
-      <option value="Thiazolidine (K)">Thiazolidine (K)</option>
-      <option value="Thiazolidine (Protein N-term)">Thiazolidine (Protein N-term)</option>
-      <option value="Thiazolidine (R)">Thiazolidine (R)</option>
-      <option value="Thiazolidine (W)">Thiazolidine (W)</option>
-      <option value="Thiazolidine (Y)">Thiazolidine (Y)</option>
-      <option value="thioacylPA (K)">thioacylPA (K)</option>
-      <option value="Thiophos-S-S-biotin (S)">Thiophos-S-S-biotin (S)</option>
-      <option value="Thiophos-S-S-biotin (T)">Thiophos-S-S-biotin (T)</option>
-      <option value="Thiophos-S-S-biotin (Y)">Thiophos-S-S-biotin (Y)</option>
-      <option value="Thiophospho (S)">Thiophospho (S)</option>
-      <option value="Thiophospho (T)">Thiophospho (T)</option>
-      <option value="Thiophospho (Y)">Thiophospho (Y)</option>
-      <option value="Thr-&gt;Ala (T)">Thr-&gt;Ala (T)</option>
-      <option value="Thr-&gt;Arg (T)">Thr-&gt;Arg (T)</option>
-      <option value="Thr-&gt;Asn (T)">Thr-&gt;Asn (T)</option>
-      <option value="Thr-&gt;Asp (T)">Thr-&gt;Asp (T)</option>
-      <option value="Thr-&gt;Cys (T)">Thr-&gt;Cys (T)</option>
-      <option value="Thr-&gt;Gln (T)">Thr-&gt;Gln (T)</option>
-      <option value="Thr-&gt;Glu (T)">Thr-&gt;Glu (T)</option>
-      <option value="Thr-&gt;Gly (T)">Thr-&gt;Gly (T)</option>
-      <option value="Thr-&gt;His (T)">Thr-&gt;His (T)</option>
-      <option value="Thr-&gt;Lys (T)">Thr-&gt;Lys (T)</option>
-      <option value="Thr-&gt;Met (T)">Thr-&gt;Met (T)</option>
-      <option value="Thr-&gt;Phe (T)">Thr-&gt;Phe (T)</option>
-      <option value="Thr-&gt;Pro (T)">Thr-&gt;Pro (T)</option>
-      <option value="Thr-&gt;Ser (T)">Thr-&gt;Ser (T)</option>
-      <option value="Thr-&gt;Trp (T)">Thr-&gt;Trp (T)</option>
-      <option value="Thr-&gt;Tyr (T)">Thr-&gt;Tyr (T)</option>
-      <option value="Thr-&gt;Val (T)">Thr-&gt;Val (T)</option>
-      <option value="Thr-&gt;Xle (T)">Thr-&gt;Xle (T)</option>
-      <option value="Thrbiotinhydrazide (T)">Thrbiotinhydrazide (T)</option>
-      <option value="Thyroxine (Y)">Thyroxine (Y)</option>
-      <option value="TMAB (K)">TMAB (K)</option>
-      <option value="TMAB (N-term)">TMAB (N-term)</option>
-      <option value="TMAB:2H(9) (K)">TMAB:2H(9) (K)</option>
-      <option value="TMAB:2H(9) (N-term)">TMAB:2H(9) (N-term)</option>
-      <option value="TMPP-Ac (K)">TMPP-Ac (K)</option>
-      <option value="TMPP-Ac (N-term)">TMPP-Ac (N-term)</option>
-      <option value="TMPP-Ac (Y)">TMPP-Ac (Y)</option>
-      <option value="TMPP-Ac:13C(9) (K)">TMPP-Ac:13C(9) (K)</option>
-      <option value="TMPP-Ac:13C(9) (N-term)">TMPP-Ac:13C(9) (N-term)</option>
-      <option value="TMPP-Ac:13C(9) (Y)">TMPP-Ac:13C(9) (Y)</option>
-      <option value="TMT (H)">TMT (H)</option>
-      <option value="TMT (K)">TMT (K)</option>
-      <option value="TMT (N-term)">TMT (N-term)</option>
-      <option value="TMT (Protein N-term)">TMT (Protein N-term)</option>
-      <option value="TMT (S)">TMT (S)</option>
-      <option value="TMT (T)">TMT (T)</option>
-      <option value="TMT2plex (H)">TMT2plex (H)</option>
-      <option value="TMT2plex (K)">TMT2plex (K)</option>
-      <option value="TMT2plex (N-term)">TMT2plex (N-term)</option>
-      <option value="TMT2plex (Protein N-term)">TMT2plex (Protein N-term)</option>
-      <option value="TMT2plex (S)">TMT2plex (S)</option>
-      <option value="TMT2plex (T)">TMT2plex (T)</option>
-      <option value="TMT6plex (H)">TMT6plex (H)</option>
-      <option value="TMT6plex (K)">TMT6plex (K)</option>
-      <option value="TMT6plex (N-term)">TMT6plex (N-term)</option>
-      <option value="TMT6plex (Protein N-term)">TMT6plex (Protein N-term)</option>
-      <option value="TMT6plex (S)">TMT6plex (S)</option>
-      <option value="TMT6plex (T)">TMT6plex (T)</option>
-      <option value="TMTpro (H)">TMTpro (H)</option>
-      <option value="TMTpro (K)">TMTpro (K)</option>
-      <option value="TMTpro (N-term)">TMTpro (N-term)</option>
-      <option value="TMTpro (Protein N-term)">TMTpro (Protein N-term)</option>
-      <option value="TMTpro (S)">TMTpro (S)</option>
-      <option value="TMTpro (T)">TMTpro (T)</option>
-      <option value="TMTpro_zero (H)">TMTpro_zero (H)</option>
-      <option value="TMTpro_zero (K)">TMTpro_zero (K)</option>
-      <option value="TMTpro_zero (N-term)">TMTpro_zero (N-term)</option>
-      <option value="TMTpro_zero (Protein N-term)">TMTpro_zero (Protein N-term)</option>
-      <option value="TMTpro_zero (S)">TMTpro_zero (S)</option>
-      <option value="TMTpro_zero (T)">TMTpro_zero (T)</option>
-      <option value="TNBS (K)">TNBS (K)</option>
-      <option value="TNBS (N-term)">TNBS (N-term)</option>
-      <option value="trifluoro (L)">trifluoro (L)</option>
-      <option value="Triiodo (Y)">Triiodo (Y)</option>
-      <option value="Triiodothyronine (Y)">Triiodothyronine (Y)</option>
-      <option value="Trimethyl (K)">Trimethyl (K)</option>
-      <option value="Trimethyl (Protein N-term A)">Trimethyl (Protein N-term A)</option>
-      <option value="Trimethyl (R)">Trimethyl (R)</option>
-      <option value="Trimethyl:13C(3)2H(9) (K)">Trimethyl:13C(3)2H(9) (K)</option>
-      <option value="Trimethyl:13C(3)2H(9) (R)">Trimethyl:13C(3)2H(9) (R)</option>
-      <option value="Trimethyl:2H(9) (K)">Trimethyl:2H(9) (K)</option>
-      <option value="Trimethyl:2H(9) (R)">Trimethyl:2H(9) (R)</option>
-      <option value="Trioxidation (C)">Trioxidation (C)</option>
-      <option value="Trioxidation (F)">Trioxidation (F)</option>
-      <option value="Trioxidation (W)">Trioxidation (W)</option>
-      <option value="Trioxidation (Y)">Trioxidation (Y)</option>
-      <option value="Tripalmitate (Protein N-term C)">Tripalmitate (Protein N-term C)</option>
-      <option value="Tris (N)">Tris (N)</option>
-      <option value="Triton (C-term)">Triton (C-term)</option>
-      <option value="Triton (N-term)">Triton (N-term)</option>
-      <option value="Trp-&gt;Ala (W)">Trp-&gt;Ala (W)</option>
-      <option value="Trp-&gt;Arg (W)">Trp-&gt;Arg (W)</option>
-      <option value="Trp-&gt;Asn (W)">Trp-&gt;Asn (W)</option>
-      <option value="Trp-&gt;Asp (W)">Trp-&gt;Asp (W)</option>
-      <option value="Trp-&gt;Cys (W)">Trp-&gt;Cys (W)</option>
-      <option value="Trp-&gt;Gln (W)">Trp-&gt;Gln (W)</option>
-      <option value="Trp-&gt;Glu (W)">Trp-&gt;Glu (W)</option>
-      <option value="Trp-&gt;Gly (W)">Trp-&gt;Gly (W)</option>
-      <option value="Trp-&gt;His (W)">Trp-&gt;His (W)</option>
-      <option value="Trp-&gt;Hydroxykynurenin (W)">Trp-&gt;Hydroxykynurenin (W)</option>
-      <option value="Trp-&gt;Kynurenin (W)">Trp-&gt;Kynurenin (W)</option>
-      <option value="Trp-&gt;Lys (W)">Trp-&gt;Lys (W)</option>
-      <option value="Trp-&gt;Met (W)">Trp-&gt;Met (W)</option>
-      <option value="Trp-&gt;Oxolactone (W)">Trp-&gt;Oxolactone (W)</option>
-      <option value="Trp-&gt;Phe (W)">Trp-&gt;Phe (W)</option>
-      <option value="Trp-&gt;Pro (W)">Trp-&gt;Pro (W)</option>
-      <option value="Trp-&gt;Ser (W)">Trp-&gt;Ser (W)</option>
-      <option value="Trp-&gt;Thr (W)">Trp-&gt;Thr (W)</option>
-      <option value="Trp-&gt;Tyr (W)">Trp-&gt;Tyr (W)</option>
-      <option value="Trp-&gt;Val (W)">Trp-&gt;Val (W)</option>
-      <option value="Trp-&gt;Xle (W)">Trp-&gt;Xle (W)</option>
-      <option value="Tween20 (N-term)">Tween20 (N-term)</option>
-      <option value="Tween80 (C-term)">Tween80 (C-term)</option>
-      <option value="Tyr-&gt;Ala (Y)">Tyr-&gt;Ala (Y)</option>
-      <option value="Tyr-&gt;Arg (Y)">Tyr-&gt;Arg (Y)</option>
-      <option value="Tyr-&gt;Asn (Y)">Tyr-&gt;Asn (Y)</option>
-      <option value="Tyr-&gt;Asp (Y)">Tyr-&gt;Asp (Y)</option>
-      <option value="Tyr-&gt;Cys (Y)">Tyr-&gt;Cys (Y)</option>
-      <option value="Tyr-&gt;Dha (Y)">Tyr-&gt;Dha (Y)</option>
-      <option value="Tyr-&gt;Gln (Y)">Tyr-&gt;Gln (Y)</option>
-      <option value="Tyr-&gt;Glu (Y)">Tyr-&gt;Glu (Y)</option>
-      <option value="Tyr-&gt;Gly (Y)">Tyr-&gt;Gly (Y)</option>
-      <option value="Tyr-&gt;His (Y)">Tyr-&gt;His (Y)</option>
-      <option value="Tyr-&gt;Lys (Y)">Tyr-&gt;Lys (Y)</option>
-      <option value="Tyr-&gt;Met (Y)">Tyr-&gt;Met (Y)</option>
-      <option value="Tyr-&gt;Phe (Y)">Tyr-&gt;Phe (Y)</option>
-      <option value="Tyr-&gt;Pro (Y)">Tyr-&gt;Pro (Y)</option>
-      <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
-      <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
-      <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
-      <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
-      <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-      <option value="Ub-amide (C)">Ub-amide (C)</option>
-      <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
-      <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
-      <option value="Ub-VME (C)">Ub-VME (C)</option>
-      <option value="UgiJoullie (D)">UgiJoullie (D)</option>
-      <option value="UgiJoullie (E)">UgiJoullie (E)</option>
-      <option value="UgiJoullieProGly (D)">UgiJoullieProGly (D)</option>
-      <option value="UgiJoullieProGly (E)">UgiJoullieProGly (E)</option>
-      <option value="UgiJoullieProGlyProGly (D)">UgiJoullieProGlyProGly (D)</option>
-      <option value="UgiJoullieProGlyProGly (E)">UgiJoullieProGlyProGly (E)</option>
-      <option value="Unknown:162 (C-term)">Unknown:162 (C-term)</option>
-      <option value="Unknown:162 (D)">Unknown:162 (D)</option>
-      <option value="Unknown:162 (E)">Unknown:162 (E)</option>
-      <option value="Unknown:162 (N-term)">Unknown:162 (N-term)</option>
-      <option value="Unknown:177 (C-term)">Unknown:177 (C-term)</option>
-      <option value="Unknown:177 (D)">Unknown:177 (D)</option>
-      <option value="Unknown:177 (E)">Unknown:177 (E)</option>
-      <option value="Unknown:177 (N-term)">Unknown:177 (N-term)</option>
-      <option value="Unknown:210 (C-term)">Unknown:210 (C-term)</option>
-      <option value="Unknown:210 (D)">Unknown:210 (D)</option>
-      <option value="Unknown:210 (E)">Unknown:210 (E)</option>
-      <option value="Unknown:210 (N-term)">Unknown:210 (N-term)</option>
-      <option value="Unknown:216 (C-term)">Unknown:216 (C-term)</option>
-      <option value="Unknown:216 (D)">Unknown:216 (D)</option>
-      <option value="Unknown:216 (E)">Unknown:216 (E)</option>
-      <option value="Unknown:216 (N-term)">Unknown:216 (N-term)</option>
-      <option value="Unknown:234 (C-term)">Unknown:234 (C-term)</option>
-      <option value="Unknown:234 (D)">Unknown:234 (D)</option>
-      <option value="Unknown:234 (E)">Unknown:234 (E)</option>
-      <option value="Unknown:234 (N-term)">Unknown:234 (N-term)</option>
-      <option value="Unknown:248 (C-term)">Unknown:248 (C-term)</option>
-      <option value="Unknown:248 (D)">Unknown:248 (D)</option>
-      <option value="Unknown:248 (E)">Unknown:248 (E)</option>
-      <option value="Unknown:248 (N-term)">Unknown:248 (N-term)</option>
-      <option value="Unknown:250 (C-term)">Unknown:250 (C-term)</option>
-      <option value="Unknown:250 (D)">Unknown:250 (D)</option>
-      <option value="Unknown:250 (E)">Unknown:250 (E)</option>
-      <option value="Unknown:250 (N-term)">Unknown:250 (N-term)</option>
-      <option value="Unknown:302 (C-term)">Unknown:302 (C-term)</option>
-      <option value="Unknown:302 (D)">Unknown:302 (D)</option>
-      <option value="Unknown:302 (E)">Unknown:302 (E)</option>
-      <option value="Unknown:302 (N-term)">Unknown:302 (N-term)</option>
-      <option value="Unknown:306 (C-term)">Unknown:306 (C-term)</option>
-      <option value="Unknown:306 (D)">Unknown:306 (D)</option>
-      <option value="Unknown:306 (E)">Unknown:306 (E)</option>
-      <option value="Unknown:306 (N-term)">Unknown:306 (N-term)</option>
-      <option value="Unknown:420 (C-term)">Unknown:420 (C-term)</option>
-      <option value="Unknown:420 (N-term)">Unknown:420 (N-term)</option>
-      <option value="Val-&gt;Ala (V)">Val-&gt;Ala (V)</option>
-      <option value="Val-&gt;Arg (V)">Val-&gt;Arg (V)</option>
-      <option value="Val-&gt;Asn (V)">Val-&gt;Asn (V)</option>
-      <option value="Val-&gt;Asp (V)">Val-&gt;Asp (V)</option>
-      <option value="Val-&gt;Cys (V)">Val-&gt;Cys (V)</option>
-      <option value="Val-&gt;Gln (V)">Val-&gt;Gln (V)</option>
-      <option value="Val-&gt;Glu (V)">Val-&gt;Glu (V)</option>
-      <option value="Val-&gt;Gly (V)">Val-&gt;Gly (V)</option>
-      <option value="Val-&gt;His (V)">Val-&gt;His (V)</option>
-      <option value="Val-&gt;Lys (V)">Val-&gt;Lys (V)</option>
-      <option value="Val-&gt;Met (V)">Val-&gt;Met (V)</option>
-      <option value="Val-&gt;Phe (V)">Val-&gt;Phe (V)</option>
-      <option value="Val-&gt;Pro (V)">Val-&gt;Pro (V)</option>
-      <option value="Val-&gt;Ser (V)">Val-&gt;Ser (V)</option>
-      <option value="Val-&gt;Thr (V)">Val-&gt;Thr (V)</option>
-      <option value="Val-&gt;Trp (V)">Val-&gt;Trp (V)</option>
-      <option value="Val-&gt;Tyr (V)">Val-&gt;Tyr (V)</option>
-      <option value="Val-&gt;Xle (V)">Val-&gt;Xle (V)</option>
-      <option value="VFQQQTGG (K)">VFQQQTGG (K)</option>
-      <option value="VIEVYQEQTGG (K)">VIEVYQEQTGG (K)</option>
-      <option value="Withaferin (C)">Withaferin (C)</option>
-      <option value="Xle-&gt;Ala (I)">Xle-&gt;Ala (I)</option>
-      <option value="Xle-&gt;Ala (L)">Xle-&gt;Ala (L)</option>
-      <option value="Xle-&gt;Arg (I)">Xle-&gt;Arg (I)</option>
-      <option value="Xle-&gt;Arg (L)">Xle-&gt;Arg (L)</option>
-      <option value="Xle-&gt;Asn (I)">Xle-&gt;Asn (I)</option>
-      <option value="Xle-&gt;Asn (L)">Xle-&gt;Asn (L)</option>
-      <option value="Xle-&gt;Asp (I)">Xle-&gt;Asp (I)</option>
-      <option value="Xle-&gt;Asp (L)">Xle-&gt;Asp (L)</option>
-      <option value="Xle-&gt;Cys (I)">Xle-&gt;Cys (I)</option>
-      <option value="Xle-&gt;Cys (L)">Xle-&gt;Cys (L)</option>
-      <option value="Xle-&gt;Gln (I)">Xle-&gt;Gln (I)</option>
-      <option value="Xle-&gt;Gln (L)">Xle-&gt;Gln (L)</option>
-      <option value="Xle-&gt;Glu (I)">Xle-&gt;Glu (I)</option>
-      <option value="Xle-&gt;Glu (L)">Xle-&gt;Glu (L)</option>
-      <option value="Xle-&gt;Gly (I)">Xle-&gt;Gly (I)</option>
-      <option value="Xle-&gt;Gly (L)">Xle-&gt;Gly (L)</option>
-      <option value="Xle-&gt;His (I)">Xle-&gt;His (I)</option>
-      <option value="Xle-&gt;His (L)">Xle-&gt;His (L)</option>
-      <option value="Xle-&gt;Lys (I)">Xle-&gt;Lys (I)</option>
-      <option value="Xle-&gt;Lys (L)">Xle-&gt;Lys (L)</option>
-      <option value="Xle-&gt;Met (I)">Xle-&gt;Met (I)</option>
-      <option value="Xle-&gt;Met (L)">Xle-&gt;Met (L)</option>
-      <option value="Xle-&gt;Phe (I)">Xle-&gt;Phe (I)</option>
-      <option value="Xle-&gt;Phe (L)">Xle-&gt;Phe (L)</option>
-      <option value="Xle-&gt;Pro (I)">Xle-&gt;Pro (I)</option>
-      <option value="Xle-&gt;Pro (L)">Xle-&gt;Pro (L)</option>
-      <option value="Xle-&gt;Ser (I)">Xle-&gt;Ser (I)</option>
-      <option value="Xle-&gt;Ser (L)">Xle-&gt;Ser (L)</option>
-      <option value="Xle-&gt;Thr (I)">Xle-&gt;Thr (I)</option>
-      <option value="Xle-&gt;Thr (L)">Xle-&gt;Thr (L)</option>
-      <option value="Xle-&gt;Trp (I)">Xle-&gt;Trp (I)</option>
-      <option value="Xle-&gt;Trp (L)">Xle-&gt;Trp (L)</option>
-      <option value="Xle-&gt;Tyr (I)">Xle-&gt;Tyr (I)</option>
-      <option value="Xle-&gt;Tyr (L)">Xle-&gt;Tyr (L)</option>
-      <option value="Xle-&gt;Val (I)">Xle-&gt;Val (I)</option>
-      <option value="Xle-&gt;Val (L)">Xle-&gt;Val (L)</option>
-      <option value="Xlink:B10621 (C)">Xlink:B10621 (C)</option>
-      <option value="Xlink:BMOE (C)">Xlink:BMOE (C)</option>
-      <option value="Xlink:BS2G[113] (K)">Xlink:BS2G[113] (K)</option>
-      <option value="Xlink:BS2G[113] (Protein N-term)">Xlink:BS2G[113] (Protein N-term)</option>
-      <option value="Xlink:BS2G[114] (K)">Xlink:BS2G[114] (K)</option>
-      <option value="Xlink:BS2G[114] (Protein N-term)">Xlink:BS2G[114] (Protein N-term)</option>
-      <option value="Xlink:BS2G[217] (K)">Xlink:BS2G[217] (K)</option>
-      <option value="Xlink:BS2G[217] (Protein N-term)">Xlink:BS2G[217] (Protein N-term)</option>
-      <option value="Xlink:BS2G[96] (K)">Xlink:BS2G[96] (K)</option>
-      <option value="Xlink:BS2G[96] (Protein N-term)">Xlink:BS2G[96] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[111] (K)">Xlink:BuUrBu[111] (K)</option>
-      <option value="Xlink:BuUrBu[111] (Protein N-term)">Xlink:BuUrBu[111] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[196] (K)">Xlink:BuUrBu[196] (K)</option>
-      <option value="Xlink:BuUrBu[196] (Protein N-term)">Xlink:BuUrBu[196] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[213] (K)">Xlink:BuUrBu[213] (K)</option>
-      <option value="Xlink:BuUrBu[213] (Protein N-term)">Xlink:BuUrBu[213] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[214] (K)">Xlink:BuUrBu[214] (K)</option>
-      <option value="Xlink:BuUrBu[214] (Protein N-term)">Xlink:BuUrBu[214] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[317] (K)">Xlink:BuUrBu[317] (K)</option>
-      <option value="Xlink:BuUrBu[317] (Protein N-term)">Xlink:BuUrBu[317] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[85] (K)">Xlink:BuUrBu[85] (K)</option>
-      <option value="Xlink:BuUrBu[85] (Protein N-term)">Xlink:BuUrBu[85] (Protein N-term)</option>
-      <option value="Xlink:DFDNB (K)">Xlink:DFDNB (K)</option>
-      <option value="Xlink:DFDNB (N)">Xlink:DFDNB (N)</option>
-      <option value="Xlink:DFDNB (Q)">Xlink:DFDNB (Q)</option>
-      <option value="Xlink:DFDNB (R)">Xlink:DFDNB (R)</option>
-      <option value="Xlink:DMP[122] (K)">Xlink:DMP[122] (K)</option>
-      <option value="Xlink:DMP[122] (Protein N-term)">Xlink:DMP[122] (Protein N-term)</option>
-      <option value="Xlink:DMP[139] (K)">Xlink:DMP[139] (K)</option>
-      <option value="Xlink:DMP[139] (Protein N-term)">Xlink:DMP[139] (Protein N-term)</option>
-      <option value="Xlink:DMP[140] (K)">Xlink:DMP[140] (K)</option>
-      <option value="Xlink:DMP[140] (Protein N-term)">Xlink:DMP[140] (Protein N-term)</option>
-      <option value="Xlink:DMP[154] (K)">Xlink:DMP[154] (K)</option>
-      <option value="Xlink:DMP[154] (Protein N-term)">Xlink:DMP[154] (Protein N-term)</option>
-      <option value="Xlink:DSS[138] (K)">Xlink:DSS[138] (K)</option>
-      <option value="Xlink:DSS[138] (Protein N-term)">Xlink:DSS[138] (Protein N-term)</option>
-      <option value="Xlink:DSS[155] (K)">Xlink:DSS[155] (K)</option>
-      <option value="Xlink:DSS[155] (Protein N-term)">Xlink:DSS[155] (Protein N-term)</option>
-      <option value="Xlink:DSS[156] (K)">Xlink:DSS[156] (K)</option>
-      <option value="Xlink:DSS[156] (Protein N-term)">Xlink:DSS[156] (Protein N-term)</option>
-      <option value="Xlink:DSS[259] (K)">Xlink:DSS[259] (K)</option>
-      <option value="Xlink:DSS[259] (Protein N-term)">Xlink:DSS[259] (Protein N-term)</option>
-      <option value="Xlink:DSSO[104] (K)">Xlink:DSSO[104] (K)</option>
-      <option value="Xlink:DSSO[104] (Protein N-term)">Xlink:DSSO[104] (Protein N-term)</option>
-      <option value="Xlink:DSSO[158] (K)">Xlink:DSSO[158] (K)</option>
-      <option value="Xlink:DSSO[158] (Protein N-term)">Xlink:DSSO[158] (Protein N-term)</option>
-      <option value="Xlink:DSSO[175] (K)">Xlink:DSSO[175] (K)</option>
-      <option value="Xlink:DSSO[175] (Protein N-term)">Xlink:DSSO[175] (Protein N-term)</option>
-      <option value="Xlink:DSSO[176] (K)">Xlink:DSSO[176] (K)</option>
-      <option value="Xlink:DSSO[176] (Protein N-term)">Xlink:DSSO[176] (Protein N-term)</option>
-      <option value="Xlink:DSSO[279] (K)">Xlink:DSSO[279] (K)</option>
-      <option value="Xlink:DSSO[279] (Protein N-term)">Xlink:DSSO[279] (Protein N-term)</option>
-      <option value="Xlink:DSSO[54] (K)">Xlink:DSSO[54] (K)</option>
-      <option value="Xlink:DSSO[54] (Protein N-term)">Xlink:DSSO[54] (Protein N-term)</option>
-      <option value="Xlink:DSSO[86] (K)">Xlink:DSSO[86] (K)</option>
-      <option value="Xlink:DSSO[86] (Protein N-term)">Xlink:DSSO[86] (Protein N-term)</option>
-      <option value="Xlink:DST[114] (K)">Xlink:DST[114] (K)</option>
-      <option value="Xlink:DST[114] (Protein N-term)">Xlink:DST[114] (Protein N-term)</option>
-      <option value="Xlink:DST[132] (K)">Xlink:DST[132] (K)</option>
-      <option value="Xlink:DST[132] (Protein N-term)">Xlink:DST[132] (Protein N-term)</option>
-      <option value="Xlink:DST[56] (K)">Xlink:DST[56] (K)</option>
-      <option value="Xlink:DST[56] (Protein N-term)">Xlink:DST[56] (Protein N-term)</option>
-      <option value="Xlink:DTBP[172] (K)">Xlink:DTBP[172] (K)</option>
-      <option value="Xlink:DTBP[172] (Protein N-term)">Xlink:DTBP[172] (Protein N-term)</option>
-      <option value="Xlink:DTBP[87] (K)">Xlink:DTBP[87] (K)</option>
-      <option value="Xlink:DTBP[87] (Protein N-term)">Xlink:DTBP[87] (Protein N-term)</option>
-      <option value="Xlink:DTSSP[174] (K)">Xlink:DTSSP[174] (K)</option>
-      <option value="Xlink:DTSSP[174] (Protein N-term)">Xlink:DTSSP[174] (Protein N-term)</option>
-      <option value="Xlink:DTSSP[192] (K)">Xlink:DTSSP[192] (K)</option>
-      <option value="Xlink:DTSSP[192] (Protein N-term)">Xlink:DTSSP[192] (Protein N-term)</option>
-      <option value="Xlink:DTSSP[88] (K)">Xlink:DTSSP[88] (K)</option>
-      <option value="Xlink:DTSSP[88] (Protein N-term)">Xlink:DTSSP[88] (Protein N-term)</option>
-      <option value="Xlink:EGS[115] (K)">Xlink:EGS[115] (K)</option>
-      <option value="Xlink:EGS[115] (Protein N-term)">Xlink:EGS[115] (Protein N-term)</option>
-      <option value="Xlink:EGS[226] (K)">Xlink:EGS[226] (K)</option>
-      <option value="Xlink:EGS[226] (Protein N-term)">Xlink:EGS[226] (Protein N-term)</option>
-      <option value="Xlink:EGS[244] (K)">Xlink:EGS[244] (K)</option>
-      <option value="Xlink:EGS[244] (Protein N-term)">Xlink:EGS[244] (Protein N-term)</option>
-      <option value="Xlink:SMCC[219] (C)">Xlink:SMCC[219] (C)</option>
-      <option value="Xlink:SMCC[219] (K)">Xlink:SMCC[219] (K)</option>
-      <option value="Xlink:SMCC[219] (Protein N-term)">Xlink:SMCC[219] (Protein N-term)</option>
-      <option value="Xlink:SMCC[237] (C)">Xlink:SMCC[237] (C)</option>
-      <option value="Xlink:SMCC[237] (K)">Xlink:SMCC[237] (K)</option>
-      <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
-      <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
-      <option value="ZGB (K)">ZGB (K)</option>
-      <option value="ZGB (N-term)">ZGB (N-term)</option>
-      <option value="ZQG (K)">ZQG (K)</option>
-      <expand macro="list_string_san" name="fixed_modifications"/>
-    </param>
-    <param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
-      <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
-      <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
-      <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
-      <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
-      <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
-      <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
-      <option value="2-succinyl (C)">2-succinyl (C)</option>
-      <option value="2HPG (R)">2HPG (R)</option>
-      <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
-      <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
-      <option value="3sulfo (N-term)">3sulfo (N-term)</option>
-      <option value="4-ONE (C)">4-ONE (C)</option>
-      <option value="4-ONE (H)">4-ONE (H)</option>
-      <option value="4-ONE (K)">4-ONE (K)</option>
-      <option value="4-ONE+Delta:H(-2)O(-1) (C)">4-ONE+Delta:H(-2)O(-1) (C)</option>
-      <option value="4-ONE+Delta:H(-2)O(-1) (H)">4-ONE+Delta:H(-2)O(-1) (H)</option>
-      <option value="4-ONE+Delta:H(-2)O(-1) (K)">4-ONE+Delta:H(-2)O(-1) (K)</option>
-      <option value="4AcAllylGal (C)">4AcAllylGal (C)</option>
-      <option value="a-type-ion (C-term)">a-type-ion (C-term)</option>
-      <option value="AccQTag (K)">AccQTag (K)</option>
-      <option value="AccQTag (N-term)">AccQTag (N-term)</option>
-      <option value="Acetyl (C)">Acetyl (C)</option>
-      <option value="Acetyl (H)">Acetyl (H)</option>
-      <option value="Acetyl (K)">Acetyl (K)</option>
-      <option value="Acetyl (N-term)">Acetyl (N-term)</option>
-      <option value="Acetyl (Protein N-term)">Acetyl (Protein N-term)</option>
-      <option value="Acetyl (R)">Acetyl (R)</option>
-      <option value="Acetyl (S)">Acetyl (S)</option>
-      <option value="Acetyl (T)">Acetyl (T)</option>
-      <option value="Acetyl (Y)">Acetyl (Y)</option>
-      <option value="Acetyl:13C(2) (K)">Acetyl:13C(2) (K)</option>
-      <option value="Acetyl:13C(2) (Protein N-term)">Acetyl:13C(2) (Protein N-term)</option>
-      <option value="Acetyl:2H(3) (H)">Acetyl:2H(3) (H)</option>
-      <option value="Acetyl:2H(3) (K)">Acetyl:2H(3) (K)</option>
-      <option value="Acetyl:2H(3) (N-term)">Acetyl:2H(3) (N-term)</option>
-      <option value="Acetyl:2H(3) (Protein N-term)">Acetyl:2H(3) (Protein N-term)</option>
-      <option value="Acetyl:2H(3) (S)">Acetyl:2H(3) (S)</option>
-      <option value="Acetyl:2H(3) (T)">Acetyl:2H(3) (T)</option>
-      <option value="Acetyl:2H(3) (Y)">Acetyl:2H(3) (Y)</option>
-      <option value="Acetyldeoxyhypusine (K)">Acetyldeoxyhypusine (K)</option>
-      <option value="Acetylhypusine (K)">Acetylhypusine (K)</option>
-      <option value="ADP-Ribosyl (C)">ADP-Ribosyl (C)</option>
-      <option value="ADP-Ribosyl (D)">ADP-Ribosyl (D)</option>
-      <option value="ADP-Ribosyl (E)">ADP-Ribosyl (E)</option>
-      <option value="ADP-Ribosyl (K)">ADP-Ribosyl (K)</option>
-      <option value="ADP-Ribosyl (N)">ADP-Ribosyl (N)</option>
-      <option value="ADP-Ribosyl (R)">ADP-Ribosyl (R)</option>
-      <option value="ADP-Ribosyl (S)">ADP-Ribosyl (S)</option>
-      <option value="ADP-Ribosyl (T)">ADP-Ribosyl (T)</option>
-      <option value="AEBS (H)">AEBS (H)</option>
-      <option value="AEBS (K)">AEBS (K)</option>
-      <option value="AEBS (Protein N-term)">AEBS (Protein N-term)</option>
-      <option value="AEBS (S)">AEBS (S)</option>
-      <option value="AEBS (Y)">AEBS (Y)</option>
-      <option value="AEC-MAEC (S)">AEC-MAEC (S)</option>
-      <option value="AEC-MAEC (T)">AEC-MAEC (T)</option>
-      <option value="AEC-MAEC:2H(4) (S)">AEC-MAEC:2H(4) (S)</option>
-      <option value="AEC-MAEC:2H(4) (T)">AEC-MAEC:2H(4) (T)</option>
-      <option value="AFB1_Dialdehyde (K)">AFB1_Dialdehyde (K)</option>
-      <option value="AHA-Alkyne (M)">AHA-Alkyne (M)</option>
-      <option value="AHA-Alkyne-KDDDD (M)">AHA-Alkyne-KDDDD (M)</option>
-      <option value="AHA-SS (M)">AHA-SS (M)</option>
-      <option value="AHA-SS_CAM (M)">AHA-SS_CAM (M)</option>
-      <option value="Ahx2+Hsl (C-term)">Ahx2+Hsl (C-term)</option>
-      <option value="Ala-&gt;Arg (A)">Ala-&gt;Arg (A)</option>
-      <option value="Ala-&gt;Asn (A)">Ala-&gt;Asn (A)</option>
-      <option value="Ala-&gt;Asp (A)">Ala-&gt;Asp (A)</option>
-      <option value="Ala-&gt;Cys (A)">Ala-&gt;Cys (A)</option>
-      <option value="Ala-&gt;Gln (A)">Ala-&gt;Gln (A)</option>
-      <option value="Ala-&gt;Glu (A)">Ala-&gt;Glu (A)</option>
-      <option value="Ala-&gt;Gly (A)">Ala-&gt;Gly (A)</option>
-      <option value="Ala-&gt;His (A)">Ala-&gt;His (A)</option>
-      <option value="Ala-&gt;Lys (A)">Ala-&gt;Lys (A)</option>
-      <option value="Ala-&gt;Met (A)">Ala-&gt;Met (A)</option>
-      <option value="Ala-&gt;Phe (A)">Ala-&gt;Phe (A)</option>
-      <option value="Ala-&gt;Pro (A)">Ala-&gt;Pro (A)</option>
-      <option value="Ala-&gt;Ser (A)">Ala-&gt;Ser (A)</option>
-      <option value="Ala-&gt;Thr (A)">Ala-&gt;Thr (A)</option>
-      <option value="Ala-&gt;Trp (A)">Ala-&gt;Trp (A)</option>
-      <option value="Ala-&gt;Tyr (A)">Ala-&gt;Tyr (A)</option>
-      <option value="Ala-&gt;Val (A)">Ala-&gt;Val (A)</option>
-      <option value="Ala-&gt;Xle (A)">Ala-&gt;Xle (A)</option>
-      <option value="Amidated (C-term)">Amidated (C-term)</option>
-      <option value="Amidated (Protein C-term)">Amidated (Protein C-term)</option>
-      <option value="Amidine (K)">Amidine (K)</option>
-      <option value="Amidine (N-term)">Amidine (N-term)</option>
-      <option value="Amidino (C)">Amidino (C)</option>
-      <option value="Amino (Y)">Amino (Y)</option>
-      <option value="Ammonia-loss (N)">Ammonia-loss (N)</option>
-      <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
-      <option value="Ammonia-loss (Protein N-term S)">Ammonia-loss (Protein N-term S)</option>
-      <option value="Ammonia-loss (Protein N-term T)">Ammonia-loss (Protein N-term T)</option>
-      <option value="Ammonium (C-term)">Ammonium (C-term)</option>
-      <option value="Ammonium (D)">Ammonium (D)</option>
-      <option value="Ammonium (E)">Ammonium (E)</option>
-      <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
-      <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
-      <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
-      <option value="Archaeol (C)">Archaeol (C)</option>
-      <option value="Arg (N-term)">Arg (N-term)</option>
-      <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
-      <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
-      <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
-      <option value="Arg-&gt;Cys (R)">Arg-&gt;Cys (R)</option>
-      <option value="Arg-&gt;Gln (R)">Arg-&gt;Gln (R)</option>
-      <option value="Arg-&gt;Glu (R)">Arg-&gt;Glu (R)</option>
-      <option value="Arg-&gt;GluSA (R)">Arg-&gt;GluSA (R)</option>
-      <option value="Arg-&gt;Gly (R)">Arg-&gt;Gly (R)</option>
-      <option value="Arg-&gt;His (R)">Arg-&gt;His (R)</option>
-      <option value="Arg-&gt;Lys (R)">Arg-&gt;Lys (R)</option>
-      <option value="Arg-&gt;Met (R)">Arg-&gt;Met (R)</option>
-      <option value="Arg-&gt;Npo (R)">Arg-&gt;Npo (R)</option>
-      <option value="Arg-&gt;Orn (R)">Arg-&gt;Orn (R)</option>
-      <option value="Arg-&gt;Phe (R)">Arg-&gt;Phe (R)</option>
-      <option value="Arg-&gt;Pro (R)">Arg-&gt;Pro (R)</option>
-      <option value="Arg-&gt;Ser (R)">Arg-&gt;Ser (R)</option>
-      <option value="Arg-&gt;Thr (R)">Arg-&gt;Thr (R)</option>
-      <option value="Arg-&gt;Trp (R)">Arg-&gt;Trp (R)</option>
-      <option value="Arg-&gt;Tyr (R)">Arg-&gt;Tyr (R)</option>
-      <option value="Arg-&gt;Val (R)">Arg-&gt;Val (R)</option>
-      <option value="Arg-&gt;Xle (R)">Arg-&gt;Xle (R)</option>
-      <option value="Arg-loss (C-term R)">Arg-loss (C-term R)</option>
-      <option value="Arg2PG (R)">Arg2PG (R)</option>
-      <option value="Argbiotinhydrazide (R)">Argbiotinhydrazide (R)</option>
-      <option value="AROD (C)">AROD (C)</option>
-      <option value="Asn-&gt;Ala (N)">Asn-&gt;Ala (N)</option>
-      <option value="Asn-&gt;Arg (N)">Asn-&gt;Arg (N)</option>
-      <option value="Asn-&gt;Asp (N)">Asn-&gt;Asp (N)</option>
-      <option value="Asn-&gt;Cys (N)">Asn-&gt;Cys (N)</option>
-      <option value="Asn-&gt;Gln (N)">Asn-&gt;Gln (N)</option>
-      <option value="Asn-&gt;Glu (N)">Asn-&gt;Glu (N)</option>
-      <option value="Asn-&gt;Gly (N)">Asn-&gt;Gly (N)</option>
-      <option value="Asn-&gt;His (N)">Asn-&gt;His (N)</option>
-      <option value="Asn-&gt;Lys (N)">Asn-&gt;Lys (N)</option>
-      <option value="Asn-&gt;Met (N)">Asn-&gt;Met (N)</option>
-      <option value="Asn-&gt;Phe (N)">Asn-&gt;Phe (N)</option>
-      <option value="Asn-&gt;Pro (N)">Asn-&gt;Pro (N)</option>
-      <option value="Asn-&gt;Ser (N)">Asn-&gt;Ser (N)</option>
-      <option value="Asn-&gt;Thr (N)">Asn-&gt;Thr (N)</option>
-      <option value="Asn-&gt;Trp (N)">Asn-&gt;Trp (N)</option>
-      <option value="Asn-&gt;Tyr (N)">Asn-&gt;Tyr (N)</option>
-      <option value="Asn-&gt;Val (N)">Asn-&gt;Val (N)</option>
-      <option value="Asn-&gt;Xle (N)">Asn-&gt;Xle (N)</option>
-      <option value="Asp-&gt;Ala (D)">Asp-&gt;Ala (D)</option>
-      <option value="Asp-&gt;Arg (D)">Asp-&gt;Arg (D)</option>
-      <option value="Asp-&gt;Asn (D)">Asp-&gt;Asn (D)</option>
-      <option value="Asp-&gt;Cys (D)">Asp-&gt;Cys (D)</option>
-      <option value="Asp-&gt;Gln (D)">Asp-&gt;Gln (D)</option>
-      <option value="Asp-&gt;Glu (D)">Asp-&gt;Glu (D)</option>
-      <option value="Asp-&gt;Gly (D)">Asp-&gt;Gly (D)</option>
-      <option value="Asp-&gt;His (D)">Asp-&gt;His (D)</option>
-      <option value="Asp-&gt;Lys (D)">Asp-&gt;Lys (D)</option>
-      <option value="Asp-&gt;Met (D)">Asp-&gt;Met (D)</option>
-      <option value="Asp-&gt;Phe (D)">Asp-&gt;Phe (D)</option>
-      <option value="Asp-&gt;Pro (D)">Asp-&gt;Pro (D)</option>
-      <option value="Asp-&gt;Ser (D)">Asp-&gt;Ser (D)</option>
-      <option value="Asp-&gt;Thr (D)">Asp-&gt;Thr (D)</option>
-      <option value="Asp-&gt;Trp (D)">Asp-&gt;Trp (D)</option>
-      <option value="Asp-&gt;Tyr (D)">Asp-&gt;Tyr (D)</option>
-      <option value="Asp-&gt;Val (D)">Asp-&gt;Val (D)</option>
-      <option value="Asp-&gt;Xle (D)">Asp-&gt;Xle (D)</option>
-      <option value="Aspartylurea (H)">Aspartylurea (H)</option>
-      <option value="Atto495Maleimide (C)">Atto495Maleimide (C)</option>
-      <option value="AzidoF (F)">AzidoF (F)</option>
-      <option value="azole (C)">azole (C)</option>
-      <option value="azole (S)">azole (S)</option>
-      <option value="Bacillosamine (N)">Bacillosamine (N)</option>
-      <option value="BADGE (C)">BADGE (C)</option>
-      <option value="BDMAPP (H)">BDMAPP (H)</option>
-      <option value="BDMAPP (K)">BDMAPP (K)</option>
-      <option value="BDMAPP (Protein N-term)">BDMAPP (Protein N-term)</option>
-      <option value="BDMAPP (W)">BDMAPP (W)</option>
-      <option value="BDMAPP (Y)">BDMAPP (Y)</option>
-      <option value="BEMAD_C (C)">BEMAD_C (C)</option>
-      <option value="BEMAD_C:2H(6) (C)">BEMAD_C:2H(6) (C)</option>
-      <option value="BEMAD_ST (S)">BEMAD_ST (S)</option>
-      <option value="BEMAD_ST (T)">BEMAD_ST (T)</option>
-      <option value="BEMAD_ST:2H(6) (S)">BEMAD_ST:2H(6) (S)</option>
-      <option value="BEMAD_ST:2H(6) (T)">BEMAD_ST:2H(6) (T)</option>
-      <option value="Benzoyl (K)">Benzoyl (K)</option>
-      <option value="Benzoyl (N-term)">Benzoyl (N-term)</option>
-      <option value="benzylguanidine (K)">benzylguanidine (K)</option>
-      <option value="betaFNA (C)">betaFNA (C)</option>
-      <option value="betaFNA (K)">betaFNA (K)</option>
-      <option value="BHT (C)">BHT (C)</option>
-      <option value="BHT (H)">BHT (H)</option>
-      <option value="BHT (K)">BHT (K)</option>
-      <option value="BHTOH (C)">BHTOH (C)</option>
-      <option value="BHTOH (H)">BHTOH (H)</option>
-      <option value="BHTOH (K)">BHTOH (K)</option>
-      <option value="Biotin (K)">Biotin (K)</option>
-      <option value="Biotin (N-term)">Biotin (N-term)</option>
-      <option value="Biotin-HPDP (C)">Biotin-HPDP (C)</option>
-      <option value="Biotin-PEG-PRA (M)">Biotin-PEG-PRA (M)</option>
-      <option value="Biotin-PEO-Amine (D)">Biotin-PEO-Amine (D)</option>
-      <option value="Biotin-PEO-Amine (E)">Biotin-PEO-Amine (E)</option>
-      <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
-      <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
-      <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
-      <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
-      <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
-      <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
-      <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
-      <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
-      <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
-      <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
-      <option value="Biotin:Thermo-21328 (K)">Biotin:Thermo-21328 (K)</option>
-      <option value="Biotin:Thermo-21328 (N-term)">Biotin:Thermo-21328 (N-term)</option>
-      <option value="Biotin:Thermo-21330 (K)">Biotin:Thermo-21330 (K)</option>
-      <option value="Biotin:Thermo-21330 (N-term)">Biotin:Thermo-21330 (N-term)</option>
-      <option value="Biotin:Thermo-21345 (Q)">Biotin:Thermo-21345 (Q)</option>
-      <option value="Biotin:Thermo-21360 (X)">Biotin:Thermo-21360 (X)</option>
-      <option value="Biotin:Thermo-21901+2H2O (C)">Biotin:Thermo-21901+2H2O (C)</option>
-      <option value="Biotin:Thermo-21901+H2O (C)">Biotin:Thermo-21901+H2O (C)</option>
-      <option value="Biotin:Thermo-21911 (C)">Biotin:Thermo-21911 (C)</option>
-      <option value="Biotin:Thermo-33033 (X)">Biotin:Thermo-33033 (X)</option>
-      <option value="Biotin:Thermo-33033-H (X)">Biotin:Thermo-33033-H (X)</option>
-      <option value="Biotin:Thermo-88310 (K)">Biotin:Thermo-88310 (K)</option>
-      <option value="Biotin:Thermo-88317 (S)">Biotin:Thermo-88317 (S)</option>
-      <option value="Biotin:Thermo-88317 (Y)">Biotin:Thermo-88317 (Y)</option>
-      <option value="biotinAcrolein298 (C)">biotinAcrolein298 (C)</option>
-      <option value="biotinAcrolein298 (H)">biotinAcrolein298 (H)</option>
-      <option value="biotinAcrolein298 (K)">biotinAcrolein298 (K)</option>
-      <option value="biotinAcrolein298 (Protein N-term)">biotinAcrolein298 (Protein N-term)</option>
-      <option value="BisANS (K)">BisANS (K)</option>
-      <option value="bisANS-sulfonates (K)">bisANS-sulfonates (K)</option>
-      <option value="bisANS-sulfonates (S)">bisANS-sulfonates (S)</option>
-      <option value="bisANS-sulfonates (T)">bisANS-sulfonates (T)</option>
-      <option value="BITC (C)">BITC (C)</option>
-      <option value="BITC (K)">BITC (K)</option>
-      <option value="BITC (N-term)">BITC (N-term)</option>
-      <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
-      <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-      <option value="Bodipy (C)">Bodipy (C)</option>
-      <option value="Brij35 (N-term)">Brij35 (N-term)</option>
-      <option value="Brij58 (N-term)">Brij58 (N-term)</option>
-      <option value="Bromo (F)">Bromo (F)</option>
-      <option value="Bromo (H)">Bromo (H)</option>
-      <option value="Bromo (W)">Bromo (W)</option>
-      <option value="Bromo (Y)">Bromo (Y)</option>
-      <option value="Bromobimane (C)">Bromobimane (C)</option>
-      <option value="Butyryl (K)">Butyryl (K)</option>
-      <option value="C8-QAT (K)">C8-QAT (K)</option>
-      <option value="C8-QAT (N-term)">C8-QAT (N-term)</option>
-      <option value="CAF (N-term)">CAF (N-term)</option>
-      <option value="CAMthiopropanoyl (K)">CAMthiopropanoyl (K)</option>
-      <option value="CAMthiopropanoyl (Protein N-term)">CAMthiopropanoyl (Protein N-term)</option>
-      <option value="Can-FP-biotin (S)">Can-FP-biotin (S)</option>
-      <option value="Can-FP-biotin (T)">Can-FP-biotin (T)</option>
-      <option value="Can-FP-biotin (Y)">Can-FP-biotin (Y)</option>
-      <option value="Carbamidomethyl (C)">Carbamidomethyl (C)</option>
-      <option value="Carbamidomethyl (D)">Carbamidomethyl (D)</option>
-      <option value="Carbamidomethyl (E)">Carbamidomethyl (E)</option>
-      <option value="Carbamidomethyl (H)">Carbamidomethyl (H)</option>
-      <option value="Carbamidomethyl (K)">Carbamidomethyl (K)</option>
-      <option value="Carbamidomethyl (M)">Carbamidomethyl (M)</option>
-      <option value="Carbamidomethyl (N-term)">Carbamidomethyl (N-term)</option>
-      <option value="Carbamidomethyl (S)">Carbamidomethyl (S)</option>
-      <option value="Carbamidomethyl (T)">Carbamidomethyl (T)</option>
-      <option value="Carbamidomethyl (U)">Carbamidomethyl (U)</option>
-      <option value="Carbamidomethyl (Y)">Carbamidomethyl (Y)</option>
-      <option value="CarbamidomethylDTT (C)">CarbamidomethylDTT (C)</option>
-      <option value="Carbamyl (C)">Carbamyl (C)</option>
-      <option value="Carbamyl (K)">Carbamyl (K)</option>
-      <option value="Carbamyl (M)">Carbamyl (M)</option>
-      <option value="Carbamyl (N-term)">Carbamyl (N-term)</option>
-      <option value="Carbamyl (Protein N-term)">Carbamyl (Protein N-term)</option>
-      <option value="Carbamyl (R)">Carbamyl (R)</option>
-      <option value="Carbamyl (S)">Carbamyl (S)</option>
-      <option value="Carbamyl (T)">Carbamyl (T)</option>
-      <option value="Carbamyl (Y)">Carbamyl (Y)</option>
-      <option value="Carbofuran (S)">Carbofuran (S)</option>
-      <option value="Carbonyl (A)">Carbonyl (A)</option>
-      <option value="Carbonyl (E)">Carbonyl (E)</option>
-      <option value="Carbonyl (I)">Carbonyl (I)</option>
-      <option value="Carbonyl (L)">Carbonyl (L)</option>
-      <option value="Carbonyl (Q)">Carbonyl (Q)</option>
-      <option value="Carbonyl (R)">Carbonyl (R)</option>
-      <option value="Carbonyl (S)">Carbonyl (S)</option>
-      <option value="Carbonyl (V)">Carbonyl (V)</option>
-      <option value="Carboxy (D)">Carboxy (D)</option>
-      <option value="Carboxy (E)">Carboxy (E)</option>
-      <option value="Carboxy (K)">Carboxy (K)</option>
-      <option value="Carboxy (Protein N-term M)">Carboxy (Protein N-term M)</option>
-      <option value="Carboxy (W)">Carboxy (W)</option>
-      <option value="Carboxy-&gt;Thiocarboxy (Protein C-term G)">Carboxy-&gt;Thiocarboxy (Protein C-term G)</option>
-      <option value="Carboxyethyl (H)">Carboxyethyl (H)</option>
-      <option value="Carboxyethyl (K)">Carboxyethyl (K)</option>
-      <option value="Carboxyethylpyrrole (K)">Carboxyethylpyrrole (K)</option>
-      <option value="Carboxymethyl (C)">Carboxymethyl (C)</option>
-      <option value="Carboxymethyl (K)">Carboxymethyl (K)</option>
-      <option value="Carboxymethyl (N-term)">Carboxymethyl (N-term)</option>
-      <option value="Carboxymethyl (U)">Carboxymethyl (U)</option>
-      <option value="Carboxymethyl (W)">Carboxymethyl (W)</option>
-      <option value="Carboxymethyl:13C(2) (C)">Carboxymethyl:13C(2) (C)</option>
-      <option value="CarboxymethylDMAP (N-term)">CarboxymethylDMAP (N-term)</option>
-      <option value="CarboxymethylDTT (C)">CarboxymethylDTT (C)</option>
-      <option value="Cation:Ag (C-term)">Cation:Ag (C-term)</option>
-      <option value="Cation:Ag (D)">Cation:Ag (D)</option>
-      <option value="Cation:Ag (E)">Cation:Ag (E)</option>
-      <option value="Cation:Al[III] (C-term)">Cation:Al[III] (C-term)</option>
-      <option value="Cation:Al[III] (D)">Cation:Al[III] (D)</option>
-      <option value="Cation:Al[III] (E)">Cation:Al[III] (E)</option>
-      <option value="Cation:Ca[II] (C-term)">Cation:Ca[II] (C-term)</option>
-      <option value="Cation:Ca[II] (D)">Cation:Ca[II] (D)</option>
-      <option value="Cation:Ca[II] (E)">Cation:Ca[II] (E)</option>
-      <option value="Cation:Cu[I] (C-term)">Cation:Cu[I] (C-term)</option>
-      <option value="Cation:Cu[I] (D)">Cation:Cu[I] (D)</option>
-      <option value="Cation:Cu[I] (E)">Cation:Cu[I] (E)</option>
-      <option value="Cation:Cu[I] (H)">Cation:Cu[I] (H)</option>
-      <option value="Cation:Fe[II] (C-term)">Cation:Fe[II] (C-term)</option>
-      <option value="Cation:Fe[II] (D)">Cation:Fe[II] (D)</option>
-      <option value="Cation:Fe[II] (E)">Cation:Fe[II] (E)</option>
-      <option value="Cation:Fe[III] (C-term)">Cation:Fe[III] (C-term)</option>
-      <option value="Cation:Fe[III] (D)">Cation:Fe[III] (D)</option>
-      <option value="Cation:Fe[III] (E)">Cation:Fe[III] (E)</option>
-      <option value="Cation:K (C-term)">Cation:K (C-term)</option>
-      <option value="Cation:K (D)">Cation:K (D)</option>
-      <option value="Cation:K (E)">Cation:K (E)</option>
-      <option value="Cation:Li (C-term)">Cation:Li (C-term)</option>
-      <option value="Cation:Li (D)">Cation:Li (D)</option>
-      <option value="Cation:Li (E)">Cation:Li (E)</option>
-      <option value="Cation:Mg[II] (C-term)">Cation:Mg[II] (C-term)</option>
-      <option value="Cation:Mg[II] (D)">Cation:Mg[II] (D)</option>
-      <option value="Cation:Mg[II] (E)">Cation:Mg[II] (E)</option>
-      <option value="Cation:Na (C-term)">Cation:Na (C-term)</option>
-      <option value="Cation:Na (D)">Cation:Na (D)</option>
-      <option value="Cation:Na (E)">Cation:Na (E)</option>
-      <option value="Cation:Ni[II] (C-term)">Cation:Ni[II] (C-term)</option>
-      <option value="Cation:Ni[II] (D)">Cation:Ni[II] (D)</option>
-      <option value="Cation:Ni[II] (E)">Cation:Ni[II] (E)</option>
-      <option value="Cation:Zn[II] (C-term)">Cation:Zn[II] (C-term)</option>
-      <option value="Cation:Zn[II] (D)">Cation:Zn[II] (D)</option>
-      <option value="Cation:Zn[II] (E)">Cation:Zn[II] (E)</option>
-      <option value="Cation:Zn[II] (H)">Cation:Zn[II] (H)</option>
-      <option value="cGMP (C)">cGMP (C)</option>
-      <option value="cGMP (S)">cGMP (S)</option>
-      <option value="cGMP+RMP-loss (C)">cGMP+RMP-loss (C)</option>
-      <option value="cGMP+RMP-loss (S)">cGMP+RMP-loss (S)</option>
-      <option value="CHDH (D)">CHDH (D)</option>
-      <option value="Chlorination (W)">Chlorination (W)</option>
-      <option value="Chlorination (Y)">Chlorination (Y)</option>
-      <option value="Cholesterol (Protein C-term)">Cholesterol (Protein C-term)</option>
-      <option value="CIGG (K)">CIGG (K)</option>
-      <option value="CLIP_TRAQ_2 (K)">CLIP_TRAQ_2 (K)</option>
-      <option value="CLIP_TRAQ_2 (N-term)">CLIP_TRAQ_2 (N-term)</option>
-      <option value="CLIP_TRAQ_2 (Y)">CLIP_TRAQ_2 (Y)</option>
-      <option value="CLIP_TRAQ_3 (K)">CLIP_TRAQ_3 (K)</option>
-      <option value="CLIP_TRAQ_3 (N-term)">CLIP_TRAQ_3 (N-term)</option>
-      <option value="CLIP_TRAQ_3 (Y)">CLIP_TRAQ_3 (Y)</option>
-      <option value="CLIP_TRAQ_4 (K)">CLIP_TRAQ_4 (K)</option>
-      <option value="CLIP_TRAQ_4 (N-term)">CLIP_TRAQ_4 (N-term)</option>
-      <option value="CLIP_TRAQ_4 (Y)">CLIP_TRAQ_4 (Y)</option>
-      <option value="CoenzymeA (C)">CoenzymeA (C)</option>
-      <option value="Cresylphosphate (H)">Cresylphosphate (H)</option>
-      <option value="Cresylphosphate (K)">Cresylphosphate (K)</option>
-      <option value="Cresylphosphate (R)">Cresylphosphate (R)</option>
-      <option value="Cresylphosphate (S)">Cresylphosphate (S)</option>
-      <option value="Cresylphosphate (T)">Cresylphosphate (T)</option>
-      <option value="Cresylphosphate (Y)">Cresylphosphate (Y)</option>
-      <option value="CresylSaligeninPhosphate (H)">CresylSaligeninPhosphate (H)</option>
-      <option value="CresylSaligeninPhosphate (K)">CresylSaligeninPhosphate (K)</option>
-      <option value="CresylSaligeninPhosphate (R)">CresylSaligeninPhosphate (R)</option>
-      <option value="CresylSaligeninPhosphate (S)">CresylSaligeninPhosphate (S)</option>
-      <option value="CresylSaligeninPhosphate (T)">CresylSaligeninPhosphate (T)</option>
-      <option value="CresylSaligeninPhosphate (Y)">CresylSaligeninPhosphate (Y)</option>
-      <option value="Crotonaldehyde (C)">Crotonaldehyde (C)</option>
-      <option value="Crotonaldehyde (H)">Crotonaldehyde (H)</option>
-      <option value="Crotonaldehyde (K)">Crotonaldehyde (K)</option>
-      <option value="Crotonyl (K)">Crotonyl (K)</option>
-      <option value="CuSMo (C)">CuSMo (C)</option>
-      <option value="CUSTOM0 (A)">CUSTOM0 (A)</option>
-      <option value="CUSTOM0 (C)">CUSTOM0 (C)</option>
-      <option value="CUSTOM0 (C-term)">CUSTOM0 (C-term)</option>
-      <option value="CUSTOM0 (D)">CUSTOM0 (D)</option>
-      <option value="CUSTOM0 (E)">CUSTOM0 (E)</option>
-      <option value="CUSTOM0 (F)">CUSTOM0 (F)</option>
-      <option value="CUSTOM0 (G)">CUSTOM0 (G)</option>
-      <option value="CUSTOM0 (H)">CUSTOM0 (H)</option>
-      <option value="CUSTOM0 (I)">CUSTOM0 (I)</option>
-      <option value="CUSTOM0 (K)">CUSTOM0 (K)</option>
-      <option value="CUSTOM0 (L)">CUSTOM0 (L)</option>
-      <option value="CUSTOM0 (M)">CUSTOM0 (M)</option>
-      <option value="CUSTOM0 (N)">CUSTOM0 (N)</option>
-      <option value="CUSTOM0 (N-term)">CUSTOM0 (N-term)</option>
-      <option value="CUSTOM0 (P)">CUSTOM0 (P)</option>
-      <option value="CUSTOM0 (Q)">CUSTOM0 (Q)</option>
-      <option value="CUSTOM0 (R)">CUSTOM0 (R)</option>
-      <option value="CUSTOM0 (S)">CUSTOM0 (S)</option>
-      <option value="CUSTOM0 (T)">CUSTOM0 (T)</option>
-      <option value="CUSTOM0 (V)">CUSTOM0 (V)</option>
-      <option value="CUSTOM0 (W)">CUSTOM0 (W)</option>
-      <option value="CUSTOM0 (Y)">CUSTOM0 (Y)</option>
-      <option value="CUSTOM1 (A)">CUSTOM1 (A)</option>
-      <option value="CUSTOM1 (C)">CUSTOM1 (C)</option>
-      <option value="CUSTOM1 (C-term)">CUSTOM1 (C-term)</option>
-      <option value="CUSTOM1 (D)">CUSTOM1 (D)</option>
-      <option value="CUSTOM1 (E)">CUSTOM1 (E)</option>
-      <option value="CUSTOM1 (F)">CUSTOM1 (F)</option>
-      <option value="CUSTOM1 (G)">CUSTOM1 (G)</option>
-      <option value="CUSTOM1 (H)">CUSTOM1 (H)</option>
-      <option value="CUSTOM1 (I)">CUSTOM1 (I)</option>
-      <option value="CUSTOM1 (K)">CUSTOM1 (K)</option>
-      <option value="CUSTOM1 (L)">CUSTOM1 (L)</option>
-      <option value="CUSTOM1 (M)">CUSTOM1 (M)</option>
-      <option value="CUSTOM1 (N)">CUSTOM1 (N)</option>
-      <option value="CUSTOM1 (N-term)">CUSTOM1 (N-term)</option>
-      <option value="CUSTOM1 (P)">CUSTOM1 (P)</option>
-      <option value="CUSTOM1 (Q)">CUSTOM1 (Q)</option>
-      <option value="CUSTOM1 (R)">CUSTOM1 (R)</option>
-      <option value="CUSTOM1 (S)">CUSTOM1 (S)</option>
-      <option value="CUSTOM1 (T)">CUSTOM1 (T)</option>
-      <option value="CUSTOM1 (V)">CUSTOM1 (V)</option>
-      <option value="CUSTOM1 (W)">CUSTOM1 (W)</option>
-      <option value="CUSTOM1 (Y)">CUSTOM1 (Y)</option>
-      <option value="CUSTOM2 (A)">CUSTOM2 (A)</option>
-      <option value="CUSTOM2 (C)">CUSTOM2 (C)</option>
-      <option value="CUSTOM2 (C-term)">CUSTOM2 (C-term)</option>
-      <option value="CUSTOM2 (D)">CUSTOM2 (D)</option>
-      <option value="CUSTOM2 (E)">CUSTOM2 (E)</option>
-      <option value="CUSTOM2 (F)">CUSTOM2 (F)</option>
-      <option value="CUSTOM2 (G)">CUSTOM2 (G)</option>
-      <option value="CUSTOM2 (H)">CUSTOM2 (H)</option>
-      <option value="CUSTOM2 (I)">CUSTOM2 (I)</option>
-      <option value="CUSTOM2 (K)">CUSTOM2 (K)</option>
-      <option value="CUSTOM2 (L)">CUSTOM2 (L)</option>
-      <option value="CUSTOM2 (M)">CUSTOM2 (M)</option>
-      <option value="CUSTOM2 (N)">CUSTOM2 (N)</option>
-      <option value="CUSTOM2 (N-term)">CUSTOM2 (N-term)</option>
-      <option value="CUSTOM2 (P)">CUSTOM2 (P)</option>
-      <option value="CUSTOM2 (Q)">CUSTOM2 (Q)</option>
-      <option value="CUSTOM2 (R)">CUSTOM2 (R)</option>
-      <option value="CUSTOM2 (S)">CUSTOM2 (S)</option>
-      <option value="CUSTOM2 (T)">CUSTOM2 (T)</option>
-      <option value="CUSTOM2 (V)">CUSTOM2 (V)</option>
-      <option value="CUSTOM2 (W)">CUSTOM2 (W)</option>
-      <option value="CUSTOM2 (Y)">CUSTOM2 (Y)</option>
-      <option value="CUSTOM3 (A)">CUSTOM3 (A)</option>
-      <option value="CUSTOM3 (C)">CUSTOM3 (C)</option>
-      <option value="CUSTOM3 (C-term)">CUSTOM3 (C-term)</option>
-      <option value="CUSTOM3 (D)">CUSTOM3 (D)</option>
-      <option value="CUSTOM3 (E)">CUSTOM3 (E)</option>
-      <option value="CUSTOM3 (F)">CUSTOM3 (F)</option>
-      <option value="CUSTOM3 (G)">CUSTOM3 (G)</option>
-      <option value="CUSTOM3 (H)">CUSTOM3 (H)</option>
-      <option value="CUSTOM3 (I)">CUSTOM3 (I)</option>
-      <option value="CUSTOM3 (K)">CUSTOM3 (K)</option>
-      <option value="CUSTOM3 (L)">CUSTOM3 (L)</option>
-      <option value="CUSTOM3 (M)">CUSTOM3 (M)</option>
-      <option value="CUSTOM3 (N)">CUSTOM3 (N)</option>
-      <option value="CUSTOM3 (N-term)">CUSTOM3 (N-term)</option>
-      <option value="CUSTOM3 (P)">CUSTOM3 (P)</option>
-      <option value="CUSTOM3 (Q)">CUSTOM3 (Q)</option>
-      <option value="CUSTOM3 (R)">CUSTOM3 (R)</option>
-      <option value="CUSTOM3 (S)">CUSTOM3 (S)</option>
-      <option value="CUSTOM3 (T)">CUSTOM3 (T)</option>
-      <option value="CUSTOM3 (V)">CUSTOM3 (V)</option>
-      <option value="CUSTOM3 (W)">CUSTOM3 (W)</option>
-      <option value="CUSTOM3 (Y)">CUSTOM3 (Y)</option>
-      <option value="CUSTOM4 (A)">CUSTOM4 (A)</option>
-      <option value="CUSTOM4 (C)">CUSTOM4 (C)</option>
-      <option value="CUSTOM4 (C-term)">CUSTOM4 (C-term)</option>
-      <option value="CUSTOM4 (D)">CUSTOM4 (D)</option>
-      <option value="CUSTOM4 (E)">CUSTOM4 (E)</option>
-      <option value="CUSTOM4 (F)">CUSTOM4 (F)</option>
-      <option value="CUSTOM4 (G)">CUSTOM4 (G)</option>
-      <option value="CUSTOM4 (H)">CUSTOM4 (H)</option>
-      <option value="CUSTOM4 (I)">CUSTOM4 (I)</option>
-      <option value="CUSTOM4 (K)">CUSTOM4 (K)</option>
-      <option value="CUSTOM4 (L)">CUSTOM4 (L)</option>
-      <option value="CUSTOM4 (M)">CUSTOM4 (M)</option>
-      <option value="CUSTOM4 (N)">CUSTOM4 (N)</option>
-      <option value="CUSTOM4 (N-term)">CUSTOM4 (N-term)</option>
-      <option value="CUSTOM4 (P)">CUSTOM4 (P)</option>
-      <option value="CUSTOM4 (Q)">CUSTOM4 (Q)</option>
-      <option value="CUSTOM4 (R)">CUSTOM4 (R)</option>
-      <option value="CUSTOM4 (S)">CUSTOM4 (S)</option>
-      <option value="CUSTOM4 (T)">CUSTOM4 (T)</option>
-      <option value="CUSTOM4 (V)">CUSTOM4 (V)</option>
-      <option value="CUSTOM4 (W)">CUSTOM4 (W)</option>
-      <option value="CUSTOM4 (Y)">CUSTOM4 (Y)</option>
-      <option value="CUSTOM5 (A)">CUSTOM5 (A)</option>
-      <option value="CUSTOM5 (C)">CUSTOM5 (C)</option>
-      <option value="CUSTOM5 (C-term)">CUSTOM5 (C-term)</option>
-      <option value="CUSTOM5 (D)">CUSTOM5 (D)</option>
-      <option value="CUSTOM5 (E)">CUSTOM5 (E)</option>
-      <option value="CUSTOM5 (F)">CUSTOM5 (F)</option>
-      <option value="CUSTOM5 (G)">CUSTOM5 (G)</option>
-      <option value="CUSTOM5 (H)">CUSTOM5 (H)</option>
-      <option value="CUSTOM5 (I)">CUSTOM5 (I)</option>
-      <option value="CUSTOM5 (K)">CUSTOM5 (K)</option>
-      <option value="CUSTOM5 (L)">CUSTOM5 (L)</option>
-      <option value="CUSTOM5 (M)">CUSTOM5 (M)</option>
-      <option value="CUSTOM5 (N)">CUSTOM5 (N)</option>
-      <option value="CUSTOM5 (N-term)">CUSTOM5 (N-term)</option>
-      <option value="CUSTOM5 (P)">CUSTOM5 (P)</option>
-      <option value="CUSTOM5 (Q)">CUSTOM5 (Q)</option>
-      <option value="CUSTOM5 (R)">CUSTOM5 (R)</option>
-      <option value="CUSTOM5 (S)">CUSTOM5 (S)</option>
-      <option value="CUSTOM5 (T)">CUSTOM5 (T)</option>
-      <option value="CUSTOM5 (V)">CUSTOM5 (V)</option>
-      <option value="CUSTOM5 (W)">CUSTOM5 (W)</option>
-      <option value="CUSTOM5 (Y)">CUSTOM5 (Y)</option>
-      <option value="CUSTOM6 (A)">CUSTOM6 (A)</option>
-      <option value="CUSTOM6 (C)">CUSTOM6 (C)</option>
-      <option value="CUSTOM6 (C-term)">CUSTOM6 (C-term)</option>
-      <option value="CUSTOM6 (D)">CUSTOM6 (D)</option>
-      <option value="CUSTOM6 (E)">CUSTOM6 (E)</option>
-      <option value="CUSTOM6 (F)">CUSTOM6 (F)</option>
-      <option value="CUSTOM6 (G)">CUSTOM6 (G)</option>
-      <option value="CUSTOM6 (H)">CUSTOM6 (H)</option>
-      <option value="CUSTOM6 (I)">CUSTOM6 (I)</option>
-      <option value="CUSTOM6 (K)">CUSTOM6 (K)</option>
-      <option value="CUSTOM6 (L)">CUSTOM6 (L)</option>
-      <option value="CUSTOM6 (M)">CUSTOM6 (M)</option>
-      <option value="CUSTOM6 (N)">CUSTOM6 (N)</option>
-      <option value="CUSTOM6 (N-term)">CUSTOM6 (N-term)</option>
-      <option value="CUSTOM6 (P)">CUSTOM6 (P)</option>
-      <option value="CUSTOM6 (Q)">CUSTOM6 (Q)</option>
-      <option value="CUSTOM6 (R)">CUSTOM6 (R)</option>
-      <option value="CUSTOM6 (S)">CUSTOM6 (S)</option>
-      <option value="CUSTOM6 (T)">CUSTOM6 (T)</option>
-      <option value="CUSTOM6 (V)">CUSTOM6 (V)</option>
-      <option value="CUSTOM6 (W)">CUSTOM6 (W)</option>
-      <option value="CUSTOM6 (Y)">CUSTOM6 (Y)</option>
-      <option value="CUSTOM7 (A)">CUSTOM7 (A)</option>
-      <option value="CUSTOM7 (C)">CUSTOM7 (C)</option>
-      <option value="CUSTOM7 (C-term)">CUSTOM7 (C-term)</option>
-      <option value="CUSTOM7 (D)">CUSTOM7 (D)</option>
-      <option value="CUSTOM7 (E)">CUSTOM7 (E)</option>
-      <option value="CUSTOM7 (F)">CUSTOM7 (F)</option>
-      <option value="CUSTOM7 (G)">CUSTOM7 (G)</option>
-      <option value="CUSTOM7 (H)">CUSTOM7 (H)</option>
-      <option value="CUSTOM7 (I)">CUSTOM7 (I)</option>
-      <option value="CUSTOM7 (K)">CUSTOM7 (K)</option>
-      <option value="CUSTOM7 (L)">CUSTOM7 (L)</option>
-      <option value="CUSTOM7 (M)">CUSTOM7 (M)</option>
-      <option value="CUSTOM7 (N)">CUSTOM7 (N)</option>
-      <option value="CUSTOM7 (N-term)">CUSTOM7 (N-term)</option>
-      <option value="CUSTOM7 (P)">CUSTOM7 (P)</option>
-      <option value="CUSTOM7 (Q)">CUSTOM7 (Q)</option>
-      <option value="CUSTOM7 (R)">CUSTOM7 (R)</option>
-      <option value="CUSTOM7 (S)">CUSTOM7 (S)</option>
-      <option value="CUSTOM7 (T)">CUSTOM7 (T)</option>
-      <option value="CUSTOM7 (V)">CUSTOM7 (V)</option>
-      <option value="CUSTOM7 (W)">CUSTOM7 (W)</option>
-      <option value="CUSTOM7 (Y)">CUSTOM7 (Y)</option>
-      <option value="CUSTOM8 (A)">CUSTOM8 (A)</option>
-      <option value="CUSTOM8 (C)">CUSTOM8 (C)</option>
-      <option value="CUSTOM8 (C-term)">CUSTOM8 (C-term)</option>
-      <option value="CUSTOM8 (D)">CUSTOM8 (D)</option>
-      <option value="CUSTOM8 (E)">CUSTOM8 (E)</option>
-      <option value="CUSTOM8 (F)">CUSTOM8 (F)</option>
-      <option value="CUSTOM8 (G)">CUSTOM8 (G)</option>
-      <option value="CUSTOM8 (H)">CUSTOM8 (H)</option>
-      <option value="CUSTOM8 (I)">CUSTOM8 (I)</option>
-      <option value="CUSTOM8 (K)">CUSTOM8 (K)</option>
-      <option value="CUSTOM8 (L)">CUSTOM8 (L)</option>
-      <option value="CUSTOM8 (M)">CUSTOM8 (M)</option>
-      <option value="CUSTOM8 (N)">CUSTOM8 (N)</option>
-      <option value="CUSTOM8 (N-term)">CUSTOM8 (N-term)</option>
-      <option value="CUSTOM8 (P)">CUSTOM8 (P)</option>
-      <option value="CUSTOM8 (Q)">CUSTOM8 (Q)</option>
-      <option value="CUSTOM8 (R)">CUSTOM8 (R)</option>
-      <option value="CUSTOM8 (S)">CUSTOM8 (S)</option>
-      <option value="CUSTOM8 (T)">CUSTOM8 (T)</option>
-      <option value="CUSTOM8 (V)">CUSTOM8 (V)</option>
-      <option value="CUSTOM8 (W)">CUSTOM8 (W)</option>
-      <option value="CUSTOM8 (Y)">CUSTOM8 (Y)</option>
-      <option value="CUSTOM9 (A)">CUSTOM9 (A)</option>
-      <option value="CUSTOM9 (C)">CUSTOM9 (C)</option>
-      <option value="CUSTOM9 (C-term)">CUSTOM9 (C-term)</option>
-      <option value="CUSTOM9 (D)">CUSTOM9 (D)</option>
-      <option value="CUSTOM9 (E)">CUSTOM9 (E)</option>
-      <option value="CUSTOM9 (F)">CUSTOM9 (F)</option>
-      <option value="CUSTOM9 (G)">CUSTOM9 (G)</option>
-      <option value="CUSTOM9 (H)">CUSTOM9 (H)</option>
-      <option value="CUSTOM9 (I)">CUSTOM9 (I)</option>
-      <option value="CUSTOM9 (K)">CUSTOM9 (K)</option>
-      <option value="CUSTOM9 (L)">CUSTOM9 (L)</option>
-      <option value="CUSTOM9 (M)">CUSTOM9 (M)</option>
-      <option value="CUSTOM9 (N)">CUSTOM9 (N)</option>
-      <option value="CUSTOM9 (N-term)">CUSTOM9 (N-term)</option>
-      <option value="CUSTOM9 (P)">CUSTOM9 (P)</option>
-      <option value="CUSTOM9 (Q)">CUSTOM9 (Q)</option>
-      <option value="CUSTOM9 (R)">CUSTOM9 (R)</option>
-      <option value="CUSTOM9 (S)">CUSTOM9 (S)</option>
-      <option value="CUSTOM9 (T)">CUSTOM9 (T)</option>
-      <option value="CUSTOM9 (V)">CUSTOM9 (V)</option>
-      <option value="CUSTOM9 (W)">CUSTOM9 (W)</option>
-      <option value="CUSTOM9 (Y)">CUSTOM9 (Y)</option>
-      <option value="Cy3-maleimide (C)">Cy3-maleimide (C)</option>
-      <option value="Cy3b-maleimide (C)">Cy3b-maleimide (C)</option>
-      <option value="Cyano (C)">Cyano (C)</option>
-      <option value="CyDye-Cy3 (C)">CyDye-Cy3 (C)</option>
-      <option value="CyDye-Cy5 (C)">CyDye-Cy5 (C)</option>
-      <option value="Cys-&gt;Ala (C)">Cys-&gt;Ala (C)</option>
-      <option value="Cys-&gt;Arg (C)">Cys-&gt;Arg (C)</option>
-      <option value="Cys-&gt;Asn (C)">Cys-&gt;Asn (C)</option>
-      <option value="Cys-&gt;Asp (C)">Cys-&gt;Asp (C)</option>
-      <option value="Cys-&gt;CamSec (C)">Cys-&gt;CamSec (C)</option>
-      <option value="Cys-&gt;Dha (C)">Cys-&gt;Dha (C)</option>
-      <option value="Cys-&gt;ethylaminoAla (C)">Cys-&gt;ethylaminoAla (C)</option>
-      <option value="Cys-&gt;Gln (C)">Cys-&gt;Gln (C)</option>
-      <option value="Cys-&gt;Glu (C)">Cys-&gt;Glu (C)</option>
-      <option value="Cys-&gt;Gly (C)">Cys-&gt;Gly (C)</option>
-      <option value="Cys-&gt;His (C)">Cys-&gt;His (C)</option>
-      <option value="Cys-&gt;Lys (C)">Cys-&gt;Lys (C)</option>
-      <option value="Cys-&gt;Met (C)">Cys-&gt;Met (C)</option>
-      <option value="Cys-&gt;methylaminoAla (C)">Cys-&gt;methylaminoAla (C)</option>
-      <option value="Cys-&gt;Oxoalanine (C)">Cys-&gt;Oxoalanine (C)</option>
-      <option value="Cys-&gt;Phe (C)">Cys-&gt;Phe (C)</option>
-      <option value="Cys-&gt;Pro (C)">Cys-&gt;Pro (C)</option>
-      <option value="Cys-&gt;PyruvicAcid (Protein N-term C)">Cys-&gt;PyruvicAcid (Protein N-term C)</option>
-      <option value="Cys-&gt;SecNEM (C)">Cys-&gt;SecNEM (C)</option>
-      <option value="Cys-&gt;SecNEM:2H(5) (C)">Cys-&gt;SecNEM:2H(5) (C)</option>
-      <option value="Cys-&gt;Ser (C)">Cys-&gt;Ser (C)</option>
-      <option value="Cys-&gt;Thr (C)">Cys-&gt;Thr (C)</option>
-      <option value="Cys-&gt;Trp (C)">Cys-&gt;Trp (C)</option>
-      <option value="Cys-&gt;Tyr (C)">Cys-&gt;Tyr (C)</option>
-      <option value="Cys-&gt;Val (C)">Cys-&gt;Val (C)</option>
-      <option value="Cys-&gt;Xle (C)">Cys-&gt;Xle (C)</option>
-      <option value="Cysteinyl (C)">Cysteinyl (C)</option>
-      <option value="cysTMT (C)">cysTMT (C)</option>
-      <option value="cysTMT6plex (C)">cysTMT6plex (C)</option>
-      <option value="Cytopiloyne (C)">Cytopiloyne (C)</option>
-      <option value="Cytopiloyne (K)">Cytopiloyne (K)</option>
-      <option value="Cytopiloyne (N-term)">Cytopiloyne (N-term)</option>
-      <option value="Cytopiloyne (P)">Cytopiloyne (P)</option>
-      <option value="Cytopiloyne (R)">Cytopiloyne (R)</option>
-      <option value="Cytopiloyne (S)">Cytopiloyne (S)</option>
-      <option value="Cytopiloyne (Y)">Cytopiloyne (Y)</option>
-      <option value="Cytopiloyne+water (C)">Cytopiloyne+water (C)</option>
-      <option value="Cytopiloyne+water (K)">Cytopiloyne+water (K)</option>
-      <option value="Cytopiloyne+water (N-term)">Cytopiloyne+water (N-term)</option>
-      <option value="Cytopiloyne+water (R)">Cytopiloyne+water (R)</option>
-      <option value="Cytopiloyne+water (S)">Cytopiloyne+water (S)</option>
-      <option value="Cytopiloyne+water (T)">Cytopiloyne+water (T)</option>
-      <option value="Cytopiloyne+water (Y)">Cytopiloyne+water (Y)</option>
-      <option value="DAET (S)">DAET (S)</option>
-      <option value="DAET (T)">DAET (T)</option>
-      <option value="Dansyl (K)">Dansyl (K)</option>
-      <option value="Dansyl (N-term)">Dansyl (N-term)</option>
-      <option value="Dap-DSP (A)">Dap-DSP (A)</option>
-      <option value="Dap-DSP (E)">Dap-DSP (E)</option>
-      <option value="Dap-DSP (K)">Dap-DSP (K)</option>
-      <option value="Deamidated (N)">Deamidated (N)</option>
-      <option value="Deamidated (Protein N-term F)">Deamidated (Protein N-term F)</option>
-      <option value="Deamidated (Q)">Deamidated (Q)</option>
-      <option value="Deamidated (R)">Deamidated (R)</option>
-      <option value="Deamidated:18O(1) (N)">Deamidated:18O(1) (N)</option>
-      <option value="Deamidated:18O(1) (Q)">Deamidated:18O(1) (Q)</option>
-      <option value="Decanoyl (S)">Decanoyl (S)</option>
-      <option value="Decanoyl (T)">Decanoyl (T)</option>
-      <option value="Decarboxylation (D)">Decarboxylation (D)</option>
-      <option value="Decarboxylation (E)">Decarboxylation (E)</option>
-      <option value="DEDGFLYMVYASQETFG (K)">DEDGFLYMVYASQETFG (K)</option>
-      <option value="Dehydrated (D)">Dehydrated (D)</option>
-      <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
-      <option value="Dehydrated (Protein C-term N)">Dehydrated (Protein C-term N)</option>
-      <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
-      <option value="Dehydrated (S)">Dehydrated (S)</option>
-      <option value="Dehydrated (T)">Dehydrated (T)</option>
-      <option value="Dehydrated (Y)">Dehydrated (Y)</option>
-      <option value="Dehydro (C)">Dehydro (C)</option>
-      <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
-      <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-      <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
-      <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
-      <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
-      <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
-      <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
-      <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
-      <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
-      <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
-      <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
-      <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-      <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
-      <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
-      <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
-      <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
-      <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
-      <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
-      <option value="Delta:H(4)C(3) (K)">Delta:H(4)C(3) (K)</option>
-      <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
-      <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
-      <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
-      <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
-      <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
-      <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
-      <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
-      <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
-      <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
-      <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
-      <option value="Delta:H(6)C(3)O(1) (K)">Delta:H(6)C(3)O(1) (K)</option>
-      <option value="Delta:H(6)C(3)O(1) (Protein N-term)">Delta:H(6)C(3)O(1) (Protein N-term)</option>
-      <option value="Delta:H(6)C(6)O(1) (K)">Delta:H(6)C(6)O(1) (K)</option>
-      <option value="Delta:H(6)C(7)O(4) (R)">Delta:H(6)C(7)O(4) (R)</option>
-      <option value="Delta:H(8)C(6)O(1) (K)">Delta:H(8)C(6)O(1) (K)</option>
-      <option value="Delta:H(8)C(6)O(1) (Protein N-term)">Delta:H(8)C(6)O(1) (Protein N-term)</option>
-      <option value="Delta:H(8)C(6)O(2) (K)">Delta:H(8)C(6)O(2) (K)</option>
-      <option value="Delta:Hg(1) (C)">Delta:Hg(1) (C)</option>
-      <option value="Delta:O(4) (W)">Delta:O(4) (W)</option>
-      <option value="Delta:S(-1)Se(1) (C)">Delta:S(-1)Se(1) (C)</option>
-      <option value="Delta:S(-1)Se(1) (M)">Delta:S(-1)Se(1) (M)</option>
-      <option value="Delta:Se(1) (C)">Delta:Se(1) (C)</option>
-      <option value="Deoxy (D)">Deoxy (D)</option>
-      <option value="Deoxy (S)">Deoxy (S)</option>
-      <option value="Deoxy (T)">Deoxy (T)</option>
-      <option value="Deoxyhypusine (K)">Deoxyhypusine (K)</option>
-      <option value="Deoxyhypusine (Q)">Deoxyhypusine (Q)</option>
-      <option value="DeStreak (C)">DeStreak (C)</option>
-      <option value="Dethiomethyl (M)">Dethiomethyl (M)</option>
-      <option value="dHex (N)">dHex (N)</option>
-      <option value="dHex (S)">dHex (S)</option>
-      <option value="dHex (T)">dHex (T)</option>
-      <option value="dHex(1)Hex(1) (S)">dHex(1)Hex(1) (S)</option>
-      <option value="dHex(1)Hex(1) (T)">dHex(1)Hex(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexA(1)HexNAc(3) (S)">dHex(1)Hex(1)HexA(1)HexNAc(3) (S)</option>
-      <option value="dHex(1)Hex(1)HexA(1)HexNAc(3) (T)">dHex(1)Hex(1)HexA(1)HexNAc(3) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)Kdn(1) (S)">dHex(1)Hex(1)HexNAc(1)Kdn(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)Kdn(1) (T)">dHex(1)Hex(1)HexNAc(1)Kdn(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(1)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(1)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(1)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(1)NeuGc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(1)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(1)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3) (S)">dHex(1)Hex(1)HexNAc(3) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3) (T)">dHex(1)Hex(1)HexNAc(3) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S)">dHex(1)Hex(1)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T)">dHex(1)Hex(1)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(1)HexNAc(4) (S)">dHex(1)Hex(1)HexNAc(4) (S)</option>
-      <option value="dHex(1)Hex(1)HexNAc(4) (T)">dHex(1)Hex(1)HexNAc(4) (T)</option>
-      <option value="dHex(1)Hex(2) (S)">dHex(1)Hex(2) (S)</option>
-      <option value="dHex(1)Hex(2) (T)">dHex(1)Hex(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexA(1) (S)">dHex(1)Hex(2)HexA(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexA(1) (T)">dHex(1)Hex(2)HexA(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(1) (S)">dHex(1)Hex(2)HexA(1)HexNAc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(1) (T)">dHex(1)Hex(2)HexA(1)HexNAc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (S)">dHex(1)Hex(2)HexA(1)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexA(1)HexNAc(2) (T)">dHex(1)Hex(2)HexA(1)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1) (S)">dHex(1)Hex(2)HexNAc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1) (T)">dHex(1)Hex(2)HexNAc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(1)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (N)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S)">dHex(1)Hex(2)HexNAc(2)NeuGc(3) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T)">dHex(1)Hex(2)HexNAc(2)NeuGc(3) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)Pent(1) (N)">dHex(1)Hex(2)HexNAc(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3) (N)">dHex(1)Hex(2)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3) (S)">dHex(1)Hex(2)HexNAc(3) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3) (T)">dHex(1)Hex(2)HexNAc(3) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(2)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4) (N)">dHex(1)Hex(2)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4) (S)">dHex(1)Hex(2)HexNAc(4) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4) (T)">dHex(1)Hex(2)HexNAc(4) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)">dHex(1)Hex(2)HexNAc(4)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-      <option value="dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(1)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-      <option value="dHex(1)Hex(3) (S)">dHex(1)Hex(3) (S)</option>
-      <option value="dHex(1)Hex(3) (T)">dHex(1)Hex(3) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(2) (S)">dHex(1)Hex(3)HexA(1)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(2) (T)">dHex(1)Hex(3)HexA(1)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexA(2)HexNAc(2) (S)">dHex(1)Hex(3)HexA(2)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(3)HexA(2)HexNAc(2) (T)">dHex(1)Hex(3)HexA(2)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(1) (S)">dHex(1)Hex(3)HexNAc(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(1) (T)">dHex(1)Hex(3)HexNAc(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(1)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(1)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2) (N)">dHex(1)Hex(3)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2) (S)">dHex(1)Hex(3)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2) (T)">dHex(1)Hex(3)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S)">dHex(1)Hex(3)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T)">dHex(1)Hex(3)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)Pent(1) (N)">dHex(1)Hex(3)HexNAc(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(2)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3) (N)">dHex(1)Hex(3)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3) (S)">dHex(1)Hex(3)HexNAc(3) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3) (T)">dHex(1)Hex(3)HexNAc(3) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(1)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(1)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Pent(1) (N)">dHex(1)Hex(3)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Pent(2) (N)">dHex(1)Hex(3)HexNAc(3)Pent(2) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Pent(3) (N)">dHex(1)Hex(3)HexNAc(3)Pent(3) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(3)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(3)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4) (N)">dHex(1)Hex(3)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4) (S)">dHex(1)Hex(3)HexNAc(4) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4) (T)">dHex(1)Hex(3)HexNAc(4) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)Pent(1) (N)">dHex(1)Hex(3)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)Pent(2) (N)">dHex(1)Hex(3)HexNAc(4)Pent(2) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)Pent(3) (N)">dHex(1)Hex(3)HexNAc(4)Pent(3) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5) (N)">dHex(1)Hex(3)HexNAc(5) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5) (S)">dHex(1)Hex(3)HexNAc(5) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5) (T)">dHex(1)Hex(3)HexNAc(5) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T)">dHex(1)Hex(3)HexNAc(5)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(5)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(5)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(6) (N)">dHex(1)Hex(3)HexNAc(6) (N)</option>
-      <option value="dHex(1)Hex(3)HexNAc(6) (S)">dHex(1)Hex(3)HexNAc(6) (S)</option>
-      <option value="dHex(1)Hex(3)HexNAc(6) (T)">dHex(1)Hex(3)HexNAc(6) (T)</option>
-      <option value="dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)">dHex(1)Hex(3)HexNAc(6)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4) (S)">dHex(1)Hex(4) (S)</option>
-      <option value="dHex(1)Hex(4) (T)">dHex(1)Hex(4) (T)</option>
-      <option value="dHex(1)Hex(4)HexA(1) (S)">dHex(1)Hex(4)HexA(1) (S)</option>
-      <option value="dHex(1)Hex(4)HexA(1) (T)">dHex(1)Hex(4)HexA(1) (T)</option>
-      <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (S)">dHex(1)Hex(4)HexA(1)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(4)HexA(1)HexNAc(2) (T)">dHex(1)Hex(4)HexA(1)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(1)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(1)Pent(1) (N)">dHex(1)Hex(4)HexNAc(1)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(2) (N)">dHex(1)Hex(4)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(2) (S)">dHex(1)Hex(4)HexNAc(2) (S)</option>
-      <option value="dHex(1)Hex(4)HexNAc(2) (T)">dHex(1)Hex(4)HexNAc(2) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(2)Pent(1) (N)">dHex(1)Hex(4)HexNAc(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3) (N)">dHex(1)Hex(4)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(4)HexNAc(3)NeuGc(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)Pent(1) (N)">dHex(1)Hex(4)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4) (N)">dHex(1)Hex(4)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4) (S)">dHex(1)Hex(4)HexNAc(4) (S)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4) (T)">dHex(1)Hex(4)HexNAc(4) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (S)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T)">dHex(1)Hex(4)HexNAc(4)NeuAc(1) (T)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)Pent(1) (N)">dHex(1)Hex(4)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(5) (N)">dHex(1)Hex(4)HexNAc(5) (N)</option>
-      <option value="dHex(1)Hex(4)HexNAc(5)Sulf(1) (N)">dHex(1)Hex(4)HexNAc(5)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5) (S)">dHex(1)Hex(5) (S)</option>
-      <option value="dHex(1)Hex(5) (T)">dHex(1)Hex(5) (T)</option>
-      <option value="dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N)">dHex(1)Hex(5)HexA(1)HexNAc(3)Sulf(2) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(2) (N)">dHex(1)Hex(5)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(2)Pent(1) (N)">dHex(1)Hex(5)HexNAc(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3) (N)">dHex(1)Hex(5)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuGc(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)NeuGc(1)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4) (N)">dHex(1)Hex(5)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N)">dHex(1)Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N)">dHex(1)Hex(5)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N)">dHex(1)Hex(5)HexNAc(4)NeuAc(2) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)Pent(1) (N)">dHex(1)Hex(5)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)Sulf(1) (N)">dHex(1)Hex(5)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(4)Sulf(2) (N)">dHex(1)Hex(5)HexNAc(4)Sulf(2) (N)</option>
-      <option value="dHex(1)Hex(5)HexNAc(5) (N)">dHex(1)Hex(5)HexNAc(5) (N)</option>
-      <option value="dHex(1)Hex(6) (S)">dHex(1)Hex(6) (S)</option>
-      <option value="dHex(1)Hex(6) (T)">dHex(1)Hex(6) (T)</option>
-      <option value="dHex(1)Hex(6)HexNAc(2) (N)">dHex(1)Hex(6)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(6)HexNAc(3) (N)">dHex(1)Hex(6)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(6)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(6)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(6)HexNAc(4) (N)">dHex(1)Hex(6)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(2) (N)">dHex(1)Hex(7)HexNAc(2) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(3) (N)">dHex(1)Hex(7)HexNAc(3) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(3)Phos(1) (N)">dHex(1)Hex(7)HexNAc(3)Phos(1) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)">dHex(1)Hex(7)HexNAc(3)Sulf(1) (N)</option>
-      <option value="dHex(1)Hex(7)HexNAc(4) (N)">dHex(1)Hex(7)HexNAc(4) (N)</option>
-      <option value="dHex(1)Hex(8)HexNAc(2) (N)">dHex(1)Hex(8)HexNAc(2) (N)</option>
-      <option value="dHex(1)HexNAc(3) (S)">dHex(1)HexNAc(3) (S)</option>
-      <option value="dHex(1)HexNAc(3) (T)">dHex(1)HexNAc(3) (T)</option>
-      <option value="dHex(1)HexNAc(4) (S)">dHex(1)HexNAc(4) (S)</option>
-      <option value="dHex(1)HexNAc(4) (T)">dHex(1)HexNAc(4) (T)</option>
-      <option value="dHex(1)HexNAc(5) (S)">dHex(1)HexNAc(5) (S)</option>
-      <option value="dHex(1)HexNAc(5) (T)">dHex(1)HexNAc(5) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(1)Kdn(1) (S)">dHex(2)Hex(1)HexNAc(1)Kdn(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(1)Kdn(1) (T)">dHex(2)Hex(1)HexNAc(1)Kdn(1) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(2)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(2)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)NeuAc(1) (S)">dHex(2)Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)NeuAc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(1)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(3) (S)">dHex(2)Hex(1)HexNAc(3) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(3) (T)">dHex(2)Hex(1)HexNAc(3) (T)</option>
-      <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)">dHex(2)Hex(1)HexNAc(4)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2) (S)">dHex(2)Hex(2) (S)</option>
-      <option value="dHex(2)Hex(2) (T)">dHex(2)Hex(2) (T)</option>
-      <option value="dHex(2)Hex(2)HexA(1) (S)">dHex(2)Hex(2)HexA(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexA(1) (T)">dHex(2)Hex(2)HexA(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexA(1)HexNAc(1) (S)">dHex(2)Hex(2)HexA(1)HexNAc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexA(1)HexNAc(1) (T)">dHex(2)Hex(2)HexA(1)HexNAc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(1) (S)">dHex(2)Hex(2)HexNAc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(1) (T)">dHex(2)Hex(2)HexNAc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2) (N)">dHex(2)Hex(2)HexNAc(2) (N)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2) (S)">dHex(2)Hex(2)HexNAc(2) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2) (T)">dHex(2)Hex(2)HexNAc(2) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(2)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(2)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(2)Sulf(2) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(2)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(2)Sulf(2) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3) (N)">dHex(2)Hex(2)HexNAc(3) (N)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3) (S)">dHex(2)Hex(2)HexNAc(3) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3) (T)">dHex(2)Hex(2)HexNAc(3) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)NeuAc(1) (S)">dHex(2)Hex(2)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(2)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)NeuGc(1) (S)">dHex(2)Hex(2)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)NeuGc(1) (T)">dHex(2)Hex(2)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(4) (S)">dHex(2)Hex(2)HexNAc(4) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(4) (T)">dHex(2)Hex(2)HexNAc(4) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(2)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(5) (S)">dHex(2)Hex(2)HexNAc(5) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(5) (T)">dHex(2)Hex(2)HexNAc(5) (T)</option>
-      <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)">dHex(2)Hex(2)HexNAc(6)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3) (S)">dHex(2)Hex(3) (S)</option>
-      <option value="dHex(2)Hex(3) (T)">dHex(2)Hex(3) (T)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(1)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(1)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(1)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(1)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2) (N)">dHex(2)Hex(3)HexNAc(2) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2) (S)">dHex(2)Hex(3)HexNAc(2) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2) (T)">dHex(2)Hex(3)HexNAc(2) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2)NeuGc(1) (S)">dHex(2)Hex(3)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2)NeuGc(1) (T)">dHex(2)Hex(3)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(2)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3) (N)">dHex(2)Hex(3)HexNAc(3) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3) (S)">dHex(2)Hex(3)HexNAc(3) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3) (T)">dHex(2)Hex(3)HexNAc(3) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)">dHex(2)Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)Pent(1) (N)">dHex(2)Hex(3)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)Pent(2) (N)">dHex(2)Hex(3)HexNAc(3)Pent(2) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(3)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4) (N)">dHex(2)Hex(3)HexNAc(4) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4) (S)">dHex(2)Hex(3)HexNAc(4) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4) (T)">dHex(2)Hex(3)HexNAc(4) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)">dHex(2)Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4)Pent(1) (N)">dHex(2)Hex(3)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(4)Pent(2) (N)">dHex(2)Hex(3)HexNAc(4)Pent(2) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(5) (N)">dHex(2)Hex(3)HexNAc(5) (N)</option>
-      <option value="dHex(2)Hex(3)HexNAc(5) (S)">dHex(2)Hex(3)HexNAc(5) (S)</option>
-      <option value="dHex(2)Hex(3)HexNAc(5) (T)">dHex(2)Hex(3)HexNAc(5) (T)</option>
-      <option value="dHex(2)Hex(3)HexNAc(6) (N)">dHex(2)Hex(3)HexNAc(6) (N)</option>
-      <option value="dHex(2)Hex(4) (S)">dHex(2)Hex(4) (S)</option>
-      <option value="dHex(2)Hex(4) (T)">dHex(2)Hex(4) (T)</option>
-      <option value="dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)">dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)">dHex(2)Hex(4)HexA(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="dHex(2)Hex(4)HexNAc(1) (S)">dHex(2)Hex(4)HexNAc(1) (S)</option>
-      <option value="dHex(2)Hex(4)HexNAc(1) (T)">dHex(2)Hex(4)HexNAc(1) (T)</option>
-      <option value="dHex(2)Hex(4)HexNAc(2) (N)">dHex(2)Hex(4)HexNAc(2) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(2) (S)">dHex(2)Hex(4)HexNAc(2) (S)</option>
-      <option value="dHex(2)Hex(4)HexNAc(2) (T)">dHex(2)Hex(4)HexNAc(2) (T)</option>
-      <option value="dHex(2)Hex(4)HexNAc(3) (N)">dHex(2)Hex(4)HexNAc(3) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)">dHex(2)Hex(4)HexNAc(3)NeuAc(1)Sulf(1) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(3)Pent(1) (N)">dHex(2)Hex(4)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4) (N)">dHex(2)Hex(4)HexNAc(4) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4) (S)">dHex(2)Hex(4)HexNAc(4) (S)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4) (T)">dHex(2)Hex(4)HexNAc(4) (T)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4)Pent(1) (N)">dHex(2)Hex(4)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(2)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(5) (N)">dHex(2)Hex(4)HexNAc(5) (N)</option>
-      <option value="dHex(2)Hex(4)HexNAc(5) (S)">dHex(2)Hex(4)HexNAc(5) (S)</option>
-      <option value="dHex(2)Hex(4)HexNAc(5) (T)">dHex(2)Hex(4)HexNAc(5) (T)</option>
-      <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (S)">dHex(2)Hex(5)HexNAc(2)Me(1) (S)</option>
-      <option value="dHex(2)Hex(5)HexNAc(2)Me(1) (T)">dHex(2)Hex(5)HexNAc(2)Me(1) (T)</option>
-      <option value="dHex(2)Hex(5)HexNAc(3)Pent(1) (N)">dHex(2)Hex(5)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(2)Hex(5)HexNAc(4) (N)">dHex(2)Hex(5)HexNAc(4) (N)</option>
-      <option value="dHex(2)HexNAc(2)Kdn(1) (S)">dHex(2)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(2)HexNAc(2)Kdn(1) (T)">dHex(2)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(2)HexNAc(5) (S)">dHex(2)HexNAc(5) (S)</option>
-      <option value="dHex(2)HexNAc(5) (T)">dHex(2)HexNAc(5) (T)</option>
-      <option value="dHex(2)HexNAc(7) (S)">dHex(2)HexNAc(7) (S)</option>
-      <option value="dHex(2)HexNAc(7) (T)">dHex(2)HexNAc(7) (T)</option>
-      <option value="dHex(3)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(3)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(3)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(3)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(3)Hex(1)HexNAc(3)Kdn(1) (S)">dHex(3)Hex(1)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(3)Hex(1)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(1)HexNAc(3)Kdn(1) (T)</option>
-      <option value="dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)">dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)">dHex(3)Hex(2)HexA(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(2) (S)">dHex(3)Hex(2)HexNAc(2) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(2) (T)">dHex(3)Hex(2)HexNAc(2) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(3)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(3) (S)">dHex(3)Hex(2)HexNAc(3) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(3) (T)">dHex(3)Hex(2)HexNAc(3) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (S)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)">dHex(3)Hex(2)HexNAc(3)Kdn(1) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(4) (S)">dHex(3)Hex(2)HexNAc(4) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(4) (T)">dHex(3)Hex(2)HexNAc(4) (T)</option>
-      <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (S)</option>
-      <option value="dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)">dHex(3)Hex(2)HexNAc(4)Sulf(2) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(1) (S)">dHex(3)Hex(3)HexNAc(1) (S)</option>
-      <option value="dHex(3)Hex(3)HexNAc(1) (T)">dHex(3)Hex(3)HexNAc(1) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(2) (S)">dHex(3)Hex(3)HexNAc(2) (S)</option>
-      <option value="dHex(3)Hex(3)HexNAc(2) (T)">dHex(3)Hex(3)HexNAc(2) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3) (S)">dHex(3)Hex(3)HexNAc(3) (S)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3) (T)">dHex(3)Hex(3)HexNAc(3) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T)">dHex(3)Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="dHex(3)Hex(3)HexNAc(3)Pent(1) (N)">dHex(3)Hex(3)HexNAc(3)Pent(1) (N)</option>
-      <option value="dHex(3)Hex(3)HexNAc(4) (N)">dHex(3)Hex(3)HexNAc(4) (N)</option>
-      <option value="dHex(3)Hex(3)HexNAc(4)Pent(1) (N)">dHex(3)Hex(3)HexNAc(4)Pent(1) (N)</option>
-      <option value="dHex(3)Hex(4)HexNAc(4) (N)">dHex(3)Hex(4)HexNAc(4) (N)</option>
-      <option value="dHex(3)Hex(4)HexNAc(4) (S)">dHex(3)Hex(4)HexNAc(4) (S)</option>
-      <option value="dHex(3)Hex(4)HexNAc(4) (T)">dHex(3)Hex(4)HexNAc(4) (T)</option>
-      <option value="dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)">dHex(3)Hex(4)HexNAc(4)Sulf(1) (N)</option>
-      <option value="dHex(3)HexNAc(3)Kdn(1) (S)">dHex(3)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(3)HexNAc(3)Kdn(1) (T)">dHex(3)HexNAc(3)Kdn(1) (T)</option>
-      <option value="dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)">dHex(4)Hex(1)HexNAc(1)Kdn(2) (S)</option>
-      <option value="dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)">dHex(4)Hex(1)HexNAc(1)Kdn(2) (T)</option>
-      <option value="dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)">dHex(4)Hex(1)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(1)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)">dHex(4)Hex(1)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)">dHex(4)Hex(1)HexNAc(3)Kdn(1) (T)</option>
-      <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (S)</option>
-      <option value="dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)">dHex(4)Hex(2)HexNAc(2)Kdn(1) (T)</option>
-      <option value="dHex(4)Hex(2)HexNAc(3) (S)">dHex(4)Hex(2)HexNAc(3) (S)</option>
-      <option value="dHex(4)Hex(2)HexNAc(3) (T)">dHex(4)Hex(2)HexNAc(3) (T)</option>
-      <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)">dHex(4)Hex(3)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="dHex(4)Hex(3)HexNAc(3) (S)">dHex(4)Hex(3)HexNAc(3) (S)</option>
-      <option value="dHex(4)Hex(3)HexNAc(3) (T)">dHex(4)Hex(3)HexNAc(3) (T)</option>
-      <option value="dHex(4)HexNAc(3)Kdn(1) (S)">dHex(4)HexNAc(3)Kdn(1) (S)</option>
-      <option value="dHex(4)HexNAc(3)Kdn(1) (T)">dHex(4)HexNAc(3)Kdn(1) (T)</option>
-      <option value="DHP (C)">DHP (C)</option>
-      <option value="Diacylglycerol (C)">Diacylglycerol (C)</option>
-      <option value="DiART6plex (K)">DiART6plex (K)</option>
-      <option value="DiART6plex (N-term)">DiART6plex (N-term)</option>
-      <option value="DiART6plex (Protein N-term)">DiART6plex (Protein N-term)</option>
-      <option value="DiART6plex (Y)">DiART6plex (Y)</option>
-      <option value="DiART6plex115 (K)">DiART6plex115 (K)</option>
-      <option value="DiART6plex115 (N-term)">DiART6plex115 (N-term)</option>
-      <option value="DiART6plex115 (Protein N-term)">DiART6plex115 (Protein N-term)</option>
-      <option value="DiART6plex115 (Y)">DiART6plex115 (Y)</option>
-      <option value="DiART6plex116/119 (K)">DiART6plex116/119 (K)</option>
-      <option value="DiART6plex116/119 (N-term)">DiART6plex116/119 (N-term)</option>
-      <option value="DiART6plex116/119 (Protein N-term)">DiART6plex116/119 (Protein N-term)</option>
-      <option value="DiART6plex116/119 (Y)">DiART6plex116/119 (Y)</option>
-      <option value="DiART6plex117 (K)">DiART6plex117 (K)</option>
-      <option value="DiART6plex117 (N-term)">DiART6plex117 (N-term)</option>
-      <option value="DiART6plex117 (Protein N-term)">DiART6plex117 (Protein N-term)</option>
-      <option value="DiART6plex117 (Y)">DiART6plex117 (Y)</option>
-      <option value="DiART6plex118 (K)">DiART6plex118 (K)</option>
-      <option value="DiART6plex118 (N-term)">DiART6plex118 (N-term)</option>
-      <option value="DiART6plex118 (Protein N-term)">DiART6plex118 (Protein N-term)</option>
-      <option value="DiART6plex118 (Y)">DiART6plex118 (Y)</option>
-      <option value="Dibromo (Y)">Dibromo (Y)</option>
-      <option value="Dicarbamidomethyl (C)">Dicarbamidomethyl (C)</option>
-      <option value="Dicarbamidomethyl (H)">Dicarbamidomethyl (H)</option>
-      <option value="Dicarbamidomethyl (K)">Dicarbamidomethyl (K)</option>
-      <option value="Dicarbamidomethyl (N-term)">Dicarbamidomethyl (N-term)</option>
-      <option value="Dicarbamidomethyl (R)">Dicarbamidomethyl (R)</option>
-      <option value="dichlorination (C)">dichlorination (C)</option>
-      <option value="dichlorination (Y)">dichlorination (Y)</option>
-      <option value="Didehydro (C-term K)">Didehydro (C-term K)</option>
-      <option value="Didehydro (S)">Didehydro (S)</option>
-      <option value="Didehydro (T)">Didehydro (T)</option>
-      <option value="Didehydro (Y)">Didehydro (Y)</option>
-      <option value="Didehydroretinylidene (K)">Didehydroretinylidene (K)</option>
-      <option value="Diethyl (K)">Diethyl (K)</option>
-      <option value="Diethyl (N-term)">Diethyl (N-term)</option>
-      <option value="Diethylphosphate (C)">Diethylphosphate (C)</option>
-      <option value="Diethylphosphate (H)">Diethylphosphate (H)</option>
-      <option value="Diethylphosphate (K)">Diethylphosphate (K)</option>
-      <option value="Diethylphosphate (N-term)">Diethylphosphate (N-term)</option>
-      <option value="Diethylphosphate (S)">Diethylphosphate (S)</option>
-      <option value="Diethylphosphate (T)">Diethylphosphate (T)</option>
-      <option value="Diethylphosphate (Y)">Diethylphosphate (Y)</option>
-      <option value="Diethylphosphothione (C)">Diethylphosphothione (C)</option>
-      <option value="Diethylphosphothione (H)">Diethylphosphothione (H)</option>
-      <option value="Diethylphosphothione (K)">Diethylphosphothione (K)</option>
-      <option value="Diethylphosphothione (S)">Diethylphosphothione (S)</option>
-      <option value="Diethylphosphothione (T)">Diethylphosphothione (T)</option>
-      <option value="Diethylphosphothione (Y)">Diethylphosphothione (Y)</option>
-      <option value="Difuran (Y)">Difuran (Y)</option>
-      <option value="Dihydroxyimidazolidine (R)">Dihydroxyimidazolidine (R)</option>
-      <option value="Diiodo (H)">Diiodo (H)</option>
-      <option value="Diiodo (Y)">Diiodo (Y)</option>
-      <option value="Diironsubcluster (C)">Diironsubcluster (C)</option>
-      <option value="Diisopropylphosphate (K)">Diisopropylphosphate (K)</option>
-      <option value="Diisopropylphosphate (N-term)">Diisopropylphosphate (N-term)</option>
-      <option value="Diisopropylphosphate (S)">Diisopropylphosphate (S)</option>
-      <option value="Diisopropylphosphate (T)">Diisopropylphosphate (T)</option>
-      <option value="Diisopropylphosphate (Y)">Diisopropylphosphate (Y)</option>
-      <option value="DiLeu4plex (K)">DiLeu4plex (K)</option>
-      <option value="DiLeu4plex (N-term)">DiLeu4plex (N-term)</option>
-      <option value="DiLeu4plex (Y)">DiLeu4plex (Y)</option>
-      <option value="DiLeu4plex115 (K)">DiLeu4plex115 (K)</option>
-      <option value="DiLeu4plex115 (N-term)">DiLeu4plex115 (N-term)</option>
-      <option value="DiLeu4plex115 (Y)">DiLeu4plex115 (Y)</option>
-      <option value="DiLeu4plex117 (K)">DiLeu4plex117 (K)</option>
-      <option value="DiLeu4plex117 (N-term)">DiLeu4plex117 (N-term)</option>
-      <option value="DiLeu4plex117 (Y)">DiLeu4plex117 (Y)</option>
-      <option value="DiLeu4plex118 (K)">DiLeu4plex118 (K)</option>
-      <option value="DiLeu4plex118 (N-term)">DiLeu4plex118 (N-term)</option>
-      <option value="DiLeu4plex118 (Y)">DiLeu4plex118 (Y)</option>
-      <option value="Dimethyl (K)">Dimethyl (K)</option>
-      <option value="Dimethyl (N)">Dimethyl (N)</option>
-      <option value="Dimethyl (N-term)">Dimethyl (N-term)</option>
-      <option value="Dimethyl (Protein N-term P)">Dimethyl (Protein N-term P)</option>
-      <option value="Dimethyl (Protein N-term)">Dimethyl (Protein N-term)</option>
-      <option value="Dimethyl (R)">Dimethyl (R)</option>
-      <option value="Dimethyl:2H(2)13C (K)">Dimethyl:2H(2)13C (K)</option>
-      <option value="Dimethyl:2H(2)13C (N)">Dimethyl:2H(2)13C (N)</option>
-      <option value="Dimethyl:2H(2)13C (N-term)">Dimethyl:2H(2)13C (N-term)</option>
-      <option value="Dimethyl:2H(2)13C (Protein N-term P)">Dimethyl:2H(2)13C (Protein N-term P)</option>
-      <option value="Dimethyl:2H(2)13C (R)">Dimethyl:2H(2)13C (R)</option>
-      <option value="Dimethyl:2H(4) (K)">Dimethyl:2H(4) (K)</option>
-      <option value="Dimethyl:2H(4) (N-term)">Dimethyl:2H(4) (N-term)</option>
-      <option value="Dimethyl:2H(4) (Protein N-term)">Dimethyl:2H(4) (Protein N-term)</option>
-      <option value="Dimethyl:2H(4) (R)">Dimethyl:2H(4) (R)</option>
-      <option value="Dimethyl:2H(4)13C(2) (K)">Dimethyl:2H(4)13C(2) (K)</option>
-      <option value="Dimethyl:2H(4)13C(2) (N-term)">Dimethyl:2H(4)13C(2) (N-term)</option>
-      <option value="Dimethyl:2H(4)13C(2) (Protein N-term)">Dimethyl:2H(4)13C(2) (Protein N-term)</option>
-      <option value="Dimethyl:2H(4)13C(2) (R)">Dimethyl:2H(4)13C(2) (R)</option>
-      <option value="Dimethyl:2H(6) (K)">Dimethyl:2H(6) (K)</option>
-      <option value="Dimethyl:2H(6) (N-term)">Dimethyl:2H(6) (N-term)</option>
-      <option value="Dimethyl:2H(6) (R)">Dimethyl:2H(6) (R)</option>
-      <option value="Dimethyl:2H(6)13C(2) (K)">Dimethyl:2H(6)13C(2) (K)</option>
-      <option value="Dimethyl:2H(6)13C(2) (N-term)">Dimethyl:2H(6)13C(2) (N-term)</option>
-      <option value="Dimethyl:2H(6)13C(2) (Protein N-term)">Dimethyl:2H(6)13C(2) (Protein N-term)</option>
-      <option value="Dimethyl:2H(6)13C(2) (R)">Dimethyl:2H(6)13C(2) (R)</option>
-      <option value="DimethylamineGMBS (C)">DimethylamineGMBS (C)</option>
-      <option value="Dimethylaminoethyl (C)">Dimethylaminoethyl (C)</option>
-      <option value="DimethylArsino (C)">DimethylArsino (C)</option>
-      <option value="Dimethylphosphothione (C)">Dimethylphosphothione (C)</option>
-      <option value="Dimethylphosphothione (H)">Dimethylphosphothione (H)</option>
-      <option value="Dimethylphosphothione (K)">Dimethylphosphothione (K)</option>
-      <option value="Dimethylphosphothione (S)">Dimethylphosphothione (S)</option>
-      <option value="Dimethylphosphothione (T)">Dimethylphosphothione (T)</option>
-      <option value="Dimethylphosphothione (Y)">Dimethylphosphothione (Y)</option>
-      <option value="DimethylpyrroleAdduct (K)">DimethylpyrroleAdduct (K)</option>
-      <option value="Dioxidation (C)">Dioxidation (C)</option>
-      <option value="Dioxidation (E)">Dioxidation (E)</option>
-      <option value="Dioxidation (F)">Dioxidation (F)</option>
-      <option value="Dioxidation (I)">Dioxidation (I)</option>
-      <option value="Dioxidation (K)">Dioxidation (K)</option>
-      <option value="Dioxidation (L)">Dioxidation (L)</option>
-      <option value="Dioxidation (M)">Dioxidation (M)</option>
-      <option value="Dioxidation (P)">Dioxidation (P)</option>
-      <option value="Dioxidation (R)">Dioxidation (R)</option>
-      <option value="Dioxidation (U)">Dioxidation (U)</option>
-      <option value="Dioxidation (V)">Dioxidation (V)</option>
-      <option value="Dioxidation (W)">Dioxidation (W)</option>
-      <option value="Dioxidation (Y)">Dioxidation (Y)</option>
-      <option value="Diphthamide (H)">Diphthamide (H)</option>
-      <option value="Dipyridyl (C)">Dipyridyl (C)</option>
-      <option value="Dipyrrolylmethanemethyl (C)">Dipyrrolylmethanemethyl (C)</option>
-      <option value="DMPO (C)">DMPO (C)</option>
-      <option value="DMPO (H)">DMPO (H)</option>
-      <option value="DMPO (Y)">DMPO (Y)</option>
-      <option value="DNCB_hapten (C)">DNCB_hapten (C)</option>
-      <option value="DNCB_hapten (H)">DNCB_hapten (H)</option>
-      <option value="DNCB_hapten (K)">DNCB_hapten (K)</option>
-      <option value="DNCB_hapten (Y)">DNCB_hapten (Y)</option>
-      <option value="dNIC (K)">dNIC (K)</option>
-      <option value="dNIC (N-term)">dNIC (N-term)</option>
-      <option value="DNPS (C)">DNPS (C)</option>
-      <option value="DNPS (W)">DNPS (W)</option>
-      <option value="DTT (C)">DTT (C)</option>
-      <option value="DyLight-maleimide (C)">DyLight-maleimide (C)</option>
-      <option value="DYn-2 (C)">DYn-2 (C)</option>
-      <option value="EDEDTIDVFQQQTGG (K)">EDEDTIDVFQQQTGG (K)</option>
-      <option value="EDT-iodoacetyl-PEO-biotin (S)">EDT-iodoacetyl-PEO-biotin (S)</option>
-      <option value="EDT-iodoacetyl-PEO-biotin (T)">EDT-iodoacetyl-PEO-biotin (T)</option>
-      <option value="EDT-maleimide-PEO-biotin (S)">EDT-maleimide-PEO-biotin (S)</option>
-      <option value="EDT-maleimide-PEO-biotin (T)">EDT-maleimide-PEO-biotin (T)</option>
-      <option value="EEEDVIEVYQEQTGG (K)">EEEDVIEVYQEQTGG (K)</option>
-      <option value="EGCG1 (C)">EGCG1 (C)</option>
-      <option value="EGCG2 (C)">EGCG2 (C)</option>
-      <option value="EHD-diphenylpentanone (C)">EHD-diphenylpentanone (C)</option>
-      <option value="EHD-diphenylpentanone (M)">EHD-diphenylpentanone (M)</option>
-      <option value="EQAT (C)">EQAT (C)</option>
-      <option value="EQAT:2H(5) (C)">EQAT:2H(5) (C)</option>
-      <option value="EQIGG (K)">EQIGG (K)</option>
-      <option value="ESP (K)">ESP (K)</option>
-      <option value="ESP (N-term)">ESP (N-term)</option>
-      <option value="ESP:2H(10) (K)">ESP:2H(10) (K)</option>
-      <option value="ESP:2H(10) (N-term)">ESP:2H(10) (N-term)</option>
-      <option value="Ethanedithiol (S)">Ethanedithiol (S)</option>
-      <option value="Ethanedithiol (T)">Ethanedithiol (T)</option>
-      <option value="Ethanolamine (C)">Ethanolamine (C)</option>
-      <option value="Ethanolamine (C-term)">Ethanolamine (C-term)</option>
-      <option value="Ethanolamine (D)">Ethanolamine (D)</option>
-      <option value="Ethanolamine (E)">Ethanolamine (E)</option>
-      <option value="Ethanolyl (C)">Ethanolyl (C)</option>
-      <option value="Ethanolyl (K)">Ethanolyl (K)</option>
-      <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-      <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
-      <option value="Ethyl (C-term)">Ethyl (C-term)</option>
-      <option value="Ethyl (D)">Ethyl (D)</option>
-      <option value="Ethyl (E)">Ethyl (E)</option>
-      <option value="Ethyl (K)">Ethyl (K)</option>
-      <option value="Ethyl (N-term)">Ethyl (N-term)</option>
-      <option value="Ethyl (Protein N-term)">Ethyl (Protein N-term)</option>
-      <option value="Ethyl+Deamidated (N)">Ethyl+Deamidated (N)</option>
-      <option value="Ethyl+Deamidated (Q)">Ethyl+Deamidated (Q)</option>
-      <option value="ethylamino (S)">ethylamino (S)</option>
-      <option value="ethylamino (T)">ethylamino (T)</option>
-      <option value="Ethylphosphate (K)">Ethylphosphate (K)</option>
-      <option value="Ethylphosphate (N-term)">Ethylphosphate (N-term)</option>
-      <option value="Ethylphosphate (S)">Ethylphosphate (S)</option>
-      <option value="Ethylphosphate (T)">Ethylphosphate (T)</option>
-      <option value="Ethylphosphate (Y)">Ethylphosphate (Y)</option>
-      <option value="ethylsulfonylethyl (C)">ethylsulfonylethyl (C)</option>
-      <option value="ethylsulfonylethyl (H)">ethylsulfonylethyl (H)</option>
-      <option value="ethylsulfonylethyl (K)">ethylsulfonylethyl (K)</option>
-      <option value="ExacTagAmine (K)">ExacTagAmine (K)</option>
-      <option value="ExacTagThiol (C)">ExacTagThiol (C)</option>
-      <option value="FAD (C)">FAD (C)</option>
-      <option value="FAD (H)">FAD (H)</option>
-      <option value="FAD (Y)">FAD (Y)</option>
-      <option value="Farnesyl (C)">Farnesyl (C)</option>
-      <option value="Fluorescein (C)">Fluorescein (C)</option>
-      <option value="Fluorescein-tyramine (Y)">Fluorescein-tyramine (Y)</option>
-      <option value="Fluoro (A)">Fluoro (A)</option>
-      <option value="Fluoro (F)">Fluoro (F)</option>
-      <option value="Fluoro (W)">Fluoro (W)</option>
-      <option value="Fluoro (Y)">Fluoro (Y)</option>
-      <option value="FMN (S)">FMN (S)</option>
-      <option value="FMN (T)">FMN (T)</option>
-      <option value="FMNC (C)">FMNC (C)</option>
-      <option value="FMNH (C)">FMNH (C)</option>
-      <option value="FMNH (H)">FMNH (H)</option>
-      <option value="FNEM (C)">FNEM (C)</option>
-      <option value="Formyl (K)">Formyl (K)</option>
-      <option value="Formyl (N-term)">Formyl (N-term)</option>
-      <option value="Formyl (Protein N-term)">Formyl (Protein N-term)</option>
-      <option value="Formyl (S)">Formyl (S)</option>
-      <option value="Formyl (T)">Formyl (T)</option>
-      <option value="Formylasparagine (H)">Formylasparagine (H)</option>
-      <option value="FormylMet (Protein N-term)">FormylMet (Protein N-term)</option>
-      <option value="FP-Biotin (K)">FP-Biotin (K)</option>
-      <option value="FP-Biotin (S)">FP-Biotin (S)</option>
-      <option value="FP-Biotin (T)">FP-Biotin (T)</option>
-      <option value="FP-Biotin (Y)">FP-Biotin (Y)</option>
-      <option value="FTC (C)">FTC (C)</option>
-      <option value="FTC (K)">FTC (K)</option>
-      <option value="FTC (P)">FTC (P)</option>
-      <option value="FTC (R)">FTC (R)</option>
-      <option value="FTC (S)">FTC (S)</option>
-      <option value="Furan (Y)">Furan (Y)</option>
-      <option value="G-H1 (R)">G-H1 (R)</option>
-      <option value="Galactosyl (K)">Galactosyl (K)</option>
-      <option value="Galactosyl (N-term)">Galactosyl (N-term)</option>
-      <option value="GEE (Q)">GEE (Q)</option>
-      <option value="GeranylGeranyl (C)">GeranylGeranyl (C)</option>
-      <option value="GG (C)">GG (C)</option>
-      <option value="GG (K)">GG (K)</option>
-      <option value="GG (Protein N-term)">GG (Protein N-term)</option>
-      <option value="GG (S)">GG (S)</option>
-      <option value="GG (T)">GG (T)</option>
-      <option value="GGQ (K)">GGQ (K)</option>
-      <option value="GIST-Quat (K)">GIST-Quat (K)</option>
-      <option value="GIST-Quat (N-term)">GIST-Quat (N-term)</option>
-      <option value="GIST-Quat:2H(3) (K)">GIST-Quat:2H(3) (K)</option>
-      <option value="GIST-Quat:2H(3) (N-term)">GIST-Quat:2H(3) (N-term)</option>
-      <option value="GIST-Quat:2H(6) (K)">GIST-Quat:2H(6) (K)</option>
-      <option value="GIST-Quat:2H(6) (N-term)">GIST-Quat:2H(6) (N-term)</option>
-      <option value="GIST-Quat:2H(9) (K)">GIST-Quat:2H(9) (K)</option>
-      <option value="GIST-Quat:2H(9) (N-term)">GIST-Quat:2H(9) (N-term)</option>
-      <option value="Gln-&gt;Ala (Q)">Gln-&gt;Ala (Q)</option>
-      <option value="Gln-&gt;Arg (Q)">Gln-&gt;Arg (Q)</option>
-      <option value="Gln-&gt;Asn (Q)">Gln-&gt;Asn (Q)</option>
-      <option value="Gln-&gt;Asp (Q)">Gln-&gt;Asp (Q)</option>
-      <option value="Gln-&gt;Cys (Q)">Gln-&gt;Cys (Q)</option>
-      <option value="Gln-&gt;Glu (Q)">Gln-&gt;Glu (Q)</option>
-      <option value="Gln-&gt;Gly (Q)">Gln-&gt;Gly (Q)</option>
-      <option value="Gln-&gt;His (Q)">Gln-&gt;His (Q)</option>
-      <option value="Gln-&gt;Lys (Q)">Gln-&gt;Lys (Q)</option>
-      <option value="Gln-&gt;Met (Q)">Gln-&gt;Met (Q)</option>
-      <option value="Gln-&gt;Phe (Q)">Gln-&gt;Phe (Q)</option>
-      <option value="Gln-&gt;Pro (Q)">Gln-&gt;Pro (Q)</option>
-      <option value="Gln-&gt;pyro-Glu (N-term Q)">Gln-&gt;pyro-Glu (N-term Q)</option>
-      <option value="Gln-&gt;Ser (Q)">Gln-&gt;Ser (Q)</option>
-      <option value="Gln-&gt;Thr (Q)">Gln-&gt;Thr (Q)</option>
-      <option value="Gln-&gt;Trp (Q)">Gln-&gt;Trp (Q)</option>
-      <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
-      <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
-      <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
-      <option value="Glu (E)">Glu (E)</option>
-      <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
-      <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
-      <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
-      <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
-      <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
-      <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
-      <option value="Glu-&gt;Gln (E)">Glu-&gt;Gln (E)</option>
-      <option value="Glu-&gt;Gly (E)">Glu-&gt;Gly (E)</option>
-      <option value="Glu-&gt;His (E)">Glu-&gt;His (E)</option>
-      <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
-      <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
-      <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
-      <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
-      <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
-      <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
-      <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
-      <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
-      <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
-      <option value="Glu-&gt;Val (E)">Glu-&gt;Val (E)</option>
-      <option value="Glu-&gt;Xle (E)">Glu-&gt;Xle (E)</option>
-      <option value="glucosone (R)">glucosone (R)</option>
-      <option value="Glucosylgalactosyl (K)">Glucosylgalactosyl (K)</option>
-      <option value="Glucuronyl (Protein N-term)">Glucuronyl (Protein N-term)</option>
-      <option value="Glucuronyl (S)">Glucuronyl (S)</option>
-      <option value="Glucuronyl (T)">Glucuronyl (T)</option>
-      <option value="GluGlu (E)">GluGlu (E)</option>
-      <option value="GluGlu (Protein C-term)">GluGlu (Protein C-term)</option>
-      <option value="GluGluGlu (E)">GluGluGlu (E)</option>
-      <option value="GluGluGlu (Protein C-term)">GluGluGlu (Protein C-term)</option>
-      <option value="GluGluGluGlu (E)">GluGluGluGlu (E)</option>
-      <option value="GluGluGluGlu (Protein C-term)">GluGluGluGlu (Protein C-term)</option>
-      <option value="Gluratylation (K)">Gluratylation (K)</option>
-      <option value="Glutathione (C)">Glutathione (C)</option>
-      <option value="Gly (K)">Gly (K)</option>
-      <option value="Gly (S)">Gly (S)</option>
-      <option value="Gly (T)">Gly (T)</option>
-      <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
-      <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
-      <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
-      <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
-      <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
-      <option value="Gly-&gt;Gln (G)">Gly-&gt;Gln (G)</option>
-      <option value="Gly-&gt;Glu (G)">Gly-&gt;Glu (G)</option>
-      <option value="Gly-&gt;His (G)">Gly-&gt;His (G)</option>
-      <option value="Gly-&gt;Lys (G)">Gly-&gt;Lys (G)</option>
-      <option value="Gly-&gt;Met (G)">Gly-&gt;Met (G)</option>
-      <option value="Gly-&gt;Phe (G)">Gly-&gt;Phe (G)</option>
-      <option value="Gly-&gt;Pro (G)">Gly-&gt;Pro (G)</option>
-      <option value="Gly-&gt;Ser (G)">Gly-&gt;Ser (G)</option>
-      <option value="Gly-&gt;Thr (G)">Gly-&gt;Thr (G)</option>
-      <option value="Gly-&gt;Trp (G)">Gly-&gt;Trp (G)</option>
-      <option value="Gly-&gt;Tyr (G)">Gly-&gt;Tyr (G)</option>
-      <option value="Gly-&gt;Val (G)">Gly-&gt;Val (G)</option>
-      <option value="Gly-&gt;Xle (G)">Gly-&gt;Xle (G)</option>
-      <option value="Gly-loss+Amide (C-term G)">Gly-loss+Amide (C-term G)</option>
-      <option value="Glycerophospho (S)">Glycerophospho (S)</option>
-      <option value="GlycerylPE (E)">GlycerylPE (E)</option>
-      <option value="glycidamide (K)">glycidamide (K)</option>
-      <option value="glycidamide (N-term)">glycidamide (N-term)</option>
-      <option value="Glycosyl (P)">Glycosyl (P)</option>
-      <option value="glyoxalAGE (R)">glyoxalAGE (R)</option>
-      <option value="GNLLFLACYCIGG (K)">GNLLFLACYCIGG (K)</option>
-      <option value="GPIanchor (Protein C-term)">GPIanchor (Protein C-term)</option>
-      <option value="Guanidinyl (K)">Guanidinyl (K)</option>
-      <option value="Guanidinyl (N-term)">Guanidinyl (N-term)</option>
-      <option value="Haloxon (C)">Haloxon (C)</option>
-      <option value="Haloxon (H)">Haloxon (H)</option>
-      <option value="Haloxon (K)">Haloxon (K)</option>
-      <option value="Haloxon (S)">Haloxon (S)</option>
-      <option value="Haloxon (T)">Haloxon (T)</option>
-      <option value="Haloxon (Y)">Haloxon (Y)</option>
-      <option value="HCysteinyl (C)">HCysteinyl (C)</option>
-      <option value="HCysThiolactone (K)">HCysThiolactone (K)</option>
-      <option value="Heme (C)">Heme (C)</option>
-      <option value="Heme (H)">Heme (H)</option>
-      <option value="Hep (K)">Hep (K)</option>
-      <option value="Hep (N)">Hep (N)</option>
-      <option value="Hep (Q)">Hep (Q)</option>
-      <option value="Hep (R)">Hep (R)</option>
-      <option value="Hep (S)">Hep (S)</option>
-      <option value="Hep (T)">Hep (T)</option>
-      <option value="Hex (C)">Hex (C)</option>
-      <option value="Hex (K)">Hex (K)</option>
-      <option value="Hex (N)">Hex (N)</option>
-      <option value="Hex (N-term)">Hex (N-term)</option>
-      <option value="Hex (R)">Hex (R)</option>
-      <option value="Hex (S)">Hex (S)</option>
-      <option value="Hex (T)">Hex (T)</option>
-      <option value="Hex (W)">Hex (W)</option>
-      <option value="Hex (Y)">Hex (Y)</option>
-      <option value="Hex(1)HexA(1) (S)">Hex(1)HexA(1) (S)</option>
-      <option value="Hex(1)HexA(1) (T)">Hex(1)HexA(1) (T)</option>
-      <option value="Hex(1)HexA(1)HexNAc(1) (S)">Hex(1)HexA(1)HexNAc(1) (S)</option>
-      <option value="Hex(1)HexA(1)HexNAc(1) (T)">Hex(1)HexA(1)HexNAc(1) (T)</option>
-      <option value="Hex(1)HexA(1)HexNAc(2) (S)">Hex(1)HexA(1)HexNAc(2) (S)</option>
-      <option value="Hex(1)HexA(1)HexNAc(2) (T)">Hex(1)HexA(1)HexNAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(1) (N)">Hex(1)HexNAc(1) (N)</option>
-      <option value="Hex(1)HexNAc(1) (S)">Hex(1)HexNAc(1) (S)</option>
-      <option value="Hex(1)HexNAc(1) (T)">Hex(1)HexNAc(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1) (N)">Hex(1)HexNAc(1)dHex(1) (N)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1) (S)">Hex(1)HexNAc(1)dHex(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1) (T)">Hex(1)HexNAc(1)dHex(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1)Me(1) (S)">Hex(1)HexNAc(1)dHex(1)Me(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1)Me(1) (T)">Hex(1)HexNAc(1)dHex(1)Me(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1)Me(2) (S)">Hex(1)HexNAc(1)dHex(1)Me(2) (S)</option>
-      <option value="Hex(1)HexNAc(1)dHex(1)Me(2) (T)">Hex(1)HexNAc(1)dHex(1)Me(2) (T)</option>
-      <option value="Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S)">Hex(1)HexNAc(1)Kdn(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T)">Hex(1)HexNAc(1)Kdn(1)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1) (N)">Hex(1)HexNAc(1)NeuAc(1) (N)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1) (S)">Hex(1)HexNAc(1)NeuAc(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1) (T)">Hex(1)HexNAc(1)NeuAc(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S)">Hex(1)HexNAc(1)NeuAc(1)Ac(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T)">Hex(1)HexNAc(1)NeuAc(1)Ac(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S)">Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T)">Hex(1)HexNAc(1)NeuAc(1)NeuGc(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T)">Hex(1)HexNAc(1)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2) (N)">Hex(1)HexNAc(1)NeuAc(2) (N)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2) (S)">Hex(1)HexNAc(1)NeuAc(2) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2) (T)">Hex(1)HexNAc(1)NeuAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S)">Hex(1)HexNAc(1)NeuAc(2)Ac(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T)">Hex(1)HexNAc(1)NeuAc(2)Ac(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S)">Hex(1)HexNAc(1)NeuAc(2)Ac(2) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T)">Hex(1)HexNAc(1)NeuAc(2)Ac(2) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(3) (S)">Hex(1)HexNAc(1)NeuAc(3) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuAc(3) (T)">Hex(1)HexNAc(1)NeuAc(3) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(1) (S)">Hex(1)HexNAc(1)NeuGc(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(1) (T)">Hex(1)HexNAc(1)NeuGc(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(2) (S)">Hex(1)HexNAc(1)NeuGc(2) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(2) (T)">Hex(1)HexNAc(1)NeuGc(2) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(3) (S)">Hex(1)HexNAc(1)NeuGc(3) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(3) (T)">Hex(1)HexNAc(1)NeuGc(3) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(4) (S)">Hex(1)HexNAc(1)NeuGc(4) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(4) (T)">Hex(1)HexNAc(1)NeuGc(4) (T)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(5) (S)">Hex(1)HexNAc(1)NeuGc(5) (S)</option>
-      <option value="Hex(1)HexNAc(1)NeuGc(5) (T)">Hex(1)HexNAc(1)NeuGc(5) (T)</option>
-      <option value="Hex(1)HexNAc(1)Phos(1) (S)">Hex(1)HexNAc(1)Phos(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)Phos(1) (T)">Hex(1)HexNAc(1)Phos(1) (T)</option>
-      <option value="Hex(1)HexNAc(1)Sulf(1) (S)">Hex(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(1)Sulf(1) (T)">Hex(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(2) (N)">Hex(1)HexNAc(2) (N)</option>
-      <option value="Hex(1)HexNAc(2) (S)">Hex(1)HexNAc(2) (S)</option>
-      <option value="Hex(1)HexNAc(2) (T)">Hex(1)HexNAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(2)dHex(1) (N)">Hex(1)HexNAc(2)dHex(1) (N)</option>
-      <option value="Hex(1)HexNAc(2)dHex(1) (S)">Hex(1)HexNAc(2)dHex(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)dHex(1) (T)">Hex(1)HexNAc(2)dHex(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)dHex(1)Pent(1) (N)">Hex(1)HexNAc(2)dHex(1)Pent(1) (N)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2) (N)">Hex(1)HexNAc(2)dHex(2) (N)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2) (S)">Hex(1)HexNAc(2)dHex(2) (S)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2) (T)">Hex(1)HexNAc(2)dHex(2) (T)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)">Hex(1)HexNAc(2)dHex(2)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(1) (S)">Hex(1)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(1) (T)">Hex(1)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(1)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(2) (S)">Hex(1)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(2) (T)">Hex(1)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S)">Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T)">Hex(1)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)NeuGc(1) (S)">Hex(1)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)NeuGc(1) (T)">Hex(1)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="Hex(1)HexNAc(2)Pent(1) (N)">Hex(1)HexNAc(2)Pent(1) (N)</option>
-      <option value="Hex(1)HexNAc(2)Sulf(1) (S)">Hex(1)HexNAc(2)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(2)Sulf(1) (T)">Hex(1)HexNAc(2)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(3) (S)">Hex(1)HexNAc(3) (S)</option>
-      <option value="Hex(1)HexNAc(3) (T)">Hex(1)HexNAc(3) (T)</option>
-      <option value="Hex(1)HexNAc(3)NeuAc(1) (S)">Hex(1)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="Hex(1)HexNAc(3)NeuAc(1) (T)">Hex(1)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="Hex(1)HexNAc(3)NeuAc(2) (S)">Hex(1)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="Hex(1)HexNAc(3)NeuAc(2) (T)">Hex(1)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="Hex(1)HexNAc(3)NeuGc(1) (S)">Hex(1)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="Hex(1)HexNAc(3)NeuGc(1) (T)">Hex(1)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="Hex(1)HexNAc(3)Sulf(1) (S)">Hex(1)HexNAc(3)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(3)Sulf(1) (T)">Hex(1)HexNAc(3)Sulf(1) (T)</option>
-      <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (S)</option>
-      <option value="Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)">Hex(1)HexNAc(4)dHex(1)Sulf(1) (T)</option>
-      <option value="Hex(1)NeuAc(1) (S)">Hex(1)NeuAc(1) (S)</option>
-      <option value="Hex(1)NeuAc(1) (T)">Hex(1)NeuAc(1) (T)</option>
-      <option value="Hex(1)NeuAc(1)Pent(1) (S)">Hex(1)NeuAc(1)Pent(1) (S)</option>
-      <option value="Hex(1)NeuAc(1)Pent(1) (T)">Hex(1)NeuAc(1)Pent(1) (T)</option>
-      <option value="Hex(1)NeuGc(1) (S)">Hex(1)NeuGc(1) (S)</option>
-      <option value="Hex(1)NeuGc(1) (T)">Hex(1)NeuGc(1) (T)</option>
-      <option value="Hex(1)Pent(1) (S)">Hex(1)Pent(1) (S)</option>
-      <option value="Hex(1)Pent(1) (T)">Hex(1)Pent(1) (T)</option>
-      <option value="Hex(1)Pent(2) (S)">Hex(1)Pent(2) (S)</option>
-      <option value="Hex(1)Pent(2) (T)">Hex(1)Pent(2) (T)</option>
-      <option value="Hex(1)Pent(2)Me(1) (S)">Hex(1)Pent(2)Me(1) (S)</option>
-      <option value="Hex(1)Pent(2)Me(1) (T)">Hex(1)Pent(2)Me(1) (T)</option>
-      <option value="Hex(1)Pent(3) (S)">Hex(1)Pent(3) (S)</option>
-      <option value="Hex(1)Pent(3) (T)">Hex(1)Pent(3) (T)</option>
-      <option value="Hex(1)Pent(3)Me(1) (S)">Hex(1)Pent(3)Me(1) (S)</option>
-      <option value="Hex(1)Pent(3)Me(1) (T)">Hex(1)Pent(3)Me(1) (T)</option>
-      <option value="Hex(10)HexNAc(1) (N)">Hex(10)HexNAc(1) (N)</option>
-      <option value="Hex(10)Phos(3) (S)">Hex(10)Phos(3) (S)</option>
-      <option value="Hex(10)Phos(3) (T)">Hex(10)Phos(3) (T)</option>
-      <option value="Hex(2) (K)">Hex(2) (K)</option>
-      <option value="Hex(2) (R)">Hex(2) (R)</option>
-      <option value="Hex(2) (S)">Hex(2) (S)</option>
-      <option value="Hex(2) (T)">Hex(2) (T)</option>
-      <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)">Hex(2)HexA(1)HexNAc(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)NeuAc(1)Pent(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (S)">Hex(2)HexA(1)Pent(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexA(1)Pent(1)Sulf(1) (T)">Hex(2)HexA(1)Pent(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(1) (N)">Hex(2)HexNAc(1) (N)</option>
-      <option value="Hex(2)HexNAc(1) (S)">Hex(2)HexNAc(1) (S)</option>
-      <option value="Hex(2)HexNAc(1) (T)">Hex(2)HexNAc(1) (T)</option>
-      <option value="Hex(2)HexNAc(1)Me(1) (S)">Hex(2)HexNAc(1)Me(1) (S)</option>
-      <option value="Hex(2)HexNAc(1)Me(1) (T)">Hex(2)HexNAc(1)Me(1) (T)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(1) (S)">Hex(2)HexNAc(1)NeuGc(1) (S)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(1) (T)">Hex(2)HexNAc(1)NeuGc(1) (T)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(2) (S)">Hex(2)HexNAc(1)NeuGc(2) (S)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(2) (T)">Hex(2)HexNAc(1)NeuGc(2) (T)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(3) (S)">Hex(2)HexNAc(1)NeuGc(3) (S)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(3) (T)">Hex(2)HexNAc(1)NeuGc(3) (T)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(4) (S)">Hex(2)HexNAc(1)NeuGc(4) (S)</option>
-      <option value="Hex(2)HexNAc(1)NeuGc(4) (T)">Hex(2)HexNAc(1)NeuGc(4) (T)</option>
-      <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (S)">Hex(2)HexNAc(1)Pent(1)HexA(1) (S)</option>
-      <option value="Hex(2)HexNAc(1)Pent(1)HexA(1) (T)">Hex(2)HexNAc(1)Pent(1)HexA(1) (T)</option>
-      <option value="Hex(2)HexNAc(1)Sulf(1) (S)">Hex(2)HexNAc(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(1)Sulf(1) (T)">Hex(2)HexNAc(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(2) (N)">Hex(2)HexNAc(2) (N)</option>
-      <option value="Hex(2)HexNAc(2) (S)">Hex(2)HexNAc(2) (S)</option>
-      <option value="Hex(2)HexNAc(2) (T)">Hex(2)HexNAc(2) (T)</option>
-      <option value="Hex(2)HexNAc(2)dHex(1) (N)">Hex(2)HexNAc(2)dHex(1) (N)</option>
-      <option value="Hex(2)HexNAc(2)dHex(1) (S)">Hex(2)HexNAc(2)dHex(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)dHex(1) (T)">Hex(2)HexNAc(2)dHex(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1) (N)">Hex(2)HexNAc(2)NeuAc(1) (N)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1) (S)">Hex(2)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1) (T)">Hex(2)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(2) (S)">Hex(2)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(2) (T)">Hex(2)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)NeuAc(2)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)NeuGc(1) (S)">Hex(2)HexNAc(2)NeuGc(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)NeuGc(1) (T)">Hex(2)HexNAc(2)NeuGc(1) (T)</option>
-      <option value="Hex(2)HexNAc(2)Pent(1) (N)">Hex(2)HexNAc(2)Pent(1) (N)</option>
-      <option value="Hex(2)HexNAc(2)Sulf(1) (S)">Hex(2)HexNAc(2)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(2)Sulf(1) (T)">Hex(2)HexNAc(2)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(3) (N)">Hex(2)HexNAc(3) (N)</option>
-      <option value="Hex(2)HexNAc(3) (S)">Hex(2)HexNAc(3) (S)</option>
-      <option value="Hex(2)HexNAc(3) (T)">Hex(2)HexNAc(3) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T)">Hex(2)HexNAc(3)NeuAc(1)NeuGc(1) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)">Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)">Hex(2)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(2) (S)">Hex(2)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(2) (T)">Hex(2)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(3) (S)">Hex(2)HexNAc(3)NeuAc(3) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuAc(3) (T)">Hex(2)HexNAc(3)NeuAc(3) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(1) (S)">Hex(2)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(1) (T)">Hex(2)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(2) (S)">Hex(2)HexNAc(3)NeuGc(2) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(2) (T)">Hex(2)HexNAc(3)NeuGc(2) (T)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(3) (S)">Hex(2)HexNAc(3)NeuGc(3) (S)</option>
-      <option value="Hex(2)HexNAc(3)NeuGc(3) (T)">Hex(2)HexNAc(3)NeuGc(3) (T)</option>
-      <option value="Hex(2)HexNAc(3)Sulf(1) (S)">Hex(2)HexNAc(3)Sulf(1) (S)</option>
-      <option value="Hex(2)HexNAc(3)Sulf(1) (T)">Hex(2)HexNAc(3)Sulf(1) (T)</option>
-      <option value="Hex(2)HexNAc(4) (N)">Hex(2)HexNAc(4) (N)</option>
-      <option value="Hex(2)HexNAc(4) (S)">Hex(2)HexNAc(4) (S)</option>
-      <option value="Hex(2)HexNAc(4) (T)">Hex(2)HexNAc(4) (T)</option>
-      <option value="Hex(2)HexNAc(4)NeuAc(1) (S)">Hex(2)HexNAc(4)NeuAc(1) (S)</option>
-      <option value="Hex(2)HexNAc(4)NeuAc(1) (T)">Hex(2)HexNAc(4)NeuAc(1) (T)</option>
-      <option value="Hex(2)HexNAc(5) (S)">Hex(2)HexNAc(5) (S)</option>
-      <option value="Hex(2)HexNAc(5) (T)">Hex(2)HexNAc(5) (T)</option>
-      <option value="Hex(2)NeuAc(1) (S)">Hex(2)NeuAc(1) (S)</option>
-      <option value="Hex(2)NeuAc(1) (T)">Hex(2)NeuAc(1) (T)</option>
-      <option value="Hex(2)Pent(2) (S)">Hex(2)Pent(2) (S)</option>
-      <option value="Hex(2)Pent(2) (T)">Hex(2)Pent(2) (T)</option>
-      <option value="Hex(2)Pent(2)Me(1) (S)">Hex(2)Pent(2)Me(1) (S)</option>
-      <option value="Hex(2)Pent(2)Me(1) (T)">Hex(2)Pent(2)Me(1) (T)</option>
-      <option value="Hex(2)Sulf(1) (S)">Hex(2)Sulf(1) (S)</option>
-      <option value="Hex(2)Sulf(1) (T)">Hex(2)Sulf(1) (T)</option>
-      <option value="Hex(3) (N)">Hex(3) (N)</option>
-      <option value="Hex(3) (S)">Hex(3) (S)</option>
-      <option value="Hex(3) (T)">Hex(3) (T)</option>
-      <option value="Hex(3)HexNAc(1) (N)">Hex(3)HexNAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(1) (S)">Hex(3)HexNAc(1) (S)</option>
-      <option value="Hex(3)HexNAc(1) (T)">Hex(3)HexNAc(1) (T)</option>
-      <option value="Hex(3)HexNAc(1)HexA(1) (S)">Hex(3)HexNAc(1)HexA(1) (S)</option>
-      <option value="Hex(3)HexNAc(1)HexA(1) (T)">Hex(3)HexNAc(1)HexA(1) (T)</option>
-      <option value="Hex(3)HexNAc(1)Me(1) (S)">Hex(3)HexNAc(1)Me(1) (S)</option>
-      <option value="Hex(3)HexNAc(1)Me(1) (T)">Hex(3)HexNAc(1)Me(1) (T)</option>
-      <option value="Hex(3)HexNAc(1)Pent(1) (N)">Hex(3)HexNAc(1)Pent(1) (N)</option>
-      <option value="Hex(3)HexNAc(2) (N)">Hex(3)HexNAc(2) (N)</option>
-      <option value="Hex(3)HexNAc(2) (S)">Hex(3)HexNAc(2) (S)</option>
-      <option value="Hex(3)HexNAc(2) (T)">Hex(3)HexNAc(2) (T)</option>
-      <option value="Hex(3)HexNAc(2)NeuAc(1) (N)">Hex(3)HexNAc(2)NeuAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(2)NeuAc(2) (S)">Hex(3)HexNAc(2)NeuAc(2) (S)</option>
-      <option value="Hex(3)HexNAc(2)NeuAc(2) (T)">Hex(3)HexNAc(2)NeuAc(2) (T)</option>
-      <option value="Hex(3)HexNAc(2)Pent(1) (N)">Hex(3)HexNAc(2)Pent(1) (N)</option>
-      <option value="Hex(3)HexNAc(2)Phos(1) (N)">Hex(3)HexNAc(2)Phos(1) (N)</option>
-      <option value="Hex(3)HexNAc(3) (N)">Hex(3)HexNAc(3) (N)</option>
-      <option value="Hex(3)HexNAc(3) (S)">Hex(3)HexNAc(3) (S)</option>
-      <option value="Hex(3)HexNAc(3) (T)">Hex(3)HexNAc(3) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(1) (S)">Hex(3)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(1) (T)">Hex(3)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(1)Sulf(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(2) (S)">Hex(3)HexNAc(3)NeuAc(2) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(2) (T)">Hex(3)HexNAc(3)NeuAc(2) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)">Hex(3)HexNAc(3)NeuAc(2)Sulf(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(3) (S)">Hex(3)HexNAc(3)NeuAc(3) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuAc(3) (T)">Hex(3)HexNAc(3)NeuAc(3) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuGc(1) (S)">Hex(3)HexNAc(3)NeuGc(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuGc(1) (T)">Hex(3)HexNAc(3)NeuGc(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)">Hex(3)HexNAc(3)NeuGc(1)Sulf(1) (T)</option>
-      <option value="Hex(3)HexNAc(3)Pent(1) (N)">Hex(3)HexNAc(3)Pent(1) (N)</option>
-      <option value="Hex(3)HexNAc(3)Sulf(1) (N)">Hex(3)HexNAc(3)Sulf(1) (N)</option>
-      <option value="Hex(3)HexNAc(3)Sulf(1) (S)">Hex(3)HexNAc(3)Sulf(1) (S)</option>
-      <option value="Hex(3)HexNAc(3)Sulf(1) (T)">Hex(3)HexNAc(3)Sulf(1) (T)</option>
-      <option value="Hex(3)HexNAc(4) (N)">Hex(3)HexNAc(4) (N)</option>
-      <option value="Hex(3)HexNAc(4) (S)">Hex(3)HexNAc(4) (S)</option>
-      <option value="Hex(3)HexNAc(4) (T)">Hex(3)HexNAc(4) (T)</option>
-      <option value="Hex(3)HexNAc(4)NeuAc(1) (N)">Hex(3)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(4)NeuAc(2) (N)">Hex(3)HexNAc(4)NeuAc(2) (N)</option>
-      <option value="Hex(3)HexNAc(4)Pent(1) (N)">Hex(3)HexNAc(4)Pent(1) (N)</option>
-      <option value="Hex(3)HexNAc(4)Sulf(1) (N)">Hex(3)HexNAc(4)Sulf(1) (N)</option>
-      <option value="Hex(3)HexNAc(5) (N)">Hex(3)HexNAc(5) (N)</option>
-      <option value="Hex(3)HexNAc(5) (S)">Hex(3)HexNAc(5) (S)</option>
-      <option value="Hex(3)HexNAc(5) (T)">Hex(3)HexNAc(5) (T)</option>
-      <option value="Hex(3)HexNAc(5)NeuAc(1) (N)">Hex(3)HexNAc(5)NeuAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(5)Sulf(1) (N)">Hex(3)HexNAc(5)Sulf(1) (N)</option>
-      <option value="Hex(3)HexNAc(6) (N)">Hex(3)HexNAc(6) (N)</option>
-      <option value="Hex(3)HexNAc(6) (S)">Hex(3)HexNAc(6) (S)</option>
-      <option value="Hex(3)HexNAc(6) (T)">Hex(3)HexNAc(6) (T)</option>
-      <option value="Hex(3)HexNAc(6)NeuAc(1) (N)">Hex(3)HexNAc(6)NeuAc(1) (N)</option>
-      <option value="Hex(3)HexNAc(6)Sulf(1) (N)">Hex(3)HexNAc(6)Sulf(1) (N)</option>
-      <option value="Hex(3)HexNAc(6)Sulf(2) (N)">Hex(3)HexNAc(6)Sulf(2) (N)</option>
-      <option value="Hex(3)HexNAc(7) (N)">Hex(3)HexNAc(7) (N)</option>
-      <option value="Hex(3)HexNAc(7)Sulf(1) (N)">Hex(3)HexNAc(7)Sulf(1) (N)</option>
-      <option value="Hex(4) (S)">Hex(4) (S)</option>
-      <option value="Hex(4) (T)">Hex(4) (T)</option>
-      <option value="Hex(4)HexA(1) (S)">Hex(4)HexA(1) (S)</option>
-      <option value="Hex(4)HexA(1) (T)">Hex(4)HexA(1) (T)</option>
-      <option value="Hex(4)HexA(1)HexNAc(1) (S)">Hex(4)HexA(1)HexNAc(1) (S)</option>
-      <option value="Hex(4)HexA(1)HexNAc(1) (T)">Hex(4)HexA(1)HexNAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(1) (N)">Hex(4)HexNAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(1) (S)">Hex(4)HexNAc(1) (S)</option>
-      <option value="Hex(4)HexNAc(1) (T)">Hex(4)HexNAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(2) (N)">Hex(4)HexNAc(2) (N)</option>
-      <option value="Hex(4)HexNAc(2)NeuAc(1) (N)">Hex(4)HexNAc(2)NeuAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(2)NeuAc(1) (S)">Hex(4)HexNAc(2)NeuAc(1) (S)</option>
-      <option value="Hex(4)HexNAc(2)NeuAc(1) (T)">Hex(4)HexNAc(2)NeuAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(2)Pent(1) (N)">Hex(4)HexNAc(2)Pent(1) (N)</option>
-      <option value="Hex(4)HexNAc(3) (N)">Hex(4)HexNAc(3) (N)</option>
-      <option value="Hex(4)HexNAc(3) (S)">Hex(4)HexNAc(3) (S)</option>
-      <option value="Hex(4)HexNAc(3) (T)">Hex(4)HexNAc(3) (T)</option>
-      <option value="Hex(4)HexNAc(3)NeuAc(1) (N)">Hex(4)HexNAc(3)NeuAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(3)NeuAc(1) (S)">Hex(4)HexNAc(3)NeuAc(1) (S)</option>
-      <option value="Hex(4)HexNAc(3)NeuAc(1) (T)">Hex(4)HexNAc(3)NeuAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(3)NeuAc(2) (N)">Hex(4)HexNAc(3)NeuAc(2) (N)</option>
-      <option value="Hex(4)HexNAc(3)NeuGc(1) (N)">Hex(4)HexNAc(3)NeuGc(1) (N)</option>
-      <option value="Hex(4)HexNAc(3)Pent(1) (N)">Hex(4)HexNAc(3)Pent(1) (N)</option>
-      <option value="Hex(4)HexNAc(4) (N)">Hex(4)HexNAc(4) (N)</option>
-      <option value="Hex(4)HexNAc(4) (S)">Hex(4)HexNAc(4) (S)</option>
-      <option value="Hex(4)HexNAc(4) (T)">Hex(4)HexNAc(4) (T)</option>
-      <option value="Hex(4)HexNAc(4)Me(2)Pent(1) (N)">Hex(4)HexNAc(4)Me(2)Pent(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1) (N)">Hex(4)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1) (S)">Hex(4)HexNAc(4)NeuAc(1) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1) (T)">Hex(4)HexNAc(4)NeuAc(1) (T)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(2) (T)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)">Hex(4)HexNAc(4)NeuAc(1)Sulf(3) (T)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1) (N)">Hex(4)HexNAc(4)NeuGc(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1) (S)">Hex(4)HexNAc(4)NeuGc(1) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1) (T)">Hex(4)HexNAc(4)NeuGc(1) (T)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (S)</option>
-      <option value="Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)">Hex(4)HexNAc(4)NeuGc(1)Sulf(2) (T)</option>
-      <option value="Hex(4)HexNAc(4)Pent(1) (N)">Hex(4)HexNAc(4)Pent(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)Sulf(1) (N)">Hex(4)HexNAc(4)Sulf(1) (N)</option>
-      <option value="Hex(4)HexNAc(4)Sulf(2) (S)">Hex(4)HexNAc(4)Sulf(2) (S)</option>
-      <option value="Hex(4)HexNAc(4)Sulf(2) (T)">Hex(4)HexNAc(4)Sulf(2) (T)</option>
-      <option value="Hex(4)HexNAc(5) (N)">Hex(4)HexNAc(5) (N)</option>
-      <option value="Hex(4)HexNAc(5)NeuAc(1) (N)">Hex(4)HexNAc(5)NeuAc(1) (N)</option>
-      <option value="Hex(4)HexNAc(5)Sulf(1) (N)">Hex(4)HexNAc(5)Sulf(1) (N)</option>
-      <option value="Hex(4)HexNAc(6) (N)">Hex(4)HexNAc(6) (N)</option>
-      <option value="Hex(4)Phos(1) (S)">Hex(4)Phos(1) (S)</option>
-      <option value="Hex(4)Phos(1) (T)">Hex(4)Phos(1) (T)</option>
-      <option value="Hex(5) (S)">Hex(5) (S)</option>
-      <option value="Hex(5) (T)">Hex(5) (T)</option>
-      <option value="Hex(5)HexA(1) (S)">Hex(5)HexA(1) (S)</option>
-      <option value="Hex(5)HexA(1) (T)">Hex(5)HexA(1) (T)</option>
-      <option value="Hex(5)HexNAc(1) (N)">Hex(5)HexNAc(1) (N)</option>
-      <option value="Hex(5)HexNAc(1) (S)">Hex(5)HexNAc(1) (S)</option>
-      <option value="Hex(5)HexNAc(1) (T)">Hex(5)HexNAc(1) (T)</option>
-      <option value="Hex(5)HexNAc(2) (N)">Hex(5)HexNAc(2) (N)</option>
-      <option value="Hex(5)HexNAc(2)Phos(1) (N)">Hex(5)HexNAc(2)Phos(1) (N)</option>
-      <option value="Hex(5)HexNAc(3) (N)">Hex(5)HexNAc(3) (N)</option>
-      <option value="Hex(5)HexNAc(3)Pent(1) (N)">Hex(5)HexNAc(3)Pent(1) (N)</option>
-      <option value="Hex(5)HexNAc(4) (N)">Hex(5)HexNAc(4) (N)</option>
-      <option value="Hex(5)HexNAc(4) (S)">Hex(5)HexNAc(4) (S)</option>
-      <option value="Hex(5)HexNAc(4) (T)">Hex(5)HexNAc(4) (T)</option>
-      <option value="Hex(5)HexNAc(4)Me(2)Pent(1) (N)">Hex(5)HexNAc(4)Me(2)Pent(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(1) (N)">Hex(5)HexNAc(4)NeuAc(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)">Hex(5)HexNAc(4)NeuAc(1)Ac(2) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)">Hex(5)HexNAc(4)NeuAc(1)Sulf(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuAc(2) (N)">Hex(5)HexNAc(4)NeuAc(2) (N)</option>
-      <option value="Hex(5)HexNAc(4)NeuGc(1) (N)">Hex(5)HexNAc(4)NeuGc(1) (N)</option>
-      <option value="Hex(5)HexNAc(4)Sulf(1) (N)">Hex(5)HexNAc(4)Sulf(1) (N)</option>
-      <option value="Hex(5)HexNAc(5) (N)">Hex(5)HexNAc(5) (N)</option>
-      <option value="Hex(5)HexNAc(5) (S)">Hex(5)HexNAc(5) (S)</option>
-      <option value="Hex(5)HexNAc(5) (T)">Hex(5)HexNAc(5) (T)</option>
-      <option value="Hex(5)Phos(1) (S)">Hex(5)Phos(1) (S)</option>
-      <option value="Hex(5)Phos(1) (T)">Hex(5)Phos(1) (T)</option>
-      <option value="Hex(5)Phos(3) (S)">Hex(5)Phos(3) (S)</option>
-      <option value="Hex(5)Phos(3) (T)">Hex(5)Phos(3) (T)</option>
-      <option value="Hex(6)HexNAc(1) (N)">Hex(6)HexNAc(1) (N)</option>
-      <option value="Hex(6)HexNAc(2) (N)">Hex(6)HexNAc(2) (N)</option>
-      <option value="Hex(6)HexNAc(2)Phos(1) (N)">Hex(6)HexNAc(2)Phos(1) (N)</option>
-      <option value="Hex(6)HexNAc(3) (N)">Hex(6)HexNAc(3) (N)</option>
-      <option value="Hex(6)HexNAc(3)Phos(1) (N)">Hex(6)HexNAc(3)Phos(1) (N)</option>
-      <option value="Hex(6)HexNAc(4) (N)">Hex(6)HexNAc(4) (N)</option>
-      <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
-      <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
-      <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
-      <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
-      <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
-      <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
-      <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
-      <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
-      <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
-      <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
-      <option value="Hex(7)HexNAc(2) (N)">Hex(7)HexNAc(2) (N)</option>
-      <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
-      <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
-      <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
-      <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
-      <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
-      <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
-      <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
-      <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
-      <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
-      <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
-      <option value="Hex(8)Phos(3) (T)">Hex(8)Phos(3) (T)</option>
-      <option value="Hex(9) (N)">Hex(9) (N)</option>
-      <option value="Hex(9)HexNAc(1) (N)">Hex(9)HexNAc(1) (N)</option>
-      <option value="Hex(9)HexNAc(2) (N)">Hex(9)HexNAc(2) (N)</option>
-      <option value="Hex(9)Phos(3) (S)">Hex(9)Phos(3) (S)</option>
-      <option value="Hex(9)Phos(3) (T)">Hex(9)Phos(3) (T)</option>
-      <option value="HexA(2)HexNAc(3) (S)">HexA(2)HexNAc(3) (S)</option>
-      <option value="HexA(2)HexNAc(3) (T)">HexA(2)HexNAc(3) (T)</option>
-      <option value="HexN (K)">HexN (K)</option>
-      <option value="HexN (N)">HexN (N)</option>
-      <option value="HexN (S)">HexN (S)</option>
-      <option value="HexN (T)">HexN (T)</option>
-      <option value="HexN (W)">HexN (W)</option>
-      <option value="HexNAc (C)">HexNAc (C)</option>
-      <option value="HexNAc (N)">HexNAc (N)</option>
-      <option value="HexNAc (S)">HexNAc (S)</option>
-      <option value="HexNAc (T)">HexNAc (T)</option>
-      <option value="HexNAc(1)dHex(1) (N)">HexNAc(1)dHex(1) (N)</option>
-      <option value="HexNAc(1)dHex(1) (S)">HexNAc(1)dHex(1) (S)</option>
-      <option value="HexNAc(1)dHex(1) (T)">HexNAc(1)dHex(1) (T)</option>
-      <option value="HexNAc(1)dHex(2) (N)">HexNAc(1)dHex(2) (N)</option>
-      <option value="HexNAc(1)Kdn(2) (S)">HexNAc(1)Kdn(2) (S)</option>
-      <option value="HexNAc(1)Kdn(2) (T)">HexNAc(1)Kdn(2) (T)</option>
-      <option value="HexNAc(1)NeuAc(1) (S)">HexNAc(1)NeuAc(1) (S)</option>
-      <option value="HexNAc(1)NeuAc(1) (T)">HexNAc(1)NeuAc(1) (T)</option>
-      <option value="HexNAc(1)NeuGc(1) (S)">HexNAc(1)NeuGc(1) (S)</option>
-      <option value="HexNAc(1)NeuGc(1) (T)">HexNAc(1)NeuGc(1) (T)</option>
-      <option value="HexNAc(1)NeuGc(2) (S)">HexNAc(1)NeuGc(2) (S)</option>
-      <option value="HexNAc(1)NeuGc(2) (T)">HexNAc(1)NeuGc(2) (T)</option>
-      <option value="HexNAc(2) (N)">HexNAc(2) (N)</option>
-      <option value="HexNAc(2) (S)">HexNAc(2) (S)</option>
-      <option value="HexNAc(2) (T)">HexNAc(2) (T)</option>
-      <option value="HexNAc(2)dHex(1) (N)">HexNAc(2)dHex(1) (N)</option>
-      <option value="HexNAc(2)dHex(2) (N)">HexNAc(2)dHex(2) (N)</option>
-      <option value="HexNAc(2)NeuAc(1) (S)">HexNAc(2)NeuAc(1) (S)</option>
-      <option value="HexNAc(2)NeuAc(1) (T)">HexNAc(2)NeuAc(1) (T)</option>
-      <option value="HexNAc(2)NeuAc(1)Sulf(1) (S)">HexNAc(2)NeuAc(1)Sulf(1) (S)</option>
-      <option value="HexNAc(2)NeuAc(1)Sulf(1) (T)">HexNAc(2)NeuAc(1)Sulf(1) (T)</option>
-      <option value="HexNAc(2)NeuGc(1) (S)">HexNAc(2)NeuGc(1) (S)</option>
-      <option value="HexNAc(2)NeuGc(1) (T)">HexNAc(2)NeuGc(1) (T)</option>
-      <option value="HexNAc(2)Sulf(1) (S)">HexNAc(2)Sulf(1) (S)</option>
-      <option value="HexNAc(2)Sulf(1) (T)">HexNAc(2)Sulf(1) (T)</option>
-      <option value="HexNAc(3) (S)">HexNAc(3) (S)</option>
-      <option value="HexNAc(3) (T)">HexNAc(3) (T)</option>
-      <option value="HexNAc(3)Sulf(1) (S)">HexNAc(3)Sulf(1) (S)</option>
-      <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
-      <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
-      <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
-      <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
-      <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
-      <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
-      <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
-      <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
-      <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
-      <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
-      <option value="His-&gt;Gln (H)">His-&gt;Gln (H)</option>
-      <option value="His-&gt;Glu (H)">His-&gt;Glu (H)</option>
-      <option value="His-&gt;Gly (H)">His-&gt;Gly (H)</option>
-      <option value="His-&gt;Lys (H)">His-&gt;Lys (H)</option>
-      <option value="His-&gt;Met (H)">His-&gt;Met (H)</option>
-      <option value="His-&gt;Phe (H)">His-&gt;Phe (H)</option>
-      <option value="His-&gt;Pro (H)">His-&gt;Pro (H)</option>
-      <option value="His-&gt;Ser (H)">His-&gt;Ser (H)</option>
-      <option value="His-&gt;Thr (H)">His-&gt;Thr (H)</option>
-      <option value="His-&gt;Trp (H)">His-&gt;Trp (H)</option>
-      <option value="His-&gt;Tyr (H)">His-&gt;Tyr (H)</option>
-      <option value="His-&gt;Val (H)">His-&gt;Val (H)</option>
-      <option value="His-&gt;Xle (H)">His-&gt;Xle (H)</option>
-      <option value="HMVK (C)">HMVK (C)</option>
-      <option value="HN2_mustard (C)">HN2_mustard (C)</option>
-      <option value="HN2_mustard (H)">HN2_mustard (H)</option>
-      <option value="HN2_mustard (K)">HN2_mustard (K)</option>
-      <option value="HN3_mustard (C)">HN3_mustard (C)</option>
-      <option value="HN3_mustard (H)">HN3_mustard (H)</option>
-      <option value="HN3_mustard (K)">HN3_mustard (K)</option>
-      <option value="HNE (A)">HNE (A)</option>
-      <option value="HNE (C)">HNE (C)</option>
-      <option value="HNE (H)">HNE (H)</option>
-      <option value="HNE (K)">HNE (K)</option>
-      <option value="HNE (L)">HNE (L)</option>
-      <option value="HNE+Delta:H(2) (C)">HNE+Delta:H(2) (C)</option>
-      <option value="HNE+Delta:H(2) (H)">HNE+Delta:H(2) (H)</option>
-      <option value="HNE+Delta:H(2) (K)">HNE+Delta:H(2) (K)</option>
-      <option value="HNE-BAHAH (C)">HNE-BAHAH (C)</option>
-      <option value="HNE-BAHAH (H)">HNE-BAHAH (H)</option>
-      <option value="HNE-BAHAH (K)">HNE-BAHAH (K)</option>
-      <option value="HNE-Delta:H(2)O (C)">HNE-Delta:H(2)O (C)</option>
-      <option value="HNE-Delta:H(2)O (H)">HNE-Delta:H(2)O (H)</option>
-      <option value="HNE-Delta:H(2)O (K)">HNE-Delta:H(2)O (K)</option>
-      <option value="Homocysteic_acid (M)">Homocysteic_acid (M)</option>
-      <option value="HPG (R)">HPG (R)</option>
-      <option value="Hydroxamic_acid (D)">Hydroxamic_acid (D)</option>
-      <option value="Hydroxamic_acid (E)">Hydroxamic_acid (E)</option>
-      <option value="Hydroxycinnamyl (C)">Hydroxycinnamyl (C)</option>
-      <option value="Hydroxyfarnesyl (C)">Hydroxyfarnesyl (C)</option>
-      <option value="Hydroxyheme (E)">Hydroxyheme (E)</option>
-      <option value="hydroxyisobutyryl (K)">hydroxyisobutyryl (K)</option>
-      <option value="Hydroxymethyl (N)">Hydroxymethyl (N)</option>
-      <option value="HydroxymethylOP (K)">HydroxymethylOP (K)</option>
-      <option value="Hydroxytrimethyl (K)">Hydroxytrimethyl (K)</option>
-      <option value="Hypusine (K)">Hypusine (K)</option>
-      <option value="IASD (C)">IASD (C)</option>
-      <option value="IBTP (C)">IBTP (C)</option>
-      <option value="ICAT-C (C)">ICAT-C (C)</option>
-      <option value="ICAT-C:13C(9) (C)">ICAT-C:13C(9) (C)</option>
-      <option value="ICAT-D (C)">ICAT-D (C)</option>
-      <option value="ICAT-D:2H(8) (C)">ICAT-D:2H(8) (C)</option>
-      <option value="ICAT-G (C)">ICAT-G (C)</option>
-      <option value="ICAT-G:2H(8) (C)">ICAT-G:2H(8) (C)</option>
-      <option value="ICAT-H (C)">ICAT-H (C)</option>
-      <option value="ICAT-H:13C(6) (C)">ICAT-H:13C(6) (C)</option>
-      <option value="ICDID (C)">ICDID (C)</option>
-      <option value="ICDID:2H(6) (C)">ICDID:2H(6) (C)</option>
-      <option value="ICPL (K)">ICPL (K)</option>
-      <option value="ICPL (N-term)">ICPL (N-term)</option>
-      <option value="ICPL (Protein N-term)">ICPL (Protein N-term)</option>
-      <option value="ICPL:13C(6) (K)">ICPL:13C(6) (K)</option>
-      <option value="ICPL:13C(6) (N-term)">ICPL:13C(6) (N-term)</option>
-      <option value="ICPL:13C(6) (Protein N-term)">ICPL:13C(6) (Protein N-term)</option>
-      <option value="ICPL:13C(6)2H(4) (K)">ICPL:13C(6)2H(4) (K)</option>
-      <option value="ICPL:13C(6)2H(4) (N-term)">ICPL:13C(6)2H(4) (N-term)</option>
-      <option value="ICPL:13C(6)2H(4) (Protein N-term)">ICPL:13C(6)2H(4) (Protein N-term)</option>
-      <option value="ICPL:2H(4) (K)">ICPL:2H(4) (K)</option>
-      <option value="ICPL:2H(4) (N-term)">ICPL:2H(4) (N-term)</option>
-      <option value="ICPL:2H(4) (Protein N-term)">ICPL:2H(4) (Protein N-term)</option>
-      <option value="IDEnT (C)">IDEnT (C)</option>
-      <option value="IED-Biotin (C)">IED-Biotin (C)</option>
-      <option value="IGBP (C)">IGBP (C)</option>
-      <option value="IGBP:13C(2) (C)">IGBP:13C(2) (C)</option>
-      <option value="IMEHex(2)NeuAc(1) (K)">IMEHex(2)NeuAc(1) (K)</option>
-      <option value="IMID (K)">IMID (K)</option>
-      <option value="IMID:2H(4) (K)">IMID:2H(4) (K)</option>
-      <option value="Iminobiotin (K)">Iminobiotin (K)</option>
-      <option value="Iminobiotin (N-term)">Iminobiotin (N-term)</option>
-      <option value="Iodo (H)">Iodo (H)</option>
-      <option value="Iodo (Y)">Iodo (Y)</option>
-      <option value="Iodoacetanilide (C)">Iodoacetanilide (C)</option>
-      <option value="Iodoacetanilide (K)">Iodoacetanilide (K)</option>
-      <option value="Iodoacetanilide (N-term)">Iodoacetanilide (N-term)</option>
-      <option value="Iodoacetanilide:13C(6) (C)">Iodoacetanilide:13C(6) (C)</option>
-      <option value="Iodoacetanilide:13C(6) (K)">Iodoacetanilide:13C(6) (K)</option>
-      <option value="Iodoacetanilide:13C(6) (N-term)">Iodoacetanilide:13C(6) (N-term)</option>
-      <option value="iodoTMT (C)">iodoTMT (C)</option>
-      <option value="iodoTMT (D)">iodoTMT (D)</option>
-      <option value="iodoTMT (E)">iodoTMT (E)</option>
-      <option value="iodoTMT (H)">iodoTMT (H)</option>
-      <option value="iodoTMT (K)">iodoTMT (K)</option>
-      <option value="iodoTMT6plex (C)">iodoTMT6plex (C)</option>
-      <option value="iodoTMT6plex (D)">iodoTMT6plex (D)</option>
-      <option value="iodoTMT6plex (E)">iodoTMT6plex (E)</option>
-      <option value="iodoTMT6plex (H)">iodoTMT6plex (H)</option>
-      <option value="iodoTMT6plex (K)">iodoTMT6plex (K)</option>
-      <option value="IodoU-AMP (F)">IodoU-AMP (F)</option>
-      <option value="IodoU-AMP (W)">IodoU-AMP (W)</option>
-      <option value="IodoU-AMP (Y)">IodoU-AMP (Y)</option>
-      <option value="ISD_z+2_ion (N-term)">ISD_z+2_ion (N-term)</option>
-      <option value="Isopropylphospho (S)">Isopropylphospho (S)</option>
-      <option value="Isopropylphospho (T)">Isopropylphospho (T)</option>
-      <option value="Isopropylphospho (Y)">Isopropylphospho (Y)</option>
-      <option value="iTRAQ4plex (C)">iTRAQ4plex (C)</option>
-      <option value="iTRAQ4plex (H)">iTRAQ4plex (H)</option>
-      <option value="iTRAQ4plex (K)">iTRAQ4plex (K)</option>
-      <option value="iTRAQ4plex (N-term)">iTRAQ4plex (N-term)</option>
-      <option value="iTRAQ4plex (Protein N-term)">iTRAQ4plex (Protein N-term)</option>
-      <option value="iTRAQ4plex (S)">iTRAQ4plex (S)</option>
-      <option value="iTRAQ4plex (T)">iTRAQ4plex (T)</option>
-      <option value="iTRAQ4plex (Y)">iTRAQ4plex (Y)</option>
-      <option value="iTRAQ4plex114 (C)">iTRAQ4plex114 (C)</option>
-      <option value="iTRAQ4plex114 (K)">iTRAQ4plex114 (K)</option>
-      <option value="iTRAQ4plex114 (N-term)">iTRAQ4plex114 (N-term)</option>
-      <option value="iTRAQ4plex114 (Y)">iTRAQ4plex114 (Y)</option>
-      <option value="iTRAQ4plex115 (C)">iTRAQ4plex115 (C)</option>
-      <option value="iTRAQ4plex115 (K)">iTRAQ4plex115 (K)</option>
-      <option value="iTRAQ4plex115 (N-term)">iTRAQ4plex115 (N-term)</option>
-      <option value="iTRAQ4plex115 (Y)">iTRAQ4plex115 (Y)</option>
-      <option value="iTRAQ8plex (C)">iTRAQ8plex (C)</option>
-      <option value="iTRAQ8plex (H)">iTRAQ8plex (H)</option>
-      <option value="iTRAQ8plex (K)">iTRAQ8plex (K)</option>
-      <option value="iTRAQ8plex (N-term)">iTRAQ8plex (N-term)</option>
-      <option value="iTRAQ8plex (Protein N-term)">iTRAQ8plex (Protein N-term)</option>
-      <option value="iTRAQ8plex (S)">iTRAQ8plex (S)</option>
-      <option value="iTRAQ8plex (T)">iTRAQ8plex (T)</option>
-      <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
-      <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
-      <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
-      <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
-      <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
-      <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
-      <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
-      <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
-      <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
-      <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
-      <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
-      <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
-      <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
-      <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
-      <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
-      <option value="Label:13C(5)15N(1) (E)">Label:13C(5)15N(1) (E)</option>
-      <option value="Label:13C(5)15N(1) (M)">Label:13C(5)15N(1) (M)</option>
-      <option value="Label:13C(5)15N(1) (P)">Label:13C(5)15N(1) (P)</option>
-      <option value="Label:13C(5)15N(1) (V)">Label:13C(5)15N(1) (V)</option>
-      <option value="Label:13C(6) (I)">Label:13C(6) (I)</option>
-      <option value="Label:13C(6) (K)">Label:13C(6) (K)</option>
-      <option value="Label:13C(6) (L)">Label:13C(6) (L)</option>
-      <option value="Label:13C(6) (R)">Label:13C(6) (R)</option>
-      <option value="Label:13C(6)+Acetyl (K)">Label:13C(6)+Acetyl (K)</option>
-      <option value="Label:13C(6)+Dimethyl (K)">Label:13C(6)+Dimethyl (K)</option>
-      <option value="Label:13C(6)+GG (K)">Label:13C(6)+GG (K)</option>
-      <option value="Label:13C(6)15N(1) (I)">Label:13C(6)15N(1) (I)</option>
-      <option value="Label:13C(6)15N(1) (L)">Label:13C(6)15N(1) (L)</option>
-      <option value="Label:13C(6)15N(2) (K)">Label:13C(6)15N(2) (K)</option>
-      <option value="Label:13C(6)15N(2)+Acetyl (K)">Label:13C(6)15N(2)+Acetyl (K)</option>
-      <option value="Label:13C(6)15N(2)+Dimethyl (K)">Label:13C(6)15N(2)+Dimethyl (K)</option>
-      <option value="Label:13C(6)15N(2)+GG (K)">Label:13C(6)15N(2)+GG (K)</option>
-      <option value="Label:13C(6)15N(4) (R)">Label:13C(6)15N(4) (R)</option>
-      <option value="Label:13C(6)15N(4)+Dimethyl (R)">Label:13C(6)15N(4)+Dimethyl (R)</option>
-      <option value="Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R)">Label:13C(6)15N(4)+Dimethyl:2H(6)13C(2) (R)</option>
-      <option value="Label:13C(6)15N(4)+Methyl (R)">Label:13C(6)15N(4)+Methyl (R)</option>
-      <option value="Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R)">Label:13C(6)15N(4)+Methyl:2H(3)13C(1) (R)</option>
-      <option value="Label:13C(9) (F)">Label:13C(9) (F)</option>
-      <option value="Label:13C(9) (Y)">Label:13C(9) (Y)</option>
-      <option value="Label:13C(9)+Phospho (Y)">Label:13C(9)+Phospho (Y)</option>
-      <option value="Label:13C(9)15N(1) (F)">Label:13C(9)15N(1) (F)</option>
-      <option value="Label:15N(1) (A)">Label:15N(1) (A)</option>
-      <option value="Label:15N(1) (C)">Label:15N(1) (C)</option>
-      <option value="Label:15N(1) (D)">Label:15N(1) (D)</option>
-      <option value="Label:15N(1) (E)">Label:15N(1) (E)</option>
-      <option value="Label:15N(1) (F)">Label:15N(1) (F)</option>
-      <option value="Label:15N(1) (G)">Label:15N(1) (G)</option>
-      <option value="Label:15N(1) (I)">Label:15N(1) (I)</option>
-      <option value="Label:15N(1) (L)">Label:15N(1) (L)</option>
-      <option value="Label:15N(1) (M)">Label:15N(1) (M)</option>
-      <option value="Label:15N(1) (P)">Label:15N(1) (P)</option>
-      <option value="Label:15N(1) (S)">Label:15N(1) (S)</option>
-      <option value="Label:15N(1) (T)">Label:15N(1) (T)</option>
-      <option value="Label:15N(1) (V)">Label:15N(1) (V)</option>
-      <option value="Label:15N(1) (Y)">Label:15N(1) (Y)</option>
-      <option value="Label:15N(2) (K)">Label:15N(2) (K)</option>
-      <option value="Label:15N(2) (N)">Label:15N(2) (N)</option>
-      <option value="Label:15N(2) (Q)">Label:15N(2) (Q)</option>
-      <option value="Label:15N(2) (W)">Label:15N(2) (W)</option>
-      <option value="Label:15N(2)2H(9) (K)">Label:15N(2)2H(9) (K)</option>
-      <option value="Label:15N(3) (H)">Label:15N(3) (H)</option>
-      <option value="Label:15N(4) (R)">Label:15N(4) (R)</option>
-      <option value="Label:18O(1) (C-term)">Label:18O(1) (C-term)</option>
-      <option value="Label:18O(1) (S)">Label:18O(1) (S)</option>
-      <option value="Label:18O(1) (T)">Label:18O(1) (T)</option>
-      <option value="Label:18O(1) (Y)">Label:18O(1) (Y)</option>
-      <option value="Label:18O(2) (C-term)">Label:18O(2) (C-term)</option>
-      <option value="Label:2H(10) (L)">Label:2H(10) (L)</option>
-      <option value="Label:2H(3) (L)">Label:2H(3) (L)</option>
-      <option value="Label:2H(3) (M)">Label:2H(3) (M)</option>
-      <option value="Label:2H(3)+Oxidation (M)">Label:2H(3)+Oxidation (M)</option>
-      <option value="Label:2H(4) (A)">Label:2H(4) (A)</option>
-      <option value="Label:2H(4) (F)">Label:2H(4) (F)</option>
-      <option value="Label:2H(4) (K)">Label:2H(4) (K)</option>
-      <option value="Label:2H(4) (U)">Label:2H(4) (U)</option>
-      <option value="Label:2H(4) (Y)">Label:2H(4) (Y)</option>
-      <option value="Label:2H(4)+Acetyl (K)">Label:2H(4)+Acetyl (K)</option>
-      <option value="Label:2H(4)+GG (K)">Label:2H(4)+GG (K)</option>
-      <option value="Label:2H(4)13C(1) (R)">Label:2H(4)13C(1) (R)</option>
-      <option value="Label:2H(6)15N(1) (P)">Label:2H(6)15N(1) (P)</option>
-      <option value="Label:2H(7)15N(4) (R)">Label:2H(7)15N(4) (R)</option>
-      <option value="Label:2H(9)13C(6)15N(2) (K)">Label:2H(9)13C(6)15N(2) (K)</option>
-      <option value="lapachenole (C)">lapachenole (C)</option>
-      <option value="Leu-&gt;MetOx (L)">Leu-&gt;MetOx (L)</option>
-      <option value="LG-anhydrolactam (K)">LG-anhydrolactam (K)</option>
-      <option value="LG-anhydrolactam (N-term)">LG-anhydrolactam (N-term)</option>
-      <option value="LG-anhyropyrrole (K)">LG-anhyropyrrole (K)</option>
-      <option value="LG-anhyropyrrole (N-term)">LG-anhyropyrrole (N-term)</option>
-      <option value="LG-Hlactam-K (K)">LG-Hlactam-K (K)</option>
-      <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
-      <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
-      <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
-      <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
-      <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
-      <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
-      <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
-      <option value="Lipoyl (K)">Lipoyl (K)</option>
-      <option value="LRGG (K)">LRGG (K)</option>
-      <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
-      <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
-      <option value="Lys (N-term)">Lys (N-term)</option>
-      <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
-      <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
-      <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
-      <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
-      <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
-      <option value="Lys-&gt;Asp (K)">Lys-&gt;Asp (K)</option>
-      <option value="Lys-&gt;CamCys (K)">Lys-&gt;CamCys (K)</option>
-      <option value="Lys-&gt;Cys (K)">Lys-&gt;Cys (K)</option>
-      <option value="Lys-&gt;Gln (K)">Lys-&gt;Gln (K)</option>
-      <option value="Lys-&gt;Glu (K)">Lys-&gt;Glu (K)</option>
-      <option value="Lys-&gt;Gly (K)">Lys-&gt;Gly (K)</option>
-      <option value="Lys-&gt;His (K)">Lys-&gt;His (K)</option>
-      <option value="Lys-&gt;Met (K)">Lys-&gt;Met (K)</option>
-      <option value="Lys-&gt;MetOx (K)">Lys-&gt;MetOx (K)</option>
-      <option value="Lys-&gt;Phe (K)">Lys-&gt;Phe (K)</option>
-      <option value="Lys-&gt;Pro (K)">Lys-&gt;Pro (K)</option>
-      <option value="Lys-&gt;Ser (K)">Lys-&gt;Ser (K)</option>
-      <option value="Lys-&gt;Thr (K)">Lys-&gt;Thr (K)</option>
-      <option value="Lys-&gt;Trp (K)">Lys-&gt;Trp (K)</option>
-      <option value="Lys-&gt;Tyr (K)">Lys-&gt;Tyr (K)</option>
-      <option value="Lys-&gt;Val (K)">Lys-&gt;Val (K)</option>
-      <option value="Lys-&gt;Xle (K)">Lys-&gt;Xle (K)</option>
-      <option value="Lys-loss (Protein C-term K)">Lys-loss (Protein C-term K)</option>
-      <option value="Lysbiotinhydrazide (K)">Lysbiotinhydrazide (K)</option>
-      <option value="maleimide (C)">maleimide (C)</option>
-      <option value="maleimide (K)">maleimide (K)</option>
-      <option value="Maleimide-PEO2-Biotin (C)">Maleimide-PEO2-Biotin (C)</option>
-      <option value="maleimide3 (C)">maleimide3 (C)</option>
-      <option value="maleimide3 (K)">maleimide3 (K)</option>
-      <option value="maleimide5 (C)">maleimide5 (C)</option>
-      <option value="maleimide5 (K)">maleimide5 (K)</option>
-      <option value="Malonyl (C)">Malonyl (C)</option>
-      <option value="Malonyl (K)">Malonyl (K)</option>
-      <option value="Malonyl (S)">Malonyl (S)</option>
-      <option value="MDCC (C)">MDCC (C)</option>
-      <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
-      <option value="Menadione (C)">Menadione (C)</option>
-      <option value="Menadione (K)">Menadione (K)</option>
-      <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
-      <option value="Menadione-HQ (K)">Menadione-HQ (K)</option>
-      <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
-      <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
-      <option value="MesitylOxide (H)">MesitylOxide (H)</option>
-      <option value="MesitylOxide (K)">MesitylOxide (K)</option>
-      <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
-      <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
-      <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
-      <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
-      <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
-      <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
-      <option value="Met-&gt;AspSA (M)">Met-&gt;AspSA (M)</option>
-      <option value="Met-&gt;Cys (M)">Met-&gt;Cys (M)</option>
-      <option value="Met-&gt;Gln (M)">Met-&gt;Gln (M)</option>
-      <option value="Met-&gt;Glu (M)">Met-&gt;Glu (M)</option>
-      <option value="Met-&gt;Gly (M)">Met-&gt;Gly (M)</option>
-      <option value="Met-&gt;His (M)">Met-&gt;His (M)</option>
-      <option value="Met-&gt;Hpg (M)">Met-&gt;Hpg (M)</option>
-      <option value="Met-&gt;Hse (C-term M)">Met-&gt;Hse (C-term M)</option>
-      <option value="Met-&gt;Hsl (C-term M)">Met-&gt;Hsl (C-term M)</option>
-      <option value="Met-&gt;Lys (M)">Met-&gt;Lys (M)</option>
-      <option value="Met-&gt;Phe (M)">Met-&gt;Phe (M)</option>
-      <option value="Met-&gt;Pro (M)">Met-&gt;Pro (M)</option>
-      <option value="Met-&gt;Ser (M)">Met-&gt;Ser (M)</option>
-      <option value="Met-&gt;Thr (M)">Met-&gt;Thr (M)</option>
-      <option value="Met-&gt;Trp (M)">Met-&gt;Trp (M)</option>
-      <option value="Met-&gt;Tyr (M)">Met-&gt;Tyr (M)</option>
-      <option value="Met-&gt;Val (M)">Met-&gt;Val (M)</option>
-      <option value="Met-&gt;Xle (M)">Met-&gt;Xle (M)</option>
-      <option value="Met-loss (Protein N-term M)">Met-loss (Protein N-term M)</option>
-      <option value="Met-loss+Acetyl (Protein N-term M)">Met-loss+Acetyl (Protein N-term M)</option>
-      <option value="Methamidophos-O (C)">Methamidophos-O (C)</option>
-      <option value="Methamidophos-O (H)">Methamidophos-O (H)</option>
-      <option value="Methamidophos-O (K)">Methamidophos-O (K)</option>
-      <option value="Methamidophos-O (S)">Methamidophos-O (S)</option>
-      <option value="Methamidophos-O (T)">Methamidophos-O (T)</option>
-      <option value="Methamidophos-O (Y)">Methamidophos-O (Y)</option>
-      <option value="Methamidophos-S (C)">Methamidophos-S (C)</option>
-      <option value="Methamidophos-S (H)">Methamidophos-S (H)</option>
-      <option value="Methamidophos-S (K)">Methamidophos-S (K)</option>
-      <option value="Methamidophos-S (S)">Methamidophos-S (S)</option>
-      <option value="Methamidophos-S (T)">Methamidophos-S (T)</option>
-      <option value="Methamidophos-S (Y)">Methamidophos-S (Y)</option>
-      <option value="Methyl (C)">Methyl (C)</option>
-      <option value="Methyl (C-term)">Methyl (C-term)</option>
-      <option value="Methyl (D)">Methyl (D)</option>
-      <option value="Methyl (E)">Methyl (E)</option>
-      <option value="Methyl (H)">Methyl (H)</option>
-      <option value="Methyl (I)">Methyl (I)</option>
-      <option value="Methyl (K)">Methyl (K)</option>
-      <option value="Methyl (L)">Methyl (L)</option>
-      <option value="Methyl (N)">Methyl (N)</option>
-      <option value="Methyl (N-term)">Methyl (N-term)</option>
-      <option value="Methyl (Protein N-term)">Methyl (Protein N-term)</option>
-      <option value="Methyl (Q)">Methyl (Q)</option>
-      <option value="Methyl (R)">Methyl (R)</option>
-      <option value="Methyl (S)">Methyl (S)</option>
-      <option value="Methyl (T)">Methyl (T)</option>
-      <option value="Methyl+Acetyl:2H(3) (K)">Methyl+Acetyl:2H(3) (K)</option>
-      <option value="Methyl+Deamidated (N)">Methyl+Deamidated (N)</option>
-      <option value="Methyl+Deamidated (Q)">Methyl+Deamidated (Q)</option>
-      <option value="Methyl-PEO12-Maleimide (C)">Methyl-PEO12-Maleimide (C)</option>
-      <option value="Methyl:2H(2) (K)">Methyl:2H(2) (K)</option>
-      <option value="Methyl:2H(2) (N-term)">Methyl:2H(2) (N-term)</option>
-      <option value="Methyl:2H(2)13C (C)">Methyl:2H(2)13C (C)</option>
-      <option value="Methyl:2H(2)13C (C-term)">Methyl:2H(2)13C (C-term)</option>
-      <option value="Methyl:2H(2)13C (D)">Methyl:2H(2)13C (D)</option>
-      <option value="Methyl:2H(2)13C (E)">Methyl:2H(2)13C (E)</option>
-      <option value="Methyl:2H(2)13C (H)">Methyl:2H(2)13C (H)</option>
-      <option value="Methyl:2H(2)13C (I)">Methyl:2H(2)13C (I)</option>
-      <option value="Methyl:2H(2)13C (K)">Methyl:2H(2)13C (K)</option>
-      <option value="Methyl:2H(2)13C (L)">Methyl:2H(2)13C (L)</option>
-      <option value="Methyl:2H(2)13C (N)">Methyl:2H(2)13C (N)</option>
-      <option value="Methyl:2H(2)13C (N-term)">Methyl:2H(2)13C (N-term)</option>
-      <option value="Methyl:2H(2)13C (Protein N-term)">Methyl:2H(2)13C (Protein N-term)</option>
-      <option value="Methyl:2H(2)13C (Q)">Methyl:2H(2)13C (Q)</option>
-      <option value="Methyl:2H(2)13C (R)">Methyl:2H(2)13C (R)</option>
-      <option value="Methyl:2H(2)13C (S)">Methyl:2H(2)13C (S)</option>
-      <option value="Methyl:2H(2)13C (T)">Methyl:2H(2)13C (T)</option>
-      <option value="Methyl:2H(3) (D)">Methyl:2H(3) (D)</option>
-      <option value="Methyl:2H(3) (E)">Methyl:2H(3) (E)</option>
-      <option value="Methyl:2H(3) (K)">Methyl:2H(3) (K)</option>
-      <option value="Methyl:2H(3) (R)">Methyl:2H(3) (R)</option>
-      <option value="Methyl:2H(3) (X)">Methyl:2H(3) (X)</option>
-      <option value="Methyl:2H(3)+Acetyl:2H(3) (K)">Methyl:2H(3)+Acetyl:2H(3) (K)</option>
-      <option value="Methyl:2H(3)13C(1) (K)">Methyl:2H(3)13C(1) (K)</option>
-      <option value="Methyl:2H(3)13C(1) (N-term)">Methyl:2H(3)13C(1) (N-term)</option>
-      <option value="Methyl:2H(3)13C(1) (R)">Methyl:2H(3)13C(1) (R)</option>
-      <option value="Methylamine (S)">Methylamine (S)</option>
-      <option value="Methylamine (T)">Methylamine (T)</option>
-      <option value="Methylmalonylation (S)">Methylmalonylation (S)</option>
-      <option value="methylol (K)">methylol (K)</option>
-      <option value="methylol (W)">methylol (W)</option>
-      <option value="methylol (Y)">methylol (Y)</option>
-      <option value="Methylphosphonate (S)">Methylphosphonate (S)</option>
-      <option value="Methylphosphonate (T)">Methylphosphonate (T)</option>
-      <option value="Methylphosphonate (Y)">Methylphosphonate (Y)</option>
-      <option value="Methylpyrroline (K)">Methylpyrroline (K)</option>
-      <option value="methylsulfonylethyl (C)">methylsulfonylethyl (C)</option>
-      <option value="methylsulfonylethyl (H)">methylsulfonylethyl (H)</option>
-      <option value="methylsulfonylethyl (K)">methylsulfonylethyl (K)</option>
-      <option value="Methylthio (C)">Methylthio (C)</option>
-      <option value="Methylthio (D)">Methylthio (D)</option>
-      <option value="Methylthio (K)">Methylthio (K)</option>
-      <option value="Methylthio (N)">Methylthio (N)</option>
-      <option value="Methylthio (N-term)">Methylthio (N-term)</option>
-      <option value="MG-H1 (R)">MG-H1 (R)</option>
-      <option value="Microcin (Protein C-term)">Microcin (Protein C-term)</option>
-      <option value="MicrocinC7 (Protein C-term)">MicrocinC7 (Protein C-term)</option>
-      <option value="MM-diphenylpentanone (C)">MM-diphenylpentanone (C)</option>
-      <option value="Molybdopterin (C)">Molybdopterin (C)</option>
-      <option value="MolybdopterinGD (C)">MolybdopterinGD (C)</option>
-      <option value="MolybdopterinGD (D)">MolybdopterinGD (D)</option>
-      <option value="MolybdopterinGD (U)">MolybdopterinGD (U)</option>
-      <option value="MolybdopterinGD+Delta:S(-1)Se(1) (C)">MolybdopterinGD+Delta:S(-1)Se(1) (C)</option>
-      <option value="monomethylphosphothione (C)">monomethylphosphothione (C)</option>
-      <option value="monomethylphosphothione (H)">monomethylphosphothione (H)</option>
-      <option value="monomethylphosphothione (K)">monomethylphosphothione (K)</option>
-      <option value="monomethylphosphothione (S)">monomethylphosphothione (S)</option>
-      <option value="monomethylphosphothione (T)">monomethylphosphothione (T)</option>
-      <option value="monomethylphosphothione (Y)">monomethylphosphothione (Y)</option>
-      <option value="mTRAQ (H)">mTRAQ (H)</option>
-      <option value="mTRAQ (K)">mTRAQ (K)</option>
-      <option value="mTRAQ (N-term)">mTRAQ (N-term)</option>
-      <option value="mTRAQ (S)">mTRAQ (S)</option>
-      <option value="mTRAQ (T)">mTRAQ (T)</option>
-      <option value="mTRAQ (Y)">mTRAQ (Y)</option>
-      <option value="mTRAQ:13C(3)15N(1) (H)">mTRAQ:13C(3)15N(1) (H)</option>
-      <option value="mTRAQ:13C(3)15N(1) (K)">mTRAQ:13C(3)15N(1) (K)</option>
-      <option value="mTRAQ:13C(3)15N(1) (N-term)">mTRAQ:13C(3)15N(1) (N-term)</option>
-      <option value="mTRAQ:13C(3)15N(1) (S)">mTRAQ:13C(3)15N(1) (S)</option>
-      <option value="mTRAQ:13C(3)15N(1) (T)">mTRAQ:13C(3)15N(1) (T)</option>
-      <option value="mTRAQ:13C(3)15N(1) (Y)">mTRAQ:13C(3)15N(1) (Y)</option>
-      <option value="mTRAQ:13C(6)15N(2) (H)">mTRAQ:13C(6)15N(2) (H)</option>
-      <option value="mTRAQ:13C(6)15N(2) (K)">mTRAQ:13C(6)15N(2) (K)</option>
-      <option value="mTRAQ:13C(6)15N(2) (N-term)">mTRAQ:13C(6)15N(2) (N-term)</option>
-      <option value="mTRAQ:13C(6)15N(2) (S)">mTRAQ:13C(6)15N(2) (S)</option>
-      <option value="mTRAQ:13C(6)15N(2) (T)">mTRAQ:13C(6)15N(2) (T)</option>
-      <option value="mTRAQ:13C(6)15N(2) (Y)">mTRAQ:13C(6)15N(2) (Y)</option>
-      <option value="MTSL (C)">MTSL (C)</option>
-      <option value="MurNAc (A)">MurNAc (A)</option>
-      <option value="Myristoleyl (Protein N-term G)">Myristoleyl (Protein N-term G)</option>
-      <option value="Myristoyl (C)">Myristoyl (C)</option>
-      <option value="Myristoyl (K)">Myristoyl (K)</option>
-      <option value="Myristoyl (N-term G)">Myristoyl (N-term G)</option>
-      <option value="Myristoyl+Delta:H(-4) (Protein N-term G)">Myristoyl+Delta:H(-4) (Protein N-term G)</option>
-      <option value="N-dimethylphosphate (S)">N-dimethylphosphate (S)</option>
-      <option value="NA-LNO2 (C)">NA-LNO2 (C)</option>
-      <option value="NA-LNO2 (H)">NA-LNO2 (H)</option>
-      <option value="NA-OA-NO2 (C)">NA-OA-NO2 (C)</option>
-      <option value="NA-OA-NO2 (H)">NA-OA-NO2 (H)</option>
-      <option value="NBS (W)">NBS (W)</option>
-      <option value="NBS:13C(6) (W)">NBS:13C(6) (W)</option>
-      <option value="NDA (K)">NDA (K)</option>
-      <option value="NDA (N-term)">NDA (N-term)</option>
-      <option value="NEIAA (C)">NEIAA (C)</option>
-      <option value="NEIAA (Y)">NEIAA (Y)</option>
-      <option value="NEIAA:2H(5) (C)">NEIAA:2H(5) (C)</option>
-      <option value="NEIAA:2H(5) (Y)">NEIAA:2H(5) (Y)</option>
-      <option value="NEM:2H(5) (C)">NEM:2H(5) (C)</option>
-      <option value="NEM:2H(5)+H2O (C)">NEM:2H(5)+H2O (C)</option>
-      <option value="NEMsulfur (C)">NEMsulfur (C)</option>
-      <option value="NEMsulfurWater (C)">NEMsulfurWater (C)</option>
-      <option value="Nethylmaleimide (C)">Nethylmaleimide (C)</option>
-      <option value="Nethylmaleimide+water (C)">Nethylmaleimide+water (C)</option>
-      <option value="Nethylmaleimide+water (K)">Nethylmaleimide+water (K)</option>
-      <option value="NeuAc (N)">NeuAc (N)</option>
-      <option value="NeuAc (S)">NeuAc (S)</option>
-      <option value="NeuAc (T)">NeuAc (T)</option>
-      <option value="NeuGc (N)">NeuGc (N)</option>
-      <option value="NeuGc (S)">NeuGc (S)</option>
-      <option value="NeuGc (T)">NeuGc (T)</option>
-      <option value="NHS-fluorescein (K)">NHS-fluorescein (K)</option>
-      <option value="NHS-LC-Biotin (K)">NHS-LC-Biotin (K)</option>
-      <option value="NHS-LC-Biotin (N-term)">NHS-LC-Biotin (N-term)</option>
-      <option value="NIC (K)">NIC (K)</option>
-      <option value="NIC (N-term)">NIC (N-term)</option>
-      <option value="NIPCAM (C)">NIPCAM (C)</option>
-      <option value="Nitrene (Y)">Nitrene (Y)</option>
-      <option value="Nitro (F)">Nitro (F)</option>
-      <option value="Nitro (W)">Nitro (W)</option>
-      <option value="Nitro (Y)">Nitro (Y)</option>
-      <option value="Nitrosyl (C)">Nitrosyl (C)</option>
-      <option value="Nitrosyl (Y)">Nitrosyl (Y)</option>
-      <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
-      <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
-      <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
-      <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
-      <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-      <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
-      <option value="NP40 (N-term)">NP40 (N-term)</option>
-      <option value="NQIGG (K)">NQIGG (K)</option>
-      <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
-      <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
-      <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
-      <option value="O-Et-N-diMePhospho (S)">O-Et-N-diMePhospho (S)</option>
-      <option value="O-Isopropylmethylphosphonate (S)">O-Isopropylmethylphosphonate (S)</option>
-      <option value="O-Isopropylmethylphosphonate (T)">O-Isopropylmethylphosphonate (T)</option>
-      <option value="O-Isopropylmethylphosphonate (Y)">O-Isopropylmethylphosphonate (Y)</option>
-      <option value="O-Methylphosphate (S)">O-Methylphosphate (S)</option>
-      <option value="O-Methylphosphate (T)">O-Methylphosphate (T)</option>
-      <option value="O-Methylphosphate (Y)">O-Methylphosphate (Y)</option>
-      <option value="O-pinacolylmethylphosphonate (H)">O-pinacolylmethylphosphonate (H)</option>
-      <option value="O-pinacolylmethylphosphonate (K)">O-pinacolylmethylphosphonate (K)</option>
-      <option value="O-pinacolylmethylphosphonate (S)">O-pinacolylmethylphosphonate (S)</option>
-      <option value="O-pinacolylmethylphosphonate (T)">O-pinacolylmethylphosphonate (T)</option>
-      <option value="O-pinacolylmethylphosphonate (Y)">O-pinacolylmethylphosphonate (Y)</option>
-      <option value="Octanoyl (C)">Octanoyl (C)</option>
-      <option value="Octanoyl (S)">Octanoyl (S)</option>
-      <option value="Octanoyl (T)">Octanoyl (T)</option>
-      <option value="OxArgBiotin (R)">OxArgBiotin (R)</option>
-      <option value="OxArgBiotinRed (R)">OxArgBiotinRed (R)</option>
-      <option value="Oxidation (C)">Oxidation (C)</option>
-      <option value="Oxidation (C-term G)">Oxidation (C-term G)</option>
-      <option value="Oxidation (D)">Oxidation (D)</option>
-      <option value="Oxidation (E)">Oxidation (E)</option>
-      <option value="Oxidation (F)">Oxidation (F)</option>
-      <option value="Oxidation (H)">Oxidation (H)</option>
-      <option value="Oxidation (I)">Oxidation (I)</option>
-      <option value="Oxidation (K)">Oxidation (K)</option>
-      <option value="Oxidation (L)">Oxidation (L)</option>
-      <option value="Oxidation (M)" selected="true">Oxidation (M)</option>
-      <option value="Oxidation (N)">Oxidation (N)</option>
-      <option value="Oxidation (P)">Oxidation (P)</option>
-      <option value="Oxidation (Q)">Oxidation (Q)</option>
-      <option value="Oxidation (R)">Oxidation (R)</option>
-      <option value="Oxidation (S)">Oxidation (S)</option>
-      <option value="Oxidation (T)">Oxidation (T)</option>
-      <option value="Oxidation (U)">Oxidation (U)</option>
-      <option value="Oxidation (V)">Oxidation (V)</option>
-      <option value="Oxidation (W)">Oxidation (W)</option>
-      <option value="Oxidation (Y)">Oxidation (Y)</option>
-      <option value="Oxidation+NEM (C)">Oxidation+NEM (C)</option>
-      <option value="OxLysBiotin (K)">OxLysBiotin (K)</option>
-      <option value="OxLysBiotinRed (K)">OxLysBiotinRed (K)</option>
-      <option value="OxProBiotin (P)">OxProBiotin (P)</option>
-      <option value="OxProBiotinRed (P)">OxProBiotinRed (P)</option>
-      <option value="Palmitoleyl (C)">Palmitoleyl (C)</option>
-      <option value="Palmitoleyl (S)">Palmitoleyl (S)</option>
-      <option value="Palmitoleyl (T)">Palmitoleyl (T)</option>
-      <option value="Palmitoyl (C)">Palmitoyl (C)</option>
-      <option value="Palmitoyl (K)">Palmitoyl (K)</option>
-      <option value="Palmitoyl (Protein N-term)">Palmitoyl (Protein N-term)</option>
-      <option value="Palmitoyl (S)">Palmitoyl (S)</option>
-      <option value="Palmitoyl (T)">Palmitoyl (T)</option>
-      <option value="PEITC (C)">PEITC (C)</option>
-      <option value="PEITC (K)">PEITC (K)</option>
-      <option value="PEITC (N-term)">PEITC (N-term)</option>
-      <option value="Pent(1)HexNAc(1) (S)">Pent(1)HexNAc(1) (S)</option>
-      <option value="Pent(1)HexNAc(1) (T)">Pent(1)HexNAc(1) (T)</option>
-      <option value="Pent(2) (S)">Pent(2) (S)</option>
-      <option value="Pent(2) (T)">Pent(2) (T)</option>
-      <option value="Pentose (S)">Pentose (S)</option>
-      <option value="Pentose (T)">Pentose (T)</option>
-      <option value="Pentylamine (Q)">Pentylamine (Q)</option>
-      <option value="PEO-Iodoacetyl-LC-Biotin (C)">PEO-Iodoacetyl-LC-Biotin (C)</option>
-      <option value="PET (S)">PET (S)</option>
-      <option value="PET (T)">PET (T)</option>
-      <option value="Phe-&gt;Ala (F)">Phe-&gt;Ala (F)</option>
-      <option value="Phe-&gt;Arg (F)">Phe-&gt;Arg (F)</option>
-      <option value="Phe-&gt;Asn (F)">Phe-&gt;Asn (F)</option>
-      <option value="Phe-&gt;Asp (F)">Phe-&gt;Asp (F)</option>
-      <option value="Phe-&gt;CamCys (F)">Phe-&gt;CamCys (F)</option>
-      <option value="Phe-&gt;Cys (F)">Phe-&gt;Cys (F)</option>
-      <option value="Phe-&gt;Gln (F)">Phe-&gt;Gln (F)</option>
-      <option value="Phe-&gt;Glu (F)">Phe-&gt;Glu (F)</option>
-      <option value="Phe-&gt;Gly (F)">Phe-&gt;Gly (F)</option>
-      <option value="Phe-&gt;His (F)">Phe-&gt;His (F)</option>
-      <option value="Phe-&gt;Lys (F)">Phe-&gt;Lys (F)</option>
-      <option value="Phe-&gt;Met (F)">Phe-&gt;Met (F)</option>
-      <option value="Phe-&gt;Pro (F)">Phe-&gt;Pro (F)</option>
-      <option value="Phe-&gt;Ser (F)">Phe-&gt;Ser (F)</option>
-      <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
-      <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
-      <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
-      <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
-      <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
-      <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
-      <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
-      <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
-      <option value="Phospho (C)">Phospho (C)</option>
-      <option value="Phospho (D)">Phospho (D)</option>
-      <option value="Phospho (E)">Phospho (E)</option>
-      <option value="Phospho (H)">Phospho (H)</option>
-      <option value="Phospho (K)">Phospho (K)</option>
-      <option value="Phospho (R)">Phospho (R)</option>
-      <option value="Phospho (S)">Phospho (S)</option>
-      <option value="Phospho (T)">Phospho (T)</option>
-      <option value="Phospho (Y)">Phospho (Y)</option>
-      <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
-      <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
-      <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
-      <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
-      <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
-      <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
-      <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
-      <option value="Phosphogluconoylation (K)">Phosphogluconoylation (K)</option>
-      <option value="Phosphogluconoylation (N-term)">Phosphogluconoylation (N-term)</option>
-      <option value="Phosphoguanosine (H)">Phosphoguanosine (H)</option>
-      <option value="Phosphoguanosine (K)">Phosphoguanosine (K)</option>
-      <option value="PhosphoHex (S)">PhosphoHex (S)</option>
-      <option value="PhosphoHex (T)">PhosphoHex (T)</option>
-      <option value="PhosphoHex(2) (N)">PhosphoHex(2) (N)</option>
-      <option value="PhosphoHex(2) (S)">PhosphoHex(2) (S)</option>
-      <option value="PhosphoHex(2) (T)">PhosphoHex(2) (T)</option>
-      <option value="PhosphoHexNAc (S)">PhosphoHexNAc (S)</option>
-      <option value="PhosphoHexNAc (T)">PhosphoHexNAc (T)</option>
-      <option value="Phosphopantetheine (S)">Phosphopantetheine (S)</option>
-      <option value="Phosphopropargyl (S)">Phosphopropargyl (S)</option>
-      <option value="Phosphopropargyl (T)">Phosphopropargyl (T)</option>
-      <option value="Phosphopropargyl (Y)">Phosphopropargyl (Y)</option>
-      <option value="phosphoRibosyl (D)">phosphoRibosyl (D)</option>
-      <option value="phosphoRibosyl (E)">phosphoRibosyl (E)</option>
-      <option value="phosphoRibosyl (R)">phosphoRibosyl (R)</option>
-      <option value="PhosphoribosyldephosphoCoA (S)">PhosphoribosyldephosphoCoA (S)</option>
-      <option value="PhosphoUridine (H)">PhosphoUridine (H)</option>
-      <option value="PhosphoUridine (Y)">PhosphoUridine (Y)</option>
-      <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
-      <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
-      <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
-      <option value="Piperidine (K)">Piperidine (K)</option>
-      <option value="Piperidine (N-term)">Piperidine (N-term)</option>
-      <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
-      <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
-      <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
-      <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
-      <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
-      <option value="Pro-&gt;Gln (P)">Pro-&gt;Gln (P)</option>
-      <option value="Pro-&gt;Glu (P)">Pro-&gt;Glu (P)</option>
-      <option value="Pro-&gt;Gly (P)">Pro-&gt;Gly (P)</option>
-      <option value="Pro-&gt;HAVA (P)">Pro-&gt;HAVA (P)</option>
-      <option value="Pro-&gt;His (P)">Pro-&gt;His (P)</option>
-      <option value="Pro-&gt;Lys (P)">Pro-&gt;Lys (P)</option>
-      <option value="Pro-&gt;Met (P)">Pro-&gt;Met (P)</option>
-      <option value="Pro-&gt;Phe (P)">Pro-&gt;Phe (P)</option>
-      <option value="Pro-&gt;pyro-Glu (P)">Pro-&gt;pyro-Glu (P)</option>
-      <option value="Pro-&gt;Pyrrolidinone (P)">Pro-&gt;Pyrrolidinone (P)</option>
-      <option value="Pro-&gt;Pyrrolidone (P)">Pro-&gt;Pyrrolidone (P)</option>
-      <option value="Pro-&gt;Ser (P)">Pro-&gt;Ser (P)</option>
-      <option value="Pro-&gt;Thr (P)">Pro-&gt;Thr (P)</option>
-      <option value="Pro-&gt;Trp (P)">Pro-&gt;Trp (P)</option>
-      <option value="Pro-&gt;Tyr (P)">Pro-&gt;Tyr (P)</option>
-      <option value="Pro-&gt;Val (P)">Pro-&gt;Val (P)</option>
-      <option value="Pro-&gt;Xle (P)">Pro-&gt;Xle (P)</option>
-      <option value="probiotinhydrazide (P)">probiotinhydrazide (P)</option>
-      <option value="Propargylamine (C-term)">Propargylamine (C-term)</option>
-      <option value="Propargylamine (D)">Propargylamine (D)</option>
-      <option value="Propargylamine (E)">Propargylamine (E)</option>
-      <option value="Propionamide (C)">Propionamide (C)</option>
-      <option value="Propionamide (K)">Propionamide (K)</option>
-      <option value="Propionamide (N-term)">Propionamide (N-term)</option>
-      <option value="Propionamide:2H(3) (C)">Propionamide:2H(3) (C)</option>
-      <option value="Propionyl (K)">Propionyl (K)</option>
-      <option value="Propionyl (N-term)">Propionyl (N-term)</option>
-      <option value="Propionyl (Protein N-term)">Propionyl (Protein N-term)</option>
-      <option value="Propionyl (S)">Propionyl (S)</option>
-      <option value="Propionyl (T)">Propionyl (T)</option>
-      <option value="Propionyl:13C(3) (K)">Propionyl:13C(3) (K)</option>
-      <option value="Propionyl:13C(3) (N-term)">Propionyl:13C(3) (N-term)</option>
-      <option value="Propiophenone (C)">Propiophenone (C)</option>
-      <option value="Propiophenone (H)">Propiophenone (H)</option>
-      <option value="Propiophenone (K)">Propiophenone (K)</option>
-      <option value="Propiophenone (R)">Propiophenone (R)</option>
-      <option value="Propiophenone (S)">Propiophenone (S)</option>
-      <option value="Propiophenone (T)">Propiophenone (T)</option>
-      <option value="Propiophenone (W)">Propiophenone (W)</option>
-      <option value="Propyl (C-term)">Propyl (C-term)</option>
-      <option value="Propyl (D)">Propyl (D)</option>
-      <option value="Propyl (E)">Propyl (E)</option>
-      <option value="Propyl (K)">Propyl (K)</option>
-      <option value="Propyl (N-term)">Propyl (N-term)</option>
-      <option value="Propyl (Protein C-term)">Propyl (Protein C-term)</option>
-      <option value="Propyl:2H(6) (K)">Propyl:2H(6) (K)</option>
-      <option value="Propyl:2H(6) (N-term)">Propyl:2H(6) (N-term)</option>
-      <option value="PropylNAGthiazoline (C)">PropylNAGthiazoline (C)</option>
-      <option value="PS_Hapten (C)">PS_Hapten (C)</option>
-      <option value="PS_Hapten (H)">PS_Hapten (H)</option>
-      <option value="PS_Hapten (K)">PS_Hapten (K)</option>
-      <option value="pupylation (K)">pupylation (K)</option>
-      <option value="Puromycin (C-term)">Puromycin (C-term)</option>
-      <option value="PyMIC (N-term)">PyMIC (N-term)</option>
-      <option value="PyridoxalPhosphate (K)">PyridoxalPhosphate (K)</option>
-      <option value="PyridoxalPhosphateH2 (K)">PyridoxalPhosphateH2 (K)</option>
-      <option value="Pyridylacetyl (K)">Pyridylacetyl (K)</option>
-      <option value="Pyridylacetyl (N-term)">Pyridylacetyl (N-term)</option>
-      <option value="Pyridylethyl (C)">Pyridylethyl (C)</option>
-      <option value="Pyro-carbamidomethyl (N-term C)">Pyro-carbamidomethyl (N-term C)</option>
-      <option value="pyrophospho (S)">pyrophospho (S)</option>
-      <option value="pyrophospho (T)">pyrophospho (T)</option>
-      <option value="PyruvicAcidIminyl (K)">PyruvicAcidIminyl (K)</option>
-      <option value="PyruvicAcidIminyl (Protein N-term C)">PyruvicAcidIminyl (Protein N-term C)</option>
-      <option value="PyruvicAcidIminyl (Protein N-term V)">PyruvicAcidIminyl (Protein N-term V)</option>
-      <option value="QAT (C)">QAT (C)</option>
-      <option value="QAT:2H(3) (C)">QAT:2H(3) (C)</option>
-      <option value="QEQTGG (K)">QEQTGG (K)</option>
-      <option value="QQQTGG (K)">QQQTGG (K)</option>
-      <option value="QTGG (K)">QTGG (K)</option>
-      <option value="Quinone (W)">Quinone (W)</option>
-      <option value="Quinone (Y)">Quinone (Y)</option>
-      <option value="Retinylidene (K)">Retinylidene (K)</option>
-      <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
-      <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
-      <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-      <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-      <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-      <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-      <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-      <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-      <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-      <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-      <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
-      <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
-      <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
-      <option value="Saligenin (H)">Saligenin (H)</option>
-      <option value="Saligenin (K)">Saligenin (K)</option>
-      <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
-      <option value="Ser-&gt;Arg (S)">Ser-&gt;Arg (S)</option>
-      <option value="Ser-&gt;Asn (S)">Ser-&gt;Asn (S)</option>
-      <option value="Ser-&gt;Asp (S)">Ser-&gt;Asp (S)</option>
-      <option value="Ser-&gt;Cys (S)">Ser-&gt;Cys (S)</option>
-      <option value="Ser-&gt;Gln (S)">Ser-&gt;Gln (S)</option>
-      <option value="Ser-&gt;Glu (S)">Ser-&gt;Glu (S)</option>
-      <option value="Ser-&gt;Gly (S)">Ser-&gt;Gly (S)</option>
-      <option value="Ser-&gt;His (S)">Ser-&gt;His (S)</option>
-      <option value="Ser-&gt;LacticAcid (Protein N-term S)">Ser-&gt;LacticAcid (Protein N-term S)</option>
-      <option value="Ser-&gt;Lys (S)">Ser-&gt;Lys (S)</option>
-      <option value="Ser-&gt;Met (S)">Ser-&gt;Met (S)</option>
-      <option value="Ser-&gt;Phe (S)">Ser-&gt;Phe (S)</option>
-      <option value="Ser-&gt;Pro (S)">Ser-&gt;Pro (S)</option>
-      <option value="Ser-&gt;Thr (S)">Ser-&gt;Thr (S)</option>
-      <option value="Ser-&gt;Trp (S)">Ser-&gt;Trp (S)</option>
-      <option value="Ser-&gt;Tyr (S)">Ser-&gt;Tyr (S)</option>
-      <option value="Ser-&gt;Val (S)">Ser-&gt;Val (S)</option>
-      <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
-      <option value="serotonylation (Q)">serotonylation (Q)</option>
-      <option value="shTMT (K)">shTMT (K)</option>
-      <option value="shTMT (N-term)">shTMT (N-term)</option>
-      <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
-      <option value="SMA (K)">SMA (K)</option>
-      <option value="SMA (N-term)">SMA (N-term)</option>
-      <option value="spermidine (Q)">spermidine (Q)</option>
-      <option value="spermine (Q)">spermine (Q)</option>
-      <option value="SPITC (K)">SPITC (K)</option>
-      <option value="SPITC (N-term)">SPITC (N-term)</option>
-      <option value="SPITC:13C(6) (K)">SPITC:13C(6) (K)</option>
-      <option value="SPITC:13C(6) (N-term)">SPITC:13C(6) (N-term)</option>
-      <option value="Succinyl (K)">Succinyl (K)</option>
-      <option value="Succinyl (N-term)">Succinyl (N-term)</option>
-      <option value="Succinyl (Protein N-term)">Succinyl (Protein N-term)</option>
-      <option value="Succinyl:13C(4) (K)">Succinyl:13C(4) (K)</option>
-      <option value="Succinyl:13C(4) (N-term)">Succinyl:13C(4) (N-term)</option>
-      <option value="Succinyl:2H(4) (K)">Succinyl:2H(4) (K)</option>
-      <option value="Succinyl:2H(4) (N-term)">Succinyl:2H(4) (N-term)</option>
-      <option value="SulfanilicAcid (C-term)">SulfanilicAcid (C-term)</option>
-      <option value="SulfanilicAcid (D)">SulfanilicAcid (D)</option>
-      <option value="SulfanilicAcid (E)">SulfanilicAcid (E)</option>
-      <option value="SulfanilicAcid:13C(6) (C-term)">SulfanilicAcid:13C(6) (C-term)</option>
-      <option value="SulfanilicAcid:13C(6) (D)">SulfanilicAcid:13C(6) (D)</option>
-      <option value="SulfanilicAcid:13C(6) (E)">SulfanilicAcid:13C(6) (E)</option>
-      <option value="Sulfide (C)">Sulfide (C)</option>
-      <option value="Sulfide (D)">Sulfide (D)</option>
-      <option value="Sulfide (W)">Sulfide (W)</option>
-      <option value="Sulfo (C)">Sulfo (C)</option>
-      <option value="Sulfo (S)">Sulfo (S)</option>
-      <option value="Sulfo (T)">Sulfo (T)</option>
-      <option value="Sulfo (Y)">Sulfo (Y)</option>
-      <option value="sulfo+amino (Y)">sulfo+amino (Y)</option>
-      <option value="Sulfo-NHS-LC-LC-Biotin (K)">Sulfo-NHS-LC-LC-Biotin (K)</option>
-      <option value="Sulfo-NHS-LC-LC-Biotin (N-term)">Sulfo-NHS-LC-LC-Biotin (N-term)</option>
-      <option value="SulfoGMBS (C)">SulfoGMBS (C)</option>
-      <option value="SulfurDioxide (C)">SulfurDioxide (C)</option>
-      <option value="SUMO2135 (K)">SUMO2135 (K)</option>
-      <option value="SUMO3549 (K)">SUMO3549 (K)</option>
-      <option value="TAMRA-FP (S)">TAMRA-FP (S)</option>
-      <option value="TAMRA-FP (Y)">TAMRA-FP (Y)</option>
-      <option value="Thiadiazole (C)">Thiadiazole (C)</option>
-      <option value="Thiazolidine (C)">Thiazolidine (C)</option>
-      <option value="Thiazolidine (F)">Thiazolidine (F)</option>
-      <option value="Thiazolidine (H)">Thiazolidine (H)</option>
-      <option value="Thiazolidine (K)">Thiazolidine (K)</option>
-      <option value="Thiazolidine (Protein N-term)">Thiazolidine (Protein N-term)</option>
-      <option value="Thiazolidine (R)">Thiazolidine (R)</option>
-      <option value="Thiazolidine (W)">Thiazolidine (W)</option>
-      <option value="Thiazolidine (Y)">Thiazolidine (Y)</option>
-      <option value="thioacylPA (K)">thioacylPA (K)</option>
-      <option value="Thiophos-S-S-biotin (S)">Thiophos-S-S-biotin (S)</option>
-      <option value="Thiophos-S-S-biotin (T)">Thiophos-S-S-biotin (T)</option>
-      <option value="Thiophos-S-S-biotin (Y)">Thiophos-S-S-biotin (Y)</option>
-      <option value="Thiophospho (S)">Thiophospho (S)</option>
-      <option value="Thiophospho (T)">Thiophospho (T)</option>
-      <option value="Thiophospho (Y)">Thiophospho (Y)</option>
-      <option value="Thr-&gt;Ala (T)">Thr-&gt;Ala (T)</option>
-      <option value="Thr-&gt;Arg (T)">Thr-&gt;Arg (T)</option>
-      <option value="Thr-&gt;Asn (T)">Thr-&gt;Asn (T)</option>
-      <option value="Thr-&gt;Asp (T)">Thr-&gt;Asp (T)</option>
-      <option value="Thr-&gt;Cys (T)">Thr-&gt;Cys (T)</option>
-      <option value="Thr-&gt;Gln (T)">Thr-&gt;Gln (T)</option>
-      <option value="Thr-&gt;Glu (T)">Thr-&gt;Glu (T)</option>
-      <option value="Thr-&gt;Gly (T)">Thr-&gt;Gly (T)</option>
-      <option value="Thr-&gt;His (T)">Thr-&gt;His (T)</option>
-      <option value="Thr-&gt;Lys (T)">Thr-&gt;Lys (T)</option>
-      <option value="Thr-&gt;Met (T)">Thr-&gt;Met (T)</option>
-      <option value="Thr-&gt;Phe (T)">Thr-&gt;Phe (T)</option>
-      <option value="Thr-&gt;Pro (T)">Thr-&gt;Pro (T)</option>
-      <option value="Thr-&gt;Ser (T)">Thr-&gt;Ser (T)</option>
-      <option value="Thr-&gt;Trp (T)">Thr-&gt;Trp (T)</option>
-      <option value="Thr-&gt;Tyr (T)">Thr-&gt;Tyr (T)</option>
-      <option value="Thr-&gt;Val (T)">Thr-&gt;Val (T)</option>
-      <option value="Thr-&gt;Xle (T)">Thr-&gt;Xle (T)</option>
-      <option value="Thrbiotinhydrazide (T)">Thrbiotinhydrazide (T)</option>
-      <option value="Thyroxine (Y)">Thyroxine (Y)</option>
-      <option value="TMAB (K)">TMAB (K)</option>
-      <option value="TMAB (N-term)">TMAB (N-term)</option>
-      <option value="TMAB:2H(9) (K)">TMAB:2H(9) (K)</option>
-      <option value="TMAB:2H(9) (N-term)">TMAB:2H(9) (N-term)</option>
-      <option value="TMPP-Ac (K)">TMPP-Ac (K)</option>
-      <option value="TMPP-Ac (N-term)">TMPP-Ac (N-term)</option>
-      <option value="TMPP-Ac (Y)">TMPP-Ac (Y)</option>
-      <option value="TMPP-Ac:13C(9) (K)">TMPP-Ac:13C(9) (K)</option>
-      <option value="TMPP-Ac:13C(9) (N-term)">TMPP-Ac:13C(9) (N-term)</option>
-      <option value="TMPP-Ac:13C(9) (Y)">TMPP-Ac:13C(9) (Y)</option>
-      <option value="TMT (H)">TMT (H)</option>
-      <option value="TMT (K)">TMT (K)</option>
-      <option value="TMT (N-term)">TMT (N-term)</option>
-      <option value="TMT (Protein N-term)">TMT (Protein N-term)</option>
-      <option value="TMT (S)">TMT (S)</option>
-      <option value="TMT (T)">TMT (T)</option>
-      <option value="TMT2plex (H)">TMT2plex (H)</option>
-      <option value="TMT2plex (K)">TMT2plex (K)</option>
-      <option value="TMT2plex (N-term)">TMT2plex (N-term)</option>
-      <option value="TMT2plex (Protein N-term)">TMT2plex (Protein N-term)</option>
-      <option value="TMT2plex (S)">TMT2plex (S)</option>
-      <option value="TMT2plex (T)">TMT2plex (T)</option>
-      <option value="TMT6plex (H)">TMT6plex (H)</option>
-      <option value="TMT6plex (K)">TMT6plex (K)</option>
-      <option value="TMT6plex (N-term)">TMT6plex (N-term)</option>
-      <option value="TMT6plex (Protein N-term)">TMT6plex (Protein N-term)</option>
-      <option value="TMT6plex (S)">TMT6plex (S)</option>
-      <option value="TMT6plex (T)">TMT6plex (T)</option>
-      <option value="TMTpro (H)">TMTpro (H)</option>
-      <option value="TMTpro (K)">TMTpro (K)</option>
-      <option value="TMTpro (N-term)">TMTpro (N-term)</option>
-      <option value="TMTpro (Protein N-term)">TMTpro (Protein N-term)</option>
-      <option value="TMTpro (S)">TMTpro (S)</option>
-      <option value="TMTpro (T)">TMTpro (T)</option>
-      <option value="TMTpro_zero (H)">TMTpro_zero (H)</option>
-      <option value="TMTpro_zero (K)">TMTpro_zero (K)</option>
-      <option value="TMTpro_zero (N-term)">TMTpro_zero (N-term)</option>
-      <option value="TMTpro_zero (Protein N-term)">TMTpro_zero (Protein N-term)</option>
-      <option value="TMTpro_zero (S)">TMTpro_zero (S)</option>
-      <option value="TMTpro_zero (T)">TMTpro_zero (T)</option>
-      <option value="TNBS (K)">TNBS (K)</option>
-      <option value="TNBS (N-term)">TNBS (N-term)</option>
-      <option value="trifluoro (L)">trifluoro (L)</option>
-      <option value="Triiodo (Y)">Triiodo (Y)</option>
-      <option value="Triiodothyronine (Y)">Triiodothyronine (Y)</option>
-      <option value="Trimethyl (K)">Trimethyl (K)</option>
-      <option value="Trimethyl (Protein N-term A)">Trimethyl (Protein N-term A)</option>
-      <option value="Trimethyl (R)">Trimethyl (R)</option>
-      <option value="Trimethyl:13C(3)2H(9) (K)">Trimethyl:13C(3)2H(9) (K)</option>
-      <option value="Trimethyl:13C(3)2H(9) (R)">Trimethyl:13C(3)2H(9) (R)</option>
-      <option value="Trimethyl:2H(9) (K)">Trimethyl:2H(9) (K)</option>
-      <option value="Trimethyl:2H(9) (R)">Trimethyl:2H(9) (R)</option>
-      <option value="Trioxidation (C)">Trioxidation (C)</option>
-      <option value="Trioxidation (F)">Trioxidation (F)</option>
-      <option value="Trioxidation (W)">Trioxidation (W)</option>
-      <option value="Trioxidation (Y)">Trioxidation (Y)</option>
-      <option value="Tripalmitate (Protein N-term C)">Tripalmitate (Protein N-term C)</option>
-      <option value="Tris (N)">Tris (N)</option>
-      <option value="Triton (C-term)">Triton (C-term)</option>
-      <option value="Triton (N-term)">Triton (N-term)</option>
-      <option value="Trp-&gt;Ala (W)">Trp-&gt;Ala (W)</option>
-      <option value="Trp-&gt;Arg (W)">Trp-&gt;Arg (W)</option>
-      <option value="Trp-&gt;Asn (W)">Trp-&gt;Asn (W)</option>
-      <option value="Trp-&gt;Asp (W)">Trp-&gt;Asp (W)</option>
-      <option value="Trp-&gt;Cys (W)">Trp-&gt;Cys (W)</option>
-      <option value="Trp-&gt;Gln (W)">Trp-&gt;Gln (W)</option>
-      <option value="Trp-&gt;Glu (W)">Trp-&gt;Glu (W)</option>
-      <option value="Trp-&gt;Gly (W)">Trp-&gt;Gly (W)</option>
-      <option value="Trp-&gt;His (W)">Trp-&gt;His (W)</option>
-      <option value="Trp-&gt;Hydroxykynurenin (W)">Trp-&gt;Hydroxykynurenin (W)</option>
-      <option value="Trp-&gt;Kynurenin (W)">Trp-&gt;Kynurenin (W)</option>
-      <option value="Trp-&gt;Lys (W)">Trp-&gt;Lys (W)</option>
-      <option value="Trp-&gt;Met (W)">Trp-&gt;Met (W)</option>
-      <option value="Trp-&gt;Oxolactone (W)">Trp-&gt;Oxolactone (W)</option>
-      <option value="Trp-&gt;Phe (W)">Trp-&gt;Phe (W)</option>
-      <option value="Trp-&gt;Pro (W)">Trp-&gt;Pro (W)</option>
-      <option value="Trp-&gt;Ser (W)">Trp-&gt;Ser (W)</option>
-      <option value="Trp-&gt;Thr (W)">Trp-&gt;Thr (W)</option>
-      <option value="Trp-&gt;Tyr (W)">Trp-&gt;Tyr (W)</option>
-      <option value="Trp-&gt;Val (W)">Trp-&gt;Val (W)</option>
-      <option value="Trp-&gt;Xle (W)">Trp-&gt;Xle (W)</option>
-      <option value="Tween20 (N-term)">Tween20 (N-term)</option>
-      <option value="Tween80 (C-term)">Tween80 (C-term)</option>
-      <option value="Tyr-&gt;Ala (Y)">Tyr-&gt;Ala (Y)</option>
-      <option value="Tyr-&gt;Arg (Y)">Tyr-&gt;Arg (Y)</option>
-      <option value="Tyr-&gt;Asn (Y)">Tyr-&gt;Asn (Y)</option>
-      <option value="Tyr-&gt;Asp (Y)">Tyr-&gt;Asp (Y)</option>
-      <option value="Tyr-&gt;Cys (Y)">Tyr-&gt;Cys (Y)</option>
-      <option value="Tyr-&gt;Dha (Y)">Tyr-&gt;Dha (Y)</option>
-      <option value="Tyr-&gt;Gln (Y)">Tyr-&gt;Gln (Y)</option>
-      <option value="Tyr-&gt;Glu (Y)">Tyr-&gt;Glu (Y)</option>
-      <option value="Tyr-&gt;Gly (Y)">Tyr-&gt;Gly (Y)</option>
-      <option value="Tyr-&gt;His (Y)">Tyr-&gt;His (Y)</option>
-      <option value="Tyr-&gt;Lys (Y)">Tyr-&gt;Lys (Y)</option>
-      <option value="Tyr-&gt;Met (Y)">Tyr-&gt;Met (Y)</option>
-      <option value="Tyr-&gt;Phe (Y)">Tyr-&gt;Phe (Y)</option>
-      <option value="Tyr-&gt;Pro (Y)">Tyr-&gt;Pro (Y)</option>
-      <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
-      <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
-      <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
-      <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
-      <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-      <option value="Ub-amide (C)">Ub-amide (C)</option>
-      <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
-      <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
-      <option value="Ub-VME (C)">Ub-VME (C)</option>
-      <option value="UgiJoullie (D)">UgiJoullie (D)</option>
-      <option value="UgiJoullie (E)">UgiJoullie (E)</option>
-      <option value="UgiJoullieProGly (D)">UgiJoullieProGly (D)</option>
-      <option value="UgiJoullieProGly (E)">UgiJoullieProGly (E)</option>
-      <option value="UgiJoullieProGlyProGly (D)">UgiJoullieProGlyProGly (D)</option>
-      <option value="UgiJoullieProGlyProGly (E)">UgiJoullieProGlyProGly (E)</option>
-      <option value="Unknown:162 (C-term)">Unknown:162 (C-term)</option>
-      <option value="Unknown:162 (D)">Unknown:162 (D)</option>
-      <option value="Unknown:162 (E)">Unknown:162 (E)</option>
-      <option value="Unknown:162 (N-term)">Unknown:162 (N-term)</option>
-      <option value="Unknown:177 (C-term)">Unknown:177 (C-term)</option>
-      <option value="Unknown:177 (D)">Unknown:177 (D)</option>
-      <option value="Unknown:177 (E)">Unknown:177 (E)</option>
-      <option value="Unknown:177 (N-term)">Unknown:177 (N-term)</option>
-      <option value="Unknown:210 (C-term)">Unknown:210 (C-term)</option>
-      <option value="Unknown:210 (D)">Unknown:210 (D)</option>
-      <option value="Unknown:210 (E)">Unknown:210 (E)</option>
-      <option value="Unknown:210 (N-term)">Unknown:210 (N-term)</option>
-      <option value="Unknown:216 (C-term)">Unknown:216 (C-term)</option>
-      <option value="Unknown:216 (D)">Unknown:216 (D)</option>
-      <option value="Unknown:216 (E)">Unknown:216 (E)</option>
-      <option value="Unknown:216 (N-term)">Unknown:216 (N-term)</option>
-      <option value="Unknown:234 (C-term)">Unknown:234 (C-term)</option>
-      <option value="Unknown:234 (D)">Unknown:234 (D)</option>
-      <option value="Unknown:234 (E)">Unknown:234 (E)</option>
-      <option value="Unknown:234 (N-term)">Unknown:234 (N-term)</option>
-      <option value="Unknown:248 (C-term)">Unknown:248 (C-term)</option>
-      <option value="Unknown:248 (D)">Unknown:248 (D)</option>
-      <option value="Unknown:248 (E)">Unknown:248 (E)</option>
-      <option value="Unknown:248 (N-term)">Unknown:248 (N-term)</option>
-      <option value="Unknown:250 (C-term)">Unknown:250 (C-term)</option>
-      <option value="Unknown:250 (D)">Unknown:250 (D)</option>
-      <option value="Unknown:250 (E)">Unknown:250 (E)</option>
-      <option value="Unknown:250 (N-term)">Unknown:250 (N-term)</option>
-      <option value="Unknown:302 (C-term)">Unknown:302 (C-term)</option>
-      <option value="Unknown:302 (D)">Unknown:302 (D)</option>
-      <option value="Unknown:302 (E)">Unknown:302 (E)</option>
-      <option value="Unknown:302 (N-term)">Unknown:302 (N-term)</option>
-      <option value="Unknown:306 (C-term)">Unknown:306 (C-term)</option>
-      <option value="Unknown:306 (D)">Unknown:306 (D)</option>
-      <option value="Unknown:306 (E)">Unknown:306 (E)</option>
-      <option value="Unknown:306 (N-term)">Unknown:306 (N-term)</option>
-      <option value="Unknown:420 (C-term)">Unknown:420 (C-term)</option>
-      <option value="Unknown:420 (N-term)">Unknown:420 (N-term)</option>
-      <option value="Val-&gt;Ala (V)">Val-&gt;Ala (V)</option>
-      <option value="Val-&gt;Arg (V)">Val-&gt;Arg (V)</option>
-      <option value="Val-&gt;Asn (V)">Val-&gt;Asn (V)</option>
-      <option value="Val-&gt;Asp (V)">Val-&gt;Asp (V)</option>
-      <option value="Val-&gt;Cys (V)">Val-&gt;Cys (V)</option>
-      <option value="Val-&gt;Gln (V)">Val-&gt;Gln (V)</option>
-      <option value="Val-&gt;Glu (V)">Val-&gt;Glu (V)</option>
-      <option value="Val-&gt;Gly (V)">Val-&gt;Gly (V)</option>
-      <option value="Val-&gt;His (V)">Val-&gt;His (V)</option>
-      <option value="Val-&gt;Lys (V)">Val-&gt;Lys (V)</option>
-      <option value="Val-&gt;Met (V)">Val-&gt;Met (V)</option>
-      <option value="Val-&gt;Phe (V)">Val-&gt;Phe (V)</option>
-      <option value="Val-&gt;Pro (V)">Val-&gt;Pro (V)</option>
-      <option value="Val-&gt;Ser (V)">Val-&gt;Ser (V)</option>
-      <option value="Val-&gt;Thr (V)">Val-&gt;Thr (V)</option>
-      <option value="Val-&gt;Trp (V)">Val-&gt;Trp (V)</option>
-      <option value="Val-&gt;Tyr (V)">Val-&gt;Tyr (V)</option>
-      <option value="Val-&gt;Xle (V)">Val-&gt;Xle (V)</option>
-      <option value="VFQQQTGG (K)">VFQQQTGG (K)</option>
-      <option value="VIEVYQEQTGG (K)">VIEVYQEQTGG (K)</option>
-      <option value="Withaferin (C)">Withaferin (C)</option>
-      <option value="Xle-&gt;Ala (I)">Xle-&gt;Ala (I)</option>
-      <option value="Xle-&gt;Ala (L)">Xle-&gt;Ala (L)</option>
-      <option value="Xle-&gt;Arg (I)">Xle-&gt;Arg (I)</option>
-      <option value="Xle-&gt;Arg (L)">Xle-&gt;Arg (L)</option>
-      <option value="Xle-&gt;Asn (I)">Xle-&gt;Asn (I)</option>
-      <option value="Xle-&gt;Asn (L)">Xle-&gt;Asn (L)</option>
-      <option value="Xle-&gt;Asp (I)">Xle-&gt;Asp (I)</option>
-      <option value="Xle-&gt;Asp (L)">Xle-&gt;Asp (L)</option>
-      <option value="Xle-&gt;Cys (I)">Xle-&gt;Cys (I)</option>
-      <option value="Xle-&gt;Cys (L)">Xle-&gt;Cys (L)</option>
-      <option value="Xle-&gt;Gln (I)">Xle-&gt;Gln (I)</option>
-      <option value="Xle-&gt;Gln (L)">Xle-&gt;Gln (L)</option>
-      <option value="Xle-&gt;Glu (I)">Xle-&gt;Glu (I)</option>
-      <option value="Xle-&gt;Glu (L)">Xle-&gt;Glu (L)</option>
-      <option value="Xle-&gt;Gly (I)">Xle-&gt;Gly (I)</option>
-      <option value="Xle-&gt;Gly (L)">Xle-&gt;Gly (L)</option>
-      <option value="Xle-&gt;His (I)">Xle-&gt;His (I)</option>
-      <option value="Xle-&gt;His (L)">Xle-&gt;His (L)</option>
-      <option value="Xle-&gt;Lys (I)">Xle-&gt;Lys (I)</option>
-      <option value="Xle-&gt;Lys (L)">Xle-&gt;Lys (L)</option>
-      <option value="Xle-&gt;Met (I)">Xle-&gt;Met (I)</option>
-      <option value="Xle-&gt;Met (L)">Xle-&gt;Met (L)</option>
-      <option value="Xle-&gt;Phe (I)">Xle-&gt;Phe (I)</option>
-      <option value="Xle-&gt;Phe (L)">Xle-&gt;Phe (L)</option>
-      <option value="Xle-&gt;Pro (I)">Xle-&gt;Pro (I)</option>
-      <option value="Xle-&gt;Pro (L)">Xle-&gt;Pro (L)</option>
-      <option value="Xle-&gt;Ser (I)">Xle-&gt;Ser (I)</option>
-      <option value="Xle-&gt;Ser (L)">Xle-&gt;Ser (L)</option>
-      <option value="Xle-&gt;Thr (I)">Xle-&gt;Thr (I)</option>
-      <option value="Xle-&gt;Thr (L)">Xle-&gt;Thr (L)</option>
-      <option value="Xle-&gt;Trp (I)">Xle-&gt;Trp (I)</option>
-      <option value="Xle-&gt;Trp (L)">Xle-&gt;Trp (L)</option>
-      <option value="Xle-&gt;Tyr (I)">Xle-&gt;Tyr (I)</option>
-      <option value="Xle-&gt;Tyr (L)">Xle-&gt;Tyr (L)</option>
-      <option value="Xle-&gt;Val (I)">Xle-&gt;Val (I)</option>
-      <option value="Xle-&gt;Val (L)">Xle-&gt;Val (L)</option>
-      <option value="Xlink:B10621 (C)">Xlink:B10621 (C)</option>
-      <option value="Xlink:BMOE (C)">Xlink:BMOE (C)</option>
-      <option value="Xlink:BS2G[113] (K)">Xlink:BS2G[113] (K)</option>
-      <option value="Xlink:BS2G[113] (Protein N-term)">Xlink:BS2G[113] (Protein N-term)</option>
-      <option value="Xlink:BS2G[114] (K)">Xlink:BS2G[114] (K)</option>
-      <option value="Xlink:BS2G[114] (Protein N-term)">Xlink:BS2G[114] (Protein N-term)</option>
-      <option value="Xlink:BS2G[217] (K)">Xlink:BS2G[217] (K)</option>
-      <option value="Xlink:BS2G[217] (Protein N-term)">Xlink:BS2G[217] (Protein N-term)</option>
-      <option value="Xlink:BS2G[96] (K)">Xlink:BS2G[96] (K)</option>
-      <option value="Xlink:BS2G[96] (Protein N-term)">Xlink:BS2G[96] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[111] (K)">Xlink:BuUrBu[111] (K)</option>
-      <option value="Xlink:BuUrBu[111] (Protein N-term)">Xlink:BuUrBu[111] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[196] (K)">Xlink:BuUrBu[196] (K)</option>
-      <option value="Xlink:BuUrBu[196] (Protein N-term)">Xlink:BuUrBu[196] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[213] (K)">Xlink:BuUrBu[213] (K)</option>
-      <option value="Xlink:BuUrBu[213] (Protein N-term)">Xlink:BuUrBu[213] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[214] (K)">Xlink:BuUrBu[214] (K)</option>
-      <option value="Xlink:BuUrBu[214] (Protein N-term)">Xlink:BuUrBu[214] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[317] (K)">Xlink:BuUrBu[317] (K)</option>
-      <option value="Xlink:BuUrBu[317] (Protein N-term)">Xlink:BuUrBu[317] (Protein N-term)</option>
-      <option value="Xlink:BuUrBu[85] (K)">Xlink:BuUrBu[85] (K)</option>
-      <option value="Xlink:BuUrBu[85] (Protein N-term)">Xlink:BuUrBu[85] (Protein N-term)</option>
-      <option value="Xlink:DFDNB (K)">Xlink:DFDNB (K)</option>
-      <option value="Xlink:DFDNB (N)">Xlink:DFDNB (N)</option>
-      <option value="Xlink:DFDNB (Q)">Xlink:DFDNB (Q)</option>
-      <option value="Xlink:DFDNB (R)">Xlink:DFDNB (R)</option>
-      <option value="Xlink:DMP[122] (K)">Xlink:DMP[122] (K)</option>
-      <option value="Xlink:DMP[122] (Protein N-term)">Xlink:DMP[122] (Protein N-term)</option>
-      <option value="Xlink:DMP[139] (K)">Xlink:DMP[139] (K)</option>
-      <option value="Xlink:DMP[139] (Protein N-term)">Xlink:DMP[139] (Protein N-term)</option>
-      <option value="Xlink:DMP[140] (K)">Xlink:DMP[140] (K)</option>
-      <option value="Xlink:DMP[140] (Protein N-term)">Xlink:DMP[140] (Protein N-term)</option>
-      <option value="Xlink:DMP[154] (K)">Xlink:DMP[154] (K)</option>
-      <option value="Xlink:DMP[154] (Protein N-term)">Xlink:DMP[154] (Protein N-term)</option>
-      <option value="Xlink:DSS[138] (K)">Xlink:DSS[138] (K)</option>
-      <option value="Xlink:DSS[138] (Protein N-term)">Xlink:DSS[138] (Protein N-term)</option>
-      <option value="Xlink:DSS[155] (K)">Xlink:DSS[155] (K)</option>
-      <option value="Xlink:DSS[155] (Protein N-term)">Xlink:DSS[155] (Protein N-term)</option>
-      <option value="Xlink:DSS[156] (K)">Xlink:DSS[156] (K)</option>
-      <option value="Xlink:DSS[156] (Protein N-term)">Xlink:DSS[156] (Protein N-term)</option>
-      <option value="Xlink:DSS[259] (K)">Xlink:DSS[259] (K)</option>
-      <option value="Xlink:DSS[259] (Protein N-term)">Xlink:DSS[259] (Protein N-term)</option>
-      <option value="Xlink:DSSO[104] (K)">Xlink:DSSO[104] (K)</option>
-      <option value="Xlink:DSSO[104] (Protein N-term)">Xlink:DSSO[104] (Protein N-term)</option>
-      <option value="Xlink:DSSO[158] (K)">Xlink:DSSO[158] (K)</option>
-      <option value="Xlink:DSSO[158] (Protein N-term)">Xlink:DSSO[158] (Protein N-term)</option>
-      <option value="Xlink:DSSO[175] (K)">Xlink:DSSO[175] (K)</option>
-      <option value="Xlink:DSSO[175] (Protein N-term)">Xlink:DSSO[175] (Protein N-term)</option>
-      <option value="Xlink:DSSO[176] (K)">Xlink:DSSO[176] (K)</option>
-      <option value="Xlink:DSSO[176] (Protein N-term)">Xlink:DSSO[176] (Protein N-term)</option>
-      <option value="Xlink:DSSO[279] (K)">Xlink:DSSO[279] (K)</option>
-      <option value="Xlink:DSSO[279] (Protein N-term)">Xlink:DSSO[279] (Protein N-term)</option>
-      <option value="Xlink:DSSO[54] (K)">Xlink:DSSO[54] (K)</option>
-      <option value="Xlink:DSSO[54] (Protein N-term)">Xlink:DSSO[54] (Protein N-term)</option>
-      <option value="Xlink:DSSO[86] (K)">Xlink:DSSO[86] (K)</option>
-      <option value="Xlink:DSSO[86] (Protein N-term)">Xlink:DSSO[86] (Protein N-term)</option>
-      <option value="Xlink:DST[114] (K)">Xlink:DST[114] (K)</option>
-      <option value="Xlink:DST[114] (Protein N-term)">Xlink:DST[114] (Protein N-term)</option>
-      <option value="Xlink:DST[132] (K)">Xlink:DST[132] (K)</option>
-      <option value="Xlink:DST[132] (Protein N-term)">Xlink:DST[132] (Protein N-term)</option>
-      <option value="Xlink:DST[56] (K)">Xlink:DST[56] (K)</option>
-      <option value="Xlink:DST[56] (Protein N-term)">Xlink:DST[56] (Protein N-term)</option>
-      <option value="Xlink:DTBP[172] (K)">Xlink:DTBP[172] (K)</option>
-      <option value="Xlink:DTBP[172] (Protein N-term)">Xlink:DTBP[172] (Protein N-term)</option>
-      <option value="Xlink:DTBP[87] (K)">Xlink:DTBP[87] (K)</option>
-      <option value="Xlink:DTBP[87] (Protein N-term)">Xlink:DTBP[87] (Protein N-term)</option>
-      <option value="Xlink:DTSSP[174] (K)">Xlink:DTSSP[174] (K)</option>
-      <option value="Xlink:DTSSP[174] (Protein N-term)">Xlink:DTSSP[174] (Protein N-term)</option>
-      <option value="Xlink:DTSSP[192] (K)">Xlink:DTSSP[192] (K)</option>
-      <option value="Xlink:DTSSP[192] (Protein N-term)">Xlink:DTSSP[192] (Protein N-term)</option>
-      <option value="Xlink:DTSSP[88] (K)">Xlink:DTSSP[88] (K)</option>
-      <option value="Xlink:DTSSP[88] (Protein N-term)">Xlink:DTSSP[88] (Protein N-term)</option>
-      <option value="Xlink:EGS[115] (K)">Xlink:EGS[115] (K)</option>
-      <option value="Xlink:EGS[115] (Protein N-term)">Xlink:EGS[115] (Protein N-term)</option>
-      <option value="Xlink:EGS[226] (K)">Xlink:EGS[226] (K)</option>
-      <option value="Xlink:EGS[226] (Protein N-term)">Xlink:EGS[226] (Protein N-term)</option>
-      <option value="Xlink:EGS[244] (K)">Xlink:EGS[244] (K)</option>
-      <option value="Xlink:EGS[244] (Protein N-term)">Xlink:EGS[244] (Protein N-term)</option>
-      <option value="Xlink:SMCC[219] (C)">Xlink:SMCC[219] (C)</option>
-      <option value="Xlink:SMCC[219] (K)">Xlink:SMCC[219] (K)</option>
-      <option value="Xlink:SMCC[219] (Protein N-term)">Xlink:SMCC[219] (Protein N-term)</option>
-      <option value="Xlink:SMCC[237] (C)">Xlink:SMCC[237] (C)</option>
-      <option value="Xlink:SMCC[237] (K)">Xlink:SMCC[237] (K)</option>
-      <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
-      <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
-      <option value="ZGB (K)">ZGB (K)</option>
-      <option value="ZGB (N-term)">ZGB (N-term)</option>
-      <option value="ZQG (K)">ZQG (K)</option>
-      <expand macro="list_string_san" name="variable_modifications"/>
-    </param>
-    <expand macro="adv_opts_macro">
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><test expect_num_outputs="1"><!-- adapted from (dysfunctional) OMS 3rdParty tests (but model selection
-             unclear https://github.com/OpenMS/OpenMS/issues/4719)-->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="PepNovo_1.mzML"/>
-    <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/>
-    <param name="model" value="LTQ_COMP"/>
-  </test>
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="PepNovo_1.mzML"/>
-    <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/>
-    <param name="model" value="LTQ_COMP"/>
-  </test>
-</tests>
-  <help><![CDATA[Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format.
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PepNovoAdapter.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/PeptideIndexer.xml b/tools/openms/PeptideIndexer.xml
index 6d0b02ca2..fd70bb1da 100644
--- a/tools/openms/PeptideIndexer.xml
+++ b/tools/openms/PeptideIndexer.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [ID Processing]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="PeptideIndexer" name="PeptideIndexer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Refreshes the protein references for all peptide hits.</description>
+  <description>Refreshes the protein references for all peptide hits</description>
   <macros>
     <token name="@EXECUTABLE@">PeptideIndexer</token>
     <import>macros.xml</import>
@@ -15,10 +14,10 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #if $fasta:
   mkdir fasta &&
-  ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' &&
+  cp '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' &&
 #end if
 mkdir out &&
 
@@ -47,17 +46,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="idxml" optional="false" label="Input idXML file containing the identifications" help=" select idxml data sets(s)"/>
+    <param argument="-in" type="data" format="idxml" label="Input idXML file containing the identifications" help=" select idxml data sets(s)"/>
     <param argument="-fasta" type="data" format="fasta" optional="true" label="Input sequence database in FASTA format" help="Leave empty for using the same DB as used for the input idXML (this might fail). Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir' select fasta data sets(s)"/>
     <param argument="-decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
       <expand macro="list_string_san" name="decoy_string"/>
     </param>
-    <param argument="-decoy_string_position" type="select" optional="true" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
+    <param argument="-decoy_string_position" type="select" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
       <option value="prefix" selected="true">prefix</option>
       <option value="suffix">suffix</option>
       <expand macro="list_string_san" name="decoy_string_position"/>
     </param>
-    <param argument="-missing_decoy_action" type="select" optional="true" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
+    <param argument="-missing_decoy_action" type="select" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
       <option value="error" selected="true">error</option>
       <option value="warn">warn</option>
       <option value="silent">silent</option>
@@ -66,19 +65,36 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
     <param argument="-write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
     <param argument="-keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
-    <param argument="-unmatched_action" type="select" optional="true" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
+    <param argument="-unmatched_action" type="select" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
       <option value="error" selected="true">error</option>
       <option value="warn">warn</option>
       <option value="remove">remove</option>
       <expand macro="list_string_san" name="unmatched_action"/>
     </param>
-    <param argument="-aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
-    <param argument="-mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
+    <param argument="-aaa_max" type="integer" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
+    <param argument="-mismatches_max" type="integer" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
     <param argument="-IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/>
+    <param argument="-allow_nterm_protein_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Allow the protein N-terminus amino acid to clip" help=""/>
     <section name="enzyme" title="" help="" expanded="false">
-      <param name="name" argument="-enzyme:name" type="select" optional="true" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
+      <param name="name" argument="-enzyme:name" type="select" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
         <option value="auto" selected="true">auto</option>
+        <option value="Trypsin">Trypsin</option>
         <option value="Arg-C">Arg-C</option>
+        <option value="cyanogen-bromide">cyanogen-bromide</option>
+        <option value="Clostripain/P">Clostripain/P</option>
+        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+        <option value="no cleavage">no cleavage</option>
+        <option value="unspecific cleavage">unspecific cleavage</option>
+        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+        <option value="2-iodobenzoate">2-iodobenzoate</option>
+        <option value="iodosobenzoate">iodosobenzoate</option>
+        <option value="staphylococcal protease/D">staphylococcal protease/D</option>
+        <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
+        <option value="Glu-C+P">Glu-C+P</option>
+        <option value="PepsinA + P">PepsinA + P</option>
+        <option value="Trypsin/P">Trypsin/P</option>
+        <option value="V8-DE">V8-DE</option>
         <option value="Arg-C/P">Arg-C/P</option>
         <option value="Asp-N">Asp-N</option>
         <option value="Asp-N/B">Asp-N/B</option>
@@ -89,31 +105,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Formic_acid">Formic_acid</option>
         <option value="Lys-C">Lys-C</option>
         <option value="Lys-N">Lys-N</option>
-        <option value="Trypsin/P">Trypsin/P</option>
-        <option value="V8-DE">V8-DE</option>
-        <option value="V8-E">V8-E</option>
-        <option value="leukocyte elastase">leukocyte elastase</option>
-        <option value="proline endopeptidase">proline endopeptidase</option>
-        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
-        <option value="2-iodobenzoate">2-iodobenzoate</option>
-        <option value="iodosobenzoate">iodosobenzoate</option>
-        <option value="staphylococcal protease/D">staphylococcal protease/D</option>
-        <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
-        <option value="Glu-C+P">Glu-C+P</option>
-        <option value="PepsinA + P">PepsinA + P</option>
-        <option value="cyanogen-bromide">cyanogen-bromide</option>
-        <option value="Clostripain/P">Clostripain/P</option>
-        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
-        <option value="no cleavage">no cleavage</option>
-        <option value="unspecific cleavage">unspecific cleavage</option>
         <option value="Lys-C/P">Lys-C/P</option>
         <option value="PepsinA">PepsinA</option>
         <option value="TrypChymo">TrypChymo</option>
-        <option value="Trypsin">Trypsin</option>
+        <option value="V8-E">V8-E</option>
+        <option value="leukocyte elastase">leukocyte elastase</option>
+        <option value="proline endopeptidase">proline endopeptidase</option>
         <expand macro="list_string_san" name="name"/>
       </param>
-      <param name="specificity" argument="-enzyme:specificity" type="select" optional="true" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
+      <param name="specificity" argument="-enzyme:specificity" type="select" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
         <option value="auto" selected="true">auto</option>
         <option value="full">full</option>
         <option value="semi">semi</option>
@@ -123,7 +123,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -137,7 +137,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_PeptideIndexer_1 -->
+  <tests>
+    <!-- TOPP_PeptideIndexer_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -145,7 +146,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="PeptideIndexer_1.idXML"/>
       <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_1_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="PeptideIndexer_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="decoy_string" value=""/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="missing_decoy_action" value="error"/>
@@ -156,6 +157,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
+      <param name="allow_nterm_protein_cleavage" value="true"/>
       <section name="enzyme">
         <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
@@ -166,6 +168,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeptideIndexer_2 -->
     <test expect_num_outputs="2">
@@ -175,7 +180,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="PeptideIndexer_1.idXML"/>
       <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_2_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="PeptideIndexer_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="decoy_string" value=""/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="missing_decoy_action" value="error"/>
@@ -186,6 +191,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
+      <param name="allow_nterm_protein_cleavage" value="true"/>
       <section name="enzyme">
         <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
@@ -196,6 +202,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeptideIndexer_3 -->
     <test expect_num_outputs="2">
@@ -205,7 +214,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="PeptideIndexer_1.idXML"/>
       <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_3_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="PeptideIndexer_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="decoy_string" value=""/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="missing_decoy_action" value="error"/>
@@ -216,6 +225,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
+      <param name="allow_nterm_protein_cleavage" value="true"/>
       <section name="enzyme">
         <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
@@ -226,6 +236,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeptideIndexer_4 -->
     <test expect_num_outputs="2">
@@ -235,7 +248,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="PeptideIndexer_1.idXML"/>
       <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_4_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="PeptideIndexer_4_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="decoy_string" value=""/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="missing_decoy_action" value="error"/>
@@ -246,6 +259,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="aaa_max" value="0"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
+      <param name="allow_nterm_protein_cleavage" value="true"/>
       <section name="enzyme">
         <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
@@ -256,6 +270,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeptideIndexer_5 -->
     <test expect_num_outputs="2">
@@ -265,7 +282,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="PeptideIndexer_1.idXML"/>
       <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_5_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="PeptideIndexer_5_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="decoy_string" value=""/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="missing_decoy_action" value="error"/>
@@ -276,6 +293,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
+      <param name="allow_nterm_protein_cleavage" value="true"/>
       <section name="enzyme">
         <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
@@ -286,6 +304,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeptideIndexer_6 -->
     <test expect_num_outputs="2">
@@ -295,7 +316,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="PeptideIndexer_2.idXML"/>
       <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_6_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="PeptideIndexer_6_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="decoy_string" value=""/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="missing_decoy_action" value="error"/>
@@ -306,6 +327,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="aaa_max" value="3"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
+      <param name="allow_nterm_protein_cleavage" value="true"/>
       <section name="enzyme">
         <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
@@ -316,6 +338,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeptideIndexer_7 -->
     <test expect_num_outputs="2">
@@ -325,7 +350,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="PeptideIndexer_3.idXML"/>
       <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_7_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="PeptideIndexer_7_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="decoy_string" value="DECOY_"/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="missing_decoy_action" value="error"/>
@@ -336,6 +361,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
+      <param name="allow_nterm_protein_cleavage" value="true"/>
       <section name="enzyme">
         <param name="name" value="auto"/>
         <param name="specificity" value="full"/>
@@ -346,6 +372,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeptideIndexer_8 -->
     <test expect_num_outputs="2">
@@ -355,7 +384,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="PeptideIndexer_3.idXML"/>
       <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_8_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="PeptideIndexer_8_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="decoy_string" value=""/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="missing_decoy_action" value="error"/>
@@ -366,6 +395,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
+      <param name="allow_nterm_protein_cleavage" value="true"/>
       <section name="enzyme">
         <param name="name" value="auto"/>
         <param name="specificity" value="semi"/>
@@ -376,6 +406,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeptideIndexer_9 -->
     <test expect_num_outputs="2">
@@ -385,7 +418,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="PeptideIndexer_3.idXML"/>
       <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_9_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="PeptideIndexer_9_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="decoy_string" value=""/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="missing_decoy_action" value="error"/>
@@ -396,6 +429,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
+      <param name="allow_nterm_protein_cleavage" value="true"/>
       <section name="enzyme">
         <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
@@ -406,6 +440,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeptideIndexer_10 -->
     <test expect_num_outputs="2">
@@ -415,7 +452,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="PeptideIndexer_10_input.idXML"/>
       <param name="fasta" value="PeptideIndexer_10_input.fasta"/>
-      <output name="out" file="PeptideIndexer_10_output.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="PeptideIndexer_10_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="decoy_string" value=""/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="missing_decoy_action" value="error"/>
@@ -426,6 +463,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="aaa_max" value="3"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="true"/>
+      <param name="allow_nterm_protein_cleavage" value="true"/>
       <section name="enzyme">
         <param name="name" value="auto"/>
         <param name="specificity" value="auto"/>
@@ -436,6 +474,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeptideIndexer_12 -->
     <test expect_num_outputs="2">
@@ -445,7 +486,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="PeptideIndexer_1.idXML"/>
       <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_12_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="PeptideIndexer_12_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="decoy_string" value=""/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="missing_decoy_action" value="error"/>
@@ -456,6 +497,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
+      <param name="allow_nterm_protein_cleavage" value="true"/>
       <section name="enzyme">
         <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
@@ -466,6 +508,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeptideIndexer_13 -->
     <test expect_num_outputs="2">
@@ -473,9 +518,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
-      <param name="in" value="empty.idXML"/>
+      <param name="in" value="empty_0.idXML"/>
       <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_13_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="empty_1.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="decoy_string" value=""/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="missing_decoy_action" value="error"/>
@@ -486,6 +531,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
+      <param name="allow_nterm_protein_cleavage" value="true"/>
       <section name="enzyme">
         <param name="name" value="auto"/>
         <param name="specificity" value="auto"/>
@@ -496,6 +542,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PeptideIndexer_14 -->
     <test expect_num_outputs="2">
@@ -505,7 +554,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="PeptideIndexer_14.idXML"/>
       <param name="fasta" value="PeptideIndexer_2.fasta"/>
-      <output name="out" file="PeptideIndexer_14_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="PeptideIndexer_14_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="decoy_string" value=""/>
       <param name="decoy_string_position" value="prefix"/>
       <param name="missing_decoy_action" value="error"/>
@@ -516,6 +565,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
+      <param name="allow_nterm_protein_cleavage" value="true"/>
       <section name="enzyme">
         <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
@@ -526,11 +576,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Refreshes the protein references for all peptide hits.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PeptideIndexer.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PeptideIndexer.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/PercolatorAdapter.xml b/tools/openms/PercolatorAdapter.xml
index c45d1a70e..53128d1ea 100644
--- a/tools/openms/PercolatorAdapter.xml
+++ b/tools/openms/PercolatorAdapter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [ID Processing]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="PercolatorAdapter" name="PercolatorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Facilitate input to Percolator and reintegrate.</description>
+  <description>Facilitate input to Percolator and reintegrate</description>
   <macros>
     <token name="@EXECUTABLE@">PercolatorAdapter</token>
     <import>macros.xml</import>
@@ -18,23 +17,23 @@
   mkdir in_cond.in &&
   #if $in_cond.in_select == "no"
   mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-  ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+  ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
   #else
-  ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+  cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
   #end if
 #end if
 #if $in_decoy_cond.in_decoy:
   mkdir in_decoy_cond.in_decoy &&
   #if $in_decoy_cond.in_decoy_select == "no"
   mkdir ${' '.join(["'in_decoy_cond.in_decoy/%s'" % (i) for i, f in enumerate($in_decoy_cond.in_decoy) if f])} && 
-  ${' '.join(["ln -s '%s' 'in_decoy_cond.in_decoy/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_decoy_cond.in_decoy) if f])}
+  ${' '.join(["cp '%s' 'in_decoy_cond.in_decoy/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_decoy_cond.in_decoy) if f])}
   #else
-  ln -s '$in_decoy_cond.in_decoy' 'in_decoy_cond.in_decoy/${re.sub("[^\w\-_]", "_", $in_decoy_cond.in_decoy.element_identifier)}.$gxy2omsext($in_decoy_cond.in_decoy.ext)' &&
+  cp '$in_decoy_cond.in_decoy' 'in_decoy_cond.in_decoy/${re.sub("[^\w\-_]", "_", $in_decoy_cond.in_decoy.element_identifier)}.$gxy2omsext($in_decoy_cond.in_decoy.ext)' &&
   #end if
 #end if
 #if $in_osw:
   mkdir in_osw &&
-  ln -s '$in_osw' 'in_osw/${re.sub("[^\w\-_]", "_", $in_osw.element_identifier)}.$gxy2omsext($in_osw.ext)' &&
+  cp '$in_osw' 'in_osw/${re.sub("[^\w\-_]", "_", $in_osw.element_identifier)}.$gxy2omsext($in_osw.ext)' &&
 #end if
 mkdir out &&
 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
@@ -55,15 +54,17 @@ mkdir out &&
 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir weights &&
 #end if
+## advanced options
   #if $adv_opts.init_weights:
     mkdir adv_opts.init_weights &&
-    ln -s '$adv_opts.init_weights' 'adv_opts.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts.init_weights.element_identifier)}.$gxy2omsext($adv_opts.init_weights.ext)' &&
+    cp '$adv_opts.init_weights' 'adv_opts.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts.init_weights.element_identifier)}.$gxy2omsext($adv_opts.init_weights.ext)' &&
   #end if
   #if $adv_opts.fasta:
     mkdir adv_opts.fasta &&
-    ln -s '$adv_opts.fasta' 'adv_opts.fasta/${re.sub("[^\w\-_]", "_", $adv_opts.fasta.element_identifier)}.$gxy2omsext($adv_opts.fasta.ext)' &&
+    cp '$adv_opts.fasta' 'adv_opts.fasta/${re.sub("[^\w\-_]", "_", $adv_opts.fasta.element_identifier)}.$gxy2omsext($adv_opts.fasta.ext)' &&
   #end if
 
+
 ## Main program call
 
 set -o pipefail &&
@@ -116,6 +117,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   -weights
   'weights/output.${gxy2omsext("tabular")}'
 #end if
+## advanced options
   #if $adv_opts.init_weights:
     -init_weights
     'adv_opts.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts.init_weights.element_identifier)}.$gxy2omsext($adv_opts.init_weights.ext)'
@@ -124,6 +126,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     -fasta
     'adv_opts.fasta/${re.sub("[^\w\-_]", "_", $adv_opts.fasta.element_identifier)}.$gxy2omsext($adv_opts.fasta.ext)'
   #end if
+
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
 #end if
@@ -165,7 +168,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param argument="-in" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
+        <param argument="-in" type="data" format="idxml,mzid" optional="true" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
       </when>
     </conditional>
     <conditional name="in_decoy_cond">
@@ -177,17 +180,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param argument="-in_decoy" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input decoy file(s) in case of separate searches" help=" select idxml,mzid data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in_decoy" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input decoy file(s) in case of separate searches" help=" select idxml,mzid data sets(s)"/>
+        <param argument="-in_decoy" type="data" format="idxml,mzid" optional="true" label="Input decoy file(s) in case of separate searches" help=" select idxml,mzid data sets(s)"/>
       </when>
     </conditional>
     <param argument="-in_osw" type="data" format="osw" optional="true" label="Input file in OSW format" help=" select osw data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
+    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
       <option value="idXML">idxml</option>
       <option value="mzid">mzid</option>
       <option value="osw">osw</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param argument="-enzyme" type="select" optional="true" label="Type of enzyme: no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin,trypsinp" help="">
+    <param argument="-enzyme" type="select" label="Type of enzyme: no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin,trypsinp" help="">
       <option value="no_enzyme">no_enzyme</option>
       <option value="elastase">elastase</option>
       <option value="pepsin">pepsin</option>
@@ -205,13 +209,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </param>
     <param argument="-peptide_level_fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculate peptide-level FDRs instead of PSM-level FDRs" help=""/>
     <param argument="-protein_level_fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the picked protein-level FDR to infer protein probabilities" help="Use the -fasta option and -decoy_pattern to set the Fasta file and decoy pattern"/>
-    <param argument="-osw_level" type="select" optional="true" label="OSW: the data level selected for scoring" help="">
+    <param argument="-osw_level" type="select" label="OSW: the data level selected for scoring" help="">
       <option value="ms1">ms1</option>
       <option value="ms2" selected="true">ms2</option>
       <option value="transition">transition</option>
       <expand macro="list_string_san" name="osw_level"/>
     </param>
-    <param argument="-score_type" type="select" optional="true" label="Type of the peptide main score" help="">
+    <param argument="-score_type" type="select" label="Type of the peptide main score" help="">
       <option value="q-value" selected="true">q-value</option>
       <option value="pep">pep</option>
       <option value="svm">svm</option>
@@ -219,37 +223,37 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-generic_feature_set" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use only generic" help="(i.e. not search engine specific) features. Generating search engine specific features for common search engines by PSMFeatureExtractor will typically boost the identification rate significantly"/>
-      <param argument="-subset_max_train" type="integer" optional="true" value="0" label="Only train an SVM on a subset of &lt;x&gt; PSMs, and use the resulting score vector to evaluate the other PSMs" help="Recommended when analyzing huge numbers (&gt;1 million) of PSMs. When set to 0, all PSMs are used for training as normal"/>
-      <param argument="-cpos" type="float" optional="true" value="0.0" label="Cpos, penalty for mistakes made on positive examples" help="Set by cross validation if not specified"/>
-      <param argument="-cneg" type="float" optional="true" value="0.0" label="Cneg, penalty for mistakes made on negative examples" help="Set by cross validation if not specified"/>
-      <param argument="-testFDR" type="float" optional="true" value="0.01" label="False discovery rate threshold for evaluating best cross validation result and the reported end result" help=""/>
-      <param argument="-trainFDR" type="float" optional="true" value="0.01" label="False discovery rate threshold to define positive examples in training" help="Set to testFDR if 0"/>
-      <param argument="-maxiter" type="integer" optional="true" value="10" label="Maximal number of iterations" help=""/>
-      <param argument="-nested_xval_bins" type="integer" optional="true" value="1" label="Number of nested cross-validation bins in the 3 splits" help=""/>
+      <param argument="-subset_max_train" type="integer" value="0" label="Only train an SVM on a subset of &lt;x&gt; PSMs, and use the resulting score vector to evaluate the other PSMs" help="Recommended when analyzing huge numbers (&gt;1 million) of PSMs. When set to 0, all PSMs are used for training as normal"/>
+      <param argument="-cpos" type="float" value="0.0" label="Cpos, penalty for mistakes made on positive examples" help="Set by cross validation if not specified"/>
+      <param argument="-cneg" type="float" value="0.0" label="Cneg, penalty for mistakes made on negative examples" help="Set by cross validation if not specified"/>
+      <param argument="-testFDR" type="float" value="0.01" label="False discovery rate threshold for evaluating best cross validation result and the reported end result" help=""/>
+      <param argument="-trainFDR" type="float" value="0.01" label="False discovery rate threshold to define positive examples in training" help="Set to testFDR if 0"/>
+      <param argument="-maxiter" type="integer" value="10" label="Maximal number of iterations" help=""/>
+      <param argument="-nested_xval_bins" type="integer" value="1" label="Number of nested cross-validation bins in the 3 splits" help=""/>
       <param argument="-quick_validation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Quicker execution by reduced internal cross-validation" help=""/>
       <param argument="-init_weights" type="data" format="tabular" optional="true" label="Read initial weights to the given file" help=" select tabular data sets(s)"/>
       <param argument="-static" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use static model (requires init-weights parameter to be set)" help=""/>
       <param argument="-default_direction" type="text" optional="true" value="" label="The most informative feature given as the feature name, can be negated to indicate that a lower value is bette" help="">
         <expand macro="list_string_san" name="default_direction"/>
       </param>
-      <param argument="-verbose" type="integer" optional="true" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help=""/>
+      <param argument="-verbose" type="integer" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help=""/>
       <param argument="-unitnorm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use unit normalization [0-1] instead of standard deviation normalization" help=""/>
       <param argument="-test_each_iteration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Measure performance on test set each iteration" help=""/>
       <param argument="-override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Override error check and do not fall back on default score vector in case of suspect score vecto" help=""/>
-      <param argument="-seed" type="integer" optional="true" value="1" label="Setting seed of the random number generato" help=""/>
-      <param argument="-doc" type="integer" optional="true" value="0" label="Include description of correct features" help=""/>
+      <param argument="-seed" type="integer" value="1" label="Setting seed of the random number generato" help=""/>
+      <param argument="-doc" type="integer" value="0" label="Include description of correct features" help=""/>
       <param argument="-klammer" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Retention time features calculated as in Klammer et al" help="Only available if -doc is set"/>
       <param argument="-fasta" type="data" format="fasta" optional="true" label="Provide the fasta file as the argument to this flag, which will be used for protein grouping based on an in-silico digest (only valid if option -protein_level_fdrs is active)" help=" select fasta data sets(s)"/>
-      <param argument="-decoy_pattern" type="text" optional="true" value="random" label="Define the text pattern to identify the decoy proteins and/or PSMs, set this up if the label that identifies the decoys in the database is not the default (Only valid if option -protein_level_fdrs is active)" help="">
+      <param argument="-decoy_pattern" type="text" value="random" label="Define the text pattern to identify the decoy proteins and/or PSMs, set this up if the label that identifies the decoys in the database is not the default (Only valid if option -protein_level_fdrs is active)" help="">
         <expand macro="list_string_san" name="decoy_pattern"/>
       </param>
       <param argument="-post_processing_tdc" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use target-decoy competition to assign q-values and PEPs" help=""/>
       <param argument="-train_best_positive" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enforce that, for each spectrum, at most one PSM is included in the positive set during each training iteration" help="If the user only provides one PSM per spectrum, this filter will have no effect"/>
-      <param argument="-ipf_max_peakgroup_pep" type="float" optional="true" value="0.7" label="OSW/IPF: Assess transitions only for candidate peak groups until maximum posterior error probability" help=""/>
-      <param argument="-ipf_max_transition_isotope_overlap" type="float" optional="true" value="0.5" label="OSW/IPF: Maximum isotope overlap to consider transitions in IPF" help=""/>
-      <param argument="-ipf_min_transition_sn" type="float" optional="true" value="0.0" label="OSW/IPF: Minimum log signal-to-noise level to consider transitions in IPF" help="Set -1 to disable this filter"/>
+      <param argument="-ipf_max_peakgroup_pep" type="float" value="0.7" label="OSW/IPF: Assess transitions only for candidate peak groups until maximum posterior error probability" help=""/>
+      <param argument="-ipf_max_transition_isotope_overlap" type="float" value="0.5" label="OSW/IPF: Maximum isotope overlap to consider transitions in IPF" help=""/>
+      <param argument="-ipf_min_transition_sn" type="float" value="0.0" label="OSW/IPF: Minimum log signal-to-noise level to consider transitions in IPF" help="Set -1 to disable this filter"/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -292,7 +296,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_PercolatorAdapter_1 -->
+  <tests>
+    <!-- TOPP_PercolatorAdapter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="generic_feature_set" value="false"/>
@@ -325,7 +330,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <conditional name="in_cond">
         <param name="in" value="PercolatorAdapter_1.idXML"/>
       </conditional>
-      <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="PercolatorAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="enzyme" value="trypsin"/>
       <param name="peptide_level_fdrs" value="false"/>
@@ -338,6 +343,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PercolatorAdapter_2 -->
     <test expect_num_outputs="2">
@@ -370,7 +378,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in_osw" value="PercolatorAdapter_2.osw"/>
-      <output name="out" file="PercolatorAdapter_2_out1.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
+      <output name="out" value="PercolatorAdapter_2_out1.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
       <param name="out_type" value="osw"/>
       <param name="enzyme" value="trypsin"/>
       <param name="peptide_level_fdrs" value="false"/>
@@ -383,6 +391,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PercolatorAdapter_3 -->
     <test expect_num_outputs="2">
@@ -415,7 +426,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in_osw" value="PercolatorAdapter_2_out1.osw"/>
-      <output name="out" file="PercolatorAdapter_3_out1.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
+      <output name="out" value="PercolatorAdapter_3_out1.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
       <param name="out_type" value="osw"/>
       <param name="enzyme" value="trypsin"/>
       <param name="peptide_level_fdrs" value="false"/>
@@ -428,6 +439,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PercolatorAdapter_4 -->
     <test expect_num_outputs="2">
@@ -460,7 +474,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in_osw" value="PercolatorAdapter_3_out1.osw"/>
-      <output name="out" file="PercolatorAdapter_4_out1.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
+      <output name="out" value="PercolatorAdapter_4_out1.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
       <param name="out_type" value="osw"/>
       <param name="enzyme" value="trypsin"/>
       <param name="peptide_level_fdrs" value="false"/>
@@ -473,6 +487,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_PercolatorAdapter_5 -->
     <test expect_num_outputs="3">
@@ -507,8 +524,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <conditional name="in_cond">
         <param name="in" value="PercolatorAdapter_1.idXML"/>
       </conditional>
-      <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <output name="out_pin" file="PercolatorAdapter_1_out1.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="PercolatorAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out_pin" value="PercolatorAdapter_1_out1.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="out_type" value="idXML"/>
       <param name="enzyme" value="trypsin"/>
       <param name="peptide_level_fdrs" value="false"/>
@@ -521,11 +538,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Facilitate input to Percolator and reintegrate.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PercolatorAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PercolatorAdapter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/PhosphoScoring.xml b/tools/openms/PhosphoScoring.xml
index 57a12af3a..438eb5a43 100644
--- a/tools/openms/PhosphoScoring.xml
+++ b/tools/openms/PhosphoScoring.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [ID Processing]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="PhosphoScoring" name="PhosphoScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Scores potential phosphorylation sites in order to localize the most probable sites.</description>
+  <description>Scores potential phosphorylation sites in order to localize the most probable sites</description>
   <macros>
     <token name="@EXECUTABLE@">PhosphoScoring</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir id &&
-ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
+cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -43,20 +42,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file with MS/MS spectra" help=" select mzml data sets(s)"/>
-    <param argument="-id" type="data" format="idxml" optional="false" label="Identification input file which contains a search against a concatenated sequence database" help=" select idxml data sets(s)"/>
-    <param argument="-fragment_mass_tolerance" type="float" optional="true" min="0.0" value="0.05" label="Fragment mass tolerance for spectrum comparisons" help=""/>
-    <param argument="-fragment_mass_unit" type="select" optional="true" label="Unit of fragment mass tolerance" help="">
+    <param argument="-in" type="data" format="mzml" label="Input file with MS/MS spectra" help=" select mzml data sets(s)"/>
+    <param argument="-id" type="data" format="idxml" label="Identification input file which contains a search against a concatenated sequence database" help=" select idxml data sets(s)"/>
+    <param argument="-fragment_mass_tolerance" type="float" min="0.0" value="0.05" label="Fragment mass tolerance for spectrum comparisons" help=""/>
+    <param argument="-fragment_mass_unit" type="select" label="Unit of fragment mass tolerance" help="">
       <option value="Da" selected="true">Da</option>
       <option value="ppm">ppm</option>
       <expand macro="list_string_san" name="fragment_mass_unit"/>
     </param>
     <expand macro="adv_opts_macro">
-      <param argument="-max_peptide_length" type="integer" optional="true" min="0" value="40" label="Restrict scoring to peptides with a length no greater than this value ('0' for 'no restriction')" help=""/>
-      <param argument="-max_num_perm" type="integer" optional="true" min="0" value="16384" label="Maximum number of permutations a sequence can have to be processed ('0' for 'no restriction')" help=""/>
-      <param argument="-unambiguous_score" type="integer" optional="true" value="1000" label="Score to use for unambiguous assignments, where all sites on a peptide are phosphorylated" help="(Note: If a peptide is not phosphorylated at all, its score is set to '-1'.)"/>
+      <param argument="-max_peptide_length" type="integer" min="0" value="40" label="Restrict scoring to peptides with a length no greater than this value ('0' for 'no restriction')" help=""/>
+      <param argument="-max_num_perm" type="integer" min="0" value="16384" label="Maximum number of permutations a sequence can have to be processed ('0' for 'no restriction')" help=""/>
+      <param argument="-unambiguous_score" type="integer" value="1000" label="Score to use for unambiguous assignments, where all sites on a peptide are phosphorylated" help="(Note: If a peptide is not phosphorylated at all, its score is set to '-1'.)"/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -70,16 +69,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="spectra.mzML"/>
-    <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/>
-    <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- same input as used in the MSGF+Adapter -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="mzml" value="spectra.mzML"/>
+      <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/>
+      <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/>
+    </test>
+  </tests>
   <help><![CDATA[Scores potential phosphorylation sites in order to localize the most probable sites.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PhosphoScoring.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PhosphoScoring.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/PrecursorIonSelector.xml b/tools/openms/PrecursorIonSelector.xml
deleted file mode 100644
index 119f5adc0..000000000
--- a/tools/openms/PrecursorIonSelector.xml
+++ /dev/null
@@ -1,378 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Targeted Experiments]-->
-<tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>PrecursorIonSelector</description>
-  <macros>
-    <token name="@EXECUTABLE@">PrecursorIonSelector</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out &&
-#end if
-#if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir next_feat &&
-#end if
-mkdir ids &&
-ln -s '$ids' 'ids/${re.sub("[^\w\-_]", "_", $ids.element_identifier)}.$gxy2omsext($ids.ext)' &&
-#if $raw_data:
-  mkdir raw_data &&
-  ln -s '$raw_data' 'raw_data/${re.sub("[^\w\-_]", "_", $raw_data.element_identifier)}.$gxy2omsext($raw_data.ext)' &&
-#end if
-#if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir sim_results &&
-#end if
-#if $db_path:
-  mkdir db_path &&
-  ln -s '$db_path' 'db_path/${re.sub("[^\w\-_]", "_", $db_path.element_identifier)}.$gxy2omsext($db_path.ext)' &&
-#end if
-#if $rt_model:
-  mkdir rt_model &&
-  ln -s '$rt_model' 'rt_model/${re.sub("[^\w\-_]", "_", $rt_model.element_identifier)}.$gxy2omsext($rt_model.ext)' &&
-#end if
-#if $dt_model:
-  mkdir dt_model &&
-  ln -s '$dt_model' 'dt_model/${re.sub("[^\w\-_]", "_", $dt_model.element_identifier)}.$gxy2omsext($dt_model.ext)' &&
-#end if
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in
-'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out
-  'out/output.${gxy2omsext("featurexml")}'
-#end if
-#if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -next_feat
-  'next_feat/output.${gxy2omsext("featurexml")}'
-#end if
--ids
-'ids/${re.sub("[^\w\-_]", "_", $ids.element_identifier)}.$gxy2omsext($ids.ext)'
-#if $raw_data:
-  -raw_data
-  'raw_data/${re.sub("[^\w\-_]", "_", $raw_data.element_identifier)}.$gxy2omsext($raw_data.ext)'
-#end if
-#if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -sim_results
-  'sim_results/output.${gxy2omsext("txt")}'
-#end if
-#if $db_path:
-  -db_path
-  'db_path/${re.sub("[^\w\-_]", "_", $db_path.element_identifier)}.$gxy2omsext($db_path.ext)'
-#end if
-#if $rt_model:
-  -rt_model
-  'rt_model/${re.sub("[^\w\-_]", "_", $rt_model.element_identifier)}.$gxy2omsext($rt_model.ext)'
-#end if
-#if $dt_model:
-  -dt_model
-  'dt_model/${re.sub("[^\w\-_]", "_", $dt_model.element_identifier)}.$gxy2omsext($dt_model.ext)'
-#end if
-#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
-  | tee '$stdout'
-#end if
-
-## Postprocessing
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
-#end if
-#if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'next_feat/output.${gxy2omsext("featurexml")}' '$next_feat'
-#end if
-#if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'sim_results/output.${gxy2omsext("txt")}' '$sim_results'
-#end if
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "algorithm": {"Preprocessing": {"tmp_dir": "\$TMP_DIR"}}}]]></configfile>
-  </configfiles>
-  <inputs>
-    <param argument="-in" type="data" format="featurexml" optional="false" label="Input feature map file (featureXML)" help=" select featurexml data sets(s)"/>
-    <param argument="-ids" type="data" format="idxml" optional="false" label="file containing results of identification" help=" select idxml data sets(s)"/>
-    <param argument="-num_precursors" type="integer" optional="true" value="1" label="number of precursors to be selected" help=""/>
-    <param argument="-raw_data" type="data" format="mzml" optional="true" label="Input profile data" help=" select mzml data sets(s)"/>
-    <param argument="-load_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is loaded from file, not calculated" help=""/>
-    <param argument="-store_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is stored" help=""/>
-    <param argument="-simulation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Simulate the whole LC-MS/MS run" help=""/>
-    <param argument="-db_path" type="data" format="fasta" optional="true" label="db file" help=" select fasta data sets(s)"/>
-    <param argument="-rt_model" type="data" format="txt" optional="true" label="SVM Model for RTPredict" help=" select txt data sets(s)"/>
-    <param argument="-dt_model" type="data" format="txt" optional="true" label="SVM Model for PTPredict" help=" select txt data sets(s)"/>
-    <param argument="-fixed_modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
-      <expand macro="list_string_val" name="fixed_modifications"/>
-      <expand macro="list_string_san" name="fixed_modifications"/>
-    </param>
-    <section name="algorithm" title="Settings for the compound list creation and rescoring" help="" expanded="false">
-      <param name="type" argument="-algorithm:type" type="select" optional="true" label="Strategy for precursor ion selection" help="">
-        <option value="ILP_IPS">ILP_IPS</option>
-        <option value="IPS" selected="true">IPS</option>
-        <option value="SPS">SPS</option>
-        <option value="Upshift">Upshift</option>
-        <option value="Downshift">Downshift</option>
-        <option value="DEX">DEX</option>
-        <expand macro="list_string_san" name="type"/>
-      </param>
-      <param name="max_iteration" argument="-algorithm:max_iteration" type="integer" optional="true" min="1" value="100" label="Maximal number of iterations" help=""/>
-      <param name="rt_bin_capacity" argument="-algorithm:rt_bin_capacity" type="integer" optional="true" min="1" value="10" label="Maximal number of precursors per rt bin" help=""/>
-      <param name="step_size" argument="-algorithm:step_size" type="integer" optional="true" min="1" value="1" label="Maximal number of precursors per iteration" help=""/>
-      <param name="peptide_min_prob" argument="-algorithm:peptide_min_prob" type="float" optional="true" value="0.2" label="Minimal peptide probability" help=""/>
-      <param name="sequential_spectrum_order" argument="-algorithm:sequential_spectrum_order" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, precursors are selected sequentially with respect to their RT" help=""/>
-      <section name="MIPFormulation" title="" help="" expanded="false">
-        <section name="thresholds" title="" help="" expanded="false">
-          <param name="min_protein_probability" argument="-algorithm:MIPFormulation:thresholds:min_protein_probability" type="float" optional="true" min="0.0" max="1.0" value="0.2" label="Minimal protein probability for a protein to be considered in the ILP" help=""/>
-          <param name="min_protein_id_probability" argument="-algorithm:MIPFormulation:thresholds:min_protein_id_probability" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="Minimal protein probability for a protein to be considered identified" help=""/>
-          <param name="min_pt_weight" argument="-algorithm:MIPFormulation:thresholds:min_pt_weight" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Minimal pt weight of a precurso" help=""/>
-          <param name="min_mz" argument="-algorithm:MIPFormulation:thresholds:min_mz" type="float" optional="true" min="0.0" value="500.0" label="Minimal mz to be considered in protein based LP formulation" help=""/>
-          <param name="max_mz" argument="-algorithm:MIPFormulation:thresholds:max_mz" type="float" optional="true" min="0.0" value="5000.0" label="Minimal mz to be considered in protein based LP formulation" help=""/>
-          <param name="min_pred_pep_prob" argument="-algorithm:MIPFormulation:thresholds:min_pred_pep_prob" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Minimal predicted peptide probability of a precurso" help=""/>
-          <param name="min_rt_weight" argument="-algorithm:MIPFormulation:thresholds:min_rt_weight" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Minimal rt weight of a precurso" help=""/>
-          <param name="use_peptide_rule" argument="-algorithm:MIPFormulation:thresholds:use_peptide_rule" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use peptide rule instead of minimal protein id probability" help=""/>
-          <param name="min_peptide_ids" argument="-algorithm:MIPFormulation:thresholds:min_peptide_ids" type="integer" optional="true" min="1" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help=""/>
-          <param name="min_peptide_probability" argument="-algorithm:MIPFormulation:thresholds:min_peptide_probability" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help=""/>
-        </section>
-        <section name="combined_ilp" title="" help="" expanded="false">
-          <param name="k1" argument="-algorithm:MIPFormulation:combined_ilp:k1" type="float" optional="true" min="0.0" value="0.2" label="combined ilp: weight for z_i" help=""/>
-          <param name="k2" argument="-algorithm:MIPFormulation:combined_ilp:k2" type="float" optional="true" min="0.0" value="0.2" label="combined ilp: weight for x_j,s*int_j,s" help=""/>
-          <param name="k3" argument="-algorithm:MIPFormulation:combined_ilp:k3" type="float" optional="true" min="0.0" value="0.4" label="combined ilp: weight for -x_j,s*w_j,s" help=""/>
-          <param name="scale_matching_probs" argument="-algorithm:MIPFormulation:combined_ilp:scale_matching_probs" type="boolean" truevalue="true" falsevalue="false" checked="true" label="flag if detectability * rt_weight shall be scaled to cover all [0,1]" help=""/>
-        </section>
-        <section name="feature_based" title="" help="" expanded="false">
-          <param name="no_intensity_normalization" argument="-algorithm:MIPFormulation:feature_based:no_intensity_normalization" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag indicating if intensities shall be scaled to be in [0,1]" help="This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1"/>
-          <param name="max_number_precursors_per_feature" argument="-algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature" type="integer" optional="true" min="1" value="1" label="The maximal number of precursors per feature" help=""/>
-        </section>
-      </section>
-      <section name="Preprocessing" title="" help="" expanded="false">
-        <param name="precursor_mass_tolerance" argument="-algorithm:Preprocessing:precursor_mass_tolerance" type="float" optional="true" min="0.0" value="10.0" label="Precursor mass tolerance which is used to query the peptide database for peptides" help=""/>
-        <param name="precursor_mass_tolerance_unit" argument="-algorithm:Preprocessing:precursor_mass_tolerance_unit" type="select" optional="true" label="Precursor mass tolerance unit" help="">
-          <option value="ppm" selected="true">ppm</option>
-          <option value="Da">Da</option>
-          <expand macro="list_string_san" name="precursor_mass_tolerance_unit"/>
-        </param>
-        <param name="preprocessed_db_path" argument="-algorithm:Preprocessing:preprocessed_db_path" type="text" optional="true" value="" label="Path where the preprocessed database should be stored" help="">
-          <expand macro="list_string_san" name="preprocessed_db_path"/>
-        </param>
-        <param name="preprocessed_db_pred_rt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_rt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help="">
-          <expand macro="list_string_san" name="preprocessed_db_pred_rt_path"/>
-        </param>
-        <param name="preprocessed_db_pred_dt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_dt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help="">
-          <expand macro="list_string_san" name="preprocessed_db_pred_dt_path"/>
-        </param>
-        <param name="max_peptides_per_run" argument="-algorithm:Preprocessing:max_peptides_per_run" type="integer" optional="true" min="1" value="100000" label="Number of peptides for that the pt and rt are parallelly predicted" help=""/>
-        <param name="missed_cleavages" argument="-algorithm:Preprocessing:missed_cleavages" type="integer" optional="true" min="0" value="1" label="Number of allowed missed cleavages" help=""/>
-        <param name="taxonomy" argument="-algorithm:Preprocessing:taxonomy" type="text" optional="true" value="" label="Taxonomy" help="">
-          <expand macro="list_string_san" name="taxonomy"/>
-        </param>
-        <param name="store_peptide_sequences" argument="-algorithm:Preprocessing:store_peptide_sequences" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag if peptide sequences should be stored" help=""/>
-        <section name="rt_settings" title="" help="" expanded="false">
-          <param name="min_rt" argument="-algorithm:Preprocessing:rt_settings:min_rt" type="float" optional="true" min="1.0" value="960.0" label="Minimal RT in the experiment (in seconds)" help=""/>
-          <param name="max_rt" argument="-algorithm:Preprocessing:rt_settings:max_rt" type="float" optional="true" value="3840.0" label="Maximal RT in the experiment (in seconds)" help=""/>
-          <param name="rt_step_size" argument="-algorithm:Preprocessing:rt_settings:rt_step_size" type="float" optional="true" value="30.0" label="Time between two consecutive spectra (in seconds)" help=""/>
-          <param name="gauss_mean" argument="-algorithm:Preprocessing:rt_settings:gauss_mean" type="float" optional="true" value="-1.0" label="mean of the gauss curve" help=""/>
-          <param name="gauss_sigma" argument="-algorithm:Preprocessing:rt_settings:gauss_sigma" type="float" optional="true" value="3.0" label="std of the gauss curve" help=""/>
-        </section>
-      </section>
-    </section>
-    <expand macro="adv_opts_macro">
-      <param argument="-solver" type="select" optional="true" label="LP solver type" help="">
-        <option value="GLPK" selected="true">GLPK</option>
-        <option value="COINOR">COINOR</option>
-        <expand macro="list_string_san" name="solver"/>
-      </param>
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="out_FLAG">out (modified feature map)</option>
-      <option value="next_feat_FLAG">next_feat (feature map (featureXML) file with the selected precursors)</option>
-      <option value="sim_results_FLAG">sim_results (File containing the results of the simulation run)</option>
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="next_feat" label="${tool.name} on ${on_string}: next_feat" format="featurexml">
-      <filter>OPTIONAL_OUTPUTS is not None and "next_feat_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="sim_results" label="${tool.name} on ${on_string}: sim_results" format="txt">
-      <filter>OPTIONAL_OUTPUTS is not None and "sim_results_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
-      <filter>OPTIONAL_OUTPUTS is None</filter>
-    </data>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><!-- TOPP_PrecursorIonSelector_1 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="solver" value="GLPK"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="PrecursorIonSelector_features.featureXML"/>
-      <param name="ids" value="PrecursorIonSelector_ids.idXML"/>
-      <param name="num_precursors" value="1"/>
-      <param name="load_preprocessing" value="false"/>
-      <param name="store_preprocessing" value="false"/>
-      <param name="simulation" value="true"/>
-      <output name="sim_results" file="PrecursorIonSelector_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
-      <param name="db_path" value="PrecursorIonSelector_db.fasta"/>
-      <param name="fixed_modifications" value=""/>
-      <section name="algorithm">
-        <param name="type" value="IPS"/>
-        <param name="max_iteration" value="10"/>
-        <param name="rt_bin_capacity" value="10"/>
-        <param name="step_size" value="1"/>
-        <param name="peptide_min_prob" value="0.2"/>
-        <param name="sequential_spectrum_order" value="false"/>
-        <section name="MIPFormulation">
-          <section name="thresholds">
-            <param name="min_protein_probability" value="0.2"/>
-            <param name="min_protein_id_probability" value="0.95"/>
-            <param name="min_pt_weight" value="0.5"/>
-            <param name="min_mz" value="500.0"/>
-            <param name="max_mz" value="5000.0"/>
-            <param name="min_pred_pep_prob" value="0.5"/>
-            <param name="min_rt_weight" value="0.5"/>
-            <param name="use_peptide_rule" value="true"/>
-            <param name="min_peptide_ids" value="2"/>
-            <param name="min_peptide_probability" value="0.95"/>
-          </section>
-          <section name="combined_ilp">
-            <param name="k1" value="0.2"/>
-            <param name="k2" value="0.2"/>
-            <param name="k3" value="0.4"/>
-            <param name="scale_matching_probs" value="true"/>
-          </section>
-          <section name="feature_based">
-            <param name="no_intensity_normalization" value="false"/>
-            <param name="max_number_precursors_per_feature" value="1"/>
-          </section>
-        </section>
-        <section name="Preprocessing">
-          <param name="precursor_mass_tolerance" value="0.9"/>
-          <param name="precursor_mass_tolerance_unit" value="Da"/>
-          <param name="preprocessed_db_path" value=""/>
-          <param name="preprocessed_db_pred_rt_path" value=""/>
-          <param name="preprocessed_db_pred_dt_path" value=""/>
-          <param name="max_peptides_per_run" value="100000"/>
-          <param name="missed_cleavages" value="1"/>
-          <param name="taxonomy" value=""/>
-          <param name="store_peptide_sequences" value="false"/>
-          <section name="rt_settings">
-            <param name="min_rt" value="960.0"/>
-            <param name="max_rt" value="3840.0"/>
-            <param name="rt_step_size" value="30.0"/>
-            <param name="gauss_mean" value="-1.0"/>
-            <param name="gauss_sigma" value="3.0"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,sim_results_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_PrecursorIonSelector_2 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="solver" value="GLPK"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="PrecursorIonSelector_features.featureXML"/>
-      <output name="out" file="PrecursorIonSelector_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <param name="ids" value="PrecursorIonSelector_ids.idXML"/>
-      <param name="num_precursors" value="1"/>
-      <param name="load_preprocessing" value="false"/>
-      <param name="store_preprocessing" value="false"/>
-      <param name="simulation" value="false"/>
-      <param name="db_path" value="PrecursorIonSelector_db.fasta"/>
-      <param name="fixed_modifications" value=""/>
-      <section name="algorithm">
-        <param name="type" value="IPS"/>
-        <param name="max_iteration" value="10"/>
-        <param name="rt_bin_capacity" value="10"/>
-        <param name="step_size" value="1"/>
-        <param name="peptide_min_prob" value="0.2"/>
-        <param name="sequential_spectrum_order" value="false"/>
-        <section name="MIPFormulation">
-          <section name="thresholds">
-            <param name="min_protein_probability" value="0.2"/>
-            <param name="min_protein_id_probability" value="0.95"/>
-            <param name="min_pt_weight" value="0.5"/>
-            <param name="min_mz" value="500.0"/>
-            <param name="max_mz" value="5000.0"/>
-            <param name="min_pred_pep_prob" value="0.5"/>
-            <param name="min_rt_weight" value="0.5"/>
-            <param name="use_peptide_rule" value="true"/>
-            <param name="min_peptide_ids" value="2"/>
-            <param name="min_peptide_probability" value="0.95"/>
-          </section>
-          <section name="combined_ilp">
-            <param name="k1" value="0.2"/>
-            <param name="k2" value="0.2"/>
-            <param name="k3" value="0.4"/>
-            <param name="scale_matching_probs" value="true"/>
-          </section>
-          <section name="feature_based">
-            <param name="no_intensity_normalization" value="false"/>
-            <param name="max_number_precursors_per_feature" value="1"/>
-          </section>
-        </section>
-        <section name="Preprocessing">
-          <param name="precursor_mass_tolerance" value="0.9"/>
-          <param name="precursor_mass_tolerance_unit" value="Da"/>
-          <param name="preprocessed_db_path" value=""/>
-          <param name="preprocessed_db_pred_rt_path" value=""/>
-          <param name="preprocessed_db_pred_dt_path" value=""/>
-          <param name="max_peptides_per_run" value="100000"/>
-          <param name="missed_cleavages" value="1"/>
-          <param name="taxonomy" value=""/>
-          <param name="store_peptide_sequences" value="false"/>
-          <section name="rt_settings">
-            <param name="min_rt" value="960.0"/>
-            <param name="max_rt" value="3840.0"/>
-            <param name="rt_step_size" value="30.0"/>
-            <param name="gauss_mean" value="-1.0"/>
-            <param name="gauss_sigma" value="3.0"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
-  <help><![CDATA[PrecursorIonSelector
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PrecursorIonSelector.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/PrecursorMassCorrector.xml b/tools/openms/PrecursorMassCorrector.xml
index 7e10f33c4..4458c01be 100644
--- a/tools/openms/PrecursorMassCorrector.xml
+++ b/tools/openms/PrecursorMassCorrector.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Mass Correction and Calibration]-->
 <tool id="PrecursorMassCorrector" name="PrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Corrects the precursor entries of MS/MS spectra, by using MS1 information.</description>
+  <description>Corrects the precursor entries of MS/MS spectra, by using MS1 information</description>
   <macros>
     <token name="@EXECUTABLE@">PrecursorMassCorrector</token>
     <import>macros.xml</import>
@@ -15,11 +14,11 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if $feature_in:
   mkdir feature_in &&
-  ln -s '$feature_in' 'feature_in/${re.sub("[^\w\-_]", "_", $feature_in.element_identifier)}.$gxy2omsext($feature_in.ext)' &&
+  cp '$feature_in' 'feature_in/${re.sub("[^\w\-_]", "_", $feature_in.element_identifier)}.$gxy2omsext($feature_in.ext)' &&
 #end if
 
 ## Main program call
@@ -47,14 +46,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input mzML file containing the spectra" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Input mzML file containing the spectra" help=" select mzml data sets(s)"/>
     <param argument="-feature_in" type="data" format="featurexml" optional="true" label="Input featureXML file, containing features; if set, the MS/MS spectra precursor entries" help="will be matched to the feature m/z values if possible select featurexml data sets(s)"/>
-    <param argument="-precursor_mass_tolerance" type="float" optional="true" min="0.0" value="1.5" label="Maximal deviation in Th which is acceptable to be corrected;" help="this value should be set to the instruments selection window"/>
+    <param argument="-precursor_mass_tolerance" type="float" min="0.0" value="1.5" label="Maximal deviation in Th which is acceptable to be corrected;" help="this value should be set to the instruments selection window"/>
     <expand macro="adv_opts_macro">
-      <param argument="-max_charge" type="integer" optional="true" value="3" label="Maximal charge that should be assumed for precursor peaks" help=""/>
-      <param argument="-intensity_threshold" type="float" optional="true" value="-1.0" label="Intensity threshold value for isotope wavelet feature finder, please look at the documentation of the class for details" help=""/>
+      <param argument="-max_charge" type="integer" value="3" label="Maximal charge that should be assumed for precursor peaks" help=""/>
+      <param argument="-intensity_threshold" type="float" value="-1.0" label="Intensity threshold value for isotope wavelet feature finder, please look at the documentation of the class for details" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -68,7 +67,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_PrecursorMassCorrector_1 -->
+  <tests>
+    <!-- TOPP_PrecursorMassCorrector_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="max_charge" value="3"/>
@@ -77,7 +77,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PrecursorMassCorrector_1_input.mzML"/>
-      <output name="out" file="PrecursorMassCorrector_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PrecursorMassCorrector_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="precursor_mass_tolerance" value="1.5"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -85,11 +85,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Corrects the precursor entries of MS/MS spectra, by using MS1 information.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PrecursorMassCorrector.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PrecursorMassCorrector.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/ProteinInference.xml b/tools/openms/ProteinInference.xml
index 7f350ed8c..eb016a50c 100644
--- a/tools/openms/ProteinInference.xml
+++ b/tools/openms/ProteinInference.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="ProteinInference" name="ProteinInference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Protein inference based on an aggregation of the scores of the identified peptides.</description>
+  <description>Protein inference based on an aggregation of the scores of the identified peptides</description>
   <macros>
     <token name="@EXECUTABLE@">ProteinInference</token>
     <import>macros.xml</import>
@@ -17,9 +16,9 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir out &&
 
@@ -54,18 +53,19 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="false" label="input file(s)" help=" select consensusxml,idxml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,idxml" multiple="true" label="input file(s)" help=" select consensusxml,idxml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="consensusxml,idxml" multiple="false" optional="false" label="input file(s)" help=" select consensusxml,idxml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,idxml" label="input file(s)" help=" select consensusxml,idxml data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="output file type" help="">
+    <param argument="-out_type" type="select" label="output file type" help="">
       <option value="consensusXML">consensusxml</option>
       <option value="idXML">idxml</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param argument="-merge_runs" type="select" optional="true" label="If your idXML contains multiple runs, merge them beforehand" help="Otherwise performs inference separately per run">
+    <param argument="-merge_runs" type="select" label="If your idXML contains multiple runs, merge them beforehand" help="Otherwise performs inference separately per run">
       <option value="no">no</option>
       <option value="all" selected="true">all</option>
       <expand macro="list_string_san" name="merge_runs"/>
@@ -76,8 +76,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <param name="allow_disagreeing_settings" argument="-Merging:allow_disagreeing_settings" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force merging of disagreeing runs" help="Use at your own risk"/>
     </section>
     <section name="Algorithm" title="" help="" expanded="false">
-      <param name="min_peptides_per_protein" argument="-Algorithm:min_peptides_per_protein" type="integer" optional="true" min="0" value="1" label="Minimal number of peptides needed for a protein identification" help="If set to zero, unmatched proteins get a score of -Infinity. If bigger than zero, proteins with less peptides are filtered and evidences removed from the PSMs. PSMs that do not reference any proteins anymore are removed but the spectrum info is kept"/>
-      <param name="score_aggregation_method" argument="-Algorithm:score_aggregation_method" type="select" optional="true" label="How to aggregate scores of peptides matching to the same protein?" help="">
+      <param name="min_peptides_per_protein" argument="-Algorithm:min_peptides_per_protein" type="integer" min="0" value="1" label="Minimal number of peptides needed for a protein identification" help="If set to zero, unmatched proteins get a score of -Infinity. If bigger than zero, proteins with less peptides are filtered and evidences removed from the PSMs. PSMs that do not reference any proteins anymore are removed but the spectrum info is kept"/>
+      <param name="score_aggregation_method" argument="-Algorithm:score_aggregation_method" type="select" label="How to aggregate scores of peptides matching to the same protein?" help="">
         <option value="best" selected="true">best</option>
         <option value="product">product</option>
         <option value="sum">sum</option>
@@ -97,13 +97,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <param argument="-picked_decoy_string" type="text" optional="true" value="" label="If using picked protein FDRs, which decoy string was used" help="Leave blank for auto-detection">
         <expand macro="list_string_san" name="picked_decoy_string"/>
       </param>
-      <param argument="-picked_decoy_prefix" type="select" optional="true" label="If using picked protein FDRs, was the decoy string a prefix or suffix" help="Ignored during auto-detection">
+      <param argument="-picked_decoy_prefix" type="select" label="If using picked protein FDRs, was the decoy string a prefix or suffix" help="Ignored during auto-detection">
         <option value="prefix" selected="true">prefix</option>
         <option value="suffix">suffix</option>
         <expand macro="list_string_san" name="picked_decoy_prefix"/>
       </param>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -121,7 +121,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_ProteinInference_1 -->
+  <tests>
+    <!-- TOPP_ProteinInference_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="conservative_fdr" value="true"/>
@@ -134,7 +135,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="ProteinInference_1_input.idXML"/>
       </conditional>
-      <output name="out" file="ProteinInference_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="ProteinInference_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="merge_runs" value="all"/>
       <param name="protein_fdr" value="false"/>
@@ -158,6 +159,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ProteinInference_2 -->
     <test expect_num_outputs="2">
@@ -172,7 +176,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="Epifany_2_input.consensusXML"/>
       </conditional>
-      <output name="out" file="ProteinInference_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="ProteinInference_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="merge_runs" value="all"/>
       <param name="protein_fdr" value="false"/>
@@ -196,6 +200,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ProteinInference_3 -->
     <test expect_num_outputs="2">
@@ -210,7 +217,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <conditional name="in_cond">
         <param name="in" value="MSstatsConverter_3_in.consensusXML"/>
       </conditional>
-      <output name="out" file="ProteinInference_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="ProteinInference_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="merge_runs" value="all"/>
       <param name="protein_fdr" value="true"/>
@@ -234,11 +241,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Protein inference based on an aggregation of the scores of the identified peptides.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinInference.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ProteinInference.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/ProteinQuantifier.xml b/tools/openms/ProteinQuantifier.xml
index 171051408..38c7ea210 100644
--- a/tools/openms/ProteinQuantifier.xml
+++ b/tools/openms/ProteinQuantifier.xml
@@ -1,4 +1,3 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Quantitation]-->
 <tool id="ProteinQuantifier" name="ProteinQuantifier" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
@@ -15,14 +14,14 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #if $protein_groups:
   mkdir protein_groups &&
-  ln -s '$protein_groups' 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' &&
+  cp '$protein_groups' 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' &&
 #end if
 #if $design:
   mkdir design &&
-  ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
+  cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
@@ -84,43 +83,50 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml,featurexml,idxml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
-    <param argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/>
+    <param argument="-in" type="data" format="consensusxml,featurexml,idxml" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
+    <param argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. via the ProteinInference tool).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/>
     <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
-    <param argument="-top" type="integer" optional="true" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/>
-    <param argument="-average" type="select" optional="true" label="Averaging method used to compute protein abundances from peptide abundances" help="">
-      <option value="median" selected="true">median</option>
-      <option value="mean">mean</option>
-      <option value="weighted_mean">weighted_mean</option>
-      <option value="sum">sum</option>
-      <expand macro="list_string_san" name="average"/>
+    <param argument="-method" type="select" label="- top - quantify based on three most abundant peptides (number can be changed in 'top')" help="- iBAQ (intensity based absolute quantification), calculate the sum of all peptide peak intensities divided by the number of theoretically observable tryptic peptides (https://rdcu.be/cND1J). Warning: only consensusXML or featureXML input is allowed!">
+      <option value="top" selected="true">top</option>
+      <option value="iBAQ">iBAQ</option>
+      <expand macro="list_string_san" name="method"/>
     </param>
-    <param argument="-include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help=""/>
     <param argument="-best_charge_and_fraction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Distinguish between fraction and charge states of a peptide" help="For peptides, abundances will be reported separately for each fraction and charge;. for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions).. By default, abundances are summed over all charge states"/>
     <param argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Pre-process identifications with greedy resolution of shared peptides based on the protein group probabilities" help="(Only works with an idXML file given as protein_groups parameter)"/>
     <param argument="-ratios" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios of the abundance values to the output" help="Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) "/>
     <param argument="-ratiosSILAC" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios for a triple SILAC experiment to the output" help="Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)"/>
+    <section name="top" title="Additional options for custom quantification using top N peptides" help="" expanded="false">
+      <param name="N" argument="-top:N" type="integer" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/>
+      <param name="aggregate" argument="-top:aggregate" type="select" label="Aggregation method used to compute protein abundances from peptide abundances" help="">
+        <option value="median" selected="true">median</option>
+        <option value="mean">mean</option>
+        <option value="weighted_mean">weighted_mean</option>
+        <option value="sum">sum</option>
+        <expand macro="list_string_san" name="aggregate"/>
+      </param>
+      <param name="include_all" argument="-top:include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'N' (no effect if 'N' is 0 or 1)" help=""/>
+    </section>
     <section name="consensus" title="Additional options for consensus maps (and identification results comprising multiple runs)" help="" expanded="false">
       <param name="normalize" argument="-consensus:normalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Scale peptide abundances so that medians of all samples are equal" help=""/>
-      <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'top 0',all peptides that occur in every sample are considered.. Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/>
+      <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'N 0',all peptides that occur in every sample are considered.. Otherwise ('N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/>
     </section>
     <section name="format" title="Output formatting options" help="" expanded="false">
       <param name="separator" argument="-format:separator" type="text" optional="true" value="" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="">
         <expand macro="list_string_san" name="separator"/>
       </param>
-      <param name="quoting" argument="-format:quoting" type="select" optional="true" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
+      <param name="quoting" argument="-format:quoting" type="select" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
         <option value="none">none</option>
         <option value="double" selected="true">double</option>
         <option value="escape">escape</option>
         <expand macro="list_string_san" name="quoting"/>
       </param>
-      <param name="replacement" argument="-format:replacement" type="text" optional="true" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="">
+      <param name="replacement" argument="-format:replacement" type="text" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="">
         <expand macro="list_string_san" name="replacement"/>
       </param>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -148,22 +154,26 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_ProteinQuantifier_1 -->
+  <tests>
+    <!-- TOPP_ProteinQuantifier_1 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.featureXML"/>
-      <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="median"/>
-      <param name="include_all" value="false"/>
+      <output name="out" value="ProteinQuantifier_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="peptide_out" value="ProteinQuantifier_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="median"/>
+        <param name="include_all" value="false"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="false"/>
@@ -179,6 +189,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ProteinQuantifier_2 -->
     <test expect_num_outputs="3">
@@ -187,15 +200,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.featureXML"/>
-      <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="2"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
+      <output name="out" value="ProteinQuantifier_2_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="peptide_out" value="ProteinQuantifier_2_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="true"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="2"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="true"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="false"/>
@@ -211,6 +227,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ProteinQuantifier_3 -->
     <test expect_num_outputs="3">
@@ -219,15 +238,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_3_input.featureXML"/>
-      <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="2"/>
-      <param name="average" value="mean"/>
-      <param name="include_all" value="true"/>
+      <output name="out" value="ProteinQuantifier_3_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="peptide_out" value="ProteinQuantifier_3_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="2"/>
+        <param name="aggregate" value="mean"/>
+        <param name="include_all" value="true"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="false"/>
@@ -243,6 +265,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ProteinQuantifier_4 -->
     <test expect_num_outputs="2">
@@ -251,14 +276,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="0"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
+      <output name="out" value="ProteinQuantifier_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="0"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="false"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="false"/>
@@ -274,6 +302,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ProteinQuantifier_5 -->
     <test expect_num_outputs="2">
@@ -282,14 +313,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
+      <output name="out" value="ProteinQuantifier_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="false"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="false"/>
@@ -305,6 +339,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ProteinQuantifier_6 -->
     <test expect_num_outputs="2">
@@ -313,14 +350,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
+      <output name="out" value="ProteinQuantifier_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="true"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="false"/>
@@ -336,6 +376,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ProteinQuantifier_7 -->
     <test expect_num_outputs="2">
@@ -344,14 +387,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="0"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
+      <output name="out" value="ProteinQuantifier_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="0"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="false"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="true"/>
@@ -367,6 +413,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ProteinQuantifier_8 -->
     <test expect_num_outputs="2">
@@ -375,14 +424,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
+      <output name="out" value="ProteinQuantifier_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="false"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="true"/>
@@ -398,6 +450,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ProteinQuantifier_9 -->
     <test expect_num_outputs="3">
@@ -406,15 +461,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
+      <output name="out" value="ProteinQuantifier_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="mztab" value="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="true"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="true"/>
@@ -430,6 +488,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ProteinQuantifier_12 -->
     <test expect_num_outputs="2">
@@ -438,14 +499,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
+      <output name="out" value="ProteinQuantifier_12_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="true"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="true"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="true"/>
@@ -461,6 +525,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ProteinQuantifier_13 -->
     <test expect_num_outputs="2">
@@ -469,14 +536,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
+      <output name="out" value="ProteinQuantifier_13_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="true"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="true"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="true"/>
@@ -492,6 +562,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ProteinQuantifier_14 -->
     <test expect_num_outputs="3">
@@ -500,15 +573,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ProteinQuantifier_input.idXML"/>
-      <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <param name="top" value="0"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
+      <output name="out" value="ProteinQuantifier_14_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="peptide_out" value="ProteinQuantifier_14_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
       <param name="best_charge_and_fraction" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="ratios" value="false"/>
       <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="0"/>
+        <param name="aggregate" value="sum"/>
+        <param name="include_all" value="false"/>
+      </section>
       <section name="consensus">
         <param name="normalize" value="false"/>
         <param name="fix_peptides" value="false"/>
@@ -524,11 +600,89 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_ProteinQuantifier_15 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
+      <output name="out" value="ProteinQuantifier_15_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="iBAQ"/>
+      <param name="best_charge_and_fraction" value="false"/>
+      <param name="greedy_group_resolution" value="false"/>
+      <param name="ratios" value="false"/>
+      <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="median"/>
+        <param name="include_all" value="false"/>
+      </section>
+      <section name="consensus">
+        <param name="normalize" value="false"/>
+        <param name="fix_peptides" value="false"/>
+      </section>
+      <section name="format">
+        <param name="separator" value=""/>
+        <param name="quoting" value="double"/>
+        <param name="replacement" value="_"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_ProteinQuantifier_16 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="ProteinQuantifier_16_input.consensusXML"/>
+      <param name="design" value="ProteinQuantifier_16_input.tsv" ftype="tabular"/>
+      <output name="out" value="ProteinQuantifier_16_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="method" value="top"/>
+      <param name="best_charge_and_fraction" value="false"/>
+      <param name="greedy_group_resolution" value="false"/>
+      <param name="ratios" value="false"/>
+      <param name="ratiosSILAC" value="false"/>
+      <section name="top">
+        <param name="N" value="3"/>
+        <param name="aggregate" value="median"/>
+        <param name="include_all" value="true"/>
+      </section>
+      <section name="consensus">
+        <param name="normalize" value="false"/>
+        <param name="fix_peptides" value="false"/>
+      </section>
+      <section name="format">
+        <param name="separator" value=""/>
+        <param name="quoting" value="double"/>
+        <param name="replacement" value="_"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Compute peptide and protein abundances
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinQuantifier.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ProteinQuantifier.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/ProteinResolver.xml b/tools/openms/ProteinResolver.xml
index 3028f6621..7143a6c40 100644
--- a/tools/openms/ProteinResolver.xml
+++ b/tools/openms/ProteinResolver.xml
@@ -1,4 +1,3 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Quantitation]-->
 <tool id="ProteinResolver" name="ProteinResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
@@ -15,19 +14,19 @@
 
 ## Preprocessing
 mkdir fasta &&
-ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' &&
+cp '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' &&
 #if $in_cond.in:
   mkdir in_cond.in &&
   #if $in_cond.in_select == "no"
   mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-  ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+  ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
   #else
-  ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+  cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
   #end if
 #end if
 #if $design:
   mkdir design &&
-  ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
+  cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
 #end if
 #if "protein_groups_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir protein_groups &&
@@ -103,7 +102,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-fasta" type="data" format="fasta" optional="false" label="Input database file" help=" select fasta data sets(s)"/>
+    <param argument="-fasta" type="data" format="fasta" label="Input database file" help=" select fasta data sets(s)"/>
     <conditional name="in_cond">
       <param name="in_select" type="select" label="Run tool in batch mode for -in">
         <option value="no">No: process all datasets jointly</option>
@@ -113,7 +112,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="consensusxml,idxml" multiple="false" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,idxml" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/>
       </when>
     </conditional>
     <param argument="-in_path" type="text" optional="true" value="" label="Path to idXMLs or consensusXMLs files" help="Ignored if 'in' is given">
@@ -121,21 +120,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </param>
     <param argument="-design" type="data" format="txt" optional="true" label="Text file containing the experimental design" help="See documentation for specific format requirements select txt data sets(s)"/>
     <section name="resolver" title="Additional options for algorithm" help="" expanded="false">
-      <param name="missed_cleavages" argument="-resolver:missed_cleavages" type="integer" optional="true" min="0" value="2" label="Number of allowed missed cleavages" help=""/>
-      <param name="min_length" argument="-resolver:min_length" type="integer" optional="true" min="1" value="6" label="Minimum length of peptide" help=""/>
-      <param name="enzyme" argument="-resolver:enzyme" type="select" optional="true" label="Digestion enzyme" help="">
+      <param name="missed_cleavages" argument="-resolver:missed_cleavages" type="integer" min="0" value="2" label="Number of allowed missed cleavages" help=""/>
+      <param name="min_length" argument="-resolver:min_length" type="integer" min="1" value="6" label="Minimum length of peptide" help=""/>
+      <param name="enzyme" argument="-resolver:enzyme" type="select" label="Digestion enzyme" help="">
         <option value="Trypsin" selected="true">Trypsin</option>
         <expand macro="list_string_san" name="enzyme"/>
       </param>
     </section>
     <section name="designer" title="Additional options for quantitative experimental design" help="" expanded="false">
-      <param name="experiment" argument="-designer:experiment" type="text" optional="true" value="ExperimentalSetting" label="Identifier for the experimental design" help="">
+      <param name="experiment" argument="-designer:experiment" type="text" value="ExperimentalSetting" label="Identifier for the experimental design" help="">
         <expand macro="list_string_san" name="experiment"/>
       </param>
-      <param name="file" argument="-designer:file" type="text" optional="true" value="File" label="Identifier for the file name" help="">
+      <param name="file" argument="-designer:file" type="text" value="File" label="Identifier for the file name" help="">
         <expand macro="list_string_san" name="file"/>
       </param>
-      <param name="separator" argument="-designer:separator" type="select" optional="true" label="Separator, which should be used to split a row into columns" help="">
+      <param name="separator" argument="-designer:separator" type="select" label="Separator, which should be used to split a row into columns" help="">
         <option value="tab" selected="true">tab</option>
         <option value="semi-colon">semi-colon</option>
         <option value="comma">comma</option>
@@ -145,7 +144,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -177,7 +176,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_ProteinResolver_1 -->
+  <tests>
+    <!-- TOPP_ProteinResolver_1 -->
     <test expect_num_outputs="4">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -188,9 +188,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="in" value="ProteinResolver_1_input.consensusXML"/>
       </conditional>
       <param name="in_path" value=""/>
-      <output name="protein_groups" file="ProteinResolver_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="peptide_table" file="ProteinResolver_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="protein_table" file="ProteinResolver_1_output3.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="protein_groups" value="ProteinResolver_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="peptide_table" value="ProteinResolver_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="protein_table" value="ProteinResolver_1_output3.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <section name="resolver">
         <param name="missed_cleavages" value="2"/>
         <param name="min_length" value="6"/>
@@ -207,11 +207,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[protein inference
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinResolver.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ProteinResolver.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/QCCalculator.xml b/tools/openms/QCCalculator.xml
index 45a1f76d6..593b0c72b 100644
--- a/tools/openms/QCCalculator.xml
+++ b/tools/openms/QCCalculator.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: []-->
 <tool id="QCCalculator" name="QCCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.</description>
+  <description>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection</description>
   <macros>
     <token name="@EXECUTABLE@">QCCalculator</token>
     <import>macros.xml</import>
@@ -15,19 +14,19 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if $id:
   mkdir id &&
-  ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
+  cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
 #end if
 #if $feature:
   mkdir feature &&
-  ln -s '$feature' 'feature/${re.sub("[^\w\-_]", "_", $feature.element_identifier)}.$gxy2omsext($feature.ext)' &&
+  cp '$feature' 'feature/${re.sub("[^\w\-_]", "_", $feature.element_identifier)}.$gxy2omsext($feature.ext)' &&
 #end if
 #if $consensus:
   mkdir consensus &&
-  ln -s '$consensus' 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)' &&
+  cp '$consensus' 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)' &&
 #end if
 
 ## Main program call
@@ -63,13 +62,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)" help=" select mzml data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
+    <param argument="-in" type="data" format="mzml" label="raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)" help=" select mzml data sets(s)"/>
+    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
       <option value="mzQC">mzqc</option>
       <option value="qcML">qcml</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param argument="-label" type="text" optional="true" value="label" label="unique name for the run that can be used in a figure label" help="">
+    <param argument="-label" type="text" value="label" label="unique name for the run that can be used in a figure label" help="">
       <expand macro="list_string_san" name="label"/>
     </param>
     <param argument="-name" type="text" optional="true" value="" label="name of the person creating this mzQC file" help="">
@@ -87,7 +87,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-remove_duplicate_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="This flag should be set, if you work with a set of merged features" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -105,14 +105,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_QCCalculator_1 -->
+  <tests>
+    <!-- TOPP_QCCalculator_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="QCCalculator_input.mzML"/>
-      <output name="out" file="QCCalculator_1.qcML" compare="sim_size" delta_frac="0.7" ftype="qcml"/>
+      <output name="out" value="QCCalculator_1_output.qcML" compare="sim_size" delta_frac="0.7" ftype="qcml"/>
       <param name="out_type" value="qcML"/>
       <param name="label" value="label"/>
       <param name="name" value=""/>
@@ -125,15 +126,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_QCCalculator_2 -->
+    <!-- TOPP_QCCalculator_2 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="QCCalculator_input.mzML"/>
-      <output name="out" file="QCCalculator_2.mzQC" compare="sim_size" delta_frac="0.7" ftype="mzqc"/>
+      <output name="out" value="QCCalculator_2_output.mzQC" compare="sim_size" delta_frac="0.7" ftype="mzqc"/>
       <param name="out_type" value="mzQC"/>
       <param name="label" value="label"/>
       <param name="name" value="name"/>
@@ -148,33 +152,39 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-  <test expect_num_outputs="1"><!-- took test data from another test w mzML input -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
-    <param name="out_type" value="qcML"/>
-    <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/>
-  </test>
-  <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,consensusXML input -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
-    <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/>
-    <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/>
-    <param name="out_type" value="qcML"/>
-    <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/>
-  </test>
-  <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,featureXML input -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/>
-    <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/>
-    <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/>
-    <param name="out_type" value="qcML"/>
-    <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/>
-  </test>
-</tests>
+    <test expect_num_outputs="1">
+      <!-- took test data from another test w mzML input -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
+      <param name="out_type" value="qcML"/>
+      <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/>
+    </test>
+    <test expect_num_outputs="1">
+      <!-- took test data from another test w mzML,idXML,consensusXML input -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
+      <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/>
+      <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/>
+      <param name="out_type" value="qcML"/>
+      <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/>
+    </test>
+    <test expect_num_outputs="1">
+      <!-- took test data from another test w mzML,idXML,featureXML input -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/>
+      <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/>
+      <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/>
+      <param name="out_type" value="qcML"/>
+      <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/>
+    </test>
+  </tests>
   <help><![CDATA[Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCCalculator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCCalculator.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/QCEmbedder.xml b/tools/openms/QCEmbedder.xml
index 02b03c59e..6be1fb1d9 100644
--- a/tools/openms/QCEmbedder.xml
+++ b/tools/openms/QCEmbedder.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: []-->
 <tool id="QCEmbedder" name="QCEmbedder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Attaches a table or an image to a given qc parameter.</description>
+  <description>Attaches a table or an image to a given qc parameter</description>
   <macros>
     <token name="@EXECUTABLE@">QCEmbedder</token>
     <import>macros.xml</import>
@@ -16,19 +15,19 @@
 ## Preprocessing
 #if $in:
   mkdir in &&
-  ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+  cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #end if
 #if $run:
   mkdir run &&
-  ln -s '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' &&
+  cp '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' &&
 #end if
 #if $plot:
   mkdir plot &&
-  ln -s '$plot' 'plot/${re.sub("[^\w\-_]", "_", $plot.element_identifier)}.$gxy2omsext($plot.ext)' &&
+  cp '$plot' 'plot/${re.sub("[^\w\-_]", "_", $plot.element_identifier)}.$gxy2omsext($plot.ext)' &&
 #end if
 #if $table:
   mkdir table &&
-  ln -s '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' &&
+  cp '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' &&
 #end if
 mkdir out &&
 
@@ -71,7 +70,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-qp_att_acc" type="text" optional="true" value="" label="Defines the qp cv accession of the qp to which the table/image is attached" help="">
       <expand macro="list_string_san" name="qp_att_acc"/>
     </param>
-    <param argument="-cv_acc" type="text" optional="false" value="" label="Defines the cv accession of the attachment" help="">
+    <param argument="-cv_acc" type="text" value="" label="Defines the cv accession of the attachment" help="">
       <expand macro="list_string_san" name="cv_acc"/>
     </param>
     <param argument="-run" type="data" format="mzml" optional="true" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="The file is only used to extract the run name from the file name select mzml data sets(s)"/>
@@ -82,7 +81,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-table" type="data" format="csv" optional="true" label="If a table is to be attached to a qp, this has to be specified here" help=" select csv data sets(s)"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -96,11 +95,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!--TODO-->
-</tests>
+  <tests>
+    <!--TODO-->
+  </tests>
   <help><![CDATA[Attaches a table or an image to a given qc parameter.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCEmbedder.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCEmbedder.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/QCExporter.xml b/tools/openms/QCExporter.xml
index 0b172b23b..6f8bd2953 100644
--- a/tools/openms/QCExporter.xml
+++ b/tools/openms/QCExporter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: []-->
 <tool id="QCExporter" name="QCExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Will extract several qp from several run/sets in a tabular format.</description>
+  <description>Will extract several qp from several run/sets in a tabular format</description>
   <macros>
     <token name="@EXECUTABLE@">QCExporter</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir mapping &&
-ln -s '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' &&
+cp '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' &&
 mkdir out_csv &&
 
 ## Main program call
@@ -43,15 +42,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/>
+    <param argument="-in" type="data" format="qcml" label="Input qcml file" help=" select qcml data sets(s)"/>
     <param argument="-names" type="text" optional="true" value="" label="The name of the target runs or sets to be exported from" help="If empty, from all will be exported (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="names"/>
       <expand macro="list_string_san" name="names"/>
     </param>
-    <param argument="-mapping" type="data" format="csv" optional="false" label="The mapping of the exported table's headers to the according qp cvs" help="The first row is considered containing the headers as for the exported the table. The second row is considered the according qp cv accessions of the qp to be exported select csv data sets(s)"/>
+    <param argument="-mapping" type="data" format="csv" label="The mapping of the exported table's headers to the according qp cvs" help="The first row is considered containing the headers as for the exported the table. The second row is considered the according qp cv accessions of the qp to be exported select csv data sets(s)"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -65,11 +64,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!--TODO-->
-</tests>
+  <tests>
+    <!--TODO-->
+  </tests>
   <help><![CDATA[Will extract several qp from several run/sets in a tabular format.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCExporter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCExporter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/QCExtractor.xml b/tools/openms/QCExtractor.xml
index 11b1910cd..65314c34e 100644
--- a/tools/openms/QCExtractor.xml
+++ b/tools/openms/QCExtractor.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: []-->
 <tool id="QCExtractor" name="QCExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Extracts a table attachment to a given qc parameter.</description>
+  <description>Extracts a table attachment to a given qc parameter</description>
   <macros>
     <token name="@EXECUTABLE@">QCExtractor</token>
     <import>macros.xml</import>
@@ -15,10 +14,10 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #if $run:
   mkdir run &&
-  ln -s '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' &&
+  cp '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' &&
 #end if
 mkdir out_csv &&
 
@@ -47,8 +46,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/>
-    <param argument="-qp" type="text" optional="false" value="" label="Target attachment qp" help="">
+    <param argument="-in" type="data" format="qcml" label="Input qcml file" help=" select qcml data sets(s)"/>
+    <param argument="-qp" type="text" value="" label="Target attachment qp" help="">
       <expand macro="list_string_san" name="qp"/>
     </param>
     <param argument="-run" type="data" format="mzml" optional="true" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="The file is only used to extract the run name from the file name select mzml data sets(s)"/>
@@ -57,7 +56,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -71,11 +70,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!--TODO-->
-</tests>
+  <tests>
+    <!--TODO-->
+  </tests>
   <help><![CDATA[Extracts a table attachment to a given qc parameter.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCExtractor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCExtractor.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/QCImporter.xml b/tools/openms/QCImporter.xml
index 1111f1503..4d25581cd 100644
--- a/tools/openms/QCImporter.xml
+++ b/tools/openms/QCImporter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: []-->
 <tool id="QCImporter" name="QCImporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Imports tables with quality control parameters into qcml files.</description>
+  <description>Imports tables with quality control parameters into qcml files</description>
   <macros>
     <token name="@EXECUTABLE@">QCImporter</token>
     <import>macros.xml</import>
@@ -16,12 +15,12 @@
 ## Preprocessing
 #if $in:
   mkdir in &&
-  ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+  cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #end if
 mkdir table &&
-ln -s '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' &&
+cp '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' &&
 mkdir mapping &&
-ln -s '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' &&
+cp '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -52,11 +51,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="qcml" optional="true" label="Input qcml file" help=" select qcml data sets(s)"/>
-    <param argument="-table" type="data" format="csv" optional="false" label="The table containing the additional qp values in the columns" help="First row is considered containing the header. The target run or set names/ids are indicated by column &quot;raw data file&quot;, so each row after the header will contain the values of qps for that run. (csv without &quot;!) select csv data sets(s)"/>
-    <param argument="-mapping" type="data" format="csv" optional="false" label="The mapping of the table header to the according qp cvs, also in csv format" help="The first row is considered containing the headers as in the table. The second row is considered the according qp cv accessions. (csv without &quot;!) select csv data sets(s)"/>
+    <param argument="-table" type="data" format="csv" label="The table containing the additional qp values in the columns" help="First row is considered containing the header. The target run or set names/ids are indicated by column &quot;raw data file&quot;, so each row after the header will contain the values of qps for that run. (csv without &quot;!) select csv data sets(s)"/>
+    <param argument="-mapping" type="data" format="csv" label="The mapping of the table header to the according qp cvs, also in csv format" help="The first row is considered containing the headers as in the table. The second row is considered the according qp cv accessions. (csv without &quot;!) select csv data sets(s)"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -70,11 +69,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!--TODO-->
-</tests>
+  <tests>
+    <!--TODO-->
+  </tests>
   <help><![CDATA[Imports tables with quality control parameters into qcml files.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCImporter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCImporter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/QCMerger.xml b/tools/openms/QCMerger.xml
index 0bde8726f..02c5e6157 100644
--- a/tools/openms/QCMerger.xml
+++ b/tools/openms/QCMerger.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: []-->
 <tool id="QCMerger" name="QCMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Merges two qcml files together.</description>
+  <description>Merges two qcml files together</description>
   <macros>
     <token name="@EXECUTABLE@">QCMerger</token>
     <import>macros.xml</import>
@@ -17,9 +16,9 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir out &&
 
@@ -54,10 +53,10 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="qcml" multiple="true" optional="false" label="List of qcml files to be merged" help=" select qcml data sets(s)"/>
+        <param argument="-in" type="data" format="qcml" multiple="true" label="List of qcml files to be merged" help=" select qcml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="qcml" multiple="false" optional="false" label="List of qcml files to be merged" help=" select qcml data sets(s)"/>
+        <param argument="-in" type="data" format="qcml" label="List of qcml files to be merged" help=" select qcml data sets(s)"/>
       </when>
     </conditional>
     <param argument="-setname" type="text" optional="true" value="" label="Use only when all given qcml files belong to one set, which will be held under the given name" help="">
@@ -65,7 +64,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -79,15 +78,17 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- just using 2 outputs from QCCalculator as input (no2 did not work) -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/>
-    <output name="out" ftype="qcml" value="QCMerger.qcML"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- just using 2 outputs from QCCalculator as input (no2 did not work) -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/>
+      <output name="out" ftype="qcml" value="QCMerger.qcML"/>
+    </test>
+  </tests>
   <help><![CDATA[Merges two qcml files together.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCMerger.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCMerger.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/QCShrinker.xml b/tools/openms/QCShrinker.xml
index 2f79f1eed..e75b2a3e8 100644
--- a/tools/openms/QCShrinker.xml
+++ b/tools/openms/QCShrinker.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: []-->
 <tool id="QCShrinker" name="QCShrinker" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.</description>
+  <description>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report</description>
   <macros>
     <token name="@EXECUTABLE@">QCShrinker</token>
     <import>macros.xml</import>
@@ -15,10 +14,10 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #if $run:
   mkdir run &&
-  ln -s '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' &&
+  cp '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' &&
 #end if
 mkdir out &&
 
@@ -47,7 +46,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/>
+    <param argument="-in" type="data" format="qcml" label="Input qcml file" help=" select qcml data sets(s)"/>
     <param argument="-qp_accessions" type="text" optional="true" value="" label="A list of cv accessions that should be removed" help="If empty, the usual suspects will be removed! (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="qp_accessions"/>
       <expand macro="list_string_san" name="qp_accessions"/>
@@ -58,7 +57,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-run" type="data" format="mzml" optional="true" label="The file from which the name of the target run that contains the requested quality parameter is taken" help="This overrides the name parameter! select mzml data sets(s)"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -72,15 +71,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- just using an output of QCCalculator as input  -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="qcml" value="QCCalculator1.qcML"/>
-    <output name="out" ftype="qcml" value="QCShrinker.qcML"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- just using an output of QCCalculator as input  -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="qcml" value="QCCalculator1.qcML"/>
+      <output name="out" ftype="qcml" value="QCShrinker.qcML"/>
+    </test>
+  </tests>
   <help><![CDATA[This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCShrinker.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCShrinker.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/QualityControl.xml b/tools/openms/QualityControl.xml
index aecd48a1a..ee06ba0c5 100644
--- a/tools/openms/QualityControl.xml
+++ b/tools/openms/QualityControl.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Quality Control]-->
 <tool id="QualityControl" name="QualityControl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get.</description>
+  <description>Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get</description>
   <macros>
     <token name="@EXECUTABLE@">QualityControl</token>
     <import>macros.xml</import>
@@ -15,23 +14,23 @@
 
 ## Preprocessing
 mkdir in_cm &&
-ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
+cp '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
 #if $in_raw_cond.in_raw:
   mkdir in_raw_cond.in_raw &&
   #if $in_raw_cond.in_raw_select == "no"
   mkdir ${' '.join(["'in_raw_cond.in_raw/%s'" % (i) for i, f in enumerate($in_raw_cond.in_raw) if f])} && 
-  ${' '.join(["ln -s '%s' 'in_raw_cond.in_raw/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_raw_cond.in_raw) if f])}
+  ${' '.join(["cp '%s' 'in_raw_cond.in_raw/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_raw_cond.in_raw) if f])}
   #else
-  ln -s '$in_raw_cond.in_raw' 'in_raw_cond.in_raw/${re.sub("[^\w\-_]", "_", $in_raw_cond.in_raw.element_identifier)}.$gxy2omsext($in_raw_cond.in_raw.ext)' &&
+  cp '$in_raw_cond.in_raw' 'in_raw_cond.in_raw/${re.sub("[^\w\-_]", "_", $in_raw_cond.in_raw.element_identifier)}.$gxy2omsext($in_raw_cond.in_raw.ext)' &&
   #end if
 #end if
 #if $in_postFDR_cond.in_postFDR:
   mkdir in_postFDR_cond.in_postFDR &&
   #if $in_postFDR_cond.in_postFDR_select == "no"
   mkdir ${' '.join(["'in_postFDR_cond.in_postFDR/%s'" % (i) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])} && 
-  ${' '.join(["ln -s '%s' 'in_postFDR_cond.in_postFDR/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])}
+  ${' '.join(["cp '%s' 'in_postFDR_cond.in_postFDR/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])}
   #else
-  ln -s '$in_postFDR_cond.in_postFDR' 'in_postFDR_cond.in_postFDR/${re.sub("[^\w\-_]", "_", $in_postFDR_cond.in_postFDR.element_identifier)}.$gxy2omsext($in_postFDR_cond.in_postFDR.ext)' &&
+  cp '$in_postFDR_cond.in_postFDR' 'in_postFDR_cond.in_postFDR/${re.sub("[^\w\-_]", "_", $in_postFDR_cond.in_postFDR.element_identifier)}.$gxy2omsext($in_postFDR_cond.in_postFDR.ext)' &&
   #end if
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
@@ -46,15 +45,19 @@ ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy
 #end if
 #if $in_contaminants:
   mkdir in_contaminants &&
-  ln -s '$in_contaminants' 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)' &&
+  cp '$in_contaminants' 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)' &&
+#end if
+#if $in_fasta:
+  mkdir in_fasta &&
+  cp '$in_fasta' 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)' &&
 #end if
 #if $in_trafo_cond.in_trafo:
   mkdir in_trafo_cond.in_trafo &&
   #if $in_trafo_cond.in_trafo_select == "no"
   mkdir ${' '.join(["'in_trafo_cond.in_trafo/%s'" % (i) for i, f in enumerate($in_trafo_cond.in_trafo) if f])} && 
-  ${' '.join(["ln -s '%s' 'in_trafo_cond.in_trafo/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_trafo_cond.in_trafo) if f])}
+  ${' '.join(["cp '%s' 'in_trafo_cond.in_trafo/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_trafo_cond.in_trafo) if f])}
   #else
-  ln -s '$in_trafo_cond.in_trafo' 'in_trafo_cond.in_trafo/${re.sub("[^\w\-_]", "_", $in_trafo_cond.in_trafo.element_identifier)}.$gxy2omsext($in_trafo_cond.in_trafo.ext)' &&
+  cp '$in_trafo_cond.in_trafo' 'in_trafo_cond.in_trafo/${re.sub("[^\w\-_]", "_", $in_trafo_cond.in_trafo.element_identifier)}.$gxy2omsext($in_trafo_cond.in_trafo.ext)' &&
   #end if
 #end if
 
@@ -98,6 +101,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   -in_contaminants
   'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)'
 #end if
+#if $in_fasta:
+  -in_fasta
+  'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)'
+#end if
 #if $in_trafo_cond.in_trafo:
   -in_trafo
   #if $in_trafo_cond.in_trafo_select == "no"
@@ -128,7 +135,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in_cm" type="data" format="consensusxml" optional="false" label="ConsensusXML input, generated by FeatureLinke" help=" select consensusxml data sets(s)"/>
+    <param argument="-in_cm" type="data" format="consensusxml" label="ConsensusXML input, generated by FeatureLinke" help=" select consensusxml data sets(s)"/>
     <conditional name="in_raw_cond">
       <param name="in_raw_select" type="select" label="Run tool in batch mode for -in_raw">
         <option value="no">No: process all datasets jointly</option>
@@ -138,7 +145,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param argument="-in_raw" type="data" format="mzml" multiple="true" optional="true" label="MzML input (after InternalCalibration, if available)" help=" select mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in_raw" type="data" format="mzml" multiple="false" optional="true" label="MzML input (after InternalCalibration, if available)" help=" select mzml data sets(s)"/>
+        <param argument="-in_raw" type="data" format="mzml" optional="true" label="MzML input (after InternalCalibration, if available)" help=" select mzml data sets(s)"/>
       </when>
     </conditional>
     <conditional name="in_postFDR_cond">
@@ -150,10 +157,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param argument="-in_postFDR" type="data" format="featurexml" multiple="true" optional="true" label="FeatureXMLs after FDR filtering" help=" select featurexml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in_postFDR" type="data" format="featurexml" multiple="false" optional="true" label="FeatureXMLs after FDR filtering" help=" select featurexml data sets(s)"/>
+        <param argument="-in_postFDR" type="data" format="featurexml" optional="true" label="FeatureXMLs after FDR filtering" help=" select featurexml data sets(s)"/>
       </when>
     </conditional>
     <param argument="-in_contaminants" type="data" format="fasta" optional="true" label="Proteins considered contaminants" help=" select fasta data sets(s)"/>
+    <param argument="-in_fasta" type="data" format="fasta" optional="true" label="FASTA file used during MS/MS identification (including decoys)" help="If the protein description contains 'GN=...' then gene names will be extracted select fasta data sets(s)"/>
     <conditional name="in_trafo_cond">
       <param name="in_trafo_select" type="select" label="Run tool in batch mode for -in_trafo">
         <option value="no">No: process all datasets jointly</option>
@@ -163,27 +171,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param argument="-in_trafo" type="data" format="trafoxml" multiple="true" optional="true" label="trafoXMLs from MapAligners" help=" select trafoxml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in_trafo" type="data" format="trafoxml" multiple="false" optional="true" label="trafoXMLs from MapAligners" help=" select trafoxml data sets(s)"/>
+        <param argument="-in_trafo" type="data" format="trafoxml" optional="true" label="trafoXMLs from MapAligners" help=" select trafoxml data sets(s)"/>
       </when>
     </conditional>
     <param argument="-out_evd" type="text" optional="true" value="" label="If a Path is given, a MQEvidence txt-file will be created in this directory" help="If the directory does not exist, it will be created as well">
       <expand macro="list_string_san" name="out_evd"/>
     </param>
+    <param argument="-out_msms" type="text" optional="true" value="" label="If a Path is given, a MQMsms txt-file will be created in this directory" help="If the directory does not exist, it will be created as well">
+      <expand macro="list_string_san" name="out_msms"/>
+    </param>
     <section name="FragmentMassError" title="Fragment Mass Error settings" help="" expanded="false">
-      <param name="unit" argument="-FragmentMassError:unit" type="select" optional="true" label="Unit for mass tolerance" help="'auto' uses information from FeatureXML">
+      <param name="unit" argument="-FragmentMassError:unit" type="select" label="Unit for mass tolerance" help="'auto' uses information from FeatureXML">
         <option value="auto" selected="true">auto</option>
         <option value="ppm">ppm</option>
         <option value="da">da</option>
         <expand macro="list_string_san" name="unit"/>
       </param>
-      <param name="tolerance" argument="-FragmentMassError:tolerance" type="float" optional="true" value="20.0" label="m/z search window for matching peaks in two spectra" help=""/>
+      <param name="tolerance" argument="-FragmentMassError:tolerance" type="float" value="20.0" label="m/z search window for matching peaks in two spectra" help=""/>
     </section>
     <section name="MS2_id_rate" title="MS2 ID Rate settings" help="" expanded="false">
       <param name="assume_all_target" argument="-MS2_id_rate:assume_all_target" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Forces the metric to run even if target/decoy annotation is missing (accepts all pep_ids as target hits)" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -212,7 +223,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_QualityControl_1 -->
+  <tests>
+    <!-- TOPP_QualityControl_1 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -225,13 +237,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <conditional name="in_postFDR_cond">
         <param name="in_postFDR" value="QualityControl_1_in1.featureXML,QualityControl_1_in2.featureXML,QualityControl_1_in3.featureXML"/>
       </conditional>
-      <output name="out" file="QualityControl_1_out.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <output name="out_cm" file="QualityControl_1_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="QualityControl_1_out.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="out_cm" value="QualityControl_1_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="in_contaminants" value="QualityControl_1.fasta"/>
+      <param name="in_fasta" value="PeptideIndexer_1.fasta"/>
       <conditional name="in_trafo_cond">
         <param name="in_trafo" value="QualityControl_1_in1.trafoXML,QualityControl_1_in2.trafoXML,QualityControl_1_in3.trafoXML"/>
       </conditional>
       <param name="out_evd" value=""/>
+      <param name="out_msms" value=""/>
       <section name="FragmentMassError">
         <param name="unit" value="auto"/>
         <param name="tolerance" value="20.0"/>
@@ -245,11 +259,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_QualityControl.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QualityControl.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/RNADigestor.xml b/tools/openms/RNADigestor.xml
index da72d4d8b..244473307 100644
--- a/tools/openms/RNADigestor.xml
+++ b/tools/openms/RNADigestor.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [RNA]-->
 <tool id="RNADigestor" name="RNADigestor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Digests an RNA sequence database in-silico.</description>
+  <description>Digests an RNA sequence database in-silico</description>
   <macros>
     <token name="@EXECUTABLE@">RNADigestor</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,19 +38,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="fasta" optional="false" label="Input file containing RNA sequences" help=" select fasta data sets(s)"/>
-    <param argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
-    <param argument="-min_length" type="integer" optional="true" value="3" label="Minimum length of a fragment" help=""/>
-    <param argument="-max_length" type="integer" optional="true" value="30" label="Maximum length of a fragment" help=""/>
-    <param argument="-enzyme" type="select" optional="true" label="Digestion enzyme (RNase)" help="">
-      <option value="RNase_U2">RNase_U2</option>
-      <option value="RNase_A">RNase_A</option>
-      <option value="RNase_MC1">RNase_MC1</option>
-      <option value="RNase_H">RNase_H</option>
-      <option value="cusativin">cusativin</option>
+    <param argument="-in" type="data" format="fasta" label="Input file containing RNA sequences" help=" select fasta data sets(s)"/>
+    <param argument="-missed_cleavages" type="integer" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
+    <param argument="-min_length" type="integer" value="3" label="Minimum length of a fragment" help=""/>
+    <param argument="-max_length" type="integer" value="30" label="Maximum length of a fragment" help=""/>
+    <param argument="-enzyme" type="select" label="Digestion enzyme (RNase)" help="">
       <option value="RNase_T1" selected="true">RNase_T1</option>
+      <option value="RNase_H">RNase_H</option>
       <option value="mazF">mazF</option>
       <option value="colicin_E5">colicin_E5</option>
+      <option value="RNase_MC1">RNase_MC1</option>
+      <option value="RNase_A">RNase_A</option>
+      <option value="RNase_U2">RNase_U2</option>
+      <option value="cusativin">cusativin</option>
       <option value="no cleavage">no cleavage</option>
       <option value="unspecific cleavage">unspecific cleavage</option>
       <expand macro="list_string_san" name="enzyme"/>
@@ -60,7 +59,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-cdna" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Input file contains cDNA sequences - replace 'T' with 'U')" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -74,15 +73,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!--random RNAsequence input -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="fasta" value="random_RNA.fa"/>
-    <output name="out" ftype="fasta" value="RNADigestor.fasta"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!--random RNAsequence input -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="fasta" value="random_RNA.fa"/>
+      <output name="out" ftype="fasta" value="RNADigestor.fasta"/>
+    </test>
+  </tests>
   <help><![CDATA[Digests an RNA sequence database in-silico.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RNADigestor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_RNADigestor.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/RNAMassCalculator.xml b/tools/openms/RNAMassCalculator.xml
index 9e47982bb..1abb63d5d 100644
--- a/tools/openms/RNAMassCalculator.xml
+++ b/tools/openms/RNAMassCalculator.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [RNA]-->
 <tool id="RNAMassCalculator" name="RNAMassCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences</description>
   <macros>
@@ -16,7 +15,7 @@
 ## Preprocessing
 #if $in:
   mkdir in &&
-  ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+  cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
@@ -57,10 +56,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <expand macro="list_string_val" name="in_seq"/>
       <expand macro="list_string_san" name="in_seq"/>
     </param>
-    <param argument="-charge" type="text" optional="true" value="0" label="List of charge states; required if 'in_seq' is given" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-charge" type="text" value="0" label="List of charge states; required if 'in_seq' is given" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_integer_valsan" name="charge"/>
     </param>
-    <param argument="-format" type="select" optional="true" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only, 'formula_only': sum formula only)" help="">
+    <param argument="-format" type="select" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only, 'formula_only': sum formula only)" help="">
       <option value="list" selected="true">list</option>
       <option value="table">table</option>
       <option value="mass_only">mass_only</option>
@@ -69,7 +68,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <expand macro="list_string_san" name="format"/>
     </param>
     <param argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) oligonucleotide masses" help=""/>
-    <param argument="-fragment_type" type="select" optional="true" label="For what type of sequence/fragment the mass should be computed" help="">
+    <param argument="-fragment_type" type="select" label="For what type of sequence/fragment the mass should be computed" help="">
       <option value="full" selected="true">full</option>
       <option value="internal">internal</option>
       <option value="5-prime">5-prime</option>
@@ -90,7 +89,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -110,14 +109,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_RNAMassCalculator_1 -->
+  <tests>
+    <!-- TOPP_RNAMassCalculator_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in_seq" value="&quot;AUCGGC&quot;"/>
-      <output name="out" file="RNAMassCalculator_1.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="RNAMassCalculator_1.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="charge" value="-1 -2"/>
       <param name="format" value="list"/>
       <param name="average_mass" value="false"/>
@@ -129,11 +129,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RNAMassCalculator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_RNAMassCalculator.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/RNPxlSearch.xml b/tools/openms/RNPxlSearch.xml
index 53fda90af..7ee3467f1 100644
--- a/tools/openms/RNPxlSearch.xml
+++ b/tools/openms/RNPxlSearch.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Cross-Linking]-->
 <tool id="RNPxlSearch" name="RNPxlSearch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Annotate RNA/DNA-peptide cross-links in MS/MS spectra.</description>
+  <description>Annotate RNA/DNA-peptide cross-links in MS/MS spectra</description>
   <macros>
     <token name="@EXECUTABLE@">RNPxlSearch</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir database &&
-ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
 mkdir out &&
 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_tsv &&
@@ -56,31 +55,31 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
-    <param argument="-database" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-database" type="data" format="fasta" label="input file" help=" select fasta data sets(s)"/>
     <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false">
-      <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Precursor mass tolerance (+/- around precursor m/z)" help=""/>
-      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
+      <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" value="10.0" label="Precursor mass tolerance (+/- around precursor m/z)" help=""/>
+      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
       </param>
-      <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/>
-      <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="5" label="Maximum precursor charge to be considered" help=""/>
-      <param name="isotopes" argument="-precursor:isotopes" type="text" optional="true" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="min_charge" argument="-precursor:min_charge" type="integer" value="2" label="Minimum precursor charge to be considered" help=""/>
+      <param name="max_charge" argument="-precursor:max_charge" type="integer" value="5" label="Maximum precursor charge to be considered" help=""/>
+      <param name="isotopes" argument="-precursor:isotopes" type="text" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_integer_valsan" name="isotopes"/>
       </param>
     </section>
     <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false">
-      <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/>
-      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="true" label="Unit of fragment m" help="">
+      <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/>
+      <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" label="Unit of fragment m" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
       </param>
     </section>
     <section name="modifications" title="Modifications Options" help="" expanded="false">
-      <param name="fixed" argument="-modifications:fixed" multiple="true" type="select" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
+      <param name="fixed" argument="-modifications:fixed" type="select" multiple="true" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
         <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -90,6 +89,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="2-succinyl (C)">2-succinyl (C)</option>
         <option value="2HPG (R)">2HPG (R)</option>
         <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+        <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+        <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+        <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+        <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
         <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
         <option value="3sulfo (N-term)">3sulfo (N-term)</option>
         <option value="4-ONE (C)">4-ONE (C)</option>
@@ -179,6 +182,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
         <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
         <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+        <option value="Andro-H2O (C)">Andro-H2O (C)</option>
         <option value="Archaeol (C)">Archaeol (C)</option>
         <option value="Arg (N-term)">Arg (N-term)</option>
         <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -282,6 +286,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
         <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
         <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+        <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
         <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
         <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
         <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -314,7 +319,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="BITC (N-term)">BITC (N-term)</option>
         <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
         <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-        <option value="Bodipy (C)">Bodipy (C)</option>
         <option value="Brij35 (N-term)">Brij35 (N-term)</option>
         <option value="Brij58 (N-term)">Brij58 (N-term)</option>
         <option value="Bromo (F)">Bromo (F)</option>
@@ -746,9 +750,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Dehydrated (T)">Dehydrated (T)</option>
         <option value="Dehydrated (Y)">Dehydrated (Y)</option>
         <option value="Dehydro (C)">Dehydro (C)</option>
+        <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
         <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-        <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
         <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
         <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -758,7 +762,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
         <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
         <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-        <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
         <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
         <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -770,6 +773,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
         <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
         <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+        <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
         <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
         <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -1342,7 +1346,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Ethanolyl (C)">Ethanolyl (C)</option>
         <option value="Ethanolyl (K)">Ethanolyl (K)</option>
         <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-        <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
         <option value="Ethyl (C-term)">Ethyl (C-term)</option>
         <option value="Ethyl (D)">Ethyl (D)</option>
         <option value="Ethyl (E)">Ethyl (E)</option>
@@ -1436,6 +1439,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
         <option value="Glu (E)">Glu (E)</option>
         <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+        <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
         <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
         <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
         <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -1450,7 +1454,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
         <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
         <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
         <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -1474,6 +1477,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gly (K)">Gly (K)</option>
         <option value="Gly (S)">Gly (S)</option>
         <option value="Gly (T)">Gly (T)</option>
+        <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
         <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
         <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
         <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -1864,6 +1868,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
         <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
         <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+        <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
         <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
         <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
         <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -1875,6 +1880,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
         <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
         <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+        <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+        <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+        <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
         <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
         <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
         <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -1930,6 +1938,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
         <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
         <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+        <option value="His+O(2) (H)">His+O(2) (H)</option>
         <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
         <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
         <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -2067,11 +2076,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+        <option value="Kdo (S)">Kdo (S)</option>
+        <option value="Kdo (T)">Kdo (T)</option>
         <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
         <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
         <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
         <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
         <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+        <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
         <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
         <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
         <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -2156,13 +2168,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
         <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
         <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+        <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
         <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
         <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
         <option value="Lipoyl (K)">Lipoyl (K)</option>
         <option value="LRGG (K)">LRGG (K)</option>
         <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
         <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+        <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
         <option value="Lys (N-term)">Lys (N-term)</option>
+        <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
         <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
         <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
         <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -2197,6 +2212,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Malonyl (C)">Malonyl (C)</option>
         <option value="Malonyl (K)">Malonyl (K)</option>
         <option value="Malonyl (S)">Malonyl (S)</option>
+        <option value="MBS+peptide (C)">MBS+peptide (C)</option>
         <option value="MDCC (C)">MDCC (C)</option>
         <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
         <option value="Menadione (C)">Menadione (C)</option>
@@ -2208,6 +2224,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="MesitylOxide (H)">MesitylOxide (H)</option>
         <option value="MesitylOxide (K)">MesitylOxide (K)</option>
         <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+        <option value="Met+O(2) (H)">Met+O(2) (H)</option>
         <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
         <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
         <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -2391,7 +2408,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
         <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
         <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-        <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
         <option value="NP40 (N-term)">NP40 (N-term)</option>
         <option value="NQIGG (K)">NQIGG (K)</option>
         <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -2479,6 +2495,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
         <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
         <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+        <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+        <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+        <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+        <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
         <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
         <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
         <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -2493,6 +2513,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phospho (Y)">Phospho (Y)</option>
         <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
         <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+        <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
         <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
         <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
         <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -2524,6 +2545,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
         <option value="Piperidine (K)">Piperidine (K)</option>
         <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+        <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
         <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
         <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
         <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -2601,18 +2623,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="QTGG (K)">QTGG (K)</option>
         <option value="Quinone (W)">Quinone (W)</option>
         <option value="Quinone (Y)">Quinone (Y)</option>
+        <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+        <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+        <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+        <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+        <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+        <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+        <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+        <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+        <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+        <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+        <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+        <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+        <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+        <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+        <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+        <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+        <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+        <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+        <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+        <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
         <option value="Retinylidene (K)">Retinylidene (K)</option>
         <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
         <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
         <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-        <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-        <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-        <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-        <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-        <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-        <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-        <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-        <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
         <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
         <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
         <option value="Saligenin (H)">Saligenin (H)</option>
@@ -2640,6 +2674,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="shTMT (K)">shTMT (K)</option>
         <option value="shTMT (N-term)">shTMT (N-term)</option>
         <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+        <option value="shTMTpro (K)">shTMTpro (K)</option>
+        <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+        <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
         <option value="SMA (K)">SMA (K)</option>
         <option value="SMA (N-term)">SMA (N-term)</option>
         <option value="spermidine (Q)">spermidine (Q)</option>
@@ -2815,7 +2852,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
         <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
         <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-        <option value="Ub-amide (C)">Ub-amide (C)</option>
         <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
         <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
         <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -3010,7 +3046,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="ZQG (K)">ZQG (K)</option>
         <expand macro="list_string_san" name="fixed"/>
       </param>
-      <param name="variable" argument="-modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'">
+      <param name="variable" argument="-modifications:variable" type="select" multiple="true" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
         <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -3020,6 +3056,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="2-succinyl (C)">2-succinyl (C)</option>
         <option value="2HPG (R)">2HPG (R)</option>
         <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+        <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+        <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+        <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+        <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
         <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
         <option value="3sulfo (N-term)">3sulfo (N-term)</option>
         <option value="4-ONE (C)">4-ONE (C)</option>
@@ -3109,6 +3149,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
         <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
         <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+        <option value="Andro-H2O (C)">Andro-H2O (C)</option>
         <option value="Archaeol (C)">Archaeol (C)</option>
         <option value="Arg (N-term)">Arg (N-term)</option>
         <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -3212,6 +3253,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
         <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
         <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+        <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
         <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
         <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
         <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -3244,7 +3286,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="BITC (N-term)">BITC (N-term)</option>
         <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
         <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-        <option value="Bodipy (C)">Bodipy (C)</option>
         <option value="Brij35 (N-term)">Brij35 (N-term)</option>
         <option value="Brij58 (N-term)">Brij58 (N-term)</option>
         <option value="Bromo (F)">Bromo (F)</option>
@@ -3676,9 +3717,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Dehydrated (T)">Dehydrated (T)</option>
         <option value="Dehydrated (Y)">Dehydrated (Y)</option>
         <option value="Dehydro (C)">Dehydro (C)</option>
+        <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
         <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-        <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
         <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
         <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -3688,7 +3729,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
         <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
         <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-        <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
         <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
         <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -3700,6 +3740,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
         <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
         <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+        <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
         <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
         <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -4272,7 +4313,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Ethanolyl (C)">Ethanolyl (C)</option>
         <option value="Ethanolyl (K)">Ethanolyl (K)</option>
         <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-        <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
         <option value="Ethyl (C-term)">Ethyl (C-term)</option>
         <option value="Ethyl (D)">Ethyl (D)</option>
         <option value="Ethyl (E)">Ethyl (E)</option>
@@ -4366,6 +4406,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
         <option value="Glu (E)">Glu (E)</option>
         <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+        <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
         <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
         <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
         <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -4380,7 +4421,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
         <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
         <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
         <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -4404,6 +4444,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Gly (K)">Gly (K)</option>
         <option value="Gly (S)">Gly (S)</option>
         <option value="Gly (T)">Gly (T)</option>
+        <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
         <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
         <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
         <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -4794,6 +4835,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
         <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
         <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+        <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
         <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
         <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
         <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -4805,6 +4847,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
         <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
         <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+        <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+        <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+        <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
         <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
         <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
         <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -4860,6 +4905,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
         <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
         <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+        <option value="His+O(2) (H)">His+O(2) (H)</option>
         <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
         <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
         <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -4997,11 +5043,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+        <option value="Kdo (S)">Kdo (S)</option>
+        <option value="Kdo (T)">Kdo (T)</option>
         <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
         <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
         <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
         <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
         <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+        <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
         <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
         <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
         <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -5086,13 +5135,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
         <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
         <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+        <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
         <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
         <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
         <option value="Lipoyl (K)">Lipoyl (K)</option>
         <option value="LRGG (K)">LRGG (K)</option>
         <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
         <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+        <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
         <option value="Lys (N-term)">Lys (N-term)</option>
+        <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
         <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
         <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
         <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -5127,6 +5179,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Malonyl (C)">Malonyl (C)</option>
         <option value="Malonyl (K)">Malonyl (K)</option>
         <option value="Malonyl (S)">Malonyl (S)</option>
+        <option value="MBS+peptide (C)">MBS+peptide (C)</option>
         <option value="MDCC (C)">MDCC (C)</option>
         <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
         <option value="Menadione (C)">Menadione (C)</option>
@@ -5138,6 +5191,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="MesitylOxide (H)">MesitylOxide (H)</option>
         <option value="MesitylOxide (K)">MesitylOxide (K)</option>
         <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+        <option value="Met+O(2) (H)">Met+O(2) (H)</option>
         <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
         <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
         <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -5321,7 +5375,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
         <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
         <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-        <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
         <option value="NP40 (N-term)">NP40 (N-term)</option>
         <option value="NQIGG (K)">NQIGG (K)</option>
         <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -5409,6 +5462,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
         <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
         <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+        <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+        <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+        <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+        <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
         <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
         <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
         <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -5423,6 +5480,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phospho (Y)">Phospho (Y)</option>
         <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
         <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+        <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
         <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
         <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
         <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -5454,6 +5512,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
         <option value="Piperidine (K)">Piperidine (K)</option>
         <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+        <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
         <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
         <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
         <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -5531,18 +5590,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="QTGG (K)">QTGG (K)</option>
         <option value="Quinone (W)">Quinone (W)</option>
         <option value="Quinone (Y)">Quinone (Y)</option>
+        <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+        <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+        <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+        <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+        <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+        <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+        <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+        <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+        <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+        <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+        <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+        <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+        <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+        <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+        <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+        <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+        <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+        <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+        <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+        <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
         <option value="Retinylidene (K)">Retinylidene (K)</option>
         <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
         <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
         <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-        <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-        <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-        <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-        <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-        <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-        <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-        <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-        <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
         <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
         <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
         <option value="Saligenin (H)">Saligenin (H)</option>
@@ -5570,6 +5641,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="shTMT (K)">shTMT (K)</option>
         <option value="shTMT (N-term)">shTMT (N-term)</option>
         <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+        <option value="shTMTpro (K)">shTMTpro (K)</option>
+        <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+        <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
         <option value="SMA (K)">SMA (K)</option>
         <option value="SMA (N-term)">SMA (N-term)</option>
         <option value="spermidine (Q)">spermidine (Q)</option>
@@ -5745,7 +5819,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
         <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
         <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-        <option value="Ub-amide (C)">Ub-amide (C)</option>
         <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
         <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
         <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -5940,58 +6013,58 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <option value="ZQG (K)">ZQG (K)</option>
         <expand macro="list_string_san" name="variable"/>
       </param>
-      <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
+      <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
     </section>
     <section name="peptide" title="Peptide Options" help="" expanded="false">
-      <param name="min_size" argument="-peptide:min_size" type="integer" optional="true" value="6" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/>
-      <param name="max_size" argument="-peptide:max_size" type="integer" optional="true" value="1000000" label="Maximum size a peptide may have after digestion to be considered in the search" help=""/>
-      <param name="missed_cleavages" argument="-peptide:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/>
-      <param name="enzyme" argument="-peptide:enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
+      <param name="min_size" argument="-peptide:min_size" type="integer" value="6" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/>
+      <param name="max_size" argument="-peptide:max_size" type="integer" value="1000000" label="Maximum size a peptide may have after digestion to be considered in the search" help=""/>
+      <param name="missed_cleavages" argument="-peptide:missed_cleavages" type="integer" value="1" label="Number of missed cleavages" help=""/>
+      <param name="enzyme" argument="-peptide:enzyme" type="select" label="The enzyme used for peptide digestion" help="">
+        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+        <option value="2-iodobenzoate">2-iodobenzoate</option>
+        <option value="iodosobenzoate">iodosobenzoate</option>
+        <option value="Lys-C/P">Lys-C/P</option>
         <option value="PepsinA">PepsinA</option>
-        <option value="TrypChymo">TrypChymo</option>
-        <option value="Trypsin/P">Trypsin/P</option>
         <option value="Trypsin" selected="true">Trypsin</option>
-        <option value="Lys-N">Lys-N</option>
-        <option value="Lys-C/P">Lys-C/P</option>
-        <option value="Clostripain/P">Clostripain/P</option>
-        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
-        <option value="no cleavage">no cleavage</option>
-        <option value="unspecific cleavage">unspecific cleavage</option>
-        <option value="Arg-C/P">Arg-C/P</option>
-        <option value="Asp-N">Asp-N</option>
-        <option value="Asp-N/B">Asp-N/B</option>
+        <option value="Chymotrypsin">Chymotrypsin</option>
+        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+        <option value="CNBr">CNBr</option>
         <option value="staphylococcal protease/D">staphylococcal protease/D</option>
         <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
         <option value="Glu-C+P">Glu-C+P</option>
         <option value="PepsinA + P">PepsinA + P</option>
         <option value="cyanogen-bromide">cyanogen-bromide</option>
-        <option value="Asp-N_ambic">Asp-N_ambic</option>
-        <option value="Chymotrypsin">Chymotrypsin</option>
-        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
-        <option value="Arg-C">Arg-C</option>
-        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
-        <option value="2-iodobenzoate">2-iodobenzoate</option>
-        <option value="iodosobenzoate">iodosobenzoate</option>
-        <option value="CNBr">CNBr</option>
         <option value="Formic_acid">Formic_acid</option>
         <option value="Lys-C">Lys-C</option>
+        <option value="Lys-N">Lys-N</option>
+        <option value="Arg-C">Arg-C</option>
+        <option value="Arg-C/P">Arg-C/P</option>
         <option value="V8-DE">V8-DE</option>
         <option value="V8-E">V8-E</option>
+        <option value="Asp-N">Asp-N</option>
+        <option value="Asp-N/B">Asp-N/B</option>
+        <option value="Asp-N_ambic">Asp-N_ambic</option>
         <option value="leukocyte elastase">leukocyte elastase</option>
         <option value="proline endopeptidase">proline endopeptidase</option>
+        <option value="TrypChymo">TrypChymo</option>
+        <option value="Trypsin/P">Trypsin/P</option>
+        <option value="Clostripain/P">Clostripain/P</option>
+        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+        <option value="no cleavage">no cleavage</option>
+        <option value="unspecific cleavage">unspecific cleavage</option>
         <expand macro="list_string_san" name="enzyme"/>
       </param>
     </section>
     <section name="report" title="Reporting Options" help="" expanded="false">
-      <param name="top_hits" argument="-report:top_hits" type="integer" optional="true" value="1" label="Maximum number of top scoring hits per spectrum that are reported" help=""/>
+      <param name="top_hits" argument="-report:top_hits" type="integer" value="1" label="Maximum number of top scoring hits per spectrum that are reported" help=""/>
     </section>
     <section name="RNPxl" title="RNPxl Options" help="" expanded="false">
-      <param name="length" argument="-RNPxl:length" type="integer" optional="true" value="2" label="Oligonucleotide maximum length" help="0 = disable search for RNA variants"/>
+      <param name="length" argument="-RNPxl:length" type="integer" value="2" label="Oligonucleotide maximum length" help="0 = disable search for RNA variants"/>
       <param name="sequence" argument="-RNPxl:sequence" type="text" optional="true" value="" label="Sequence to restrict the generation of oligonucleotide chains" help="(disabled for empty sequence)">
         <expand macro="list_string_san" name="sequence"/>
       </param>
-      <param name="target_nucleotides" argument="-RNPxl:target_nucleotides" type="text" optional="true" value="A=C10H14N5O7P C=C9H14N3O8P G=C10H14N5O8P U=C9H13N2O9P" label="format:  target nucleotide=empirical formula of nucleoside monophosphate" help="e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS  where X represents e.g. tU .  or e.g. Y=C10H14N5O7PS where Y represents tG (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="target_nucleotides" argument="-RNPxl:target_nucleotides" type="text" value="A=C10H14N5O7P C=C9H14N3O8P G=C10H14N5O8P U=C9H13N2O9P" label="format:  target nucleotide=empirical formula of nucleoside monophosphate" help="e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS  where X represents e.g. tU .  or e.g. Y=C10H14N5O7PS where Y represents tG (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="target_nucleotides"/>
         <expand macro="list_string_san" name="target_nucleotides"/>
       </param>
@@ -5999,22 +6072,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <expand macro="list_string_val" name="nt_groups"/>
         <expand macro="list_string_san" name="nt_groups"/>
       </param>
-      <param name="mapping" argument="-RNPxl:mapping" type="text" optional="true" value="A-&gt;A C-&gt;C G-&gt;G U-&gt;U" label="format: source-&gt;target e.g. A-&gt;A, ..., U-&gt;U, U-&gt;X" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="mapping" argument="-RNPxl:mapping" type="text" value="A-&gt;A C-&gt;C G-&gt;G U-&gt;U" label="format: source-&gt;target e.g. A-&gt;A, ..., U-&gt;U, U-&gt;X" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="mapping"/>
         <expand macro="list_string_san" name="mapping"/>
       </param>
-      <param name="can_cross_link" argument="-RNPxl:can_cross_link" type="text" optional="true" value="U" label="format: 'U' if only U forms cross-links" help="'CATG' if C, A, G, and T form cross-links">
+      <param name="can_cross_link" argument="-RNPxl:can_cross_link" type="text" value="U" label="format: 'U' if only U forms cross-links" help="'CATG' if C, A, G, and T form cross-links">
         <expand macro="list_string_san" name="can_cross_link"/>
       </param>
-      <param name="fragment_adducts" argument="-RNPxl:fragment_adducts" type="text" optional="true" value="U:C9H10N2O5;U-H3PO4 U:C4H4N2O2;U' U:C4H2N2O1;U'-H2O U:C3O;C3O U:C9H13N2O9P1;U U:C9H11N2O8P1;U-H2O U:C9H12N2O6;U-HPO3" label="format: [target nucleotide]:[formula] or [precursor adduct]-&gt;[fragment adduct formula];[name]:" help="e.g., 'U:C9H10N2O5;U-H3PO4' or 'U:U-H2O-&gt;C9H11N2O8P1;U-H2O', (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="fragment_adducts" argument="-RNPxl:fragment_adducts" type="text" value="U:C9H10N2O5;U-H3PO4 U:C4H4N2O2;U' U:C4H2N2O1;U'-H2O U:C3O;C3O U:C9H13N2O9P1;U U:C9H11N2O8P1;U-H2O U:C9H12N2O6;U-HPO3" label="format: [target nucleotide]:[formula] or [precursor adduct]-&gt;[fragment adduct formula];[name]:" help="e.g., 'U:C9H10N2O5;U-H3PO4' or 'U:U-H2O-&gt;C9H11N2O8P1;U-H2O', (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="fragment_adducts"/>
         <expand macro="list_string_san" name="fragment_adducts"/>
       </param>
-      <param name="modifications" argument="-RNPxl:modifications" type="text" optional="true" value="U: U:-H2O U:-H2O-HPO3 U:-HPO3" label="format: empirical formula e.g -H2O, ..., H2O+PO3" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="modifications" argument="-RNPxl:modifications" type="text" value="U: U:-H2O U:-H2O-HPO3 U:-HPO3" label="format: empirical formula e.g -H2O, ..., H2O+PO3" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_string_val" name="modifications"/>
         <expand macro="list_string_san" name="modifications"/>
       </param>
-      <param name="scoring" argument="-RNPxl:scoring" type="select" optional="true" label="Scoring algorithm used in prescoring (fast: total-loss, slow: all losses)" help="">
+      <param name="scoring" argument="-RNPxl:scoring" type="select" label="Scoring algorithm used in prescoring (fast: total-loss, slow: all losses)" help="">
         <option value="fast" selected="true">fast</option>
         <option value="slow">slow</option>
         <expand macro="list_string_san" name="scoring"/>
@@ -6024,12 +6097,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="filter_fractional_mass" argument="-RNPxl:filter_fractional_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag to filter non-crosslinks by fractional mass" help=""/>
       <param name="carbon_labeled_fragments" argument="-RNPxl:carbon_labeled_fragments" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate fragment shifts assuming full labeling of carbon" help="(e.g. completely labeled U13)"/>
       <param name="only_xl" argument="-RNPxl:only_xl" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only search cross-links and ignore non-cross-linked peptides" help=""/>
-      <param name="filter_small_peptide_mass" argument="-RNPxl:filter_small_peptide_mass" type="float" optional="true" value="600.0" label="Filter precursor that can only correspond to non-crosslinks by mass" help=""/>
-      <param name="marker_ions_tolerance" argument="-RNPxl:marker_ions_tolerance" type="float" optional="true" value="0.05" label="Tolerance used to determine marker ions (Da)" help=""/>
+      <param name="filter_small_peptide_mass" argument="-RNPxl:filter_small_peptide_mass" type="float" value="600.0" label="Filter precursor that can only correspond to non-crosslinks by mass" help=""/>
+      <param name="marker_ions_tolerance" argument="-RNPxl:marker_ions_tolerance" type="float" value="0.05" label="Tolerance used to determine marker ions (Da)" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -6047,7 +6120,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_RNPxlSearch_1 -->
+  <tests>
+    <!-- TOPP_RNPxlSearch_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -6055,7 +6129,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="RNPxlSearch_1_input.mzML"/>
       <param name="database" value="RNPxlSearch_1_input.fasta"/>
-      <output name="out" file="RNPxlSearch_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="RNPxlSearch_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <section name="precursor">
         <param name="mass_tolerance" value="20.0"/>
         <param name="mass_tolerance_unit" value="ppm"/>
@@ -6068,7 +6142,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="mass_tolerance_unit" value="ppm"/>
       </section>
       <section name="modifications">
-        <param name="fixed"/>
         <param name="variable" value="Oxidation (M)"/>
         <param name="variable_max_per_peptide" value="2"/>
       </section>
@@ -6085,7 +6158,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="length" value="2"/>
         <param name="sequence" value="GUA"/>
         <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
-        <param name="nt_groups" value=""/>
         <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
         <param name="can_cross_link" value="U"/>
         <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
@@ -6105,6 +6177,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_RNPxlSearch_2 -->
     <test expect_num_outputs="2">
@@ -6114,7 +6189,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="RNPxlSearch_1_input.mzML"/>
       <param name="database" value="RNPxlSearch_1_input.fasta"/>
-      <output name="out" file="RNPxlSearch_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="RNPxlSearch_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <section name="precursor">
         <param name="mass_tolerance" value="20.0"/>
         <param name="mass_tolerance_unit" value="ppm"/>
@@ -6127,7 +6202,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="mass_tolerance_unit" value="ppm"/>
       </section>
       <section name="modifications">
-        <param name="fixed"/>
         <param name="variable" value="Oxidation (M)"/>
         <param name="variable_max_per_peptide" value="2"/>
       </section>
@@ -6144,7 +6218,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="length" value="2"/>
         <param name="sequence" value="GUA"/>
         <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
-        <param name="nt_groups" value=""/>
         <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
         <param name="can_cross_link" value="U"/>
         <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
@@ -6164,6 +6237,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_RNPxlSearch_3 -->
     <test expect_num_outputs="3">
@@ -6173,8 +6249,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="RNPxlSearch_1_input.mzML"/>
       <param name="database" value="RNPxlSearch_1_input.fasta"/>
-      <output name="out" file="RNPxlSearch_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <output name="out_tsv" file="RNPxlSearch_3_output2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="RNPxlSearch_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out_tsv" value="RNPxlSearch_3_output2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <section name="precursor">
         <param name="mass_tolerance" value="10.0"/>
         <param name="mass_tolerance_unit" value="ppm"/>
@@ -6187,8 +6263,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="mass_tolerance_unit" value="ppm"/>
       </section>
       <section name="modifications">
-        <param name="fixed"/>
-        <param name="variable"/>
         <param name="variable_max_per_peptide" value="2"/>
       </section>
       <section name="peptide">
@@ -6204,7 +6278,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="length" value="2"/>
         <param name="sequence" value=""/>
         <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
-        <param name="nt_groups" value=""/>
         <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
         <param name="can_cross_link" value="U"/>
         <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
@@ -6224,6 +6297,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_RNPxlSearch_4 -->
     <test expect_num_outputs="3">
@@ -6233,8 +6309,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </section>
       <param name="in" value="RNPxlSearch_1_input.mzML"/>
       <param name="database" value="RNPxlSearch_1_input.fasta"/>
-      <output name="out" file="RNPxlSearch_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <output name="out_tsv" file="RNPxlSearch_4_output2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="RNPxlSearch_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out_tsv" value="RNPxlSearch_4_output2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <section name="precursor">
         <param name="mass_tolerance" value="10.0"/>
         <param name="mass_tolerance_unit" value="ppm"/>
@@ -6247,8 +6323,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="mass_tolerance_unit" value="ppm"/>
       </section>
       <section name="modifications">
-        <param name="fixed"/>
-        <param name="variable"/>
         <param name="variable_max_per_peptide" value="2"/>
       </section>
       <section name="peptide">
@@ -6264,7 +6338,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="length" value="2"/>
         <param name="sequence" value=""/>
         <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
-        <param name="nt_groups" value=""/>
         <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
         <param name="can_cross_link" value="U"/>
         <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
@@ -6284,11 +6357,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Annotate RNA/DNA-peptide cross-links in MS/MS spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RNPxlSearch.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_RNPxlSearch.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/RNPxlXICFilter.xml b/tools/openms/RNPxlXICFilter.xml
index e11c988f9..6805ab786 100644
--- a/tools/openms/RNPxlXICFilter.xml
+++ b/tools/openms/RNPxlXICFilter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Cross-Linking]-->
 <tool id="RNPxlXICFilter" name="RNPxlXICFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Remove MS2 spectra from treatment based on the fold change between control and treatment.</description>
+  <description>Remove MS2 spectra from treatment based on the fold change between control and treatment</description>
   <macros>
     <token name="@EXECUTABLE@">RNPxlXICFilter</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir control &&
-ln -s '$control' 'control/${re.sub("[^\w\-_]", "_", $control.element_identifier)}.$gxy2omsext($control.ext)' &&
+cp '$control' 'control/${re.sub("[^\w\-_]", "_", $control.element_identifier)}.$gxy2omsext($control.ext)' &&
 mkdir treatment &&
-ln -s '$treatment' 'treatment/${re.sub("[^\w\-_]", "_", $treatment.element_identifier)}.$gxy2omsext($treatment.ext)' &&
+cp '$treatment' 'treatment/${re.sub("[^\w\-_]", "_", $treatment.element_identifier)}.$gxy2omsext($treatment.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -43,14 +42,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-control" type="data" format="mzml" optional="false" label="input mzML file" help=" select mzml data sets(s)"/>
-    <param argument="-treatment" type="data" format="mzml" optional="false" label="input mzML file" help=" select mzml data sets(s)"/>
-    <param argument="-fold_change" type="float" optional="true" value="2.0" label="fold change between XICs" help=""/>
-    <param argument="-rt_tol" type="float" optional="true" value="20.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/>
-    <param argument="-mz_tol" type="float" optional="true" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/>
+    <param argument="-control" type="data" format="mzml" label="input mzML file" help=" select mzml data sets(s)"/>
+    <param argument="-treatment" type="data" format="mzml" label="input mzML file" help=" select mzml data sets(s)"/>
+    <param argument="-fold_change" type="float" value="2.0" label="fold change between XICs" help=""/>
+    <param argument="-rt_tol" type="float" value="20.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/>
+    <param argument="-mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -64,16 +63,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input (2x the same which is likely nonsense, but sufficient for the test) and autgenerated output-->
-    <param name="adv_opts|test" value="true"/>
-    <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/>
-    <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/>
-    <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- just chosen an arbitrary input (2x the same which is likely nonsense, but sufficient for the test) and autgenerated output-->
+      <param name="adv_opts|test" value="true"/>
+      <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/>
+      <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/>
+      <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/>
+    </test>
+  </tests>
   <help><![CDATA[Remove MS2 spectra from treatment based on the fold change between control and treatment.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RNPxlXICFilter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_RNPxlXICFilter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/RTEvaluation.xml b/tools/openms/RTEvaluation.xml
deleted file mode 100644
index 0ae73381b..000000000
--- a/tools/openms/RTEvaluation.xml
+++ /dev/null
@@ -1,83 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
-<tool id="RTEvaluation" name="RTEvaluation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</description>
-  <macros>
-    <token name="@EXECUTABLE@">RTEvaluation</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-#if $sequences_file:
-  mkdir sequences_file &&
-  ln -s '$sequences_file' 'sequences_file/${re.sub("[^\w\-_]", "_", $sequences_file.element_identifier)}.$gxy2omsext($sequences_file.ext)' &&
-#end if
-mkdir out &&
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in
-'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-#if $sequences_file:
-  -sequences_file
-  'sequences_file/${re.sub("[^\w\-_]", "_", $sequences_file.element_identifier)}.$gxy2omsext($sequences_file.ext)'
-#end if
--out
-'out/output.${gxy2omsext("tabular")}'
-
-## Postprocessing
-&& mv 'out/output.${gxy2omsext("tabular")}' '$out'
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
-  </configfiles>
-  <inputs>
-    <param argument="-in" type="data" format="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/>
-    <param argument="-sequences_file" type="data" format="fasta" optional="true" label="Fasta File" help=" select fasta data sets(s)"/>
-    <param argument="-latex" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Indicates whether the output file format of the table should be LaTeX or TSV (default)" help=""/>
-    <param argument="-p_value_dim_1" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Significance level of first dimension RT filte" help=""/>
-    <param argument="-p_value_dim_2" type="float" optional="true" min="0.0" max="1.0" value="0.05" label="Significance level of second dimension RT filte" help=""/>
-    <expand macro="adv_opts_macro">
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="tabular"/>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><!-- just chosen an arbitrary input and autgenerated output-->
-  <test expect_num_outputs="1">
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/>
-    <output name="out" ftype="tabular" value="RTEvaluation.tsv"/>
-  </test>
-</tests>
-  <help><![CDATA[Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RTEvaluation.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/RTModel.xml b/tools/openms/RTModel.xml
deleted file mode 100644
index 4c6eba7b1..000000000
--- a/tools/openms/RTModel.xml
+++ /dev/null
@@ -1,356 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Peptide property prediction]-->
-<tool id="RTModel" name="RTModel" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Trains a model for the retention time prediction of peptides from a training set.</description>
-  <macros>
-    <token name="@EXECUTABLE@">RTModel</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-#if $in:
-  mkdir in &&
-  ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-#end if
-#if $in_positive:
-  mkdir in_positive &&
-  ln -s '$in_positive' 'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)' &&
-#end if
-#if $in_negative:
-  mkdir in_negative &&
-  ln -s '$in_negative' 'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)' &&
-#end if
-mkdir out &&
-#if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out_oligo_params &&
-#end if
-#if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out_oligo_trainset &&
-#end if
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-#if $in:
-  -in
-  'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-#end if
-#if $in_positive:
-  -in_positive
-  'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)'
-#end if
-#if $in_negative:
-  -in_negative
-  'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)'
-#end if
--out
-'out/output.${gxy2omsext("txt")}'
-#if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out_oligo_params
-  'out_oligo_params/output.${gxy2omsext("paramxml")}'
-#end if
-#if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out_oligo_trainset
-  'out_oligo_trainset/output.${gxy2omsext("txt")}'
-#end if
-#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
-  | tee '$stdout'
-#end if
-
-## Postprocessing
-&& mv 'out/output.${gxy2omsext("txt")}' '$out'
-#if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out_oligo_params/output.${gxy2omsext("paramxml")}' '$out_oligo_params'
-#end if
-#if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out_oligo_trainset/output.${gxy2omsext("txt")}' '$out_oligo_trainset'
-#end if
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
-  </configfiles>
-  <inputs>
-    <param argument="-in" type="data" format="idxml,txt" optional="true" label="This is the name of the input file (RT prediction)" help="It is assumed that the file type is idXML. Alternatively you can provide a .txt file having a sequence and the corresponding rt per line..  select idxml,txt data sets(s)"/>
-    <param argument="-in_positive" type="data" format="idxml" optional="true" label="input file with positive examples (peptide separation prediction)" help=" select idxml data sets(s)"/>
-    <param argument="-in_negative" type="data" format="idxml" optional="true" label="input file with negative examples (peptide separation prediction)" help=" select idxml data sets(s)"/>
-    <param argument="-svm_type" type="select" optional="true" label="the type of the svm (NU_SVR or EPSILON_SVR for RT prediction, automatically set" help="to C_SVC for separation prediction). ">
-      <option value="NU_SVR" selected="true">NU_SVR</option>
-      <option value="NU_SVC">NU_SVC</option>
-      <option value="EPSILON_SVR">EPSILON_SVR</option>
-      <option value="C_SVC">C_SVC</option>
-      <expand macro="list_string_san" name="svm_type"/>
-    </param>
-    <param argument="-nu" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="the nu parameter [0..1] of the svm (for nu-SVR)" help=""/>
-    <param argument="-p" type="float" optional="true" value="0.1" label="the epsilon parameter of the svm (for epsilon-SVR)" help=""/>
-    <param argument="-c" type="float" optional="true" value="1.0" label="the penalty parameter of the svm" help=""/>
-    <param argument="-kernel_type" type="select" optional="true" label="the kernel type of the svm" help="">
-      <option value="LINEAR">LINEAR</option>
-      <option value="RBF">RBF</option>
-      <option value="POLY">POLY</option>
-      <option value="OLIGO" selected="true">OLIGO</option>
-      <expand macro="list_string_san" name="kernel_type"/>
-    </param>
-    <param argument="-degree" type="integer" optional="true" min="1" value="1" label="the degree parameter of the kernel function of the svm (POLY kernel)" help=""/>
-    <param argument="-border_length" type="integer" optional="true" min="1" value="22" label="length of the POBK" help=""/>
-    <param argument="-max_std" type="float" optional="true" min="0.0" value="10.0" label="max standard deviation for a peptide to be included (if there are several ones for one peptide string)(median is taken)" help=""/>
-    <param argument="-k_mer_length" type="integer" optional="true" min="1" value="1" label="k_mer length of the POBK" help=""/>
-    <param argument="-sigma" type="float" optional="true" value="5.0" label="sigma of the POBK" help=""/>
-    <param argument="-total_gradient_time" type="float" optional="true" min="1e-05" value="1.0" label="the time (in seconds) of the gradient (only for RT prediction)" help=""/>
-    <param argument="-first_dim_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if set the model will be built for first_dim_rt" help=""/>
-    <param argument="-additive_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if the step sizes should be interpreted additively (otherwise the actual value is multiplied" help="with the step size to get the new value"/>
-    <section name="cv" title="Parameters for the grid search / cross validation:" help="" expanded="false">
-      <param name="skip_cv" argument="-cv:skip_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to enable Cross-Validation or set to true if the model should just be trained with 1 set of specified parameters" help=""/>
-      <param name="number_of_runs" argument="-cv:number_of_runs" type="integer" optional="true" min="1" value="1" label="number of runs for the CV (each run creates a new random partition of the data)" help=""/>
-      <param name="number_of_partitions" argument="-cv:number_of_partitions" type="integer" optional="true" min="2" value="10" label="number of CV partitions" help=""/>
-      <param name="degree_start" argument="-cv:degree_start" type="integer" optional="true" min="1" value="1" label="starting point of degree" help=""/>
-      <param name="degree_step_size" argument="-cv:degree_step_size" type="integer" optional="true" value="2" label="step size point of degree" help=""/>
-      <param name="degree_stop" argument="-cv:degree_stop" type="integer" optional="true" value="4" label="stopping point of degree" help=""/>
-      <param name="p_start" argument="-cv:p_start" type="float" optional="true" value="1.0" label="starting point of p" help=""/>
-      <param name="p_step_size" argument="-cv:p_step_size" type="float" optional="true" value="10.0" label="step size point of p" help=""/>
-      <param name="p_stop" argument="-cv:p_stop" type="float" optional="true" value="1000.0" label="stopping point of p" help=""/>
-      <param name="c_start" argument="-cv:c_start" type="float" optional="true" value="1.0" label="starting point of c" help=""/>
-      <param name="c_step_size" argument="-cv:c_step_size" type="float" optional="true" value="10.0" label="step size of c" help=""/>
-      <param name="c_stop" argument="-cv:c_stop" type="float" optional="true" value="1000.0" label="stopping point of c" help=""/>
-      <param name="nu_start" argument="-cv:nu_start" type="float" optional="true" min="0.0" max="1.0" value="0.3" label="starting point of nu" help=""/>
-      <param name="nu_step_size" argument="-cv:nu_step_size" type="float" optional="true" value="1.2" label="step size of nu" help=""/>
-      <param name="nu_stop" argument="-cv:nu_stop" type="float" optional="true" min="0.0" max="1.0" value="0.7" label="stopping point of nu" help=""/>
-      <param name="sigma_start" argument="-cv:sigma_start" type="float" optional="true" value="1.0" label="starting point of sigma" help=""/>
-      <param name="sigma_step_size" argument="-cv:sigma_step_size" type="float" optional="true" value="1.3" label="step size of sigma" help=""/>
-      <param name="sigma_stop" argument="-cv:sigma_stop" type="float" optional="true" value="15.0" label="stopping point of sigma" help=""/>
-    </section>
-    <expand macro="adv_opts_macro">
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="out_oligo_params_FLAG">out_oligo_params (output file with additional model parameters when using the OLIGO kernel)</option>
-      <option value="out_oligo_trainset_FLAG">out_oligo_trainset (output file with the used training dataset when using the OLIGO kernel)</option>
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
-    <data name="out_oligo_params" label="${tool.name} on ${on_string}: out_oligo_params" format="paramxml">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_oligo_params_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="out_oligo_trainset" label="${tool.name} on ${on_string}: out_oligo_trainset" format="txt">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_oligo_trainset_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><!-- TOPP_RTModel_1 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="RTModel_1_input.idXML"/>
-      <output name="out" file="RTModel_1_output.model" compare="sim_size" delta_frac="0.7" ftype="txt"/>
-      <param name="svm_type" value="NU_SVR"/>
-      <param name="nu" value="0.5"/>
-      <param name="p" value="0.1"/>
-      <param name="c" value="0.1"/>
-      <param name="kernel_type" value="POLY"/>
-      <param name="degree" value="1"/>
-      <param name="border_length" value="22"/>
-      <param name="max_std" value="10.0"/>
-      <param name="k_mer_length" value="1"/>
-      <param name="sigma" value="5.0"/>
-      <param name="total_gradient_time" value="3000.0"/>
-      <param name="first_dim_rt" value="false"/>
-      <param name="additive_cv" value="false"/>
-      <section name="cv">
-        <param name="skip_cv" value="true"/>
-        <param name="number_of_runs" value="10"/>
-        <param name="number_of_partitions" value="10"/>
-        <param name="degree_start" value="1"/>
-        <param name="degree_step_size" value="2"/>
-        <param name="degree_stop" value="4"/>
-        <param name="p_start" value="1.0"/>
-        <param name="p_step_size" value="10.0"/>
-        <param name="p_stop" value="1000.0"/>
-        <param name="c_start" value="1.0"/>
-        <param name="c_step_size" value="10.0"/>
-        <param name="c_stop" value="1000.0"/>
-        <param name="nu_start" value="0.3"/>
-        <param name="nu_step_size" value="1.2"/>
-        <param name="nu_stop" value="0.7"/>
-        <param name="sigma_start" value="1.0"/>
-        <param name="sigma_step_size" value="1.3"/>
-        <param name="sigma_stop" value="15.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_RTModel_2 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in_positive" value="RTModel_2_input_positive.idXML"/>
-      <param name="in_negative" value="RTModel_2_input_negative.idXML"/>
-      <output name="out" file="RTModel_2_output.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/>
-      <param name="svm_type" value="NU_SVR"/>
-      <param name="nu" value="0.5"/>
-      <param name="p" value="0.1"/>
-      <param name="c" value="0.5"/>
-      <param name="kernel_type" value="OLIGO"/>
-      <param name="degree" value="1"/>
-      <param name="border_length" value="22"/>
-      <param name="max_std" value="10.0"/>
-      <param name="k_mer_length" value="1"/>
-      <param name="sigma" value="5.0"/>
-      <param name="total_gradient_time" value="1.0"/>
-      <param name="first_dim_rt" value="false"/>
-      <param name="additive_cv" value="false"/>
-      <section name="cv">
-        <param name="skip_cv" value="true"/>
-        <param name="number_of_runs" value="10"/>
-        <param name="number_of_partitions" value="10"/>
-        <param name="degree_start" value="1"/>
-        <param name="degree_step_size" value="2"/>
-        <param name="degree_stop" value="4"/>
-        <param name="p_start" value="1.0"/>
-        <param name="p_step_size" value="10.0"/>
-        <param name="p_stop" value="1000.0"/>
-        <param name="c_start" value="1.0"/>
-        <param name="c_step_size" value="10.0"/>
-        <param name="c_stop" value="1000.0"/>
-        <param name="nu_start" value="0.3"/>
-        <param name="nu_step_size" value="1.2"/>
-        <param name="nu_stop" value="0.7"/>
-        <param name="sigma_start" value="1.0"/>
-        <param name="sigma_step_size" value="1.3"/>
-        <param name="sigma_stop" value="15.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_RTModel_3 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="RTModel_3_input.idXML"/>
-      <output name="out" file="RTModel_3_output.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/>
-      <param name="svm_type" value="NU_SVR"/>
-      <param name="nu" value="0.5"/>
-      <param name="p" value="0.1"/>
-      <param name="c" value="0.001953125"/>
-      <param name="kernel_type" value="OLIGO"/>
-      <param name="degree" value="1"/>
-      <param name="border_length" value="22"/>
-      <param name="max_std" value="10.0"/>
-      <param name="k_mer_length" value="1"/>
-      <param name="sigma" value="1.0"/>
-      <param name="total_gradient_time" value="1.0"/>
-      <param name="first_dim_rt" value="false"/>
-      <param name="additive_cv" value="false"/>
-      <section name="cv">
-        <param name="skip_cv" value="false"/>
-        <param name="number_of_runs" value="1"/>
-        <param name="number_of_partitions" value="5"/>
-        <param name="degree_start" value="1"/>
-        <param name="degree_step_size" value="2"/>
-        <param name="degree_stop" value="4"/>
-        <param name="p_start" value="1.0"/>
-        <param name="p_step_size" value="10.0"/>
-        <param name="p_stop" value="1000.0"/>
-        <param name="c_start" value="0.001953125"/>
-        <param name="c_step_size" value="2.0"/>
-        <param name="c_stop" value="0.001953125"/>
-        <param name="nu_start" value="0.4"/>
-        <param name="nu_step_size" value="1.2"/>
-        <param name="nu_stop" value="0.4"/>
-        <param name="sigma_start" value="5.0"/>
-        <param name="sigma_step_size" value="1.221055"/>
-        <param name="sigma_stop" value="5.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_RTModel_4 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="RTModel_4_input.txt" ftype="txt"/>
-      <output name="out" file="RTModel_4_output.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/>
-      <param name="svm_type" value="NU_SVR"/>
-      <param name="nu" value="0.5"/>
-      <param name="p" value="0.1"/>
-      <param name="c" value="0.001953125"/>
-      <param name="kernel_type" value="OLIGO"/>
-      <param name="degree" value="1"/>
-      <param name="border_length" value="22"/>
-      <param name="max_std" value="10.0"/>
-      <param name="k_mer_length" value="1"/>
-      <param name="sigma" value="1.0"/>
-      <param name="total_gradient_time" value="1.0"/>
-      <param name="first_dim_rt" value="false"/>
-      <param name="additive_cv" value="false"/>
-      <section name="cv">
-        <param name="skip_cv" value="false"/>
-        <param name="number_of_runs" value="1"/>
-        <param name="number_of_partitions" value="5"/>
-        <param name="degree_start" value="1"/>
-        <param name="degree_step_size" value="2"/>
-        <param name="degree_stop" value="4"/>
-        <param name="p_start" value="1.0"/>
-        <param name="p_step_size" value="10.0"/>
-        <param name="p_stop" value="1000.0"/>
-        <param name="c_start" value="0.001953125"/>
-        <param name="c_step_size" value="2.0"/>
-        <param name="c_stop" value="0.001953125"/>
-        <param name="nu_start" value="0.4"/>
-        <param name="nu_step_size" value="1.2"/>
-        <param name="nu_stop" value="0.4"/>
-        <param name="sigma_start" value="5.0"/>
-        <param name="sigma_step_size" value="1.221055"/>
-        <param name="sigma_stop" value="5.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
-  <help><![CDATA[Trains a model for the retention time prediction of peptides from a training set.
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_RTModel.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/MyriMatchAdapter.xml b/tools/openms/SageAdapter.xml
similarity index 94%
rename from tools/openms/MyriMatchAdapter.xml
rename to tools/openms/SageAdapter.xml
index 8a2de1db5..a86b083c1 100644
--- a/tools/openms/MyriMatchAdapter.xml
+++ b/tools/openms/SageAdapter.xml
@@ -1,10 +1,9 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
-<tool id="MyriMatchAdapter" name="MyriMatchAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Annotates MS/MS spectra using MyriMatch.</description>
+<!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
+<tool id="SageAdapter" name="SageAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+  <description>Annotates MS/MS spectra using Sage</description>
   <macros>
-    <token name="@EXECUTABLE@">MyriMatchAdapter</token>
+    <token name="@EXECUTABLE@">SageAdapter</token>
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
@@ -14,11 +13,16 @@
 #import re
 
 ## Preprocessing
-mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir in_cond.in &&
+#if $in_cond.in_select == "no"
+mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+#else
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+#end if
 mkdir out &&
 mkdir database &&
-ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
 
 ## Main program call
 
@@ -27,7 +31,11 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+#if $in_cond.in_select == "no"
+${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+#else
+'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
+#end if
 -out
 'out/output.${gxy2omsext("idxml")}'
 -database
@@ -40,25 +48,77 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 #end if]]></command>
   <configfiles>
     <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"myrimatch_executable": "myrimatch", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+    <configfile name="hardcoded_json"><![CDATA[{"sage_executable": "sage", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
-    <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance" help=""/>
-    <param argument="-precursor_mass_tolerance_unit" type="select" optional="true" label="Unit to be used for precursor mass tolerance" help="">
+    <conditional name="in_cond">
+      <param name="in_select" type="select" label="Run tool in batch mode for -in">
+        <option value="no">No: process all datasets jointly</option>
+        <option value="yes">Yes: process each dataset in an independent job</option>
+      </param>
+      <when value="no">
+        <param argument="-in" type="data" format="mzml" multiple="true" label="Input files separated by blank" help=" select mzml data sets(s)"/>
+      </when>
+      <when value="yes">
+        <param argument="-in" type="data" format="mzml" label="Input files separated by blank" help=" select mzml data sets(s)"/>
+      </when>
+    </conditional>
+    <param argument="-database" type="data" format="fasta" label="FASTA file" help=" select fasta data sets(s)"/>
+    <param argument="-decoy_prefix" type="text" value="DECOY_" label="Prefix on protein accession used to distinguish decoy from target proteins" help="NOTE: Decoy suffix is currently not supported by sage">
+      <expand macro="list_string_san" name="decoy_prefix"/>
+    </param>
+    <param argument="-batch_size" type="integer" value="0" label="Number of files to load and search in parallel (default = # of CPUs/2)" help=""/>
+    <param argument="-precursor_tol_left" type="float" value="-6.0" label="Start (left side) of the precursor tolerance window w.r.t" help="precursor location. Usually used with negative values smaller or equal to the 'right' counterpart"/>
+    <param argument="-precursor_tol_right" type="float" value="6.0" label="End (right side) of the precursor tolerance window w.r.t" help="precursor location. Usually used with positive values larger or equal to the 'left' counterpart"/>
+    <param argument="-precursor_tol_unit" type="select" label="Unit of precursor tolerance (ppm or Da)" help="">
+      <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
+      <expand macro="list_string_san" name="precursor_tol_unit"/>
+    </param>
+    <param argument="-fragment_tol_left" type="float" value="-20.0" label="Start (left side) of the fragment tolerance window w.r.t" help="precursor location. Usually used with negative values smaller or equal to the 'right' counterpart"/>
+    <param argument="-fragment_tol_right" type="float" value="20.0" label="End (right side) of the fragment tolerance window w.r.t" help="precursor location. Usually used with positive values larger or equal to the 'left' counterpart"/>
+    <param argument="-fragment_tol_unit" type="select" label="Unit of fragment tolerance (ppm or Da)" help="">
       <option value="ppm" selected="true">ppm</option>
-      <expand macro="list_string_san" name="precursor_mass_tolerance_unit"/>
+      <option value="Da">Da</option>
+      <expand macro="list_string_san" name="fragment_tol_unit"/>
     </param>
-    <param argument="-precursor_mass_tolerance_avg" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set, the average mass is used in the precursor mass tolerance" help=""/>
-    <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.3" label="Fragment mass error in Dalton" help=""/>
-    <param argument="-fragment_mass_tolerance_unit" type="select" optional="true" label="Unit to be used for fragment mass tolerance" help="">
-      <option value="Da" selected="true">Da</option>
-      <option value="ppm">ppm</option>
-      <expand macro="list_string_san" name="fragment_mass_tolerance_unit"/>
+    <param argument="-enzyme" type="select" label="The enzyme used for peptide digestion" help="">
+      <option value="Arg-C/P">Arg-C/P</option>
+      <option value="Asp-N">Asp-N</option>
+      <option value="Asp-N/B">Asp-N/B</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
+      <option value="Arg-C">Arg-C</option>
+      <option value="Clostripain/P">Clostripain/P</option>
+      <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+      <option value="no cleavage">no cleavage</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="staphylococcal protease/D">staphylococcal protease/D</option>
+      <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
+      <option value="Glu-C+P">Glu-C+P</option>
+      <option value="PepsinA + P">PepsinA + P</option>
+      <option value="cyanogen-bromide">cyanogen-bromide</option>
+      <option value="leukocyte elastase">leukocyte elastase</option>
+      <option value="proline endopeptidase">proline endopeptidase</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
+      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+      <option value="CNBr">CNBr</option>
+      <option value="Formic_acid">Formic_acid</option>
+      <option value="Lys-C">Lys-C</option>
+      <option value="Lys-N">Lys-N</option>
+      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="PepsinA">PepsinA</option>
+      <option value="TrypChymo">TrypChymo</option>
+      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="V8-DE">V8-DE</option>
+      <option value="V8-E">V8-E</option>
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+      <option value="2-iodobenzoate">2-iodobenzoate</option>
+      <option value="iodosobenzoate">iodosobenzoate</option>
+      <expand macro="list_string_san" name="enzyme"/>
     </param>
-    <param argument="-database" type="data" format="fasta" optional="false" label="FASTA protein database" help=" select fasta data sets(s)"/>
-    <param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
+    <param argument="-fixed_modifications" type="select" multiple="true" optional="false" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
       <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
       <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
       <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -68,6 +128,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="2-succinyl (C)">2-succinyl (C)</option>
       <option value="2HPG (R)">2HPG (R)</option>
       <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+      <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+      <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+      <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+      <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
       <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
       <option value="3sulfo (N-term)">3sulfo (N-term)</option>
       <option value="4-ONE (C)">4-ONE (C)</option>
@@ -157,6 +221,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
       <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
       <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+      <option value="Andro-H2O (C)">Andro-H2O (C)</option>
       <option value="Archaeol (C)">Archaeol (C)</option>
       <option value="Arg (N-term)">Arg (N-term)</option>
       <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -260,6 +325,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
       <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
       <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+      <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
       <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
       <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
       <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -292,7 +358,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="BITC (N-term)">BITC (N-term)</option>
       <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
       <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-      <option value="Bodipy (C)">Bodipy (C)</option>
       <option value="Brij35 (N-term)">Brij35 (N-term)</option>
       <option value="Brij58 (N-term)">Brij58 (N-term)</option>
       <option value="Bromo (F)">Bromo (F)</option>
@@ -724,9 +789,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Dehydrated (T)">Dehydrated (T)</option>
       <option value="Dehydrated (Y)">Dehydrated (Y)</option>
       <option value="Dehydro (C)">Dehydro (C)</option>
+      <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
       <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-      <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
       <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
       <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -736,7 +801,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
       <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
       <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-      <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
       <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
       <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -748,6 +812,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
       <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
       <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+      <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
       <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
       <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -1320,7 +1385,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Ethanolyl (C)">Ethanolyl (C)</option>
       <option value="Ethanolyl (K)">Ethanolyl (K)</option>
       <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-      <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
       <option value="Ethyl (C-term)">Ethyl (C-term)</option>
       <option value="Ethyl (D)">Ethyl (D)</option>
       <option value="Ethyl (E)">Ethyl (E)</option>
@@ -1414,6 +1478,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
       <option value="Glu (E)">Glu (E)</option>
       <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+      <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
       <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
       <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
       <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -1428,7 +1493,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
       <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
       <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
       <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -1452,6 +1516,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gly (K)">Gly (K)</option>
       <option value="Gly (S)">Gly (S)</option>
       <option value="Gly (T)">Gly (T)</option>
+      <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
       <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
       <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
       <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -1842,6 +1907,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
       <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
       <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+      <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
       <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
       <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
       <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -1853,6 +1919,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
       <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
       <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+      <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+      <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+      <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
       <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
       <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
       <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -1908,6 +1977,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
       <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
       <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+      <option value="His+O(2) (H)">His+O(2) (H)</option>
       <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
       <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
       <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -2045,11 +2115,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+      <option value="Kdo (S)">Kdo (S)</option>
+      <option value="Kdo (T)">Kdo (T)</option>
       <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
       <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
       <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
       <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
       <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+      <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
       <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
       <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
       <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -2134,13 +2207,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
       <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
       <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+      <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
       <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
       <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
       <option value="Lipoyl (K)">Lipoyl (K)</option>
       <option value="LRGG (K)">LRGG (K)</option>
       <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
       <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+      <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
       <option value="Lys (N-term)">Lys (N-term)</option>
+      <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
       <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
       <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
       <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -2175,6 +2251,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Malonyl (C)">Malonyl (C)</option>
       <option value="Malonyl (K)">Malonyl (K)</option>
       <option value="Malonyl (S)">Malonyl (S)</option>
+      <option value="MBS+peptide (C)">MBS+peptide (C)</option>
       <option value="MDCC (C)">MDCC (C)</option>
       <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
       <option value="Menadione (C)">Menadione (C)</option>
@@ -2186,6 +2263,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="MesitylOxide (H)">MesitylOxide (H)</option>
       <option value="MesitylOxide (K)">MesitylOxide (K)</option>
       <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+      <option value="Met+O(2) (H)">Met+O(2) (H)</option>
       <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
       <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
       <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -2369,7 +2447,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
       <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
       <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-      <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
       <option value="NP40 (N-term)">NP40 (N-term)</option>
       <option value="NQIGG (K)">NQIGG (K)</option>
       <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -2457,6 +2534,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
       <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
       <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+      <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+      <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+      <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+      <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
       <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
       <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
       <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -2471,6 +2552,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phospho (Y)">Phospho (Y)</option>
       <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
       <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+      <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
       <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
       <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
       <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -2502,6 +2584,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
       <option value="Piperidine (K)">Piperidine (K)</option>
       <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+      <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
       <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
       <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
       <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -2579,18 +2662,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="QTGG (K)">QTGG (K)</option>
       <option value="Quinone (W)">Quinone (W)</option>
       <option value="Quinone (Y)">Quinone (Y)</option>
+      <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+      <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+      <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+      <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+      <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+      <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+      <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+      <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+      <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+      <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+      <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+      <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+      <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+      <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+      <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+      <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+      <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+      <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+      <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+      <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
       <option value="Retinylidene (K)">Retinylidene (K)</option>
       <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
       <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
       <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-      <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-      <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-      <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-      <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-      <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-      <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-      <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-      <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
       <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
       <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
       <option value="Saligenin (H)">Saligenin (H)</option>
@@ -2618,6 +2713,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="shTMT (K)">shTMT (K)</option>
       <option value="shTMT (N-term)">shTMT (N-term)</option>
       <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+      <option value="shTMTpro (K)">shTMTpro (K)</option>
+      <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+      <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
       <option value="SMA (K)">SMA (K)</option>
       <option value="SMA (N-term)">SMA (N-term)</option>
       <option value="spermidine (Q)">spermidine (Q)</option>
@@ -2793,7 +2891,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
       <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
       <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-      <option value="Ub-amide (C)">Ub-amide (C)</option>
       <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
       <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
       <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -2988,7 +3085,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="ZQG (K)">ZQG (K)</option>
       <expand macro="list_string_san" name="fixed_modifications"/>
     </param>
-    <param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
+    <param argument="-variable_modifications" type="select" multiple="true" optional="false" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
       <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
       <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
       <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -2998,6 +3095,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="2-succinyl (C)">2-succinyl (C)</option>
       <option value="2HPG (R)">2HPG (R)</option>
       <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+      <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+      <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+      <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+      <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
       <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
       <option value="3sulfo (N-term)">3sulfo (N-term)</option>
       <option value="4-ONE (C)">4-ONE (C)</option>
@@ -3087,6 +3188,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
       <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
       <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+      <option value="Andro-H2O (C)">Andro-H2O (C)</option>
       <option value="Archaeol (C)">Archaeol (C)</option>
       <option value="Arg (N-term)">Arg (N-term)</option>
       <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -3190,6 +3292,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
       <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
       <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+      <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
       <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
       <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
       <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -3222,7 +3325,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="BITC (N-term)">BITC (N-term)</option>
       <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
       <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-      <option value="Bodipy (C)">Bodipy (C)</option>
       <option value="Brij35 (N-term)">Brij35 (N-term)</option>
       <option value="Brij58 (N-term)">Brij58 (N-term)</option>
       <option value="Bromo (F)">Bromo (F)</option>
@@ -3654,9 +3756,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Dehydrated (T)">Dehydrated (T)</option>
       <option value="Dehydrated (Y)">Dehydrated (Y)</option>
       <option value="Dehydro (C)">Dehydro (C)</option>
+      <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
       <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-      <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
       <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
       <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -3666,7 +3768,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
       <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
       <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-      <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
       <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
       <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -3678,6 +3779,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
       <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
       <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+      <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
       <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
       <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -4250,7 +4352,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Ethanolyl (C)">Ethanolyl (C)</option>
       <option value="Ethanolyl (K)">Ethanolyl (K)</option>
       <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-      <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
       <option value="Ethyl (C-term)">Ethyl (C-term)</option>
       <option value="Ethyl (D)">Ethyl (D)</option>
       <option value="Ethyl (E)">Ethyl (E)</option>
@@ -4344,6 +4445,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
       <option value="Glu (E)">Glu (E)</option>
       <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+      <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
       <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
       <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
       <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -4358,7 +4460,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
       <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
       <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
       <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -4382,6 +4483,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gly (K)">Gly (K)</option>
       <option value="Gly (S)">Gly (S)</option>
       <option value="Gly (T)">Gly (T)</option>
+      <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
       <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
       <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
       <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -4772,6 +4874,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
       <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
       <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+      <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
       <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
       <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
       <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -4783,6 +4886,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
       <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
       <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+      <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+      <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+      <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
       <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
       <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
       <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -4838,6 +4944,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
       <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
       <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+      <option value="His+O(2) (H)">His+O(2) (H)</option>
       <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
       <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
       <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -4975,11 +5082,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+      <option value="Kdo (S)">Kdo (S)</option>
+      <option value="Kdo (T)">Kdo (T)</option>
       <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
       <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
       <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
       <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
       <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+      <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
       <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
       <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
       <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -5064,13 +5174,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
       <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
       <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+      <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
       <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
       <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
       <option value="Lipoyl (K)">Lipoyl (K)</option>
       <option value="LRGG (K)">LRGG (K)</option>
       <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
       <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+      <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
       <option value="Lys (N-term)">Lys (N-term)</option>
+      <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
       <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
       <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
       <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -5105,6 +5218,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Malonyl (C)">Malonyl (C)</option>
       <option value="Malonyl (K)">Malonyl (K)</option>
       <option value="Malonyl (S)">Malonyl (S)</option>
+      <option value="MBS+peptide (C)">MBS+peptide (C)</option>
       <option value="MDCC (C)">MDCC (C)</option>
       <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
       <option value="Menadione (C)">Menadione (C)</option>
@@ -5116,6 +5230,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="MesitylOxide (H)">MesitylOxide (H)</option>
       <option value="MesitylOxide (K)">MesitylOxide (K)</option>
       <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+      <option value="Met+O(2) (H)">Met+O(2) (H)</option>
       <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
       <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
       <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -5299,7 +5414,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
       <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
       <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-      <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
       <option value="NP40 (N-term)">NP40 (N-term)</option>
       <option value="NQIGG (K)">NQIGG (K)</option>
       <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -5387,6 +5501,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
       <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
       <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+      <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+      <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+      <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+      <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
       <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
       <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
       <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -5401,6 +5519,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phospho (Y)">Phospho (Y)</option>
       <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
       <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+      <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
       <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
       <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
       <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -5432,6 +5551,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
       <option value="Piperidine (K)">Piperidine (K)</option>
       <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+      <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
       <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
       <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
       <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -5509,18 +5629,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="QTGG (K)">QTGG (K)</option>
       <option value="Quinone (W)">Quinone (W)</option>
       <option value="Quinone (Y)">Quinone (Y)</option>
+      <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+      <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+      <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+      <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+      <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+      <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+      <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+      <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+      <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+      <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+      <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+      <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+      <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+      <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+      <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+      <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+      <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+      <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+      <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+      <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
       <option value="Retinylidene (K)">Retinylidene (K)</option>
       <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
       <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
       <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-      <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-      <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-      <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-      <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-      <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-      <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-      <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-      <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
       <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
       <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
       <option value="Saligenin (H)">Saligenin (H)</option>
@@ -5548,6 +5680,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="shTMT (K)">shTMT (K)</option>
       <option value="shTMT (N-term)">shTMT (N-term)</option>
       <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+      <option value="shTMTpro (K)">shTMTpro (K)</option>
+      <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+      <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
       <option value="SMA (K)">SMA (K)</option>
       <option value="SMA (N-term)">SMA (N-term)</option>
       <option value="spermidine (Q)">spermidine (Q)</option>
@@ -5723,7 +5858,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
       <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
       <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-      <option value="Ub-amide (C)">Ub-amide (C)</option>
       <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
       <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
       <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -5918,52 +6052,105 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="ZQG (K)">ZQG (K)</option>
       <expand macro="list_string_san" name="variable_modifications"/>
     </param>
-    <param argument="-NumChargeStates" type="integer" optional="true" value="3" label="The number of charge states that MyriMatch will handle during all stages of the program" help=""/>
-    <param argument="-TicCutoffPercentage" type="float" optional="true" value="0.98" label="Noise peaks are filtered out by sorting the original peaks in descending order of intensity, and then picking peaks from that list until the cumulative ion current of the picked peaks divided by the total ion current (TIC) is greater than or equal to this paramete" help=""/>
-    <param argument="-MaxDynamicMods" type="integer" optional="true" value="2" label="This parameter sets the maximum number of modified residues that may be in any candidate sequence" help=""/>
-    <param argument="-MaxResultRank" type="integer" optional="true" value="5" label="This parameter sets the maximum rank of peptide-spectrum-matches to report for each spectrum" help=""/>
-    <param argument="-CleavageRules" type="select" optional="true" label="This parameter allows the user to control the way peptides are generated from the protein database" help="For more details, see http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MS&amp;termId=MS:1001045&amp;termName=cleavage%20agent%20name ">
-      <option value="Trypsin">Trypsin</option>
-      <option value="Trypsin/P">Trypsin/P</option>
-      <option value="Arg-C">Arg-C</option>
-      <option value="Asp-N">Asp-N</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="CNBr">CNBr</option>
-      <option value="Chymotrypsin">Chymotrypsin</option>
-      <option value="Formic_acid">Formic_acid</option>
-      <option value="Lys-C">Lys-C</option>
-      <option value="Lys-C/P">Lys-C/P</option>
-      <option value="PepsinA">PepsinA</option>
-      <option value="TrypChymo">TrypChymo</option>
-      <option value="V8-DE">V8-DE</option>
-      <option value="V8-E">V8-E</option>
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="leukocyte elastase">leukocyte elastase</option>
-      <option value="no cleavage">no cleavage</option>
-      <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="unspecific cleavage">unspecific cleavage</option>
-      <expand macro="list_string_san" name="CleavageRules"/>
-    </param>
-    <param argument="-MinTerminiCleavages" type="integer" optional="true" value="2" label="By default, when generating peptides from the protein database, a peptide must start and end at a valid cleavage site" help="Setting this parameter to 0 or 1 will reduce that requirement, so that neither terminus or only one terminus of the peptide must match one of the cleavage rules specified in the CleavageRules parameter. This parameter is useful to turn a tryptic digest into a semi-tryptic digest"/>
-    <param argument="-MaxMissedCleavages" type="integer" optional="true" value="-1" label="By default, when generating peptides from the protein database, a peptide may contain any number of missed cleavages" help="A missed cleavage is a site within the peptide that matches one of the cleavage rules (refer to CleavageRules). Settings this parameter to some other number will stop generating peptides from a sequence if it contains more than the specified number of missed cleavages"/>
+    <param argument="-reindex" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Recalculate peptide to protein association using OpenMS" help="Annotates target-decoy information"/>
+    <section name="PeptideIndexing" title="" help="" expanded="false">
+      <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
+        <expand macro="list_string_san" name="decoy_string"/>
+      </param>
+      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
+        <option value="prefix" selected="true">prefix</option>
+        <option value="suffix">suffix</option>
+        <expand macro="list_string_san" name="decoy_string_position"/>
+      </param>
+      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
+        <option value="error">error</option>
+        <option value="warn" selected="true">warn</option>
+        <option value="silent">silent</option>
+        <expand macro="list_string_san" name="missing_decoy_action"/>
+      </param>
+      <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
+      <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
+      <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
+      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
+        <option value="error" selected="true">error</option>
+        <option value="warn">warn</option>
+        <option value="remove">remove</option>
+        <expand macro="list_string_san" name="unmatched_action"/>
+      </param>
+      <param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
+      <param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
+      <param name="IL_equivalent" argument="-PeptideIndexing:IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/>
+      <param name="allow_nterm_protein_cleavage" argument="-PeptideIndexing:allow_nterm_protein_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Allow the protein N-terminus amino acid to clip" help=""/>
+      <section name="enzyme" title="" help="" expanded="false">
+        <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
+          <option value="auto" selected="true">auto</option>
+          <option value="Trypsin">Trypsin</option>
+          <option value="TrypChymo">TrypChymo</option>
+          <option value="Trypsin/P">Trypsin/P</option>
+          <option value="V8-DE">V8-DE</option>
+          <option value="V8-E">V8-E</option>
+          <option value="leukocyte elastase">leukocyte elastase</option>
+          <option value="proline endopeptidase">proline endopeptidase</option>
+          <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
+          <option value="Glu-C+P">Glu-C+P</option>
+          <option value="PepsinA + P">PepsinA + P</option>
+          <option value="cyanogen-bromide">cyanogen-bromide</option>
+          <option value="Clostripain/P">Clostripain/P</option>
+          <option value="Lys-C/P">Lys-C/P</option>
+          <option value="PepsinA">PepsinA</option>
+          <option value="Arg-C">Arg-C</option>
+          <option value="Arg-C/P">Arg-C/P</option>
+          <option value="Asp-N">Asp-N</option>
+          <option value="Asp-N/B">Asp-N/B</option>
+          <option value="Asp-N_ambic">Asp-N_ambic</option>
+          <option value="Chymotrypsin">Chymotrypsin</option>
+          <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+          <option value="CNBr">CNBr</option>
+          <option value="Formic_acid">Formic_acid</option>
+          <option value="Lys-C">Lys-C</option>
+          <option value="Lys-N">Lys-N</option>
+          <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+          <option value="no cleavage">no cleavage</option>
+          <option value="unspecific cleavage">unspecific cleavage</option>
+          <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+          <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+          <option value="2-iodobenzoate">2-iodobenzoate</option>
+          <option value="iodosobenzoate">iodosobenzoate</option>
+          <option value="staphylococcal protease/D">staphylococcal protease/D</option>
+          <expand macro="list_string_san" name="name"/>
+        </param>
+        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
+          <option value="auto" selected="true">auto</option>
+          <option value="full">full</option>
+          <option value="semi">semi</option>
+          <option value="none">none</option>
+          <expand macro="list_string_san" name="specificity"/>
+        </param>
+      </section>
+    </section>
     <expand macro="adv_opts_macro">
-      <param argument="-MinPeptideMass" type="float" optional="true" value="0.0" label="When preprocessing the experimental spectra, any spectrum with a precursor mass that is less than the specified mass will be disqualified" help=""/>
-      <param argument="-MaxPeptideMass" type="float" optional="true" value="10000.0" label="When preprocessing the experimental spectra, any spectrum with a precursor mass that exceeds the specified mass will be disqualified" help=""/>
-      <param argument="-MinPeptideLength" type="integer" optional="true" value="5" label="When digesting proteins, any peptide which does not meet or exceed the specified length will be disqualified" help=""/>
-      <param argument="-MaxPeptideLength" type="integer" optional="true" value="75" label="When digesting proteins, any peptide which exceeds this specified length will be disqualified" help=""/>
-      <param argument="-UseSmartPlusThreeModel" type="boolean" truevalue="true" falsevalue="false" checked="false" label="When this parameter is set, then for each peptide bond, an internal calculation is done to estimate the basicity of the b and y fragment sequence" help="The precursors protons are distributed to those ions based on that calculation, with the more basic sequence generally getting more of the protons"/>
-      <param argument="-NumIntensityClasses" type="integer" optional="true" value="3" label="Before scoring any candidates, experimental spectra have their peaks stratified into the number of intensity classes specified by this paramete" help=""/>
-      <param argument="-ClassSizeMultiplier" type="float" optional="true" value="2.0" label="When stratifying peaks into a specified, fixed number of intensity classes, this parameter controls the size of each class relative to the class above it (where the peaks are more intense)" help=""/>
-      <param argument="-MonoisotopeAdjustmentSet" type="text" optional="true" value="0" label="This parameter defines a set of isotopes (0 being the instrument-called monoisotope) to try as the monoisotopic precursor m/z" help="To disable this technique, set the value to '0'">
-        <expand macro="list_string_san" name="MonoisotopeAdjustmentSet"/>
+      <param argument="-min_matched_peaks" type="integer" value="6" label="Minimum number of b+y ions required to match for PSM to be reported" help=""/>
+      <param argument="-min_peaks" type="integer" value="15" label="Minimum number of peaks required for a spectrum to be considered" help=""/>
+      <param argument="-max_peaks" type="integer" value="150" label="Take the top N most intense MS2 peaks only for matching" help=""/>
+      <param argument="-report_psms" type="integer" value="1" label="Number of hits (PSMs) to report for each spectrum" help=""/>
+      <param argument="-bucket_size" type="integer" value="8192" label="How many fragments are in each internal mass bucket (default: 8192 for hi-res data)" help="Try increasing it to 32k or 64k for low-res. See also: fragment_tol_*"/>
+      <param argument="-min_len" type="integer" value="5" label="Minimum peptide length" help=""/>
+      <param argument="-max_len" type="integer" value="50" label="Maximum peptide length" help=""/>
+      <param argument="-missed_cleavages" type="integer" value="2" label="Number of missed cleavages" help=""/>
+      <param argument="-fragment_min_mz" type="float" value="200.0" label="Minimum fragment m/z" help=""/>
+      <param argument="-fragment_max_mz" type="float" value="2000.0" label="Maximum fragment m/z" help=""/>
+      <param argument="-peptide_min_mass" type="float" value="500.0" label="Minimum monoisotopic peptide mass to consider a peptide from the DB" help=""/>
+      <param argument="-peptide_max_mass" type="float" value="5000.0" label="Maximum monoisotopic peptide mass to consider a peptide from the DB" help=""/>
+      <param argument="-min_ion_index" type="integer" value="2" label="Minimum ion index to consider for preliminary scoring" help="Default = 2 to skip b1/y1 AND (sic) b2/y2 ions that are often missing"/>
+      <param argument="-max_variable_mods" type="integer" value="2" label="Maximum number of variable modifications" help=""/>
+      <param argument="-isotope_error_range" type="text" value="-1, 3" label="Range of (C13) isotope errors to consider for precursor.Can be negative" help="E.g. '-1,3' for considering '-1/0/1/2/3'">
+        <expand macro="list_string_san" name="isotope_error_range"/>
       </param>
-      <param argument="-SpectrumListFilters" type="text" optional="true" value="" label="Optional set of filters as described in the MyriMatch documentation" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
-        <expand macro="list_string_val" name="SpectrumListFilters"/>
-        <expand macro="list_string_san" name="SpectrumListFilters"/>
+      <param argument="-charges" type="text" value="2, 5" label="Range of precursor charges to consider if not annotated in the file" help="">
+        <expand macro="list_string_san" name="charges"/>
       </param>
-      <param argument="-ignoreConfigErrors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Ignore wrong parameter names or values" help="Use with maximum caution!"/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -5977,50 +6164,77 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MyriMatchAdapter_1 -->
+  <tests>
+    <!-- TOPP_SageAdapter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
-        <param name="MinPeptideMass" value="0.0"/>
-        <param name="MaxPeptideMass" value="10000.0"/>
-        <param name="MinPeptideLength" value="5"/>
-        <param name="MaxPeptideLength" value="75"/>
-        <param name="UseSmartPlusThreeModel" value="false"/>
-        <param name="NumIntensityClasses" value="3"/>
-        <param name="ClassSizeMultiplier" value="2.0"/>
-        <param name="MonoisotopeAdjustmentSet" value="[-1,2]"/>
-        <param name="SpectrumListFilters" value=""/>
-        <param name="ignoreConfigErrors" value="false"/>
+        <param name="min_matched_peaks" value="6"/>
+        <param name="min_peaks" value="15"/>
+        <param name="max_peaks" value="150"/>
+        <param name="report_psms" value="1"/>
+        <param name="bucket_size" value="8192"/>
+        <param name="min_len" value="5"/>
+        <param name="max_len" value="50"/>
+        <param name="missed_cleavages" value="2"/>
+        <param name="fragment_min_mz" value="200.0"/>
+        <param name="fragment_max_mz" value="2000.0"/>
+        <param name="peptide_min_mass" value="500.0"/>
+        <param name="peptide_max_mass" value="5000.0"/>
+        <param name="min_ion_index" value="2"/>
+        <param name="max_variable_mods" value="2"/>
+        <param name="isotope_error_range" value="-1, 3"/>
+        <param name="charges" value="2, 5"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
-      <param name="in" value="spectra.mzML"/>
-      <output name="out" file="MyriMatchAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <param name="precursor_mass_tolerance" value="5.0"/>
-      <param name="precursor_mass_tolerance_unit" value="ppm"/>
-      <param name="precursor_mass_tolerance_avg" value="false"/>
-      <param name="fragment_mass_tolerance" value="0.3"/>
-      <param name="fragment_mass_tolerance_unit" value="Da"/>
-      <param name="database" value="proteins.fasta"/>
-      <param name="fixed_modifications"/>
+      <conditional name="in_cond">
+        <param name="in" value="SageAdapter_1.mzML"/>
+      </conditional>
+      <output name="out" value="SageAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="database" value="SageAdapter_1.fasta"/>
+      <param name="decoy_prefix" value="DECOY_"/>
+      <param name="batch_size" value="0"/>
+      <param name="precursor_tol_left" value="-6.0"/>
+      <param name="precursor_tol_right" value="6.0"/>
+      <param name="precursor_tol_unit" value="ppm"/>
+      <param name="fragment_tol_left" value="-20.0"/>
+      <param name="fragment_tol_right" value="20.0"/>
+      <param name="fragment_tol_unit" value="ppm"/>
+      <param name="enzyme" value="Trypsin"/>
+      <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
       <param name="variable_modifications" value="Oxidation (M)"/>
-      <param name="NumChargeStates" value="3"/>
-      <param name="TicCutoffPercentage" value="0.98"/>
-      <param name="MaxDynamicMods" value="2"/>
-      <param name="MaxResultRank" value="5"/>
-      <param name="CleavageRules"/>
-      <param name="MinTerminiCleavages" value="2"/>
-      <param name="MaxMissedCleavages" value="-1"/>
+      <param name="reindex" value="true"/>
+      <section name="PeptideIndexing">
+        <param name="decoy_string" value=""/>
+        <param name="decoy_string_position" value="prefix"/>
+        <param name="missing_decoy_action" value="warn"/>
+        <param name="write_protein_sequence" value="false"/>
+        <param name="write_protein_description" value="false"/>
+        <param name="keep_unreferenced_proteins" value="false"/>
+        <param name="unmatched_action" value="error"/>
+        <param name="aaa_max" value="3"/>
+        <param name="mismatches_max" value="0"/>
+        <param name="IL_equivalent" value="false"/>
+        <param name="allow_nterm_protein_cleavage" value="true"/>
+        <section name="enzyme">
+          <param name="name" value="auto"/>
+          <param name="specificity" value="auto"/>
+        </section>
+      </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
-  <help><![CDATA[Annotates MS/MS spectra using MyriMatch.
+  <help><![CDATA[Annotates MS/MS spectra using Sage.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MyriMatchAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SageAdapter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SeedListGenerator.xml b/tools/openms/SeedListGenerator.xml
index b130244de..18b2b75c6 100644
--- a/tools/openms/SeedListGenerator.xml
+++ b/tools/openms/SeedListGenerator.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Quantitation]-->
 <tool id="SeedListGenerator" name="SeedListGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Generates seed lists for feature detection.</description>
+  <description>Generates seed lists for feature detection</description>
   <macros>
     <token name="@EXECUTABLE@">SeedListGenerator</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out_prefix &&
 
 ## Main program call
@@ -38,11 +37,11 @@ out_prefix/
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="featurexml,idxml,mzml" optional="false" label="Input file (see below for details)" help=" select featurexml,idxml,mzml data sets(s)"/>
+    <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" label="Input file (see below for details)" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
     <param argument="-use_peptide_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -58,10 +57,11 @@ out_prefix/
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_SeedListGenerator_1 -->
+  <tests>
+    <!-- TOPP_SeedListGenerator_1 -->
     <!-- TOPP_SeedListGenerator_2 -->
     <!-- TOPP_SeedListGenerator_3 -->
-  <test expect_num_outputs="2">
+    <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="test" value="true"/>
       </section>
@@ -76,7 +76,8 @@ out_prefix/
           <is_valid_xml/>
         </assert_contents>
       </output>
-    </test><test expect_num_outputs="2">
+    </test>
+    <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="test" value="true"/>
       </section>
@@ -91,7 +92,8 @@ out_prefix/
           <is_valid_xml/>
         </assert_contents>
       </output>
-    </test><test expect_num_outputs="2">
+    </test>
+    <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="test" value="true"/>
       </section>
@@ -108,10 +110,10 @@ out_prefix/
         </assert_contents>
       </output>
     </test>
-</tests>
+  </tests>
   <help><![CDATA[Generates seed lists for feature detection.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SeedListGenerator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SeedListGenerator.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SemanticValidator.xml b/tools/openms/SemanticValidator.xml
index 42b94376a..e267f1264 100644
--- a/tools/openms/SemanticValidator.xml
+++ b/tools/openms/SemanticValidator.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [[for Developers]]-->
 <tool id="SemanticValidator" name="SemanticValidator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>SemanticValidator for semantically validating certain XML files.</description>
+  <description>SemanticValidator for semantically validating certain XML files</description>
   <macros>
     <token name="@EXECUTABLE@">SemanticValidator</token>
     <import>macros.xml</import>
@@ -15,16 +14,16 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir mapping_file &&
-ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
+cp '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
 #if $cv_cond.cv:
   mkdir cv_cond.cv &&
   #if $cv_cond.cv_select == "no"
   mkdir ${' '.join(["'cv_cond.cv/%s'" % (i) for i, f in enumerate($cv_cond.cv) if f])} && 
-  ${' '.join(["ln -s '%s' 'cv_cond.cv/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_cond.cv) if f])}
+  ${' '.join(["cp '%s' 'cv_cond.cv/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_cond.cv) if f])}
   #else
-  ln -s '$cv_cond.cv' 'cv_cond.cv/${re.sub("[^\w\-_]", "_", $cv_cond.cv.element_identifier)}.$gxy2omsext($cv_cond.cv.ext)' &&
+  cp '$cv_cond.cv' 'cv_cond.cv/${re.sub("[^\w\-_]", "_", $cv_cond.cv.element_identifier)}.$gxy2omsext($cv_cond.cv.ext)' &&
   #end if
 #end if
 
@@ -57,8 +56,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzdata,mzid,mzml,traml,xml" optional="false" label="Input file (any xml file)" help=" select mzdata,mzid,mzml,traml,xml data sets(s)"/>
-    <param argument="-mapping_file" type="data" format="xml" optional="false" label="Mapping file which is used to semantically validate the given XML file against this mapping file (see 'share/OpenMS/MAPPING' for templates)" help=" select xml data sets(s)"/>
+    <param argument="-in" type="data" format="mzdata,mzid,mzml,traml,xml" label="Input file (any xml file)" help=" select mzdata,mzid,mzml,traml,xml data sets(s)"/>
+    <param argument="-mapping_file" type="data" format="xml" label="Mapping file which is used to semantically validate the given XML file against this mapping file (see 'share/OpenMS/MAPPING' for templates)" help=" select xml data sets(s)"/>
     <conditional name="cv_cond">
       <param name="cv_select" type="select" label="Run tool in batch mode for -cv">
         <option value="no">No: process all datasets jointly</option>
@@ -68,12 +67,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param argument="-cv" type="data" format="obo" multiple="true" optional="true" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help=" select obo data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-cv" type="data" format="obo" multiple="false" optional="true" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help=" select obo data sets(s)"/>
+        <param argument="-cv" type="data" format="obo" optional="true" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help=" select obo data sets(s)"/>
       </when>
     </conditional>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -89,18 +88,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output-->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
-    <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/>
-    <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4">
-       <assert_contents><has_text text="Congratulations, the file is valid!"/></assert_contents>
-    </output>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output-->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
+      <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/>
+      <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4">
+        <assert_contents>
+          <has_text text="Congratulations, the file is valid!"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
   <help><![CDATA[SemanticValidator for semantically validating certain XML files.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SemanticValidator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SemanticValidator.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SequenceCoverageCalculator.xml b/tools/openms/SequenceCoverageCalculator.xml
index 05f7048f3..128481cbc 100644
--- a/tools/openms/SequenceCoverageCalculator.xml
+++ b/tools/openms/SequenceCoverageCalculator.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="SequenceCoverageCalculator" name="SequenceCoverageCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Prints information about idXML files.</description>
+  <description>Prints information about idXML files</description>
   <macros>
     <token name="@EXECUTABLE@">SequenceCoverageCalculator</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in_database &&
-ln -s '$in_database' 'in_database/${re.sub("[^\w\-_]", "_", $in_database.element_identifier)}.$gxy2omsext($in_database.ext)' &&
+cp '$in_database' 'in_database/${re.sub("[^\w\-_]", "_", $in_database.element_identifier)}.$gxy2omsext($in_database.ext)' &&
 mkdir in_peptides &&
-ln -s '$in_peptides' 'in_peptides/${re.sub("[^\w\-_]", "_", $in_peptides.element_identifier)}.$gxy2omsext($in_peptides.ext)' &&
+cp '$in_peptides' 'in_peptides/${re.sub("[^\w\-_]", "_", $in_peptides.element_identifier)}.$gxy2omsext($in_peptides.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -43,11 +42,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in_database" type="data" format="fasta" optional="false" label="input file containing the database in FASTA format" help=" select fasta data sets(s)"/>
-    <param argument="-in_peptides" type="data" format="idxml" optional="false" label="input file containing the identified peptides" help=" select idxml data sets(s)"/>
+    <param argument="-in_database" type="data" format="fasta" label="input file containing the database in FASTA format" help=" select fasta data sets(s)"/>
+    <param argument="-in_peptides" type="data" format="idxml" label="input file containing the identified peptides" help=" select idxml data sets(s)"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -61,16 +60,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- took test data from another tool that also takes idXML and fasta as input -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in_database" value="PeptideIndexer_1.fasta" ftype="fasta"/>
-    <param name="in_peptides" value="SequenceCoverageCalculator_1.idXML" ftype="idxml"/>
-    <output name="out" value="SequenceCoverageCalculator.txt" ftype="txt" compare="sim_size"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- took test data from another tool that also takes idXML and fasta as input -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in_database" value="PeptideIndexer_1.fasta" ftype="fasta"/>
+      <param name="in_peptides" value="SequenceCoverageCalculator_1.idXML" ftype="idxml"/>
+      <output name="out" value="SequenceCoverageCalculator.txt" ftype="txt" compare="sim_size"/>
+    </test>
+  </tests>
   <help><![CDATA[Prints information about idXML files.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SequenceCoverageCalculator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SequenceCoverageCalculator.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SimpleSearchEngine.xml b/tools/openms/SimpleSearchEngine.xml
index 28f1a4e7b..5c73d5bbd 100644
--- a/tools/openms/SimpleSearchEngine.xml
+++ b/tools/openms/SimpleSearchEngine.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: []-->
 <tool id="SimpleSearchEngine" name="SimpleSearchEngine" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Annotates MS/MS spectra using SimpleSearchEngine.</description>
+  <description>Annotates MS/MS spectra using SimpleSearchEngine</description>
   <macros>
     <token name="@EXECUTABLE@">SimpleSearchEngine</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir database &&
-ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -43,69 +42,69 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
-    <param argument="-database" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-database" type="data" format="fasta" label="input file" help=" select fasta data sets(s)"/>
     <section name="Search" title="" help="" expanded="false">
-      <param name="enzyme" argument="-Search:enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
-        <option value="Trypsin" selected="true">Trypsin</option>
+      <param name="enzyme" argument="-Search:enzyme" type="select" label="The enzyme used for peptide digestion" help="">
+        <option value="Asp-N">Asp-N</option>
+        <option value="Asp-N/B">Asp-N/B</option>
+        <option value="Asp-N_ambic">Asp-N_ambic</option>
+        <option value="V8-E">V8-E</option>
+        <option value="leukocyte elastase">leukocyte elastase</option>
+        <option value="proline endopeptidase">proline endopeptidase</option>
+        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+        <option value="2-iodobenzoate">2-iodobenzoate</option>
+        <option value="iodosobenzoate">iodosobenzoate</option>
         <option value="staphylococcal protease/D">staphylococcal protease/D</option>
         <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
+        <option value="Trypsin" selected="true">Trypsin</option>
         <option value="Glu-C+P">Glu-C+P</option>
         <option value="PepsinA + P">PepsinA + P</option>
         <option value="cyanogen-bromide">cyanogen-bromide</option>
         <option value="Clostripain/P">Clostripain/P</option>
         <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
-        <option value="CNBr">CNBr</option>
-        <option value="Formic_acid">Formic_acid</option>
-        <option value="Lys-C">Lys-C</option>
+        <option value="no cleavage">no cleavage</option>
+        <option value="unspecific cleavage">unspecific cleavage</option>
+        <option value="Arg-C">Arg-C</option>
         <option value="Arg-C/P">Arg-C/P</option>
-        <option value="Asp-N">Asp-N</option>
-        <option value="Asp-N/B">Asp-N/B</option>
-        <option value="PepsinA">PepsinA</option>
+        <option value="Chymotrypsin">Chymotrypsin</option>
+        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+        <option value="CNBr">CNBr</option>
         <option value="TrypChymo">TrypChymo</option>
         <option value="Trypsin/P">Trypsin/P</option>
         <option value="V8-DE">V8-DE</option>
-        <option value="V8-E">V8-E</option>
-        <option value="leukocyte elastase">leukocyte elastase</option>
-        <option value="proline endopeptidase">proline endopeptidase</option>
-        <option value="no cleavage">no cleavage</option>
-        <option value="unspecific cleavage">unspecific cleavage</option>
-        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
-        <option value="2-iodobenzoate">2-iodobenzoate</option>
-        <option value="iodosobenzoate">iodosobenzoate</option>
-        <option value="Arg-C">Arg-C</option>
+        <option value="Formic_acid">Formic_acid</option>
+        <option value="Lys-C">Lys-C</option>
         <option value="Lys-N">Lys-N</option>
         <option value="Lys-C/P">Lys-C/P</option>
-        <option value="Asp-N_ambic">Asp-N_ambic</option>
-        <option value="Chymotrypsin">Chymotrypsin</option>
-        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+        <option value="PepsinA">PepsinA</option>
         <expand macro="list_string_san" name="enzyme"/>
       </param>
       <param name="decoys" argument="-Search:decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Should decoys be generated?" help=""/>
       <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false">
-        <param name="mass_tolerance" argument="-Search:precursor:mass_tolerance" type="float" optional="true" value="10.0" label="+/- tolerance for precursor mass" help=""/>
-        <param name="mass_tolerance_unit" argument="-Search:precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
+        <param name="mass_tolerance" argument="-Search:precursor:mass_tolerance" type="float" value="10.0" label="+/- tolerance for precursor mass" help=""/>
+        <param name="mass_tolerance_unit" argument="-Search:precursor:mass_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
           <option value="ppm" selected="true">ppm</option>
           <option value="Da">Da</option>
           <expand macro="list_string_san" name="mass_tolerance_unit"/>
         </param>
-        <param name="min_charge" argument="-Search:precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/>
-        <param name="max_charge" argument="-Search:precursor:max_charge" type="integer" optional="true" value="5" label="Maximum precursor charge to be considered" help=""/>
-        <param name="isotopes" argument="-Search:precursor:isotopes" type="text" optional="true" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+        <param name="min_charge" argument="-Search:precursor:min_charge" type="integer" value="2" label="Minimum precursor charge to be considered" help=""/>
+        <param name="max_charge" argument="-Search:precursor:max_charge" type="integer" value="5" label="Maximum precursor charge to be considered" help=""/>
+        <param name="isotopes" argument="-Search:precursor:isotopes" type="text" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
           <expand macro="list_integer_valsan" name="isotopes"/>
         </param>
       </section>
       <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false">
-        <param name="mass_tolerance" argument="-Search:fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance" help=""/>
-        <param name="mass_tolerance_unit" argument="-Search:fragment:mass_tolerance_unit" type="select" optional="true" label="Unit of fragment m" help="">
+        <param name="mass_tolerance" argument="-Search:fragment:mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance" help=""/>
+        <param name="mass_tolerance_unit" argument="-Search:fragment:mass_tolerance_unit" type="select" label="Unit of fragment m" help="">
           <option value="ppm" selected="true">ppm</option>
           <option value="Da">Da</option>
           <expand macro="list_string_san" name="mass_tolerance_unit"/>
         </param>
       </section>
       <section name="modifications" title="Modifications Options" help="" expanded="false">
-        <param name="fixed" argument="-Search:modifications:fixed" multiple="true" type="select" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
+        <param name="fixed" argument="-Search:modifications:fixed" type="select" multiple="true" optional="false" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
           <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
           <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
           <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -115,6 +114,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="2-succinyl (C)">2-succinyl (C)</option>
           <option value="2HPG (R)">2HPG (R)</option>
           <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+          <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+          <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+          <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+          <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
           <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
           <option value="3sulfo (N-term)">3sulfo (N-term)</option>
           <option value="4-ONE (C)">4-ONE (C)</option>
@@ -204,6 +207,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
           <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
           <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+          <option value="Andro-H2O (C)">Andro-H2O (C)</option>
           <option value="Archaeol (C)">Archaeol (C)</option>
           <option value="Arg (N-term)">Arg (N-term)</option>
           <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -307,6 +311,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
           <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
           <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+          <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
           <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
           <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
           <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -339,7 +344,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="BITC (N-term)">BITC (N-term)</option>
           <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
           <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-          <option value="Bodipy (C)">Bodipy (C)</option>
           <option value="Brij35 (N-term)">Brij35 (N-term)</option>
           <option value="Brij58 (N-term)">Brij58 (N-term)</option>
           <option value="Bromo (F)">Bromo (F)</option>
@@ -771,9 +775,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Dehydrated (T)">Dehydrated (T)</option>
           <option value="Dehydrated (Y)">Dehydrated (Y)</option>
           <option value="Dehydro (C)">Dehydro (C)</option>
+          <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
           <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
           <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-          <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
           <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
           <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
           <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -783,7 +787,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
           <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
           <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-          <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
           <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
           <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
           <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -795,6 +798,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
           <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
           <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+          <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
           <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
           <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
           <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -1367,7 +1371,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Ethanolyl (C)">Ethanolyl (C)</option>
           <option value="Ethanolyl (K)">Ethanolyl (K)</option>
           <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-          <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
           <option value="Ethyl (C-term)">Ethyl (C-term)</option>
           <option value="Ethyl (D)">Ethyl (D)</option>
           <option value="Ethyl (E)">Ethyl (E)</option>
@@ -1461,6 +1464,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
           <option value="Glu (E)">Glu (E)</option>
           <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+          <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
           <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
           <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
           <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -1475,7 +1479,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
           <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
           <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-          <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
           <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
           <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
           <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -1499,6 +1502,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Gly (K)">Gly (K)</option>
           <option value="Gly (S)">Gly (S)</option>
           <option value="Gly (T)">Gly (T)</option>
+          <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
           <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
           <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
           <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -1889,6 +1893,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
           <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
           <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+          <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
           <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
           <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
           <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -1900,6 +1905,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
           <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
           <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+          <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+          <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+          <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
           <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
           <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
           <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -1955,6 +1963,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
           <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
           <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+          <option value="His+O(2) (H)">His+O(2) (H)</option>
           <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
           <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
           <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -2092,11 +2101,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
           <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
           <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+          <option value="Kdo (S)">Kdo (S)</option>
+          <option value="Kdo (T)">Kdo (T)</option>
           <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
           <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
           <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
           <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
           <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+          <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
           <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
           <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
           <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -2181,13 +2193,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
           <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
           <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+          <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
           <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
           <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
           <option value="Lipoyl (K)">Lipoyl (K)</option>
           <option value="LRGG (K)">LRGG (K)</option>
           <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
           <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+          <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
           <option value="Lys (N-term)">Lys (N-term)</option>
+          <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
           <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
           <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
           <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -2222,6 +2237,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Malonyl (C)">Malonyl (C)</option>
           <option value="Malonyl (K)">Malonyl (K)</option>
           <option value="Malonyl (S)">Malonyl (S)</option>
+          <option value="MBS+peptide (C)">MBS+peptide (C)</option>
           <option value="MDCC (C)">MDCC (C)</option>
           <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
           <option value="Menadione (C)">Menadione (C)</option>
@@ -2233,6 +2249,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="MesitylOxide (H)">MesitylOxide (H)</option>
           <option value="MesitylOxide (K)">MesitylOxide (K)</option>
           <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+          <option value="Met+O(2) (H)">Met+O(2) (H)</option>
           <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
           <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
           <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -2416,7 +2433,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
           <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
           <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-          <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
           <option value="NP40 (N-term)">NP40 (N-term)</option>
           <option value="NQIGG (K)">NQIGG (K)</option>
           <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -2504,6 +2520,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
           <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
           <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+          <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+          <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+          <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+          <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
           <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
           <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
           <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -2518,6 +2538,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Phospho (Y)">Phospho (Y)</option>
           <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
           <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+          <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
           <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
           <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
           <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -2549,6 +2570,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
           <option value="Piperidine (K)">Piperidine (K)</option>
           <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+          <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
           <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
           <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
           <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -2626,18 +2648,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="QTGG (K)">QTGG (K)</option>
           <option value="Quinone (W)">Quinone (W)</option>
           <option value="Quinone (Y)">Quinone (Y)</option>
+          <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+          <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+          <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+          <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+          <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+          <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+          <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+          <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+          <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+          <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+          <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+          <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+          <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+          <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+          <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+          <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+          <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+          <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+          <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+          <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
           <option value="Retinylidene (K)">Retinylidene (K)</option>
           <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
           <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
           <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-          <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-          <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-          <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-          <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-          <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-          <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-          <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-          <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
           <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
           <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
           <option value="Saligenin (H)">Saligenin (H)</option>
@@ -2665,6 +2699,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="shTMT (K)">shTMT (K)</option>
           <option value="shTMT (N-term)">shTMT (N-term)</option>
           <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+          <option value="shTMTpro (K)">shTMTpro (K)</option>
+          <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+          <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
           <option value="SMA (K)">SMA (K)</option>
           <option value="SMA (N-term)">SMA (N-term)</option>
           <option value="spermidine (Q)">spermidine (Q)</option>
@@ -2840,7 +2877,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
           <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
           <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-          <option value="Ub-amide (C)">Ub-amide (C)</option>
           <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
           <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
           <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -3035,7 +3071,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="ZQG (K)">ZQG (K)</option>
           <expand macro="list_string_san" name="fixed"/>
         </param>
-        <param name="variable" argument="-Search:modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'">
+        <param name="variable" argument="-Search:modifications:variable" type="select" multiple="true" optional="false" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'">
           <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
           <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
           <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -3045,6 +3081,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="2-succinyl (C)">2-succinyl (C)</option>
           <option value="2HPG (R)">2HPG (R)</option>
           <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+          <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+          <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+          <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+          <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
           <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
           <option value="3sulfo (N-term)">3sulfo (N-term)</option>
           <option value="4-ONE (C)">4-ONE (C)</option>
@@ -3134,6 +3174,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
           <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
           <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+          <option value="Andro-H2O (C)">Andro-H2O (C)</option>
           <option value="Archaeol (C)">Archaeol (C)</option>
           <option value="Arg (N-term)">Arg (N-term)</option>
           <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -3237,6 +3278,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
           <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
           <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+          <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
           <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
           <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
           <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -3269,7 +3311,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="BITC (N-term)">BITC (N-term)</option>
           <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
           <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-          <option value="Bodipy (C)">Bodipy (C)</option>
           <option value="Brij35 (N-term)">Brij35 (N-term)</option>
           <option value="Brij58 (N-term)">Brij58 (N-term)</option>
           <option value="Bromo (F)">Bromo (F)</option>
@@ -3701,9 +3742,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Dehydrated (T)">Dehydrated (T)</option>
           <option value="Dehydrated (Y)">Dehydrated (Y)</option>
           <option value="Dehydro (C)">Dehydro (C)</option>
+          <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
           <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
           <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-          <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
           <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
           <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
           <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -3713,7 +3754,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
           <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
           <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-          <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
           <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
           <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
           <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -3725,6 +3765,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
           <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
           <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+          <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
           <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
           <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
           <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -4297,7 +4338,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Ethanolyl (C)">Ethanolyl (C)</option>
           <option value="Ethanolyl (K)">Ethanolyl (K)</option>
           <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-          <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
           <option value="Ethyl (C-term)">Ethyl (C-term)</option>
           <option value="Ethyl (D)">Ethyl (D)</option>
           <option value="Ethyl (E)">Ethyl (E)</option>
@@ -4391,6 +4431,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
           <option value="Glu (E)">Glu (E)</option>
           <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+          <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
           <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
           <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
           <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -4405,7 +4446,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
           <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
           <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-          <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
           <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
           <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
           <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -4429,6 +4469,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Gly (K)">Gly (K)</option>
           <option value="Gly (S)">Gly (S)</option>
           <option value="Gly (T)">Gly (T)</option>
+          <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
           <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
           <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
           <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -4819,6 +4860,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
           <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
           <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+          <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
           <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
           <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
           <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -4830,6 +4872,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
           <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
           <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+          <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+          <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+          <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
           <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
           <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
           <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -4885,6 +4930,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
           <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
           <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+          <option value="His+O(2) (H)">His+O(2) (H)</option>
           <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
           <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
           <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -5022,11 +5068,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
           <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
           <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+          <option value="Kdo (S)">Kdo (S)</option>
+          <option value="Kdo (T)">Kdo (T)</option>
           <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
           <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
           <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
           <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
           <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+          <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
           <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
           <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
           <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -5111,13 +5160,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
           <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
           <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+          <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
           <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
           <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
           <option value="Lipoyl (K)">Lipoyl (K)</option>
           <option value="LRGG (K)">LRGG (K)</option>
           <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
           <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+          <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
           <option value="Lys (N-term)">Lys (N-term)</option>
+          <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
           <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
           <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
           <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -5152,6 +5204,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Malonyl (C)">Malonyl (C)</option>
           <option value="Malonyl (K)">Malonyl (K)</option>
           <option value="Malonyl (S)">Malonyl (S)</option>
+          <option value="MBS+peptide (C)">MBS+peptide (C)</option>
           <option value="MDCC (C)">MDCC (C)</option>
           <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
           <option value="Menadione (C)">Menadione (C)</option>
@@ -5163,6 +5216,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="MesitylOxide (H)">MesitylOxide (H)</option>
           <option value="MesitylOxide (K)">MesitylOxide (K)</option>
           <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+          <option value="Met+O(2) (H)">Met+O(2) (H)</option>
           <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
           <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
           <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -5346,7 +5400,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
           <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
           <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-          <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
           <option value="NP40 (N-term)">NP40 (N-term)</option>
           <option value="NQIGG (K)">NQIGG (K)</option>
           <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -5434,6 +5487,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
           <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
           <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+          <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+          <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+          <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+          <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
           <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
           <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
           <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -5448,6 +5505,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Phospho (Y)">Phospho (Y)</option>
           <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
           <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+          <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
           <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
           <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
           <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -5479,6 +5537,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
           <option value="Piperidine (K)">Piperidine (K)</option>
           <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+          <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
           <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
           <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
           <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -5556,18 +5615,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="QTGG (K)">QTGG (K)</option>
           <option value="Quinone (W)">Quinone (W)</option>
           <option value="Quinone (Y)">Quinone (Y)</option>
+          <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+          <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+          <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+          <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+          <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+          <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+          <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+          <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+          <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+          <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+          <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+          <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+          <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+          <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+          <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+          <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+          <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+          <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+          <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+          <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
           <option value="Retinylidene (K)">Retinylidene (K)</option>
           <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
           <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
           <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-          <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-          <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-          <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-          <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-          <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-          <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-          <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-          <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
           <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
           <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
           <option value="Saligenin (H)">Saligenin (H)</option>
@@ -5595,6 +5666,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="shTMT (K)">shTMT (K)</option>
           <option value="shTMT (N-term)">shTMT (N-term)</option>
           <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+          <option value="shTMTpro (K)">shTMTpro (K)</option>
+          <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+          <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
           <option value="SMA (K)">SMA (K)</option>
           <option value="SMA (N-term)">SMA (N-term)</option>
           <option value="spermidine (Q)">spermidine (Q)</option>
@@ -5770,7 +5844,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
           <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
           <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-          <option value="Ub-amide (C)">Ub-amide (C)</option>
           <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
           <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
           <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -5965,10 +6038,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <option value="ZQG (K)">ZQG (K)</option>
           <expand macro="list_string_san" name="variable"/>
         </param>
-        <param name="variable_max_per_peptide" argument="-Search:modifications:variable_max_per_peptide" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
+        <param name="variable_max_per_peptide" argument="-Search:modifications:variable_max_per_peptide" type="integer" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
       </section>
       <section name="annotate" title="Annotation Options" help="" expanded="false">
-        <param name="PSM" argument="-Search:annotate:PSM" multiple="true" type="select" optional="true" label="Annotations added to each PSM" help="">
+        <param name="PSM" argument="-Search:annotate:PSM" type="select" multiple="true" optional="false" label="Annotations added to each PSM" help="">
           <option value="ALL" selected="true">ALL</option>
           <option value="fragment_mz_error_median_ppm">fragment_mz_error_median_ppm</option>
           <option value="precursor_mz_error_ppm">precursor_mz_error_ppm</option>
@@ -5978,20 +6051,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         </param>
       </section>
       <section name="peptide" title="Peptide Options" help="" expanded="false">
-        <param name="min_size" argument="-Search:peptide:min_size" type="integer" optional="true" value="7" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/>
-        <param name="max_size" argument="-Search:peptide:max_size" type="integer" optional="true" value="40" label="Maximum size a peptide must have after digestion to be considered in the search (0 = disabled)" help=""/>
-        <param name="missed_cleavages" argument="-Search:peptide:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/>
+        <param name="min_size" argument="-Search:peptide:min_size" type="integer" value="7" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/>
+        <param name="max_size" argument="-Search:peptide:max_size" type="integer" value="40" label="Maximum size a peptide must have after digestion to be considered in the search (0 = disabled)" help=""/>
+        <param name="missed_cleavages" argument="-Search:peptide:missed_cleavages" type="integer" value="1" label="Number of missed cleavages" help=""/>
         <param name="motif" argument="-Search:peptide:motif" type="text" optional="true" value="" label="If set, only peptides that contain this motif (provided as RegEx) will be considered" help="">
           <expand macro="list_string_san" name="motif"/>
         </param>
       </section>
       <section name="report" title="Reporting Options" help="" expanded="false">
-        <param name="top_hits" argument="-Search:report:top_hits" type="integer" optional="true" value="1" label="Maximum number of top scoring hits per spectrum that are reported" help=""/>
+        <param name="top_hits" argument="-Search:report:top_hits" type="integer" value="1" label="Maximum number of top scoring hits per spectrum that are reported" help=""/>
       </section>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -6005,106 +6078,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_SimpleSearchEngine_1 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="SimpleSearchEngine_1.mzML"/>
-      <param name="database" value="SimpleSearchEngine_1.fasta"/>
-      <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <section name="Search">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="decoys" value="false"/>
-        <section name="precursor">
-          <param name="mass_tolerance" value="5.0"/>
-          <param name="mass_tolerance_unit" value="ppm"/>
-          <param name="min_charge" value="2"/>
-          <param name="max_charge" value="5"/>
-          <param name="isotopes" value="0 1"/>
-        </section>
-        <section name="fragment">
-          <param name="mass_tolerance" value="0.3"/>
-          <param name="mass_tolerance_unit" value="Da"/>
-        </section>
-        <section name="modifications">
-          <param name="fixed"/>
-          <param name="variable" value="Oxidation (M)"/>
-          <param name="variable_max_per_peptide" value="2"/>
-        </section>
-        <section name="annotate">
-          <param name="PSM" value="ALL"/>
-        </section>
-        <section name="peptide">
-          <param name="min_size" value="7"/>
-          <param name="max_size" value="40"/>
-          <param name="missed_cleavages" value="1"/>
-          <param name="motif" value=""/>
-        </section>
-        <section name="report">
-          <param name="top_hits" value="1"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- UTILS_SimpleSearchEngine_2 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="SimpleSearchEngine_1.mzML"/>
-      <param name="database" value="SimpleSearchEngine_1.fasta"/>
-      <output name="out" file="SimpleSearchEngine_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <section name="Search">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="decoys" value="false"/>
-        <section name="precursor">
-          <param name="mass_tolerance" value="10.0"/>
-          <param name="mass_tolerance_unit" value="ppm"/>
-          <param name="min_charge" value="2"/>
-          <param name="max_charge" value="5"/>
-          <param name="isotopes" value="0 1"/>
-        </section>
-        <section name="fragment">
-          <param name="mass_tolerance" value="10.0"/>
-          <param name="mass_tolerance_unit" value="ppm"/>
-        </section>
-        <section name="modifications">
-          <param name="fixed" value="Carbamidomethyl (C)"/>
-          <param name="variable" value="Oxidation (M)"/>
-          <param name="variable_max_per_peptide" value="2"/>
-        </section>
-        <section name="annotate">
-          <param name="PSM" value="ALL"/>
-        </section>
-        <section name="peptide">
-          <param name="min_size" value="7"/>
-          <param name="max_size" value="40"/>
-          <param name="missed_cleavages" value="1"/>
-          <param name="motif" value=""/>
-        </section>
-        <section name="report">
-          <param name="top_hits" value="1"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
+  <tests/>
   <help><![CDATA[Annotates MS/MS spectra using SimpleSearchEngine.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SimpleSearchEngine.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SimpleSearchEngine.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SiriusAdapter.xml b/tools/openms/SiriusAdapter.xml
index 3b3e33634..73becd038 100644
--- a/tools/openms/SiriusAdapter.xml
+++ b/tools/openms/SiriusAdapter.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: []-->
 <tool id="SiriusAdapter" name="SiriusAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Tool for metabolite identification using single and tandem mass spectrometry</description>
   <macros>
@@ -14,15 +13,11 @@
 #import re
 
 ## Preprocessing
-#if $sirius_executable:
-  mkdir sirius_executable &&
-  ln -s '$sirius_executable' 'sirius_executable/${re.sub("[^\w\-_]", "_", $sirius_executable.element_identifier)}.$gxy2omsext($sirius_executable.ext)' &&
-#end if
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #if $in_featureinfo:
   mkdir in_featureinfo &&
-  ln -s '$in_featureinfo' 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)' &&
+  cp '$in_featureinfo' 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)' &&
 #end if
 #if "out_sirius_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_sirius &&
@@ -33,6 +28,9 @@ ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($
 #if "out_ms_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_ms &&
 #end if
+#if "out_annotated_spectra_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_annotated_spectra &&
+#end if
 
 ## Main program call
 
@@ -40,10 +38,6 @@ set -o pipefail &&
 @EXECUTABLE@ -write_ctd ./ &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
-#if $sirius_executable:
-  -sirius_executable
-  'sirius_executable/${re.sub("[^\w\-_]", "_", $sirius_executable.element_identifier)}.$gxy2omsext($sirius_executable.ext)'
-#end if
 -in
 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
 #if $in_featureinfo:
@@ -62,6 +56,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   -out_ms
   'out_ms/output.${gxy2omsext("sirius.ms")}'
 #end if
+#if "out_annotated_spectra_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_annotated_spectra
+  'out_annotated_spectra/output.${gxy2omsext("mzml")}'
+#end if
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
 #end if
@@ -76,84 +74,98 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 #if "out_ms_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   && mv 'out_ms/output.${gxy2omsext("sirius.ms")}' '$out_ms'
 #end if
+#if "out_annotated_spectra_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_annotated_spectra/output.${gxy2omsext("mzml")}' '$out_annotated_spectra'
+#end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
   <configfiles>
     <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+    <configfile name="hardcoded_json"><![CDATA[{"sirius_executable": "\$(which sirius)", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-sirius_executable" type="data" format="txt" optional="true" value="sirius" label="The Sirius executable" help="Provide a full or relative path, or make sure it can be found in your PATH environment select txt data sets(s)"/>
-    <param argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="MzML Input file" help=" select mzml data sets(s)"/>
     <param argument="-in_featureinfo" type="data" format="featurexml" optional="true" label="FeatureXML input with feature and adduct information" help=" select featurexml data sets(s)"/>
     <param argument="-out_project_space" type="text" optional="true" value="" label="Output directory for SIRIUS project space" help="">
       <expand macro="list_string_san" name="out_project_space"/>
     </param>
+    <param argument="-sirius_user_email" type="text" optional="true" value="" label="E-mail for your SIRIUS account" help="">
+      <expand macro="list_string_san" name="sirius_user_email"/>
+    </param>
+    <param argument="-sirius_user_password" type="text" optional="true" value="" label="Password for your SIRIUS account" help="">
+      <expand macro="list_string_san" name="sirius_user_password"/>
+    </param>
     <section name="preprocessing" title="" help="" expanded="false">
-      <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" optional="true" min="1" value="1" label="Number of mass traces each feature has to have to be included" help="To use this parameter, setting the feature_only flag is necessary"/>
-      <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" optional="true" value="10.0" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/>
-      <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" optional="true" label="Unit of the precursor_mz_tolerance" help="">
+      <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" min="1" value="1" label="Number of mass traces each feature has to have to be included" help="To use this parameter, setting the feature_only flag is necessary"/>
+      <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" value="10.0" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/>
+      <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" label="Unit of the precursor_mz_tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="precursor_mz_tolerance_unit"/>
       </param>
-      <param name="precursor_rt_tolerance" argument="-preprocessing:precursor_rt_tolerance" type="float" optional="true" value="5.0" label="Tolerance window (left and right) for precursor selection [seconds]" help=""/>
-      <param name="isotope_pattern_iterations" argument="-preprocessing:isotope_pattern_iterations" type="integer" optional="true" value="3" label="Number of iterations that should be performed to extract the C13 isotope pattern" help="If no peak is found (C13 distance) the function will abort. Be careful with noisy data - since this can lead to wrong isotope patterns"/>
+      <param name="precursor_rt_tolerance" argument="-preprocessing:precursor_rt_tolerance" type="float" value="5.0" label="Tolerance window (left and right) for precursor selection [seconds]" help=""/>
+      <param name="isotope_pattern_iterations" argument="-preprocessing:isotope_pattern_iterations" type="integer" value="3" label="Number of iterations that should be performed to extract the C13 isotope pattern" help="If no peak is found (C13 distance) the function will abort. Be careful with noisy data - since this can lead to wrong isotope patterns"/>
       <param name="feature_only" argument="-preprocessing:feature_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Uses the feature information from in_featureinfo to reduce the search space to MS2 associated with a feature" help=""/>
       <param name="no_masstrace_info_isotope_pattern" argument="-preprocessing:no_masstrace_info_isotope_pattern" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if the masstrace information from a feature should be discarded and the isotope_pattern_iterations should be used instead" help=""/>
     </section>
     <section name="project" title="" help="" expanded="false">
-      <param name="processors" argument="-project:processors" type="integer" optional="true" value="1" label="Number of cpu cores to use" help="If not specified SIRIUS uses all available cores"/>
+      <param name="maxmz" argument="-project:maxmz" type="integer" value="-1" label="Just consider compounds with a precursor mz lower or equal" help="this maximum mz. All other compounds in the input file. are ignored"/>
+      <param name="loglevel" argument="-project:loglevel" type="text" optional="true" value="" label="Set logging level of the Jobs SIRIUS will execute" help="Valid values: SEVERE, WARNING, INFO, FINER, ALL. Default: WARNING">
+        <expand macro="list_string_san" name="loglevel"/>
+      </param>
       <param name="ignore_formula" argument="-project:ignore_formula" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Ignore given molecular formula in internal .ms format, while processing" help=""/>
       <param name="q" argument="-project:q" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress shell output" help=""/>
     </section>
     <section name="sirius" title="" help="" expanded="false">
-      <param name="ppm_max" argument="-sirius:ppm_max" type="float" optional="true" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses [ppm]" help=""/>
-      <param name="ppm_max_ms2" argument="-sirius:ppm_max_ms2" type="float" optional="true" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses in MS2 [ppm].If not specified, the same value as for the MS1 is used" help=""/>
-      <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" optional="true" min="0" value="0" label="Time out in seconds per fragmentation tree computations" help="0 for an infinite amount of time"/>
-      <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" optional="true" min="0" value="100" label="Maximal computation time in seconds for a single compound" help="0 for an infinite amount of time"/>
+      <param name="ppm_max" argument="-sirius:ppm_max" type="float" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses [ppm]" help=""/>
+      <param name="ppm_max_ms2" argument="-sirius:ppm_max_ms2" type="float" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses in MS2 [ppm].If not specified, the same value as for the MS1 is used" help=""/>
+      <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" min="0" value="100" label="Time out in seconds per fragmentation tree computations" help="0 for an infinite amount of time"/>
+      <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" min="0" value="100" label="Maximal computation time in seconds for a single compound" help="0 for an infinite amount of time"/>
       <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable recalibration of input spectra" help=""/>
-      <param name="profile" argument="-sirius:profile" type="select" optional="true" label="Name of the configuration profile" help="">
-        <option value="default">default</option>
-        <option value="qtof" selected="true">qtof</option>
+      <param name="profile" argument="-sirius:profile" type="select" label="Name of the configuration profile" help="">
+        <option value="default" selected="true">default</option>
+        <option value="qtof">qtof</option>
         <option value="orbitrap">orbitrap</option>
         <option value="fticr">fticr</option>
         <expand macro="list_string_san" name="profile"/>
       </param>
-      <param name="formula" argument="-sirius:formula" type="text" optional="true" value="" label="Specify the neutral molecular formula of the measured compound to compute its tree or a list of candidate formulas the method should discriminate" help="Omit this option if you want to consider all possible molecular formulas">
-        <expand macro="list_string_san" name="formula"/>
+      <param name="formulas" argument="-sirius:formulas" type="text" optional="true" value="" label="Specify the neutral molecular formula of the measured compound to compute its tree or a list of candidate formulas the method should discriminate" help="Omit this option if you want to consider all possible molecular formulas">
+        <expand macro="list_string_san" name="formulas"/>
       </param>
       <param name="ions_enforced" argument="-sirius:ions_enforced" type="text" optional="true" value="" label="The iontype/adduct of the MS/MS data" help="Example: [M+H]+, . [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a . comma separated list of adducts">
         <expand macro="list_string_san" name="ions_enforced"/>
       </param>
-      <param name="candidates" argument="-sirius:candidates" type="integer" optional="true" min="1" value="5" label="The number of formula candidates in the SIRIUS output" help=""/>
-      <param name="candidates_per_ion" argument="-sirius:candidates_per_ion" type="integer" optional="true" value="-1" label="Minimum number of candidates in the output for each ionization" help="Set to force output of results for each possible ionization, even if not part of highest ranked results. -1 omits parameter in Sirius"/>
-      <param name="elements_considered" argument="-sirius:elements_considered" type="text" optional="true" value="" label="Set the allowed elements for rare element detection" help="Write SBrClBSe to allow the elements S,Br,Cl,B and Se">
+      <param name="candidates" argument="-sirius:candidates" type="integer" min="0" value="10" label="The number of formula candidates in the SIRIUS output" help=""/>
+      <param name="candidates_per_ion" argument="-sirius:candidates_per_ion" type="integer" value="1" label="Minimum number of candidates in the output for each ionization" help="Set to force output of results for each possible ionization, even if not part of highest ranked results"/>
+      <param name="elements_considered" argument="-sirius:elements_considered" type="text" value="SBrClBSe" label="Set the allowed elements for rare element detection" help="Write SBrClBSe to allow the elements S,Br,Cl,B and Se">
         <expand macro="list_string_san" name="elements_considered"/>
       </param>
-      <param name="elements_enforced" argument="-sirius:elements_enforced" type="text" optional="true" value="" label="Enforce elements for molecular formula determination" help="Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the minimal and maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1-2]. When one number is given then it is interpreted as upper bound. Default is CHNOP">
+      <param name="elements_enforced" argument="-sirius:elements_enforced" type="text" value="CHNOP" label="Enforce elements for molecular formula determination" help="Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the minimal and maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1-2]. When one number is given then it is interpreted as upper bound">
         <expand macro="list_string_san" name="elements_enforced"/>
       </param>
       <param name="no_isotope_score" argument="-sirius:no_isotope_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable isotope pattern score" help=""/>
       <param name="no_isotope_filter" argument="-sirius:no_isotope_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable molecular formula filte" help="When filtering is enabled, molecular formulas are excluded if their theoretical isotope pattern does not match the theoretical one, even if their MS/MS pattern has high score"/>
-      <param name="ions_considered" argument="-sirius:ions_considered" type="text" optional="true" value="" label="the iontype/adduct of the MS/MS data" help="Example: [M+H]+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a comma separated list of adducts">
+      <param name="ions_considered" argument="-sirius:ions_considered" type="text" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-" label="the iontype/adduct of the MS/MS data" help="Example: [M+H]+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a comma separated list of adducts">
         <expand macro="list_string_san" name="ions_considered"/>
       </param>
-      <param name="db" argument="-sirius:db" type="text" optional="true" value="" label="Search formulas in the Union of the given databases db-name1,db-name2,db-name3" help="If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE">
+      <param name="db" argument="-sirius:db" type="text" value="none" label="Search formulas in the Union of the given databases db-name1,db-name2,db-name3" help="If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE">
         <expand macro="list_string_san" name="db"/>
       </param>
+      <param name="solver" argument="-sirius:solver" type="text" value="CLP" label="For GUROBI and CPLEX environment variables need to be configured" help="(see SIRIUS manual: https://boecker-lab.github.io/docs.sirius.github.io/install/)">
+        <expand macro="list_string_san" name="solver"/>
+      </param>
     </section>
     <section name="fingerid" title="" help="" expanded="false">
-      <param name="candidates" argument="-fingerid:candidates" type="integer" optional="true" min="1" value="10" label="Number of molecular structure candidates in the output" help=""/>
-      <param name="db" argument="-fingerid:db" type="text" optional="true" value="BIO" label="Search formulas in the Union of the given databases db-name1,db-name2,db-name3" help="If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE">
+      <param name="db" argument="-fingerid:db" type="text" optional="true" value="" label="Search structures in the Union of the given databases db-name1,db-name2,db-name3" help="If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE">
         <expand macro="list_string_san" name="db"/>
       </param>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-converter_mode" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag in combination with the out_ms file to convert the input mzML and featureXML to a .ms file" help="Without further SIRIUS processing"/>
+      <param argument="-read_sirius_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Read and print the standard output and error of the Sirius executable, even if it succeeds" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -161,6 +173,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="out_sirius_FLAG">out_sirius (MzTab output file for SIRIUS results)</option>
       <option value="out_fingerid_FLAG">out_fingerid (MzTab output file for CSI:FingerID, if this parameter is given, SIRIUS will search for a molecular structure using CSI:FingerID after determining the sum formula)</option>
       <option value="out_ms_FLAG">out_ms (Internal SIRIUS .ms format after OpenMS preprocessing)</option>
+      <option value="out_annotated_spectra_FLAG">out_annotated_spectra (Export spectra with fragment annotations from SIRIUS)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
@@ -174,6 +187,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <data name="out_ms" label="${tool.name} on ${on_string}: out_ms" format="sirius.ms">
       <filter>OPTIONAL_OUTPUTS is not None and "out_ms_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
+    <data name="out_annotated_spectra" label="${tool.name} on ${on_string}: out_annotated_spectra" format="mzml">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_annotated_spectra_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
     <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
       <filter>OPTIONAL_OUTPUTS is None</filter>
     </data>
@@ -181,496 +197,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_SiriusAdapter_1 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="SiriusAdapter_1_input.mzML"/>
-      <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value="all"/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_SiriusAdapter_2 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="SiriusAdapter_2_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="3"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value="all"/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_SiriusAdapter_3 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="SiriusAdapter_3_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="3"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value="all"/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_SiriusAdapter_5 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="converter_mode" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="SiriusAdapter_3_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
-      <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta_frac="0.7" ftype="sirius.ms"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_SiriusAdapter_6 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="converter_mode" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="SiriusAdapter_4_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
-      <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta_frac="0.7" ftype="sirius.ms"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value=""/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_SiriusAdapter_8 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
-      <param name="in_featureinfo" value="AssayGeneratorMetabo_decoy_generation_input_multids.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_8_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value="all"/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_SiriusAdapter_9 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
-      <param name="in_featureinfo" value="AssayGeneratorMetabo_decoy_generation_input_multids.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_9_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value="all"/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_SiriusAdapter_7 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="SiriusAdapter_4_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value="all"/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_SiriusAdapter_4 -->
-    <test expect_num_outputs="3">
-      <section name="adv_opts">
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="SiriusAdapter_2_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <param name="out_project_space" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5.0"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="project">
-        <param name="processors" value="1"/>
-        <param name="ignore_formula" value="false"/>
-        <param name="q" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="ppm_max" value="10.0"/>
-        <param name="ppm_max_ms2" value="10.0"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="profile" value="qtof"/>
-        <param name="formula" value=""/>
-        <param name="ions_enforced" value=""/>
-        <param name="candidates" value="5"/>
-        <param name="candidates_per_ion" value="-1"/>
-        <param name="elements_considered" value=""/>
-        <param name="elements_enforced" value=""/>
-        <param name="no_isotope_score" value="false"/>
-        <param name="no_isotope_filter" value="false"/>
-        <param name="ions_considered" value=""/>
-        <param name="db" value="ALL"/>
-      </section>
-      <section name="fingerid">
-        <param name="candidates" value="10"/>
-        <param name="db" value="BIO"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG,out_fingerid_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
+  <tests/>
   <help><![CDATA[Tool for metabolite identification using single and tandem mass spectrometry
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SiriusAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SiriusAdapter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SpecLibCreator.xml b/tools/openms/SpecLibCreator.xml
index 40de2a959..16c1e8b18 100644
--- a/tools/openms/SpecLibCreator.xml
+++ b/tools/openms/SpecLibCreator.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="SpecLibCreator" name="SpecLibCreator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Creates an MSP formatted spectral library.</description>
+  <description>Creates an MSP formatted spectral library</description>
   <macros>
     <token name="@EXECUTABLE@">SpecLibCreator</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir info &&
-ln -s '$info' 'info/${re.sub("[^\w\-_]", "_", $info.element_identifier)}.$gxy2omsext($info.ext)' &&
+cp '$info' 'info/${re.sub("[^\w\-_]", "_", $info.element_identifier)}.$gxy2omsext($info.ext)' &&
 mkdir spec &&
-ln -s '$spec' 'spec/${re.sub("[^\w\-_]", "_", $spec.element_identifier)}.$gxy2omsext($spec.ext)' &&
+cp '$spec' 'spec/${re.sub("[^\w\-_]", "_", $spec.element_identifier)}.$gxy2omsext($spec.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -43,15 +42,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-info" type="data" format="csv" optional="false" label="Holds id, peptide, retention time etc" help=" select csv data sets(s)"/>
-    <param argument="-itemseperator" type="text" optional="true" value="," label=" Separator between items. e.g. ," help="">
+    <param argument="-info" type="data" format="csv" label="Holds id, peptide, retention time etc" help=" select csv data sets(s)"/>
+    <param argument="-itemseperator" type="text" value="," label=" Separator between items. e.g. ," help="">
       <expand macro="list_string_san" name="itemseperator"/>
     </param>
     <param argument="-itemenclosed" type="boolean" truevalue="true" falsevalue="false" checked="false" label="'true' or 'false' if true every item is enclosed" help="e.g. '$peptide$,$run$"/>
-    <param argument="-spec" type="data" format="mzdata,mzxml" optional="false" label="spectra" help=" select mzdata,mzxml data sets(s)"/>
+    <param argument="-spec" type="data" format="mzdata,mzxml" label="spectra" help=" select mzdata,mzxml data sets(s)"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -65,11 +64,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!--TODO could not find test data -->
-</tests>
+  <tests>
+    <!--TODO could not find test data -->
+  </tests>
   <help><![CDATA[Creates an MSP formatted spectral library.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SpecLibCreator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpecLibCreator.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SpecLibSearcher.xml b/tools/openms/SpecLibSearcher.xml
index 3de47782e..cf000859f 100644
--- a/tools/openms/SpecLibSearcher.xml
+++ b/tools/openms/SpecLibSearcher.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
 <tool id="SpecLibSearcher" name="SpecLibSearcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.</description>
+  <description>Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library</description>
   <macros>
     <token name="@EXECUTABLE@">SpecLibSearcher</token>
     <import>macros.xml</import>
@@ -17,12 +16,12 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir lib &&
-ln -s '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' &&
+cp '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' &&
 mkdir out &&
 mkdir ${' '.join(["'out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
 
@@ -59,14 +58,14 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" multiple="true" label="Input files" help=" select mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input files" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" label="Input files" help=" select mzml data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-lib" type="data" format="msp" optional="false" label="searchable spectral library (MSP format)" help=" select msp data sets(s)"/>
-    <param argument="-compare_function" type="select" optional="true" label="function for similarity comparison" help="">
+    <param argument="-lib" type="data" format="msp" label="searchable spectral library (MSP format)" help=" select msp data sets(s)"/>
+    <param argument="-compare_function" type="select" label="function for similarity comparison" help="">
       <option value="PeakAlignment">PeakAlignment</option>
       <option value="SpectrumAlignmentScore">SpectrumAlignmentScore</option>
       <option value="SpectrumCheapDPCorr">SpectrumCheapDPCorr</option>
@@ -76,32 +75,32 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
       <expand macro="list_string_san" name="compare_function"/>
     </param>
     <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false">
-      <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Width of precursor mass tolerance window" help=""/>
-      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
+      <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" value="10.0" label="Width of precursor mass tolerance window" help=""/>
+      <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_tolerance_unit"/>
       </param>
-      <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/>
-      <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="5" label="Maximum precursor charge to be considered" help=""/>
-      <param name="isotopes" argument="-precursor:isotopes" type="text" optional="true" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <param name="min_charge" argument="-precursor:min_charge" type="integer" value="2" label="Minimum precursor charge to be considered" help=""/>
+      <param name="max_charge" argument="-precursor:max_charge" type="integer" value="5" label="Maximum precursor charge to be considered" help=""/>
+      <param name="isotopes" argument="-precursor:isotopes" type="text" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
         <expand macro="list_integer_valsan" name="isotopes"/>
       </param>
     </section>
     <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false">
-      <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance" help=""/>
+      <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance" help=""/>
     </section>
     <section name="report" title="Reporting Options" help="" expanded="false">
-      <param name="top_hits" argument="-report:top_hits" type="integer" optional="true" value="10" label="Maximum number of top scoring hits per spectrum that are reported" help=""/>
+      <param name="top_hits" argument="-report:top_hits" type="integer" value="10" label="Maximum number of top scoring hits per spectrum that are reported" help=""/>
     </section>
     <section name="filter" title="Filtering options" help="Most are especially useful when the query spectra are raw" expanded="false">
-      <param name="remove_peaks_below_threshold" argument="-filter:remove_peaks_below_threshold" type="float" optional="true" value="2.01" label="All peaks of a query spectrum with intensities below &lt;threshold&gt; will be zeroed" help=""/>
-      <param name="min_peaks" argument="-filter:min_peaks" type="integer" optional="true" value="5" label="required minimum number of peaks for a query spectrum" help=""/>
-      <param name="max_peaks" argument="-filter:max_peaks" type="integer" optional="true" value="150" label="Use only the top &lt;number&gt; of peaks" help=""/>
-      <param name="cut_peaks_below" argument="-filter:cut_peaks_below" type="integer" optional="true" value="1000" label="Remove all peaks which are lower than 1/&lt;number&gt; of the highest peaks" help="Default equals all peaks which are lower than 0.001 of the maximum intensity peak"/>
+      <param name="remove_peaks_below_threshold" argument="-filter:remove_peaks_below_threshold" type="float" value="2.01" label="All peaks of a query spectrum with intensities below &lt;threshold&gt; will be zeroed" help=""/>
+      <param name="min_peaks" argument="-filter:min_peaks" type="integer" value="5" label="required minimum number of peaks for a query spectrum" help=""/>
+      <param name="max_peaks" argument="-filter:max_peaks" type="integer" value="150" label="Use only the top &lt;number&gt; of peaks" help=""/>
+      <param name="cut_peaks_below" argument="-filter:cut_peaks_below" type="integer" value="1000" label="Remove all peaks which are lower than 1/&lt;number&gt; of the highest peaks" help="Default equals all peaks which are lower than 0.001 of the maximum intensity peak"/>
     </section>
     <section name="modifications" title="Modifications Options" help="" expanded="false">
-      <param name="fixed" argument="-modifications:fixed" multiple="true" type="select" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
+      <param name="fixed" argument="-modifications:fixed" type="select" multiple="true" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
         <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -111,6 +110,10 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="2-succinyl (C)">2-succinyl (C)</option>
         <option value="2HPG (R)">2HPG (R)</option>
         <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+        <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+        <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+        <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+        <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
         <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
         <option value="3sulfo (N-term)">3sulfo (N-term)</option>
         <option value="4-ONE (C)">4-ONE (C)</option>
@@ -200,6 +203,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
         <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
         <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+        <option value="Andro-H2O (C)">Andro-H2O (C)</option>
         <option value="Archaeol (C)">Archaeol (C)</option>
         <option value="Arg (N-term)">Arg (N-term)</option>
         <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -303,6 +307,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
         <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
         <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+        <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
         <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
         <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
         <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -335,7 +340,6 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="BITC (N-term)">BITC (N-term)</option>
         <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
         <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-        <option value="Bodipy (C)">Bodipy (C)</option>
         <option value="Brij35 (N-term)">Brij35 (N-term)</option>
         <option value="Brij58 (N-term)">Brij58 (N-term)</option>
         <option value="Bromo (F)">Bromo (F)</option>
@@ -767,9 +771,9 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Dehydrated (T)">Dehydrated (T)</option>
         <option value="Dehydrated (Y)">Dehydrated (Y)</option>
         <option value="Dehydro (C)">Dehydro (C)</option>
+        <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
         <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-        <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
         <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
         <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -779,7 +783,6 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
         <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
         <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-        <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
         <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
         <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -791,6 +794,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
         <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
         <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+        <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
         <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
         <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -1363,7 +1367,6 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Ethanolyl (C)">Ethanolyl (C)</option>
         <option value="Ethanolyl (K)">Ethanolyl (K)</option>
         <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-        <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
         <option value="Ethyl (C-term)">Ethyl (C-term)</option>
         <option value="Ethyl (D)">Ethyl (D)</option>
         <option value="Ethyl (E)">Ethyl (E)</option>
@@ -1457,6 +1460,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
         <option value="Glu (E)">Glu (E)</option>
         <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+        <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
         <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
         <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
         <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -1471,7 +1475,6 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
         <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
         <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
         <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -1495,6 +1498,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Gly (K)">Gly (K)</option>
         <option value="Gly (S)">Gly (S)</option>
         <option value="Gly (T)">Gly (T)</option>
+        <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
         <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
         <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
         <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -1885,6 +1889,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
         <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
         <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+        <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
         <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
         <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
         <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -1896,6 +1901,9 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
         <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
         <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+        <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+        <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+        <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
         <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
         <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
         <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -1951,6 +1959,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
         <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
         <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+        <option value="His+O(2) (H)">His+O(2) (H)</option>
         <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
         <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
         <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -2088,11 +2097,14 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+        <option value="Kdo (S)">Kdo (S)</option>
+        <option value="Kdo (T)">Kdo (T)</option>
         <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
         <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
         <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
         <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
         <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+        <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
         <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
         <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
         <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -2177,13 +2189,16 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
         <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
         <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+        <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
         <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
         <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
         <option value="Lipoyl (K)">Lipoyl (K)</option>
         <option value="LRGG (K)">LRGG (K)</option>
         <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
         <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+        <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
         <option value="Lys (N-term)">Lys (N-term)</option>
+        <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
         <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
         <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
         <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -2218,6 +2233,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Malonyl (C)">Malonyl (C)</option>
         <option value="Malonyl (K)">Malonyl (K)</option>
         <option value="Malonyl (S)">Malonyl (S)</option>
+        <option value="MBS+peptide (C)">MBS+peptide (C)</option>
         <option value="MDCC (C)">MDCC (C)</option>
         <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
         <option value="Menadione (C)">Menadione (C)</option>
@@ -2229,6 +2245,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="MesitylOxide (H)">MesitylOxide (H)</option>
         <option value="MesitylOxide (K)">MesitylOxide (K)</option>
         <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+        <option value="Met+O(2) (H)">Met+O(2) (H)</option>
         <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
         <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
         <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -2412,7 +2429,6 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
         <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
         <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-        <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
         <option value="NP40 (N-term)">NP40 (N-term)</option>
         <option value="NQIGG (K)">NQIGG (K)</option>
         <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -2500,6 +2516,10 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
         <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
         <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+        <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+        <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+        <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+        <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
         <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
         <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
         <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -2514,6 +2534,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Phospho (Y)">Phospho (Y)</option>
         <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
         <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+        <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
         <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
         <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
         <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -2545,6 +2566,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
         <option value="Piperidine (K)">Piperidine (K)</option>
         <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+        <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
         <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
         <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
         <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -2622,18 +2644,30 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="QTGG (K)">QTGG (K)</option>
         <option value="Quinone (W)">Quinone (W)</option>
         <option value="Quinone (Y)">Quinone (Y)</option>
+        <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+        <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+        <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+        <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+        <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+        <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+        <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+        <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+        <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+        <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+        <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+        <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+        <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+        <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+        <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+        <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+        <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+        <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+        <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+        <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
         <option value="Retinylidene (K)">Retinylidene (K)</option>
         <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
         <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
         <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-        <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-        <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-        <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-        <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-        <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-        <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-        <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-        <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
         <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
         <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
         <option value="Saligenin (H)">Saligenin (H)</option>
@@ -2661,6 +2695,9 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="shTMT (K)">shTMT (K)</option>
         <option value="shTMT (N-term)">shTMT (N-term)</option>
         <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+        <option value="shTMTpro (K)">shTMTpro (K)</option>
+        <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+        <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
         <option value="SMA (K)">SMA (K)</option>
         <option value="SMA (N-term)">SMA (N-term)</option>
         <option value="spermidine (Q)">spermidine (Q)</option>
@@ -2836,7 +2873,6 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
         <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
         <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-        <option value="Ub-amide (C)">Ub-amide (C)</option>
         <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
         <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
         <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -3031,7 +3067,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="ZQG (K)">ZQG (K)</option>
         <expand macro="list_string_san" name="fixed"/>
       </param>
-      <param name="variable" argument="-modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'">
+      <param name="variable" argument="-modifications:variable" type="select" multiple="true" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
         <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -3041,6 +3077,10 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="2-succinyl (C)">2-succinyl (C)</option>
         <option value="2HPG (R)">2HPG (R)</option>
         <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+        <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+        <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+        <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+        <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
         <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
         <option value="3sulfo (N-term)">3sulfo (N-term)</option>
         <option value="4-ONE (C)">4-ONE (C)</option>
@@ -3130,6 +3170,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
         <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
         <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+        <option value="Andro-H2O (C)">Andro-H2O (C)</option>
         <option value="Archaeol (C)">Archaeol (C)</option>
         <option value="Arg (N-term)">Arg (N-term)</option>
         <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -3233,6 +3274,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
         <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
         <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+        <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
         <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
         <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
         <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -3265,7 +3307,6 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="BITC (N-term)">BITC (N-term)</option>
         <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
         <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-        <option value="Bodipy (C)">Bodipy (C)</option>
         <option value="Brij35 (N-term)">Brij35 (N-term)</option>
         <option value="Brij58 (N-term)">Brij58 (N-term)</option>
         <option value="Bromo (F)">Bromo (F)</option>
@@ -3697,9 +3738,9 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Dehydrated (T)">Dehydrated (T)</option>
         <option value="Dehydrated (Y)">Dehydrated (Y)</option>
         <option value="Dehydro (C)">Dehydro (C)</option>
+        <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
         <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-        <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
         <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
         <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
         <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -3709,7 +3750,6 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
         <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
         <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-        <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
         <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
         <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -3721,6 +3761,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
         <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
         <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+        <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
         <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
         <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
         <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -4293,7 +4334,6 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Ethanolyl (C)">Ethanolyl (C)</option>
         <option value="Ethanolyl (K)">Ethanolyl (K)</option>
         <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-        <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
         <option value="Ethyl (C-term)">Ethyl (C-term)</option>
         <option value="Ethyl (D)">Ethyl (D)</option>
         <option value="Ethyl (E)">Ethyl (E)</option>
@@ -4387,6 +4427,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
         <option value="Glu (E)">Glu (E)</option>
         <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+        <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
         <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
         <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
         <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -4401,7 +4442,6 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
         <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-        <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
         <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
         <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
         <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -4425,6 +4465,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Gly (K)">Gly (K)</option>
         <option value="Gly (S)">Gly (S)</option>
         <option value="Gly (T)">Gly (T)</option>
+        <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
         <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
         <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
         <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -4815,6 +4856,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
         <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
         <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+        <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
         <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
         <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
         <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -4826,6 +4868,9 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
         <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
         <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+        <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+        <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+        <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
         <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
         <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
         <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -4881,6 +4926,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
         <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
         <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+        <option value="His+O(2) (H)">His+O(2) (H)</option>
         <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
         <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
         <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -5018,11 +5064,14 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
         <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+        <option value="Kdo (S)">Kdo (S)</option>
+        <option value="Kdo (T)">Kdo (T)</option>
         <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
         <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
         <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
         <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
         <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+        <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
         <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
         <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
         <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -5107,13 +5156,16 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
         <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
         <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+        <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
         <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
         <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
         <option value="Lipoyl (K)">Lipoyl (K)</option>
         <option value="LRGG (K)">LRGG (K)</option>
         <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
         <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+        <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
         <option value="Lys (N-term)">Lys (N-term)</option>
+        <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
         <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
         <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
         <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -5148,6 +5200,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Malonyl (C)">Malonyl (C)</option>
         <option value="Malonyl (K)">Malonyl (K)</option>
         <option value="Malonyl (S)">Malonyl (S)</option>
+        <option value="MBS+peptide (C)">MBS+peptide (C)</option>
         <option value="MDCC (C)">MDCC (C)</option>
         <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
         <option value="Menadione (C)">Menadione (C)</option>
@@ -5159,6 +5212,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="MesitylOxide (H)">MesitylOxide (H)</option>
         <option value="MesitylOxide (K)">MesitylOxide (K)</option>
         <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+        <option value="Met+O(2) (H)">Met+O(2) (H)</option>
         <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
         <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
         <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -5342,7 +5396,6 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
         <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
         <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-        <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
         <option value="NP40 (N-term)">NP40 (N-term)</option>
         <option value="NQIGG (K)">NQIGG (K)</option>
         <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -5430,6 +5483,10 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
         <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
         <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+        <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+        <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+        <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+        <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
         <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
         <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
         <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -5444,6 +5501,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Phospho (Y)">Phospho (Y)</option>
         <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
         <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+        <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
         <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
         <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
         <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -5475,6 +5533,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
         <option value="Piperidine (K)">Piperidine (K)</option>
         <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+        <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
         <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
         <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
         <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -5552,18 +5611,30 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="QTGG (K)">QTGG (K)</option>
         <option value="Quinone (W)">Quinone (W)</option>
         <option value="Quinone (Y)">Quinone (Y)</option>
+        <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+        <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+        <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+        <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+        <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+        <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+        <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+        <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+        <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+        <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+        <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+        <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+        <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+        <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+        <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+        <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+        <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+        <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+        <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+        <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
         <option value="Retinylidene (K)">Retinylidene (K)</option>
         <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
         <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
         <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-        <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-        <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-        <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-        <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-        <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-        <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-        <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-        <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
         <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
         <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
         <option value="Saligenin (H)">Saligenin (H)</option>
@@ -5591,6 +5662,9 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="shTMT (K)">shTMT (K)</option>
         <option value="shTMT (N-term)">shTMT (N-term)</option>
         <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+        <option value="shTMTpro (K)">shTMTpro (K)</option>
+        <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+        <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
         <option value="SMA (K)">SMA (K)</option>
         <option value="SMA (N-term)">SMA (N-term)</option>
         <option value="spermidine (Q)">spermidine (Q)</option>
@@ -5766,7 +5840,6 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
         <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
         <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-        <option value="Ub-amide (C)">Ub-amide (C)</option>
         <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
         <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
         <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -5961,11 +6034,11 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <option value="ZQG (K)">ZQG (K)</option>
         <expand macro="list_string_san" name="variable"/>
       </param>
-      <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
+      <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -5981,7 +6054,8 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_SpecLibSearcher_1 -->
+  <tests>
+    <!-- TOPP_SpecLibSearcher_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -6013,8 +6087,6 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
         <param name="cut_peaks_below" value="1000"/>
       </section>
       <section name="modifications">
-        <param name="fixed"/>
-        <param name="variable"/>
         <param name="variable_max_per_peptide" value="2"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -6023,11 +6095,14 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpecLibSearcher.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpecLibSearcher.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SpectraFilterBernNorm.xml b/tools/openms/SpectraFilterBernNorm.xml
index b68fc4784..690465db0 100644
--- a/tools/openms/SpectraFilterBernNorm.xml
+++ b/tools/openms/SpectraFilterBernNorm.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="SpectraFilterBernNorm" name="SpectraFilterBernNorm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies thresholdfilter to peak spectra.</description>
+  <description>Applies thresholdfilter to peak spectra</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraFilterBernNorm</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,15 +38,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
-      <param name="C1" argument="-algorithm:C1" type="float" optional="true" value="28.0" label="C1 value of the normalization" help=""/>
-      <param name="C2" argument="-algorithm:C2" type="float" optional="true" value="400.0" label="C2 value of the normalization" help=""/>
-      <param name="threshold" argument="-algorithm:threshold" type="float" optional="true" value="0.1" label="Threshold of the Bern et al. normalization" help=""/>
+      <param name="C1" argument="-algorithm:C1" type="float" value="28.0" label="C1 value of the normalization" help=""/>
+      <param name="C2" argument="-algorithm:C2" type="float" value="400.0" label="C2 value of the normalization" help=""/>
+      <param name="threshold" argument="-algorithm:threshold" type="float" value="0.1" label="Threshold of the Bern et al. normalization" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -61,15 +60,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterBernNorm.mzML" compare="sim_size"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
+      <output name="out" value="SpectraFilterBernNorm.mzML" compare="sim_size"/>
+    </test>
+  </tests>
   <help><![CDATA[Applies thresholdfilter to peak spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterBernNorm.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraFilterBernNorm.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SpectraFilterMarkerMower.xml b/tools/openms/SpectraFilterMarkerMower.xml
index 325df2318..3cb371ac7 100644
--- a/tools/openms/SpectraFilterMarkerMower.xml
+++ b/tools/openms/SpectraFilterMarkerMower.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="SpectraFilterMarkerMower" name="SpectraFilterMarkerMower" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies thresholdfilter to peak spectra.</description>
+  <description>Applies thresholdfilter to peak spectra</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraFilterMarkerMower</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,10 +38,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -56,15 +55,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterMarkerMower.mzML" compare="sim_size"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
+      <output name="out" value="SpectraFilterMarkerMower.mzML" compare="sim_size"/>
+    </test>
+  </tests>
   <help><![CDATA[Applies thresholdfilter to peak spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterMarkerMower.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraFilterMarkerMower.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SpectraFilterNLargest.xml b/tools/openms/SpectraFilterNLargest.xml
index 40c161fd8..61989a7c5 100644
--- a/tools/openms/SpectraFilterNLargest.xml
+++ b/tools/openms/SpectraFilterNLargest.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="SpectraFilterNLargest" name="SpectraFilterNLargest" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies thresholdfilter to peak spectra.</description>
+  <description>Applies thresholdfilter to peak spectra</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraFilterNLargest</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,13 +38,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
-      <param name="n" argument="-algorithm:n" type="integer" optional="true" value="200" label="The number of peaks to keep" help=""/>
+      <param name="n" argument="-algorithm:n" type="integer" value="200" label="The number of peaks to keep" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -59,15 +58,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterNLargest.mzML" compare="sim_size"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
+      <output name="out" value="SpectraFilterNLargest.mzML" compare="sim_size"/>
+    </test>
+  </tests>
   <help><![CDATA[Applies thresholdfilter to peak spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterNLargest.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraFilterNLargest.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SpectraFilterNormalizer.xml b/tools/openms/SpectraFilterNormalizer.xml
index 9a1984ce9..38607665b 100644
--- a/tools/openms/SpectraFilterNormalizer.xml
+++ b/tools/openms/SpectraFilterNormalizer.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="SpectraFilterNormalizer" name="SpectraFilterNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Normalizes intensity of peak spectra.</description>
+  <description>Normalizes intensity of peak spectra</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraFilterNormalizer</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,9 +38,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
-      <param name="method" argument="-algorithm:method" type="select" optional="true" label="Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max" help="intensity of one ('to_one') per spectrum">
+      <param name="method" argument="-algorithm:method" type="select" label="Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max" help="intensity of one ('to_one') per spectrum">
         <option value="to_one" selected="true">to_one</option>
         <option value="to_TIC">to_TIC</option>
         <expand macro="list_string_san" name="method"/>
@@ -49,7 +48,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -63,15 +62,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
+      <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/>
+    </test>
+  </tests>
   <help><![CDATA[Normalizes intensity of peak spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterNormalizer.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraFilterNormalizer.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SpectraFilterParentPeakMower.xml b/tools/openms/SpectraFilterParentPeakMower.xml
index 85bc9e403..eceec7e10 100644
--- a/tools/openms/SpectraFilterParentPeakMower.xml
+++ b/tools/openms/SpectraFilterParentPeakMower.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies thresholdfilter to peak spectra.</description>
+  <description>Applies thresholdfilter to peak spectra</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,20 +38,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
-      <param name="window_size" argument="-algorithm:window_size" type="float" optional="true" value="2.0" label="The size of the m/z window where the peaks are removed, +/- window_size" help=""/>
-      <param name="default_charge" argument="-algorithm:default_charge" type="integer" optional="true" value="2" label="If the precursor has no charge set, the default charge is assumed" help=""/>
-      <param name="clean_all_charge_states" argument="-algorithm:clean_all_charge_states" type="integer" optional="true" value="1" label="Set to 1 if precursor ions of all possible charge states should be removed" help=""/>
-      <param name="consider_NH3_loss" argument="-algorithm:consider_NH3_loss" type="integer" optional="true" value="1" label="Whether NH3 loss peaks from the precursor should be removed" help=""/>
-      <param name="consider_H2O_loss" argument="-algorithm:consider_H2O_loss" type="integer" optional="true" value="1" label="Whether H2O loss peaks from the precursor should be removed" help=""/>
-      <param name="reduce_by_factor" argument="-algorithm:reduce_by_factor" type="integer" optional="true" value="0" label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" help=""/>
-      <param name="factor" argument="-algorithm:factor" type="float" optional="true" value="1000.0" label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" help=""/>
-      <param name="set_to_zero" argument="-algorithm:set_to_zero" type="integer" optional="true" value="1" label="Reduce the intensities of the precursor and related ions to zero" help=""/>
+      <param name="window_size" argument="-algorithm:window_size" type="float" value="2.0" label="The size of the m/z window where the peaks are removed, +/- window_size" help=""/>
+      <param name="default_charge" argument="-algorithm:default_charge" type="integer" value="2" label="If the precursor has no charge set, the default charge is assumed" help=""/>
+      <param name="clean_all_charge_states" argument="-algorithm:clean_all_charge_states" type="integer" value="1" label="Set to 1 if precursor ions of all possible charge states should be removed" help=""/>
+      <param name="consider_NH3_loss" argument="-algorithm:consider_NH3_loss" type="integer" value="1" label="Whether NH3 loss peaks from the precursor should be removed" help=""/>
+      <param name="consider_H2O_loss" argument="-algorithm:consider_H2O_loss" type="integer" value="1" label="Whether H2O loss peaks from the precursor should be removed" help=""/>
+      <param name="reduce_by_factor" argument="-algorithm:reduce_by_factor" type="integer" value="0" label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" help=""/>
+      <param name="factor" argument="-algorithm:factor" type="float" value="1000.0" label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" help=""/>
+      <param name="set_to_zero" argument="-algorithm:set_to_zero" type="integer" value="1" label="Reduce the intensities of the precursor and related ions to zero" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -66,15 +65,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
+      <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/>
+    </test>
+  </tests>
   <help><![CDATA[Applies thresholdfilter to peak spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterParentPeakMower.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraFilterParentPeakMower.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SpectraFilterScaler.xml b/tools/openms/SpectraFilterScaler.xml
index e1e70bba2..b6081b1b4 100644
--- a/tools/openms/SpectraFilterScaler.xml
+++ b/tools/openms/SpectraFilterScaler.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="SpectraFilterScaler" name="SpectraFilterScaler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies thresholdfilter to peak spectra.</description>
+  <description>Applies thresholdfilter to peak spectra</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraFilterScaler</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,10 +38,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -56,15 +55,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"> <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterScaler.mzML" compare="sim_size"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
+      <output name="out" value="SpectraFilterScaler.mzML" compare="sim_size"/>
+    </test>
+  </tests>
   <help><![CDATA[Applies thresholdfilter to peak spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterScaler.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraFilterScaler.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SpectraFilterSqrtMower.xml b/tools/openms/SpectraFilterSqrtMower.xml
index 2d9d42b52..425071b9e 100644
--- a/tools/openms/SpectraFilterSqrtMower.xml
+++ b/tools/openms/SpectraFilterSqrtMower.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="SpectraFilterSqrtMower" name="SpectraFilterSqrtMower" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies thresholdfilter to peak spectra.</description>
+  <description>Applies thresholdfilter to peak spectra</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraFilterSqrtMower</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,10 +38,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -56,25 +55,29 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_SpectraFilterSqrtMower_1 -->
+  <tests>
+    <!-- TOPP_SpectraFilterSqrtMower_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-      <output name="out" file="SpectraFilterSqrtMower_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="SpectraFilterSqrtMower_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Applies thresholdfilter to peak spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterSqrtMower.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraFilterSqrtMower.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SpectraFilterThresholdMower.xml b/tools/openms/SpectraFilterThresholdMower.xml
index 0733aac77..d40a04c27 100644
--- a/tools/openms/SpectraFilterThresholdMower.xml
+++ b/tools/openms/SpectraFilterThresholdMower.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="SpectraFilterThresholdMower" name="SpectraFilterThresholdMower" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies thresholdfilter to peak spectra.</description>
+  <description>Applies thresholdfilter to peak spectra</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraFilterThresholdMower</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,13 +38,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
-      <param name="threshold" argument="-algorithm:threshold" type="float" optional="true" value="0.05" label="Intensity threshold, peaks below this threshold are discarded" help=""/>
+      <param name="threshold" argument="-algorithm:threshold" type="float" value="0.05" label="Intensity threshold, peaks below this threshold are discarded" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -59,15 +58,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterThresholdMower.mzML" compare="sim_size"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
+      <output name="out" value="SpectraFilterThresholdMower.mzML" compare="sim_size"/>
+    </test>
+  </tests>
   <help><![CDATA[Applies thresholdfilter to peak spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterThresholdMower.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraFilterThresholdMower.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SpectraFilterWindowMower.xml b/tools/openms/SpectraFilterWindowMower.xml
index d325298f1..0d6f30913 100644
--- a/tools/openms/SpectraFilterWindowMower.xml
+++ b/tools/openms/SpectraFilterWindowMower.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="SpectraFilterWindowMower" name="SpectraFilterWindowMower" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies thresholdfilter to peak spectra.</description>
+  <description>Applies thresholdfilter to peak spectra</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraFilterWindowMower</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,11 +38,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
-      <param name="windowsize" argument="-algorithm:windowsize" type="float" optional="true" value="50.0" label="The size of the sliding window along the m/z axis" help=""/>
-      <param name="peakcount" argument="-algorithm:peakcount" type="integer" optional="true" value="2" label="The number of peaks that should be kept" help=""/>
-      <param name="movetype" argument="-algorithm:movetype" type="select" optional="true" label="Whether sliding window (one peak steps) or jumping window (window size steps) should be used" help="">
+      <param name="windowsize" argument="-algorithm:windowsize" type="float" value="50.0" label="The size of the sliding window along the m/z axis" help=""/>
+      <param name="peakcount" argument="-algorithm:peakcount" type="integer" value="2" label="The number of peaks that should be kept" help=""/>
+      <param name="movetype" argument="-algorithm:movetype" type="select" label="Whether sliding window (one peak steps) or jumping window (window size steps) should be used" help="">
         <option value="slide" selected="true">slide</option>
         <option value="jump">jump</option>
         <expand macro="list_string_san" name="movetype"/>
@@ -51,7 +50,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -65,14 +64,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_SpectraFilterWindowMower_1 -->
+  <tests>
+    <!-- TOPP_SpectraFilterWindowMower_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="SpectraFilterWindowMower_1_input.mzML"/>
-      <output name="out" file="SpectraFilterWindowMower_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="SpectraFilterWindowMower_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="windowsize" value="50.0"/>
         <param name="peakcount" value="2"/>
@@ -84,6 +84,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_SpectraFilterWindowMower_2 -->
     <test expect_num_outputs="2">
@@ -92,7 +95,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="SpectraFilterWindowMower_2_input.mzML"/>
-      <output name="out" file="SpectraFilterWindowMower_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="SpectraFilterWindowMower_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="windowsize" value="20.0"/>
         <param name="peakcount" value="4"/>
@@ -104,11 +107,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Applies thresholdfilter to peak spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterWindowMower.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraFilterWindowMower.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SpectraMerger.xml b/tools/openms/SpectraMerger.xml
index 8dc753b31..d22051bc5 100644
--- a/tools/openms/SpectraMerger.xml
+++ b/tools/openms/SpectraMerger.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Spectrum processing: Misc / Helpers]-->
 <tool id="SpectraMerger" name="SpectraMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Merges spectra (each MS level separately), increasing S/N ratios.</description>
+  <description>Merges spectra (each MS level separately), increasing S/N ratios</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraMerger</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,8 +38,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input mzML file" help=" select mzml data sets(s)"/>
-    <param argument="-merging_method" type="select" optional="true" label="Method of merging which should be used" help="">
+    <param argument="-in" type="data" format="mzml" label="Input mzML file" help=" select mzml data sets(s)"/>
+    <param argument="-merging_method" type="select" label="Method of merging which should be used" help="">
       <option value="average_gaussian" selected="true">average_gaussian</option>
       <option value="average_tophat">average_tophat</option>
       <option value="precursor_method">precursor_method</option>
@@ -48,61 +47,64 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <expand macro="list_string_san" name="merging_method"/>
     </param>
     <section name="algorithm" title="Algorithm section for merging spectra" help="" expanded="false">
-      <param name="mz_binning_width" argument="-algorithm:mz_binning_width" type="float" optional="true" min="0.0" value="5.0" label="minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct" help="Closer data points or peaks will be merged"/>
-      <param name="mz_binning_width_unit" argument="-algorithm:mz_binning_width_unit" type="select" optional="true" label="Unit in which the distance between two data points or peaks is given" help="">
+      <param name="mz_binning_width" argument="-algorithm:mz_binning_width" type="float" min="0.0" value="5.0" label="minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct" help="Closer data points or peaks will be merged"/>
+      <param name="mz_binning_width_unit" argument="-algorithm:mz_binning_width_unit" type="select" label="Unit in which the distance between two data points or peaks is given" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mz_binning_width_unit"/>
       </param>
-      <param name="sort_blocks" argument="-algorithm:sort_blocks" type="select" optional="true" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help="">
+      <param name="sort_blocks" argument="-algorithm:sort_blocks" type="select" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help="">
         <option value="RT_ascending" selected="true">RT_ascending</option>
         <option value="RT_descending">RT_descending</option>
         <expand macro="list_string_san" name="sort_blocks"/>
       </param>
       <section name="average_gaussian" title="" help="" expanded="false">
-        <param name="spectrum_type" argument="-algorithm:average_gaussian:spectrum_type" type="select" optional="true" label="Spectrum type of the MS level to be averaged" help="">
+        <param name="spectrum_type" argument="-algorithm:average_gaussian:spectrum_type" type="select" label="Spectrum type of the MS level to be averaged" help="">
           <option value="profile">profile</option>
           <option value="centroid">centroid</option>
           <option value="automatic" selected="true">automatic</option>
           <expand macro="list_string_san" name="spectrum_type"/>
         </param>
-        <param name="ms_level" argument="-algorithm:average_gaussian:ms_level" type="integer" optional="true" min="1" value="1" label="Average spectra of this level" help="All other spectra remain unchanged"/>
-        <param name="rt_FWHM" argument="-algorithm:average_gaussian:rt_FWHM" type="float" optional="true" min="0.0" max="100000000000.0" value="5.0" label="FWHM of Gauss curve in seconds to be averaged ove" help=""/>
-        <param name="cutoff" argument="-algorithm:average_gaussian:cutoff" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Intensity cutoff for Gaussian" help="The Gaussian RT profile decreases from 1 at its apex to 0 at infinity. Spectra for which the intensity of the Gaussian drops below the cutoff do not contribute to the average"/>
+        <param name="ms_level" argument="-algorithm:average_gaussian:ms_level" type="integer" min="0" value="1" label="If set to be 0, each MS level will be merged from 1 to max" help="Otherwise, average spectra of this level. All other spectra remain unchanged"/>
+        <param name="rt_FWHM" argument="-algorithm:average_gaussian:rt_FWHM" type="float" min="0.0" max="100000000000.0" value="5.0" label="FWHM of Gauss curve in seconds to be averaged ove" help=""/>
+        <param name="cutoff" argument="-algorithm:average_gaussian:cutoff" type="float" min="0.0" max="1.0" value="0.01" label="Intensity cutoff for Gaussian" help="The Gaussian RT profile decreases from 1 at its apex to 0 at infinity. Spectra for which the intensity of the Gaussian drops below the cutoff do not contribute to the average"/>
+        <param name="precursor_mass_tol" argument="-algorithm:average_gaussian:precursor_mass_tol" type="float" min="0.0" value="0.0" label="PPM mass tolerance for precursor mass" help="If set, MSn (n&gt;2) spectra of precursor masses within the tolerance are averaged"/>
+        <param name="precursor_max_charge" argument="-algorithm:average_gaussian:precursor_max_charge" type="integer" min="1" value="1" label="Possible maximum precursor ion charge" help="Effective only when average_gaussian:precursor_mass_tol option is active"/>
       </section>
       <section name="average_tophat" title="" help="" expanded="false">
-        <param name="spectrum_type" argument="-algorithm:average_tophat:spectrum_type" type="select" optional="true" label="Spectrum type of the MS level to be averaged" help="">
+        <param name="spectrum_type" argument="-algorithm:average_tophat:spectrum_type" type="select" label="Spectrum type of the MS level to be averaged" help="">
           <option value="profile">profile</option>
           <option value="centroid">centroid</option>
           <option value="automatic" selected="true">automatic</option>
           <expand macro="list_string_san" name="spectrum_type"/>
         </param>
-        <param name="ms_level" argument="-algorithm:average_tophat:ms_level" type="integer" optional="true" min="1" value="1" label="Average spectra of this level" help="All other spectra remain unchanged"/>
-        <param name="rt_range" argument="-algorithm:average_tophat:rt_range" type="float" optional="true" min="0.0" max="100000000000.0" value="5.0" label="RT range to be averaged ove" help="i.e. +/-(RT range)/2 from each spectrum"/>
-        <param name="rt_unit" argument="-algorithm:average_tophat:rt_unit" type="select" optional="true" label="Unit for RT range" help="">
+        <param name="ms_level" argument="-algorithm:average_tophat:ms_level" type="integer" min="0" value="1" label="If set to be 0, each MS level will be merged from 1 to max" help="Otherwise, average spectra of this level. All other spectra remain unchanged"/>
+        <param name="rt_range" argument="-algorithm:average_tophat:rt_range" type="float" min="0.0" max="100000000000.0" value="5.0" label="RT range to be averaged ove" help="i.e. +/-(RT range)/2 from each spectrum"/>
+        <param name="rt_unit" argument="-algorithm:average_tophat:rt_unit" type="select" label="Unit for RT range" help="">
           <option value="scans" selected="true">scans</option>
           <option value="seconds">seconds</option>
           <expand macro="list_string_san" name="rt_unit"/>
         </param>
       </section>
       <section name="block_method" title="" help="" expanded="false">
-        <param name="ms_levels" argument="-algorithm:block_method:ms_levels" type="text" optional="true" value="1" label="Merge spectra of this level" help="All spectra with other MS levels remain untouched (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+        <param name="ms_levels" argument="-algorithm:block_method:ms_levels" type="text" value="1" label="Merge spectra of this level" help="All spectra with other MS levels remain untouched (space separated list, in order to allow for spaces in list items surround them by single quotes)">
           <expand macro="list_integer_valsan" name="ms_levels">
             <validator type="expression" message="a space separated list of integer values in the range 1: is required"><![CDATA[len(value.split(' ')) == len([_ for _ in value.split(' ') if  1 <= int(_)])
 ]]></validator>
           </expand>
         </param>
-        <param name="rt_block_size" argument="-algorithm:block_method:rt_block_size" type="integer" optional="true" min="1" value="5" label="Maximum number of scans to be summed up" help=""/>
-        <param name="rt_max_length" argument="-algorithm:block_method:rt_max_length" type="float" optional="true" min="0.0" max="100000000000.0" value="0.0" label="Maximum RT size of the block in seconds (0.0 = no size restriction)" help=""/>
+        <param name="rt_block_size" argument="-algorithm:block_method:rt_block_size" type="integer" min="1" value="5" label="Maximum number of scans to be summed up" help=""/>
+        <param name="rt_max_length" argument="-algorithm:block_method:rt_max_length" type="float" min="0.0" max="100000000000.0" value="0.0" label="Maximum RT size of the block in seconds (0.0 = no size restriction)" help=""/>
       </section>
       <section name="precursor_method" title="" help="" expanded="false">
-        <param name="mz_tolerance" argument="-algorithm:precursor_method:mz_tolerance" type="float" optional="true" min="0.0" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" help=""/>
-        <param name="rt_tolerance" argument="-algorithm:precursor_method:rt_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Max RT distance of the precursor entries of two spectra to be merged in [s]" help=""/>
+        <param name="mz_tolerance" argument="-algorithm:precursor_method:mz_tolerance" type="float" min="0.0" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" help=""/>
+        <param name="mass_tolerance" argument="-algorithm:precursor_method:mass_tolerance" type="float" min="0.0" value="0.0" label="Max mass distance of the precursor entries of two spectra to be merged in [Da]" help="Active when set to a positive value"/>
+        <param name="rt_tolerance" argument="-algorithm:precursor_method:rt_tolerance" type="float" min="0.0" value="5.0" label="Max RT distance of the precursor entries of two spectra to be merged in [s]" help=""/>
       </section>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -116,15 +118,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/>
-    <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- just chosen an arbitrary input and autgenerated output-->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/>
+      <section name="algorithm">
+        <section name="average_gaussian">
+          <param name="ms_level" value="2"/>
+        </section>
+      </section>
+      <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/>
+    </test>
+  </tests>
   <help><![CDATA[Merges spectra (each MS level separately), increasing S/N ratios.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraMerger.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraMerger.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SpectraSTSearchAdapter.xml b/tools/openms/SpectraSTSearchAdapter.xml
index f9e7767b1..456d72660 100644
--- a/tools/openms/SpectraSTSearchAdapter.xml
+++ b/tools/openms/SpectraSTSearchAdapter.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
 <tool id="SpectraSTSearchAdapter" name="SpectraSTSearchAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Interface to the SEARCH Mode of the SpectraST executable</description>
   <macros>
@@ -17,27 +16,29 @@
 mkdir spectra_files_cond.spectra_files &&
 #if $spectra_files_cond.spectra_files_select == "no"
 mkdir ${' '.join(["'spectra_files_cond.spectra_files/%s'" % (i) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} && 
-${' '.join(["ln -s '%s' 'spectra_files_cond.spectra_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($spectra_files_cond.spectra_files) if f])}
+${' '.join(["cp '%s' 'spectra_files_cond.spectra_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($spectra_files_cond.spectra_files) if f])}
 #else
-ln -s '$spectra_files_cond.spectra_files' 'spectra_files_cond.spectra_files/${re.sub("[^\w\-_]", "_", $spectra_files_cond.spectra_files.element_identifier)}.$gxy2omsext($spectra_files_cond.spectra_files.ext)' &&
+cp '$spectra_files_cond.spectra_files' 'spectra_files_cond.spectra_files/${re.sub("[^\w\-_]", "_", $spectra_files_cond.spectra_files.element_identifier)}.$gxy2omsext($spectra_files_cond.spectra_files.ext)' &&
 #end if
 mkdir output_files &&
 mkdir ${' '.join(["'output_files/%s'" % (i) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} && 
 mkdir library_file &&
-ln -s '$library_file' 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)' &&
+cp '$library_file' 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)' &&
 #if $sequence_database_file:
   mkdir sequence_database_file &&
-  ln -s '$sequence_database_file' 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)' &&
+  cp '$sequence_database_file' 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)' &&
 #end if
 #if $search_file:
   mkdir search_file &&
-  ln -s '$search_file' 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' &&
+  cp '$search_file' 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' &&
 #end if
+## advanced options
   #if $adv_opts.user_mod_file:
     mkdir adv_opts.user_mod_file &&
-    ln -s '$adv_opts.user_mod_file' 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)' &&
+    cp '$adv_opts.user_mod_file' 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)' &&
   #end if
 
+
 ## Main program call
 
 set -o pipefail &&
@@ -62,11 +63,13 @@ ${' '.join(["'output_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_iden
   -search_file
   'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)'
 #end if
+## advanced options
   #if $adv_opts.user_mod_file:
     -user_mod_file
     'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)'
   #end if
 
+
 ## Postprocessing
 ${' '.join(["&& mv -n 'output_files/%(bn)s/%(id)s.%(omsext)s' 'output_files/%(bn)s/%(id)s.%(gext)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "omsext":$output_files_type, "gext": $oms2gxyext(str($output_files_type))} for i, f in enumerate($spectra_files_cond.spectra_files) if f])}
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
@@ -83,34 +86,34 @@ ${' '.join(["&& mv -n 'output_files/%(bn)s/%(id)s.%(omsext)s' 'output_files/%(bn
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" multiple="true" optional="false" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/>
+        <param argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" multiple="true" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" multiple="false" optional="false" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/>
+        <param argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/>
       </when>
     </conditional>
-    <param name="output_files_type" type="select" optional="false" label="File type of output output_files (Output files. Make sure to specify one output file for each input file)">
+    <param name="output_files_type" type="select" label="File type of output output_files (Output files. Make sure to specify one output file for each input file)">
       <option value="txt">txt</option>
       <option value="tsv">tabular (tsv)</option>
       <option value="pep.xml">pepxml (pep.xml)</option>
       <option value="pepXML">pepxml</option>
       <option value="html">html</option>
     </param>
-    <param argument="-library_file" type="data" format="splib" optional="false" label="Specify library file" help=" select splib data sets(s)"/>
+    <param argument="-library_file" type="data" format="splib" label="Specify library file" help=" select splib data sets(s)"/>
     <param argument="-sequence_database_file" type="data" format="fasta" optional="true" label="The sequence database" help=" select fasta data sets(s)"/>
-    <param argument="-sequence_database_type" type="select" optional="true" label="Specify type of sequence database" help="">
+    <param argument="-sequence_database_type" type="select" label="Specify type of sequence database" help="">
       <option value="DNA">DNA</option>
       <option value="AA" selected="true">AA</option>
       <expand macro="list_string_san" name="sequence_database_type"/>
     </param>
     <param argument="-search_file" type="data" format="txt" optional="true" label="Only search a subset of the query spectra in the search file" help=" select txt data sets(s)"/>
-    <param argument="-precursor_mz_tolerance" type="float" optional="true" min="0.0" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="Monoisotopic mass is assumed"/>
+    <param argument="-precursor_mz_tolerance" type="float" min="0.0" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="Monoisotopic mass is assumed"/>
     <expand macro="adv_opts_macro">
       <param argument="-use_isotopically_averaged_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use isotopically averaged mass instead of monoisotopic mass" help=""/>
       <param argument="-use_all_charge_states" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Search library spectra of all charge states" help="i.e., ignore specified charge state (if any) of the query spectrum"/>
       <param argument="-user_mod_file" type="data" format="txt" optional="true" label="Specify name of user-defined modifications file" help="Default is &quot;spectrast.usermods&quot; select txt data sets(s)"/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -126,12 +129,13 @@ ${' '.join(["&& mv -n 'output_files/%(bn)s/%(id)s.%(omsext)s' 'output_files/%(bn
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_SpectrastSearchAdapter_1 -->
+  <tests>
+    <!-- TOPP_SpectrastSearchAdapter_1 -->
     <!-- TOPP_SpectrastSearchAdapter_2 -->
   </tests>
   <help><![CDATA[Interface to the SEARCH Mode of the SpectraST executable
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SpectraSTSearchAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraSTSearchAdapter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/StaticModification.xml b/tools/openms/StaticModification.xml
index ece061f6c..f9582dc97 100644
--- a/tools/openms/StaticModification.xml
+++ b/tools/openms/StaticModification.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="StaticModification" name="StaticModification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies a set of modifications to all PeptideIDs in an idXML file.</description>
+  <description>Applies a set of modifications to all PeptideIDs in an idXML file</description>
   <macros>
     <token name="@EXECUTABLE@">StaticModification</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,8 +38,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="idxml" optional="false" label="Input: identification results" help=" select idxml data sets(s)"/>
-    <param argument="-mods" multiple="true" type="select" optional="true" label="List of manual modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
+    <param argument="-in" type="data" format="idxml" label="Input: identification results" help=" select idxml data sets(s)"/>
+    <param argument="-mods" type="select" multiple="true" optional="true" label="List of manual modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
       <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
       <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
       <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -50,6 +49,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="2-succinyl (C)">2-succinyl (C)</option>
       <option value="2HPG (R)">2HPG (R)</option>
       <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+      <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+      <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+      <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+      <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
       <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
       <option value="3sulfo (N-term)">3sulfo (N-term)</option>
       <option value="4-ONE (C)">4-ONE (C)</option>
@@ -139,6 +142,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
       <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
       <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+      <option value="Andro-H2O (C)">Andro-H2O (C)</option>
       <option value="Archaeol (C)">Archaeol (C)</option>
       <option value="Arg (N-term)">Arg (N-term)</option>
       <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -242,6 +246,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
       <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
       <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+      <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
       <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
       <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
       <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -274,7 +279,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="BITC (N-term)">BITC (N-term)</option>
       <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
       <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-      <option value="Bodipy (C)">Bodipy (C)</option>
       <option value="Brij35 (N-term)">Brij35 (N-term)</option>
       <option value="Brij58 (N-term)">Brij58 (N-term)</option>
       <option value="Bromo (F)">Bromo (F)</option>
@@ -706,9 +710,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Dehydrated (T)">Dehydrated (T)</option>
       <option value="Dehydrated (Y)">Dehydrated (Y)</option>
       <option value="Dehydro (C)">Dehydro (C)</option>
+      <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
       <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-      <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
       <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
       <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -718,7 +722,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
       <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
       <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-      <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
       <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
       <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -730,6 +733,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
       <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
       <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+      <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
       <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
       <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -1302,7 +1306,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Ethanolyl (C)">Ethanolyl (C)</option>
       <option value="Ethanolyl (K)">Ethanolyl (K)</option>
       <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-      <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
       <option value="Ethyl (C-term)">Ethyl (C-term)</option>
       <option value="Ethyl (D)">Ethyl (D)</option>
       <option value="Ethyl (E)">Ethyl (E)</option>
@@ -1396,6 +1399,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
       <option value="Glu (E)">Glu (E)</option>
       <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+      <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
       <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
       <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
       <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -1410,7 +1414,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
       <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
       <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
       <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -1434,6 +1437,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gly (K)">Gly (K)</option>
       <option value="Gly (S)">Gly (S)</option>
       <option value="Gly (T)">Gly (T)</option>
+      <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
       <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
       <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
       <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -1824,6 +1828,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
       <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
       <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+      <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
       <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
       <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
       <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -1835,6 +1840,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
       <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
       <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+      <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+      <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+      <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
       <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
       <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
       <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -1890,6 +1898,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
       <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
       <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+      <option value="His+O(2) (H)">His+O(2) (H)</option>
       <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
       <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
       <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -2027,11 +2036,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+      <option value="Kdo (S)">Kdo (S)</option>
+      <option value="Kdo (T)">Kdo (T)</option>
       <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
       <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
       <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
       <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
       <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+      <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
       <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
       <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
       <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -2116,13 +2128,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
       <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
       <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+      <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
       <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
       <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
       <option value="Lipoyl (K)">Lipoyl (K)</option>
       <option value="LRGG (K)">LRGG (K)</option>
       <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
       <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+      <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
       <option value="Lys (N-term)">Lys (N-term)</option>
+      <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
       <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
       <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
       <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -2157,6 +2172,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Malonyl (C)">Malonyl (C)</option>
       <option value="Malonyl (K)">Malonyl (K)</option>
       <option value="Malonyl (S)">Malonyl (S)</option>
+      <option value="MBS+peptide (C)">MBS+peptide (C)</option>
       <option value="MDCC (C)">MDCC (C)</option>
       <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
       <option value="Menadione (C)">Menadione (C)</option>
@@ -2168,6 +2184,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="MesitylOxide (H)">MesitylOxide (H)</option>
       <option value="MesitylOxide (K)">MesitylOxide (K)</option>
       <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+      <option value="Met+O(2) (H)">Met+O(2) (H)</option>
       <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
       <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
       <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -2351,7 +2368,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
       <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
       <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-      <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
       <option value="NP40 (N-term)">NP40 (N-term)</option>
       <option value="NQIGG (K)">NQIGG (K)</option>
       <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -2439,6 +2455,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
       <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
       <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+      <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+      <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+      <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+      <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
       <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
       <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
       <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -2453,6 +2473,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phospho (Y)">Phospho (Y)</option>
       <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
       <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+      <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
       <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
       <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
       <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -2484,6 +2505,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
       <option value="Piperidine (K)">Piperidine (K)</option>
       <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+      <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
       <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
       <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
       <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -2561,18 +2583,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="QTGG (K)">QTGG (K)</option>
       <option value="Quinone (W)">Quinone (W)</option>
       <option value="Quinone (Y)">Quinone (Y)</option>
+      <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+      <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+      <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+      <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+      <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+      <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+      <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+      <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+      <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+      <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+      <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+      <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+      <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+      <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+      <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+      <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+      <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+      <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+      <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+      <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
       <option value="Retinylidene (K)">Retinylidene (K)</option>
       <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
       <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
       <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-      <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-      <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-      <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-      <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-      <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-      <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-      <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-      <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
       <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
       <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
       <option value="Saligenin (H)">Saligenin (H)</option>
@@ -2600,6 +2634,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="shTMT (K)">shTMT (K)</option>
       <option value="shTMT (N-term)">shTMT (N-term)</option>
       <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+      <option value="shTMTpro (K)">shTMTpro (K)</option>
+      <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+      <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
       <option value="SMA (K)">SMA (K)</option>
       <option value="SMA (N-term)">SMA (N-term)</option>
       <option value="spermidine (Q)">spermidine (Q)</option>
@@ -2775,7 +2812,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
       <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
       <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-      <option value="Ub-amide (C)">Ub-amide (C)</option>
       <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
       <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
       <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -2970,14 +3006,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="ZQG (K)">ZQG (K)</option>
       <expand macro="list_string_san" name="mods"/>
     </param>
-    <param argument="-presets" type="select" optional="true" label="Add predefined sets, as shortcut to manually specifying a lot of modifications" help="">
+    <param argument="-presets" type="select" label="Add predefined sets, as shortcut to manually specifying a lot of modifications" help="">
       <option value="none" selected="true">none</option>
       <option value="N15">N15</option>
       <expand macro="list_string_san" name="presets"/>
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -2995,6 +3031,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   <help><![CDATA[Applies a set of modifications to all PeptideIDs in an idXML file.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_StaticModification.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_StaticModification.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/SvmTheoreticalSpectrumGeneratorTrainer.xml b/tools/openms/SvmTheoreticalSpectrumGeneratorTrainer.xml
deleted file mode 100644
index 0bf0d0cf5..000000000
--- a/tools/openms/SvmTheoreticalSpectrumGeneratorTrainer.xml
+++ /dev/null
@@ -1,141 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
-<tool id="SvmTheoreticalSpectrumGeneratorTrainer" name="SvmTheoreticalSpectrumGeneratorTrainer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator</description>
-  <macros>
-    <token name="@EXECUTABLE@">SvmTheoreticalSpectrumGeneratorTrainer</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in_spectra &&
-ln -s '$in_spectra' 'in_spectra/${re.sub("[^\w\-_]", "_", $in_spectra.element_identifier)}.$gxy2omsext($in_spectra.ext)' &&
-mkdir in_identifications &&
-ln -s '$in_identifications' 'in_identifications/${re.sub("[^\w\-_]", "_", $in_identifications.element_identifier)}.$gxy2omsext($in_identifications.ext)' &&
-mkdir model_output_file &&
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in_spectra
-'in_spectra/${re.sub("[^\w\-_]", "_", $in_spectra.element_identifier)}.$gxy2omsext($in_spectra.ext)'
--in_identifications
-'in_identifications/${re.sub("[^\w\-_]", "_", $in_identifications.element_identifier)}.$gxy2omsext($in_identifications.ext)'
--model_output_file
-'model_output_file/output.${gxy2omsext("txt")}'
-
-## Postprocessing
-&& mv 'model_output_file/output.${gxy2omsext("txt")}' '$model_output_file'
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
-  </configfiles>
-  <inputs>
-    <param argument="-in_spectra" type="data" format="mzml" optional="false" label="Input Training Spectra in mzML" help=" select mzml data sets(s)"/>
-    <param argument="-in_identifications" type="data" format="idxml" optional="false" label="Input file with corresponding sequences in idXML" help=" select idxml data sets(s)"/>
-    <param argument="-precursor_charge" type="integer" optional="true" min="1" max="3" value="2" label="Precursor charge state used for model training" help=""/>
-    <param argument="-write_training_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No models are trained but input training files for libSVM command line tools are produced" help=""/>
-    <section name="algorithm" title="" help="" expanded="false">
-      <param name="number_intensity_levels" argument="-algorithm:number_intensity_levels" type="integer" optional="true" value="7" label="The number of intensity bins (for secondary type models)" help=""/>
-      <param name="number_regions" argument="-algorithm:number_regions" type="integer" optional="true" value="3" label="The number of regions each spectrum is split to (for secondary type models)" help=""/>
-      <param name="parent_tolerance" argument="-algorithm:parent_tolerance" type="float" optional="true" value="2.5" label="The maximum difference between theoretical and experimental parent mass to accept training spectrum" help=""/>
-      <param name="peak_tolerance" argument="-algorithm:peak_tolerance" type="float" optional="true" value="0.5" label="The maximum mass error for a peak to the expected mass of some ion type" help=""/>
-      <param name="add_b_ions" argument="-algorithm:add_b_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Train simulator for b-ions" help=""/>
-      <param name="add_y_ions" argument="-algorithm:add_y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Train simulator for y-ions" help=""/>
-      <param name="add_a_ions" argument="-algorithm:add_a_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Train simulator for a-ions" help=""/>
-      <param name="add_c_ions" argument="-algorithm:add_c_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Train simulator for c-ions" help=""/>
-      <param name="add_x_ions" argument="-algorithm:add_x_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Train simulator for x-ions" help=""/>
-      <param name="add_z_ions" argument="-algorithm:add_z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Train simulator for z-ions" help=""/>
-      <param name="add_losses" argument="-algorithm:add_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Train simulator for neutral losses of H2O and NH3 for b-ions and y-ions" help=""/>
-      <param name="add_b2_ions" argument="-algorithm:add_b2_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Train simulator for doubly charged b-ions" help=""/>
-      <param name="add_y2_ions" argument="-algorithm:add_y2_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Train simulator for double charged y-ions" help=""/>
-      <section name="svm" title="Parameters controlling SVM trainig behaviou" help="All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation" expanded="false">
-        <param name="svc_type" argument="-algorithm:svm:svc_type" type="integer" optional="true" min="0" max="1" value="0" label="Type of the SVC: 0=C_SVC 1=NU_SVC" help=""/>
-        <param name="svr_type" argument="-algorithm:svm:svr_type" type="integer" optional="true" min="0" max="1" value="1" label="Type of the SVR: 0=EPSILON_SVR 1=NU_SVR" help=""/>
-        <param name="scaling" argument="-algorithm:svm:scaling" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Apply scaling of feature values" help=""/>
-        <param name="scaling_lower" argument="-algorithm:svm:scaling_lower" type="float" optional="true" value="0.0" label="Lower bound for scaling" help=""/>
-        <param name="scaling_upper" argument="-algorithm:svm:scaling_upper" type="float" optional="true" value="1.0" label="Upper bound for scaling" help=""/>
-        <param name="n_fold" argument="-algorithm:svm:n_fold" type="integer" optional="true" min="1" value="5" label="n_fold cross validation is performed" help=""/>
-        <param name="grid" argument="-algorithm:svm:grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform grid search" help=""/>
-        <param name="additive_cv" argument="-algorithm:svm:additive_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Additive step size (if false multiplicative)" help=""/>
-        <section name="svc" title="Parameters for svm - classification of missing/abundant" help="" expanded="false">
-          <param name="kernel_type" argument="-algorithm:svm:svc:kernel_type" type="integer" optional="true" min="0" max="3" value="2" label="Type of the kernel:  0=LINEAR 1=POLY 2=RBF 3=SIGMOID" help=""/>
-          <param name="degree" argument="-algorithm:svm:svc:degree" type="integer" optional="true" min="1" value="3" label="For POLY" help=""/>
-          <param name="gamma" argument="-algorithm:svm:svc:gamma" type="float" optional="true" min="0.0" value="0.0" label="For POLY/RBF/SIGMOID" help=""/>
-          <param name="C" argument="-algorithm:svm:svc:C" type="float" optional="true" value="1.0" label="Cost of constraint violation" help=""/>
-          <param name="nu" argument="-algorithm:svm:svc:nu" type="float" optional="true" value="0.5" label="For NU_SVC, ONE_CLASS and NU_SVR" help=""/>
-          <param name="balancing" argument="-algorithm:svm:svc:balancing" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use class balanced SVC training" help=""/>
-          <param name="degree_start" argument="-algorithm:svm:svc:degree_start" type="integer" optional="true" min="1" value="1" label="starting point of degree" help=""/>
-          <param name="degree_step_size" argument="-algorithm:svm:svc:degree_step_size" type="integer" optional="true" value="2" label="step size point of degree" help=""/>
-          <param name="degree_stop" argument="-algorithm:svm:svc:degree_stop" type="integer" optional="true" value="4" label="stopping point of degree" help=""/>
-          <param name="gamma_start" argument="-algorithm:svm:svc:gamma_start" type="float" optional="true" min="0.0" max="1.0" value="1e-05" label="starting point of gamma" help=""/>
-          <param name="gamma_step_size" argument="-algorithm:svm:svc:gamma_step_size" type="integer" optional="true" value="100" label="step size point of gamma" help=""/>
-          <param name="gamma_stop" argument="-algorithm:svm:svc:gamma_stop" type="float" optional="true" value="0.1" label="stopping point of gamma" help=""/>
-          <param name="c_start" argument="-algorithm:svm:svc:c_start" type="float" optional="true" value="0.1" label="starting point of c" help=""/>
-          <param name="c_step_size" argument="-algorithm:svm:svc:c_step_size" type="integer" optional="true" value="100" label="step size of c" help=""/>
-          <param name="c_stop" argument="-algorithm:svm:svc:c_stop" type="integer" optional="true" value="1000" label="stopping point of c" help=""/>
-          <param name="nu_start" argument="-algorithm:svm:svc:nu_start" type="float" optional="true" min="0.0" max="1.0" value="0.3" label="starting point of nu" help=""/>
-          <param name="nu_step_size" argument="-algorithm:svm:svc:nu_step_size" type="integer" optional="true" value="2" label="step size of nu" help=""/>
-          <param name="nu_stop" argument="-algorithm:svm:svc:nu_stop" type="float" optional="true" min="0.0" max="1.0" value="0.6" label="stopping point of nu" help=""/>
-        </section>
-        <section name="svr" title="Parameters for svm - regression of peak intensities" help="" expanded="false">
-          <param name="kernel_type" argument="-algorithm:svm:svr:kernel_type" type="integer" optional="true" min="0" max="3" value="2" label="Type of the kernel:  0=LINEAR 1=POLY 2=RBF 3=SIGMOID" help=""/>
-          <param name="degree" argument="-algorithm:svm:svr:degree" type="integer" optional="true" min="1" value="3" label="For POLY" help=""/>
-          <param name="gamma" argument="-algorithm:svm:svr:gamma" type="float" optional="true" min="0.0" value="0.0" label="For POLY/RBF/SIGMOID" help=""/>
-          <param name="C" argument="-algorithm:svm:svr:C" type="float" optional="true" value="1.0" label="Cost of constraint violation" help=""/>
-          <param name="p" argument="-algorithm:svm:svr:p" type="float" optional="true" value="0.1" label="The epsilon for the loss function in epsilon-SVR" help=""/>
-          <param name="nu" argument="-algorithm:svm:svr:nu" type="float" optional="true" value="0.5" label="For NU_SVC, ONE_CLASS and NU_SVR" help=""/>
-          <param name="degree_start" argument="-algorithm:svm:svr:degree_start" type="integer" optional="true" min="1" value="1" label="starting point of degree" help=""/>
-          <param name="degree_step_size" argument="-algorithm:svm:svr:degree_step_size" type="integer" optional="true" value="2" label="step size point of degree" help=""/>
-          <param name="degree_stop" argument="-algorithm:svm:svr:degree_stop" type="integer" optional="true" value="4" label="stopping point of degree" help=""/>
-          <param name="gamma_start" argument="-algorithm:svm:svr:gamma_start" type="float" optional="true" min="0.0" max="1.0" value="1e-05" label="starting point of gamma" help=""/>
-          <param name="gamma_step_size" argument="-algorithm:svm:svr:gamma_step_size" type="integer" optional="true" value="100" label="step size point of gamma" help=""/>
-          <param name="gamma_stop" argument="-algorithm:svm:svr:gamma_stop" type="float" optional="true" value="0.1" label="stopping point of gamma" help=""/>
-          <param name="p_start" argument="-algorithm:svm:svr:p_start" type="float" optional="true" value="1e-05" label="starting point of p" help=""/>
-          <param name="p_step_size" argument="-algorithm:svm:svr:p_step_size" type="integer" optional="true" value="100" label="step size point of p" help=""/>
-          <param name="p_stop" argument="-algorithm:svm:svr:p_stop" type="float" optional="true" value="0.1" label="stopping point of p" help=""/>
-          <param name="c_start" argument="-algorithm:svm:svr:c_start" type="float" optional="true" value="0.1" label="starting point of c" help=""/>
-          <param name="c_step_size" argument="-algorithm:svm:svr:c_step_size" type="integer" optional="true" value="100" label="step size of c" help=""/>
-          <param name="c_stop" argument="-algorithm:svm:svr:c_stop" type="integer" optional="true" value="1000" label="stopping point of c" help=""/>
-          <param name="nu_start" argument="-algorithm:svm:svr:nu_start" type="float" optional="true" min="0.0" max="1.0" value="0.3" label="starting point of nu" help=""/>
-          <param name="nu_step_size" argument="-algorithm:svm:svr:nu_step_size" type="integer" optional="true" value="2" label="step size of nu" help=""/>
-          <param name="nu_stop" argument="-algorithm:svm:svr:nu_stop" type="float" optional="true" min="0.0" max="1.0" value="0.6" label="stopping point of nu" help=""/>
-        </section>
-      </section>
-    </section>
-    <expand macro="adv_opts_macro">
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="model_output_file" label="${tool.name} on ${on_string}: model_output_file" format="txt"/>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><!-- -TODO model_output_file creates multiple files-->
-</tests>
-  <help><![CDATA[Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SvmTheoreticalSpectrumGeneratorTrainer.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/TICCalculator.xml b/tools/openms/TICCalculator.xml
index 4dc0d2108..1b6f31ace 100644
--- a/tools/openms/TICCalculator.xml
+++ b/tools/openms/TICCalculator.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: []-->
 <tool id="TICCalculator" name="TICCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).</description>
+  <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking)</description>
   <macros>
     <token name="@EXECUTABLE@">TICCalculator</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 
 ## Main program call
 
@@ -36,8 +35,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular" optional="false" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular data sets(s)"/>
-    <param argument="-read_method" type="select" optional="true" label="Method to read the file" help="">
+    <param argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular data sets(s)"/>
+    <param argument="-read_method" type="select" label="Method to read the file" help="">
       <option value="regular" selected="true">regular</option>
       <option value="indexed">indexed</option>
       <option value="indexed_parallel">indexed_parallel</option>
@@ -49,7 +48,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-loadData" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to actually load and decode the binary data (or whether to skip decoding the binary data)" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -65,7 +64,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_TICCalculator_1 -->
+  <tests>
+    <!-- TOPP_TICCalculator_1 -->
     <test expect_num_outputs="1">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -80,8 +80,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_TICCalculator_2 -->
+    <!-- TOPP_TICCalculator_2 -->
     <test expect_num_outputs="1">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -96,8 +99,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_TICCalculator_3 -->
+    <!-- TOPP_TICCalculator_3 -->
     <test expect_num_outputs="1">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -112,8 +118,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_TICCalculator_4 -->
+    <!-- TOPP_TICCalculator_4 -->
     <test expect_num_outputs="1">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -128,8 +137,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_TICCalculator_5 -->
+    <!-- TOPP_TICCalculator_5 -->
     <test expect_num_outputs="1">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -144,11 +156,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TICCalculator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TICCalculator.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/TOFCalibration.xml b/tools/openms/TOFCalibration.xml
index 30767249b..f41d1e153 100644
--- a/tools/openms/TOFCalibration.xml
+++ b/tools/openms/TOFCalibration.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Mass Correction and Calibration]-->
 <tool id="TOFCalibration" name="TOFCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies time of flight calibration.</description>
+  <description>Applies time of flight calibration</description>
   <macros>
     <token name="@EXECUTABLE@">TOFCalibration</token>
     <import>macros.xml</import>
@@ -15,14 +14,14 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 mkdir ext_calibrants &&
-ln -s '$ext_calibrants' 'ext_calibrants/${re.sub("[^\w\-_]", "_", $ext_calibrants.element_identifier)}.$gxy2omsext($ext_calibrants.ext)' &&
+cp '$ext_calibrants' 'ext_calibrants/${re.sub("[^\w\-_]", "_", $ext_calibrants.element_identifier)}.$gxy2omsext($ext_calibrants.ext)' &&
 mkdir ref_masses &&
-ln -s '$ref_masses' 'ref_masses/${re.sub("[^\w\-_]", "_", $ref_masses.element_identifier)}.$gxy2omsext($ref_masses.ext)' &&
+cp '$ref_masses' 'ref_masses/${re.sub("[^\w\-_]", "_", $ref_masses.element_identifier)}.$gxy2omsext($ref_masses.ext)' &&
 mkdir tof_const &&
-ln -s '$tof_const' 'tof_const/${re.sub("[^\w\-_]", "_", $tof_const.element_identifier)}.$gxy2omsext($tof_const.ext)' &&
+cp '$tof_const' 'tof_const/${re.sub("[^\w\-_]", "_", $tof_const.element_identifier)}.$gxy2omsext($tof_const.ext)' &&
 
 ## Main program call
 
@@ -51,77 +50,77 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input peak or raw data file" help=" select mzml data sets(s)"/>
-    <param argument="-ext_calibrants" type="data" format="mzml" optional="false" label="input file containing the external calibrant spectra (peak or raw data)" help=" select mzml data sets(s)"/>
-    <param argument="-ref_masses" type="data" format="tabular,txt" optional="false" label="input file containing reference masses of the external calibrant spectra (one per line)" help=" select tabular,txt data sets(s)"/>
-    <param argument="-tof_const" type="data" format="tabular" optional="false" label="File containing TOF conversion constants" help="These can be either two or three constants. per set, depending on the conversion type. Either one set for all calibrant spectra . (tab separated), or one for each spectrum.. For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line) select tabular data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input peak or raw data file" help=" select mzml data sets(s)"/>
+    <param argument="-ext_calibrants" type="data" format="mzml" label="input file containing the external calibrant spectra (peak or raw data)" help=" select mzml data sets(s)"/>
+    <param argument="-ref_masses" type="data" format="tabular,txt" label="input file containing reference masses of the external calibrant spectra (one per line)" help=" select tabular,txt data sets(s)"/>
+    <param argument="-tof_const" type="data" format="tabular" label="File containing TOF conversion constants" help="These can be either two or three constants. per set, depending on the conversion type. Either one set for all calibrant spectra . (tab separated), or one for each spectrum.. For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line) select tabular data sets(s)"/>
     <param argument="-peak_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI file)" help=""/>
     <section name="algorithm" title="Algorithm section for peak picking" help="" expanded="false">
       <section name="PeakPicker" title="" help="" expanded="false">
-        <param name="signal_to_noise" argument="-algorithm:PeakPicker:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/>
-        <param name="centroid_percentage" argument="-algorithm:PeakPicker:centroid_percentage" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" help="If it is 1 the centroid position corresponds to the position of the highest intensity"/>
-        <param name="peak_width" argument="-algorithm:PeakPicker:peak_width" type="float" optional="true" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/>
+        <param name="signal_to_noise" argument="-algorithm:PeakPicker:signal_to_noise" type="float" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/>
+        <param name="centroid_percentage" argument="-algorithm:PeakPicker:centroid_percentage" type="float" min="0.0" max="1.0" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" help="If it is 1 the centroid position corresponds to the position of the highest intensity"/>
+        <param name="peak_width" argument="-algorithm:PeakPicker:peak_width" type="float" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/>
         <param name="estimate_peak_width" argument="-algorithm:PeakPicker:estimate_peak_width" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag if the average peak width shall be estimated" help="Attention: when this flag is set, the peak_width is ignored"/>
-        <param name="fwhm_lower_bound_factor" argument="-algorithm:PeakPicker:fwhm_lower_bound_factor" type="float" optional="true" min="0.0" value="0.7" label="Factor that calculates the minimal fwhm value from the peak_width" help="All peaks with width smaller than fwhm_bound_factor * peak_width are discarded"/>
-        <param name="fwhm_upper_bound_factor" argument="-algorithm:PeakPicker:fwhm_upper_bound_factor" type="float" optional="true" min="0.0" value="20.0" label="Factor that calculates the maximal fwhm value from the peak_width" help="All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded"/>
+        <param name="fwhm_lower_bound_factor" argument="-algorithm:PeakPicker:fwhm_lower_bound_factor" type="float" min="0.0" value="0.7" label="Factor that calculates the minimal fwhm value from the peak_width" help="All peaks with width smaller than fwhm_bound_factor * peak_width are discarded"/>
+        <param name="fwhm_upper_bound_factor" argument="-algorithm:PeakPicker:fwhm_upper_bound_factor" type="float" min="0.0" value="20.0" label="Factor that calculates the maximal fwhm value from the peak_width" help="All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded"/>
         <section name="optimization" title="" help="" expanded="false">
-          <param name="iterations" argument="-algorithm:PeakPicker:optimization:iterations" type="integer" optional="true" min="1" value="400" label="maximal number of iterations for the fitting step" help=""/>
+          <param name="iterations" argument="-algorithm:PeakPicker:optimization:iterations" type="integer" min="1" value="400" label="maximal number of iterations for the fitting step" help=""/>
           <section name="penalties" title="" help="" expanded="false">
-            <param name="position" argument="-algorithm:PeakPicker:optimization:penalties:position" type="float" optional="true" min="0.0" value="0.0" label="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized" help=""/>
-            <param name="left_width" argument="-algorithm:PeakPicker:optimization:penalties:left_width" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized" help=""/>
-            <param name="right_width" argument="-algorithm:PeakPicker:optimization:penalties:right_width" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized" help=""/>
-            <param name="height" argument="-algorithm:PeakPicker:optimization:penalties:height" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized" help=""/>
+            <param name="position" argument="-algorithm:PeakPicker:optimization:penalties:position" type="float" min="0.0" value="0.0" label="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized" help=""/>
+            <param name="left_width" argument="-algorithm:PeakPicker:optimization:penalties:left_width" type="float" min="0.0" value="1.0" label="penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized" help=""/>
+            <param name="right_width" argument="-algorithm:PeakPicker:optimization:penalties:right_width" type="float" min="0.0" value="1.0" label="penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized" help=""/>
+            <param name="height" argument="-algorithm:PeakPicker:optimization:penalties:height" type="float" min="0.0" value="1.0" label="penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized" help=""/>
           </section>
           <section name="2d" title="" help="" expanded="false">
-            <param name="tolerance_mz" argument="-algorithm:PeakPicker:optimization:2d:tolerance_mz" type="float" optional="true" min="0.0" value="2.2" label="mz tolerance for cluster construction" help=""/>
-            <param name="max_peak_distance" argument="-algorithm:PeakPicker:optimization:2d:max_peak_distance" type="float" optional="true" min="0.0" value="1.2" label="maximal peak distance in mz in a cluste" help=""/>
+            <param name="tolerance_mz" argument="-algorithm:PeakPicker:optimization:2d:tolerance_mz" type="float" min="0.0" value="2.2" label="mz tolerance for cluster construction" help=""/>
+            <param name="max_peak_distance" argument="-algorithm:PeakPicker:optimization:2d:max_peak_distance" type="float" min="0.0" value="1.2" label="maximal peak distance in mz in a cluste" help=""/>
           </section>
         </section>
         <section name="thresholds" title="" help="" expanded="false">
-          <param name="peak_bound" argument="-algorithm:PeakPicker:thresholds:peak_bound" type="float" optional="true" min="0.0" value="10.0" label="Minimal peak intensity" help=""/>
-          <param name="peak_bound_ms2_level" argument="-algorithm:PeakPicker:thresholds:peak_bound_ms2_level" type="float" optional="true" min="0.0" value="10.0" label="Minimal peak intensity for MS/MS peaks" help=""/>
-          <param name="correlation" argument="-algorithm:PeakPicker:thresholds:correlation" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="minimal correlation of a peak and the raw signal" help="If a peak has a lower correlation it is skipped"/>
-          <param name="noise_level" argument="-algorithm:PeakPicker:thresholds:noise_level" type="float" optional="true" min="0.0" value="0.1" label="noise level for the search of the peak endpoints" help=""/>
-          <param name="search_radius" argument="-algorithm:PeakPicker:thresholds:search_radius" type="integer" optional="true" min="0" value="3" label="search radius for the search of the maximum in the signal after a maximum in the cwt was found" help=""/>
+          <param name="peak_bound" argument="-algorithm:PeakPicker:thresholds:peak_bound" type="float" min="0.0" value="10.0" label="Minimal peak intensity" help=""/>
+          <param name="peak_bound_ms2_level" argument="-algorithm:PeakPicker:thresholds:peak_bound_ms2_level" type="float" min="0.0" value="10.0" label="Minimal peak intensity for MS/MS peaks" help=""/>
+          <param name="correlation" argument="-algorithm:PeakPicker:thresholds:correlation" type="float" min="0.0" max="1.0" value="0.5" label="minimal correlation of a peak and the raw signal" help="If a peak has a lower correlation it is skipped"/>
+          <param name="noise_level" argument="-algorithm:PeakPicker:thresholds:noise_level" type="float" min="0.0" value="0.1" label="noise level for the search of the peak endpoints" help=""/>
+          <param name="search_radius" argument="-algorithm:PeakPicker:thresholds:search_radius" type="integer" min="0" value="3" label="search radius for the search of the maximum in the signal after a maximum in the cwt was found" help=""/>
         </section>
         <section name="wavelet_transform" title="" help="" expanded="false">
-          <param name="spacing" argument="-algorithm:PeakPicker:wavelet_transform:spacing" type="float" optional="true" min="0.0" value="0.001" label="Spacing of the CWT" help="Note that the accuracy of the picked peak's centroid position depends in the Raw data spacing, i.e., 50% of raw peak distance at most"/>
+          <param name="spacing" argument="-algorithm:PeakPicker:wavelet_transform:spacing" type="float" min="0.0" value="0.001" label="Spacing of the CWT" help="Note that the accuracy of the picked peak's centroid position depends in the Raw data spacing, i.e., 50% of raw peak distance at most"/>
         </section>
         <section name="deconvolution" title="" help="" expanded="false">
           <param name="deconvolution" argument="-algorithm:PeakPicker:deconvolution:deconvolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If you want heavily overlapping peaks to be separated set this value to &quot;true&quot;" help=""/>
-          <param name="asym_threshold" argument="-algorithm:PeakPicker:deconvolution:asym_threshold" type="float" optional="true" min="0.0" value="0.3" label="If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started" help=""/>
-          <param name="left_width" argument="-algorithm:PeakPicker:deconvolution:left_width" type="float" optional="true" min="0.0" value="2.0" label="1/left_width is the initial value for the left width of the peaks found in the deconvolution step" help=""/>
-          <param name="right_width" argument="-algorithm:PeakPicker:deconvolution:right_width" type="float" optional="true" min="0.0" value="2.0" label="1/right_width is the initial value for the right width of the peaks found in the deconvolution step" help=""/>
-          <param name="scaling" argument="-algorithm:PeakPicker:deconvolution:scaling" type="float" optional="true" min="0.0" value="0.12" label="Initial scaling of the cwt used in the separation of heavily overlapping peaks" help="The initial value is used for charge 1, for higher charges it is adapted to scaling/charge"/>
+          <param name="asym_threshold" argument="-algorithm:PeakPicker:deconvolution:asym_threshold" type="float" min="0.0" value="0.3" label="If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started" help=""/>
+          <param name="left_width" argument="-algorithm:PeakPicker:deconvolution:left_width" type="float" min="0.0" value="2.0" label="1/left_width is the initial value for the left width of the peaks found in the deconvolution step" help=""/>
+          <param name="right_width" argument="-algorithm:PeakPicker:deconvolution:right_width" type="float" min="0.0" value="2.0" label="1/right_width is the initial value for the right width of the peaks found in the deconvolution step" help=""/>
+          <param name="scaling" argument="-algorithm:PeakPicker:deconvolution:scaling" type="float" min="0.0" value="0.12" label="Initial scaling of the cwt used in the separation of heavily overlapping peaks" help="The initial value is used for charge 1, for higher charges it is adapted to scaling/charge"/>
           <section name="fitting" title="" help="" expanded="false">
-            <param name="fwhm_threshold" argument="-algorithm:PeakPicker:deconvolution:fitting:fwhm_threshold" type="float" optional="true" min="0.0" value="0.7" label="If the FWHM of a peak is higher than 'fwhm_thresholds' it is assumed that it consists of more than one peak and the deconvolution procedure is started" help=""/>
-            <param name="eps_abs" argument="-algorithm:PeakPicker:deconvolution:fitting:eps_abs" type="float" optional="true" min="0.0" value="9.999999747378752e-06" label="if the absolute error gets smaller than this value the fitting is stopped" help=""/>
-            <param name="eps_rel" argument="-algorithm:PeakPicker:deconvolution:fitting:eps_rel" type="float" optional="true" min="0.0" value="9.999999747378752e-06" label="if the relative error gets smaller than this value the fitting is stopped" help=""/>
-            <param name="max_iteration" argument="-algorithm:PeakPicker:deconvolution:fitting:max_iteration" type="integer" optional="true" min="1" value="10" label="maximal number of iterations for the fitting step" help=""/>
+            <param name="fwhm_threshold" argument="-algorithm:PeakPicker:deconvolution:fitting:fwhm_threshold" type="float" min="0.0" value="0.7" label="If the FWHM of a peak is higher than 'fwhm_thresholds' it is assumed that it consists of more than one peak and the deconvolution procedure is started" help=""/>
+            <param name="eps_abs" argument="-algorithm:PeakPicker:deconvolution:fitting:eps_abs" type="float" min="0.0" value="9.999999747378752e-06" label="if the absolute error gets smaller than this value the fitting is stopped" help=""/>
+            <param name="eps_rel" argument="-algorithm:PeakPicker:deconvolution:fitting:eps_rel" type="float" min="0.0" value="9.999999747378752e-06" label="if the relative error gets smaller than this value the fitting is stopped" help=""/>
+            <param name="max_iteration" argument="-algorithm:PeakPicker:deconvolution:fitting:max_iteration" type="integer" min="1" value="10" label="maximal number of iterations for the fitting step" help=""/>
             <section name="penalties" title="" help="" expanded="false">
-              <param name="position" argument="-algorithm:PeakPicker:deconvolution:fitting:penalties:position" type="float" optional="true" min="0.0" value="0.0" label="penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule" help=""/>
-              <param name="height" argument="-algorithm:PeakPicker:deconvolution:fitting:penalties:height" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized" help=""/>
-              <param name="left_width" argument="-algorithm:PeakPicker:deconvolution:fitting:penalties:left_width" type="float" optional="true" min="0.0" value="0.0" label="penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized" help=""/>
-              <param name="right_width" argument="-algorithm:PeakPicker:deconvolution:fitting:penalties:right_width" type="float" optional="true" min="0.0" value="0.0" label="penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized" help=""/>
+              <param name="position" argument="-algorithm:PeakPicker:deconvolution:fitting:penalties:position" type="float" min="0.0" value="0.0" label="penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule" help=""/>
+              <param name="height" argument="-algorithm:PeakPicker:deconvolution:fitting:penalties:height" type="float" min="0.0" value="1.0" label="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized" help=""/>
+              <param name="left_width" argument="-algorithm:PeakPicker:deconvolution:fitting:penalties:left_width" type="float" min="0.0" value="0.0" label="penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized" help=""/>
+              <param name="right_width" argument="-algorithm:PeakPicker:deconvolution:fitting:penalties:right_width" type="float" min="0.0" value="0.0" label="penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized" help=""/>
             </section>
           </section>
         </section>
         <section name="SignalToNoiseEstimationParameter" title="" help="" expanded="false">
-          <param name="max_intensity" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:max_intensity" type="integer" optional="true" min="-1" value="-1" label="maximal intensity considered for histogram construction" help="By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will not be added to the histogram. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime)"/>
-          <param name="auto_max_stdev_factor" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_stdev_factor" type="float" optional="true" min="0.0" max="999.0" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help=""/>
-          <param name="auto_max_percentile" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_percentile" type="integer" optional="true" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/>
-          <param name="auto_mode" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_mode" type="integer" optional="true" min="-1" max="1" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help=""/>
-          <param name="win_len" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:win_len" type="float" optional="true" min="1.0" value="200.0" label="window length in Thomson" help=""/>
-          <param name="bin_count" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:bin_count" type="integer" optional="true" min="3" value="30" label="number of bins for intensity values" help=""/>
-          <param name="stdev_mp" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:stdev_mp" type="float" optional="true" min="0.01" max="999.0" value="3.0" label="multiplier for stdev" help=""/>
-          <param name="min_required_elements" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:min_required_elements" type="integer" optional="true" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/>
-          <param name="noise_for_empty_window" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/>
+          <param name="max_intensity" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:max_intensity" type="integer" min="-1" value="-1" label="maximal intensity considered for histogram construction" help="By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will not be added to the histogram. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime)"/>
+          <param name="auto_max_stdev_factor" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_stdev_factor" type="float" min="0.0" max="999.0" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help=""/>
+          <param name="auto_max_percentile" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_percentile" type="integer" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/>
+          <param name="auto_mode" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_mode" type="integer" min="-1" max="1" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help=""/>
+          <param name="win_len" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:win_len" type="float" min="1.0" value="200.0" label="window length in Thomson" help=""/>
+          <param name="bin_count" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:bin_count" type="integer" min="3" value="30" label="number of bins for intensity values" help=""/>
+          <param name="stdev_mp" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:stdev_mp" type="float" min="0.01" max="999.0" value="3.0" label="multiplier for stdev" help=""/>
+          <param name="min_required_elements" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:min_required_elements" type="integer" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/>
+          <param name="noise_for_empty_window" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help=""/>
         </section>
       </section>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -135,14 +134,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_TOFCalibration_1 -->
+  <tests>
+    <!-- TOPP_TOFCalibration_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TOFCalibration_1_input.mzML"/>
-      <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="TOFCalibration.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/>
       <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
       <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
@@ -216,6 +216,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TOFCalibration_2 -->
     <test expect_num_outputs="2">
@@ -224,7 +227,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TOFCalibration_2_input.mzML"/>
-      <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="TOFCalibration_2.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/>
       <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
       <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
@@ -298,11 +301,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Applies time of flight calibration.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_TOFCalibration.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TOFCalibration.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/TargetedFileConverter.xml b/tools/openms/TargetedFileConverter.xml
index 763063312..e02942365 100644
--- a/tools/openms/TargetedFileConverter.xml
+++ b/tools/openms/TargetedFileConverter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Targeted Experiments]-->
+<!--Proposed Tool Section: [File Converter]-->
 <tool id="TargetedFileConverter" name="TargetedFileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Converts different transition files for targeted proteomics / metabolomics analysis.</description>
+  <description>Converts different transition files for targeted proteomics / metabolomics analysis</description>
   <macros>
     <token name="@EXECUTABLE@">TargetedFileConverter</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,15 +38,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file to convert" help="See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file select mrm,pqp,tabular,traml data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: not all conversion paths work or make sense">
+    <param argument="-in" type="data" format="mrm,pqp,tabular,traml" label="Input file to convert" help="See http://www.openms.de/current_doxygen/html/TOPP_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file select mrm,pqp,tabular,traml data sets(s)"/>
+    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="Note: not all conversion paths work or make sense">
       <option value="TraML">traml</option>
       <option value="pqp">pqp</option>
       <option value="tsv">tabular (tsv)</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="retentionTimeInterpretation" argument="-algorithm:retentionTimeInterpretation" type="select" optional="true" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="">
+      <param name="retentionTimeInterpretation" argument="-algorithm:retentionTimeInterpretation" type="select" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="">
         <option value="iRT" selected="true">iRT</option>
         <option value="seconds">seconds</option>
         <option value="minutes">minutes</option>
@@ -59,7 +59,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <expand macro="adv_opts_macro">
       <param argument="-legacy_traml_id" type="boolean" truevalue="true" falsevalue="false" checked="false" label="PQP to TraML: Should legacy TraML IDs be used?" help=""/>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -78,7 +78,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_ConvertTSVToTraML_test_1 -->
+  <tests>
+    <!-- TOPP_ConvertTSVToTraML_test_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="legacy_traml_id" value="false"/>
@@ -86,7 +87,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ConvertTSVToTraML_1_input.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="ConvertTSVToTraML_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -99,6 +100,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ConvertTSVToTraML_test_2 -->
     <test expect_num_outputs="2">
@@ -108,7 +112,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_2_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="ConvertTSVToTraML_2_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="minutes"/>
@@ -121,6 +125,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ConvertTSVToTraML_test_3 -->
     <test expect_num_outputs="2">
@@ -130,7 +137,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_3_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="ConvertTSVToTraML_3_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="seconds"/>
@@ -143,6 +150,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ConvertTSVToTraML_test_4 -->
     <test expect_num_outputs="2">
@@ -152,7 +162,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ConvertTSVToTraML_4_input.mrm" ftype="mrm"/>
-      <output name="out" file="ConvertTSVToTraML_4_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="ConvertTSVToTraML_4_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -165,6 +175,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ConvertTSVToTraML_test_5 -->
     <test expect_num_outputs="2">
@@ -174,7 +187,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ConvertTSVToTraML_5_input.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_5_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="ConvertTSVToTraML_5_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -187,6 +200,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ConvertTSVToTraML_test_6 -->
     <test expect_num_outputs="2">
@@ -196,7 +212,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ConvertTSVToTraML_6_input.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_6_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="ConvertTSVToTraML_6_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -209,6 +225,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_ConvertTSVToTraML_test_7 -->
     <test expect_num_outputs="2">
@@ -218,7 +237,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ConvertTSVToTraML_7_input_Skyline.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_7_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="ConvertTSVToTraML_7_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -231,6 +250,34 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_TargetedFileConverter_test_1_prepare -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="legacy_traml_id" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="TargetedFileConverter_1_input.TraML"/>
+      <output name="out" value="TargetedFileConverter_1_output.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/>
+      <param name="out_type" value="pqp"/>
+      <section name="algorithm">
+        <param name="retentionTimeInterpretation" value="iRT"/>
+        <param name="override_group_label_check" value="false"/>
+        <param name="force_invalid_mods" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TargetedFileConverter_test_1 -->
     <test expect_num_outputs="2">
@@ -240,7 +287,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_1_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="TargetedFileConverter_1_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -253,6 +300,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TargetedFileConverter_test_2 -->
     <test expect_num_outputs="2">
@@ -262,7 +312,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_2_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="TargetedFileConverter_2_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -275,6 +325,34 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_TargetedFileConverter_test_3_prepare -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="legacy_traml_id" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="TargetedFileConverter_3_input.TraML"/>
+      <output name="out" value="TargetedFileConverter_3_output.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/>
+      <param name="out_type" value="pqp"/>
+      <section name="algorithm">
+        <param name="retentionTimeInterpretation" value="iRT"/>
+        <param name="override_group_label_check" value="false"/>
+        <param name="force_invalid_mods" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TargetedFileConverter_test_3 -->
     <test expect_num_outputs="2">
@@ -284,7 +362,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_3_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="TargetedFileConverter_3_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -297,6 +375,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TargetedFileConverter_test_4 -->
     <test expect_num_outputs="2">
@@ -306,7 +387,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_4_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="TargetedFileConverter_4_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -319,6 +400,34 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_TargetedFileConverter_test_10_prepare -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="legacy_traml_id" value="true"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="TargetedFileConverter_10_input.pqp"/>
+      <output name="out" value="TargetedFileConverter_10_output.TraML.tmp" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <param name="out_type" value="TraML"/>
+      <section name="algorithm">
+        <param name="retentionTimeInterpretation" value="iRT"/>
+        <param name="override_group_label_check" value="false"/>
+        <param name="force_invalid_mods" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TargetedFileConverter_test_10 -->
     <test expect_num_outputs="2">
@@ -328,7 +437,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TargetedFileConverter_10_output.TraML.tmp"/>
-      <output name="out" file="TargetedFileConverter_10_output.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="TargetedFileConverter_10_output.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="out_type" value="tsv"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -341,6 +450,34 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_TargetedFileConverter_test_11_prepare -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="legacy_traml_id" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="TargetedFileConverter_11_input.TraML"/>
+      <output name="out" value="TargetedFileConverter_11_output.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/>
+      <param name="out_type" value="pqp"/>
+      <section name="algorithm">
+        <param name="retentionTimeInterpretation" value="iRT"/>
+        <param name="override_group_label_check" value="false"/>
+        <param name="force_invalid_mods" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TargetedFileConverter_test_11 -->
     <test expect_num_outputs="2">
@@ -350,7 +487,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TargetedFileConverter_11_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_11_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="TargetedFileConverter_11_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -363,6 +500,34 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_TargetedFileConverter_test_8_prepare -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="legacy_traml_id" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="TargetedFileConverter_8_input.tsv" ftype="tabular"/>
+      <output name="out" value="TargetedFileConverter_8_output.TraML.tmp" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <param name="out_type" value="TraML"/>
+      <section name="algorithm">
+        <param name="retentionTimeInterpretation" value="iRT"/>
+        <param name="override_group_label_check" value="true"/>
+        <param name="force_invalid_mods" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TargetedFileConverter_test_8 -->
     <test expect_num_outputs="2">
@@ -372,7 +537,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TargetedFileConverter_8_output.TraML.tmp"/>
-      <output name="out" file="TargetedFileConverter_8_input.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="TargetedFileConverter_8_input.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="out_type" value="tsv"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -385,6 +550,34 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_TargetedFileConverter_test_9_prepare -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="legacy_traml_id" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="TargetedFileConverter_9_input.TraML"/>
+      <output name="out" value="TargetedFileConverter_9_output.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/>
+      <param name="out_type" value="pqp"/>
+      <section name="algorithm">
+        <param name="retentionTimeInterpretation" value="iRT"/>
+        <param name="override_group_label_check" value="true"/>
+        <param name="force_invalid_mods" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TargetedFileConverter_test_9 -->
     <test expect_num_outputs="2">
@@ -394,7 +587,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TargetedFileConverter_9_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_9_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="TargetedFileConverter_9_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -407,6 +600,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TargetedFileConverter_test_5 -->
     <test expect_num_outputs="2">
@@ -416,7 +612,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ConvertTSVToTraML_output.TraML"/>
-      <output name="out" file="ConvertTraMLToTSV_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="ConvertTraMLToTSV_output.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="out_type" value="tsv"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -429,6 +625,34 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_TargetedFileConverter_test_12_prepare -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="legacy_traml_id" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="TargetedFileConverter_12_input.TraML"/>
+      <output name="out" value="TargetedFileConverter_12_output.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/>
+      <param name="out_type" value="pqp"/>
+      <section name="algorithm">
+        <param name="retentionTimeInterpretation" value="iRT"/>
+        <param name="override_group_label_check" value="true"/>
+        <param name="force_invalid_mods" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TargetedFileConverter_test_12 -->
     <test expect_num_outputs="2">
@@ -438,7 +662,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TargetedFileConverter_12_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_12_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="TargetedFileConverter_12_input.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -451,6 +675,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TargetedFileConverter_test_13 -->
     <test expect_num_outputs="2">
@@ -460,7 +687,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TargetedFileConverter_12_input.tsv" ftype="tabular"/>
-      <output name="out" file="TargetedFileConverter_13_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="TargetedFileConverter_13_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -473,6 +700,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TargetedFileConverter_test_6 -->
     <test expect_num_outputs="2">
@@ -482,7 +712,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ConvertTSVToTraML_5_output.TraML"/>
-      <output name="out" file="ConvertTraMLToTSV_output_2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="ConvertTraMLToTSV_output_2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="out_type" value="tsv"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -495,8 +725,86 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_OpenSwathWorkflow_13_prepare -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="legacy_traml_id" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="OpenSwathWorkflow_1_input.TraML"/>
+      <output name="out" value="OpenSwathWorkflow_13_input.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/>
+      <param name="out_type" value="pqp"/>
+      <section name="algorithm">
+        <param name="retentionTimeInterpretation" value="iRT"/>
+        <param name="override_group_label_check" value="false"/>
+        <param name="force_invalid_mods" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_OpenSwathWorkflow_14_prepare -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="legacy_traml_id" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="OpenSwathWorkflow_1_input.TraML"/>
+      <output name="out" value="OpenSwathWorkflow_14_input.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/>
+      <param name="out_type" value="pqp"/>
+      <section name="algorithm">
+        <param name="retentionTimeInterpretation" value="iRT"/>
+        <param name="override_group_label_check" value="false"/>
+        <param name="force_invalid_mods" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
+    </test>
+    <!-- TOPP_OpenSwathWorkflow_17_b_prepare -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="legacy_traml_id" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
+      <output name="out" value="OpenSwathWorkflow_17_input.pqp.tmp" compare="sim_size" delta_frac="0.7" ftype="pqp"/>
+      <param name="out_type" value="pqp"/>
+      <section name="algorithm">
+        <param name="retentionTimeInterpretation" value="iRT"/>
+        <param name="override_group_label_check" value="false"/>
+        <param name="force_invalid_mods" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
-    <!-- UTILS_AssayGeneratorMetabo_6 -->
+    <!-- TOPP_AssayGeneratorMetabo_6 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="legacy_traml_id" value="false"/>
@@ -504,7 +812,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" ftype="tabular"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus_traml.tmp.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="AssayGeneratorMetabo_ams_uku_output_consensus_traml.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="out_type" value="TraML"/>
       <section name="algorithm">
         <param name="retentionTimeInterpretation" value="iRT"/>
@@ -517,11 +825,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Converts different transition files for targeted proteomics / metabolomics analysis.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TargetedFileConverter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TargetedFileConverter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/TextExporter.xml b/tools/openms/TextExporter.xml
index ca50fe1b7..8869300be 100644
--- a/tools/openms/TextExporter.xml
+++ b/tools/openms/TextExporter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [File Handling]-->
+<!--Proposed Tool Section: [File Converter]-->
 <tool id="TextExporter" name="TextExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Exports various XML formats to a text file.</description>
+  <description>Exports various XML formats to a text file</description>
   <macros>
     <token name="@EXECUTABLE@">TextExporter</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir consensus_centroids &&
@@ -72,17 +71,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension, ambiguous file extensions are interpreted as tsv" help="">
+    <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" label="Input file" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
+    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension, ambiguous file extensions are interpreted as tsv" help="">
       <option value="csv">csv</option>
       <option value="tsv">tabular (tsv)</option>
       <option value="txt">txt</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param argument="-replacement" type="text" optional="true" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help="">
+    <param argument="-replacement" type="text" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help="">
       <expand macro="list_string_san" name="replacement"/>
     </param>
-    <param argument="-quoting" type="select" optional="true" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
+    <param argument="-quoting" type="select" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
       <option value="none" selected="true">none</option>
       <option value="double">double</option>
       <option value="escape">escape</option>
@@ -91,19 +91,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <param argument="-no_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppresses output of identification data" help=""/>
     <section name="feature" title="Options for featureXML input files" help="" expanded="false">
       <param name="minimal" argument="-feature:minimal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag to write only three attributes: RT, m/z, and intensity" help=""/>
-      <param name="add_metavalues" argument="-feature:add_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
+      <param name="add_metavalues" argument="-feature:add_metavalues" type="integer" min="-1" max="100" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
     </section>
     <section name="id" title="Options for idXML input files" help="" expanded="false">
       <param name="proteins_only" argument="-id:proteins_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want only protein information from an idXML file" help=""/>
       <param name="peptides_only" argument="-id:peptides_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want only peptide information from an idXML file" help=""/>
       <param name="protein_groups" argument="-id:protein_groups" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want to also write indist" help="group information from an idXML file"/>
       <param name="first_dim_rt" argument="-id:first_dim_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set the first_dim RT of the peptide hits will also be printed (if present)" help=""/>
-      <param name="add_metavalues" argument="-id:add_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideID (=spectrum) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
-      <param name="add_hit_metavalues" argument="-id:add_hit_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideHit (=PSM) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
-      <param name="add_protein_hit_metavalues" argument="-id:add_protein_hit_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values on protein level which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
+      <param name="add_metavalues" argument="-id:add_metavalues" type="integer" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideID (=spectrum) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
+      <param name="add_hit_metavalues" argument="-id:add_hit_metavalues" type="integer" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideHit (=PSM) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
+      <param name="add_protein_hit_metavalues" argument="-id:add_protein_hit_metavalues" type="integer" min="-1" max="100" value="-1" label="Add columns for meta values on protein level which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
     </section>
     <section name="consensus" title="Options for consensusXML input files" help="" expanded="false">
-      <param name="sorting_method" argument="-consensus:sorting_method" type="select" optional="true" label="Sorting options can be combined" help="The precedence is: sort_by_size, sort_by_maps, sorting_method">
+      <param name="sorting_method" argument="-consensus:sorting_method" type="select" label="Sorting options can be combined" help="The precedence is: sort_by_size, sort_by_maps, sorting_method">
         <option value="none" selected="true">none</option>
         <option value="RT">RT</option>
         <option value="MZ">MZ</option>
@@ -115,10 +115,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       </param>
       <param name="sort_by_maps" argument="-consensus:sort_by_maps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by the covered maps, lexicographically" help=""/>
       <param name="sort_by_size" argument="-consensus:sort_by_size" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by decreasing size" help="(i.e., the number of elements)"/>
+      <param name="add_metavalues" argument="-consensus:add_metavalues" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add columns for ConsensusFeature meta values" help=""/>
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -149,14 +150,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_TextExporter_1 -->
+  <tests>
+    <!-- TOPP_TextExporter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_1_input.featureXML"/>
-      <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="TextExporter_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="out_type" value="txt"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -178,6 +180,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="sorting_method" value="none"/>
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
+        <param name="add_metavalues" value="false"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -185,6 +188,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TextExporter_2 -->
     <test expect_num_outputs="5">
@@ -193,7 +199,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_2_input.consensusXML"/>
-      <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="out_type" value="tsv"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -215,16 +221,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="sorting_method" value="RT_then_MZ"/>
         <param name="sort_by_maps" value="true"/>
         <param name="sort_by_size" value="true"/>
+        <param name="add_metavalues" value="true"/>
       </section>
-      <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="consensus_centroids" value="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="consensus_elements" value="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="consensus_features" value="TextExporter_2_consensus_features.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TextExporter_3 -->
     <test expect_num_outputs="2">
@@ -233,7 +243,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_3_input.idXML"/>
-      <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="TextExporter_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="out_type" value="txt"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -255,6 +265,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="sorting_method" value="none"/>
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
+        <param name="add_metavalues" value="false"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -262,6 +273,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TextExporter_4 -->
     <test expect_num_outputs="2">
@@ -270,7 +284,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_3_input.idXML"/>
-      <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="TextExporter_4_output_proteins.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="out_type" value="txt"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -292,6 +306,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="sorting_method" value="none"/>
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
+        <param name="add_metavalues" value="false"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -299,6 +314,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TextExporter_5 -->
     <test expect_num_outputs="2">
@@ -307,7 +325,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_5_input.idXML"/>
-      <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="TextExporter_5_output_peptides.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="out_type" value="txt"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -329,6 +347,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="sorting_method" value="none"/>
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
+        <param name="add_metavalues" value="false"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -336,6 +355,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TextExporter_6 -->
     <test expect_num_outputs="2">
@@ -344,7 +366,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_6_input.featureXML"/>
-      <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="TextExporter_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="out_type" value="txt"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -366,6 +388,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="sorting_method" value="none"/>
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
+        <param name="add_metavalues" value="false"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -373,6 +396,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TextExporter_7 -->
     <test expect_num_outputs="2">
@@ -381,7 +407,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_7_input.consensusXML"/>
-      <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="out_type" value="tsv"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -403,6 +429,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="sorting_method" value="RT_then_MZ"/>
         <param name="sort_by_maps" value="true"/>
         <param name="sort_by_size" value="true"/>
+        <param name="add_metavalues" value="false"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -410,6 +437,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TextExporter_8 -->
     <test expect_num_outputs="2">
@@ -418,7 +448,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_1_input.featureXML"/>
-      <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="TextExporter_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="out_type" value="txt"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -440,6 +470,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="sorting_method" value="none"/>
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
+        <param name="add_metavalues" value="false"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -447,6 +478,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_TextExporter_9 -->
     <test expect_num_outputs="2">
@@ -455,7 +489,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_9_input.idXML"/>
-      <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="TextExporter_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="out_type" value="txt"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -477,6 +511,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="sorting_method" value="none"/>
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
+        <param name="add_metavalues" value="false"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -484,11 +519,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Exports various XML formats to a text file.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_TextExporter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TextExporter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/TransformationEvaluation.xml b/tools/openms/TransformationEvaluation.xml
deleted file mode 100644
index b860e6d3d..000000000
--- a/tools/openms/TransformationEvaluation.xml
+++ /dev/null
@@ -1,89 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
-<tool id="TransformationEvaluation" name="TransformationEvaluation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies a transformation to a range of values</description>
-  <macros>
-    <token name="@EXECUTABLE@">TransformationEvaluation</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
-@EXT_FOO@
-#import re
-
-## Preprocessing
-mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out &&
-#end if
-
-## Main program call
-
-set -o pipefail &&
-@EXECUTABLE@ -write_ctd ./ &&
-python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
-@EXECUTABLE@ -ini @EXECUTABLE@.ctd
--in
-'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out
-  'out/output.${gxy2omsext("trafoxml")}'
-#end if
-#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
-  | tee '$stdout'
-#end if
-
-## Postprocessing
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out/output.${gxy2omsext("trafoxml")}' '$out'
-#end if
-#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
-  && mv '@EXECUTABLE@.ctd' '$ctd_out'
-#end if]]></command>
-  <configfiles>
-    <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
-  </configfiles>
-  <inputs>
-    <param argument="-in" type="data" format="trafoxml" optional="false" label="Input file containing the transformation description" help=" select trafoxml data sets(s)"/>
-    <param argument="-min" type="float" optional="true" value="0.0" label="Minimum value to transform" help=""/>
-    <param argument="-max" type="float" optional="true" value="0.0" label="Maximum value to transform (if at or below 'min', select a suitable maximum based on the transformation description)" help=""/>
-    <param argument="-step" type="float" optional="true" min="0.001" value="1.0" label="Step size between 'min' and 'max'" help=""/>
-    <expand macro="adv_opts_macro">
-      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san" name="test"/>
-      </param>
-    </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="out_FLAG">out (Output file containing original and transformed values; if empty, output is written to the screen)</option>
-      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="trafoxml">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
-      <filter>OPTIONAL_OUTPUTS is None</filter>
-    </data>
-    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
-      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
-  </outputs>
-  <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="trafoxml" value="FileInfo_16_input.trafoXML"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
-    <output name="out" ftype="trafoxml" value="TransformationEvaluation.trafoXML" compare="sim_size" delta="100000000"/>
-  </test>
-</tests>
-  <help><![CDATA[Applies a transformation to a range of values
-
-
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TransformationEvaluation.html]]></help>
-  <expand macro="references"/>
-</tool>
diff --git a/tools/openms/TriqlerConverter.xml b/tools/openms/TriqlerConverter.xml
index 07f9ba8b2..ed28e1cc3 100644
--- a/tools/openms/TriqlerConverter.xml
+++ b/tools/openms/TriqlerConverter.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [File Converter]-->
 <tool id="TriqlerConverter" name="TriqlerConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Converter to input for Triqler</description>
   <macros>
@@ -15,20 +14,22 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir in_design &&
-ln -s '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' &&
+cp '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' &&
 mkdir out &&
+## advanced options
   #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
     mkdir adv_opts.reannotate_filenames_cond.reannotate_filenames &&
     #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
     mkdir ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s'" % (i) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} && 
-    ${' '.join(["ln -s '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])}
+    ${' '.join(["cp '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])}
     #else
-    ln -s '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' &&
+    cp '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' &&
     #end if
   #end if
 
+
 ## Main program call
 
 set -o pipefail &&
@@ -41,6 +42,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)'
 -out
 'out/output.${gxy2omsext("csv")}'
+## advanced options
   #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
     -reannotate_filenames
     #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
@@ -50,6 +52,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     #end if
   #end if
 
+
 ## Postprocessing
 && mv 'out/output.${gxy2omsext("csv")}' '$out'
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
@@ -60,9 +63,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml" optional="false" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/>
-    <param argument="-in_design" type="data" format="tabular" optional="false" label="Experimental Design file" help=" select tabular data sets(s)"/>
-    <param argument="-Triqler_condition" type="text" optional="true" value="Triqler_Condition" label="Which column in the condition table should be used for Triqler 'Condition'" help="">
+    <param argument="-in" type="data" format="consensusxml" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/>
+    <param argument="-in_design" type="data" format="tabular" label="Experimental Design file" help=" select tabular data sets(s)"/>
+    <param argument="-Triqler_condition" type="text" value="Triqler_Condition" label="Which column in the condition table should be used for Triqler 'Condition'" help="">
       <expand macro="list_string_san" name="Triqler_condition"/>
     </param>
     <expand macro="adv_opts_macro">
@@ -75,11 +78,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <param argument="-reannotate_filenames" type="data" format="mzml" multiple="true" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
         </when>
         <when value="yes">
-          <param argument="-reannotate_filenames" type="data" format="mzml" multiple="false" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
+          <param argument="-reannotate_filenames" type="data" format="mzml" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
         </when>
       </conditional>
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -97,6 +100,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   <help><![CDATA[Converter to input for Triqler
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TriqlerConverter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TriqlerConverter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/XFDR.xml b/tools/openms/XFDR.xml
index fe13090e2..a04816401 100644
--- a/tools/openms/XFDR.xml
+++ b/tools/openms/XFDR.xml
@@ -1,6 +1,5 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [ID Processing]-->
+<!--Proposed Tool Section: [Cross-Linking]-->
 <tool id="XFDR" name="XFDR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Calculates false discovery rate estimates on crosslink identifications</description>
   <macros>
@@ -16,7 +15,7 @@
 ## Preprocessing
 #if $in:
   mkdir in &&
-  ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+  cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #end if
 #if "out_idXML_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_idXML &&
@@ -73,20 +72,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="idxml,mzid,xquest.xml" optional="true" label="Crosslink Identifications in either xquest.xml, idXML, or mzIdentML format (as produced by OpenPepXL)" help=" select idxml,mzid,xquest.xml data sets(s)"/>
-    <param argument="-decoy_string" type="text" optional="true" value="DECOY_" label="Prefix of decoy protein ids" help="The correspondig target protein id should be retrievable by deleting this prefix">
+    <param argument="-decoy_string" type="text" value="DECOY_" label="Prefix of decoy protein ids" help="The correspondig target protein id should be retrievable by deleting this prefix">
       <expand macro="list_string_san" name="decoy_string"/>
     </param>
-    <param argument="-minborder" type="float" optional="true" value="-50.0" label="Filter for minimum precursor mass error (ppm) before FDR estimation" help="Values outside of the tolerance window of the original search will effectively disable this filter"/>
-    <param argument="-maxborder" type="float" optional="true" value="50.0" label="Filter for maximum precursor mass error (ppm) before FDR estimation" help="Values outside of the tolerance window of the original search will effectively disable this filter"/>
-    <param argument="-mindeltas" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Filter for delta score, 0 disables the filte" help="Minimum delta score required, hits are rejected if larger or equal. The delta score is a ratio of the score of a hit and the score of the next best hit to the same spectrum, so the value range is between 0 and 1 with 1.0 meaning the scores are equal and 0.5 meaning the next best score is half as high as the current one"/>
-    <param argument="-minionsmatched" type="integer" optional="true" min="0" value="0" label="Filter for minimum matched ions per peptide" help=""/>
+    <param argument="-minborder" type="float" value="-50.0" label="Filter for minimum precursor mass error (ppm) before FDR estimation" help="Values outside of the tolerance window of the original search will effectively disable this filter"/>
+    <param argument="-maxborder" type="float" value="50.0" label="Filter for maximum precursor mass error (ppm) before FDR estimation" help="Values outside of the tolerance window of the original search will effectively disable this filter"/>
+    <param argument="-mindeltas" type="float" min="0.0" max="1.0" value="0.0" label="Filter for delta score, 0 disables the filte" help="Minimum delta score required, hits are rejected if larger or equal. The delta score is a ratio of the score of a hit and the score of the next best hit to the same spectrum, so the value range is between 0 and 1 with 1.0 meaning the scores are equal and 0.5 meaning the next best score is half as high as the current one"/>
+    <param argument="-minionsmatched" type="integer" min="0" value="0" label="Filter for minimum matched ions per peptide" help=""/>
     <param argument="-uniquexl" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculate statistics based only on unique IDs" help="For a set of IDs from equal candidates (same pair of peptides, modifications and cross-linked positions), only the highest scoring hit will be considered. By default the score distribution will be estimated using all 1st ranked candidates"/>
     <param argument="-no_qvalues" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not transform simple FDR to q-values" help=""/>
-    <param argument="-minscore" type="float" optional="true" value="-10.0" label="Minimum score to be considered for FDR calculation" help="A number lower than the lowest score will effectively disable this filter"/>
-    <param argument="-binsize" type="float" optional="true" min="0.0" value="0.0001" label="Bin size for the cumulative histograms for score distributions" help="Should be about the same size as the smallest expected difference between scores. Smaller numbers will make XFDR more robust, but much slower. Negative numbers are not allowed. Should only be changed if the range of the main score changes or another score than the OpenPepXL score is used"/>
+    <param argument="-minscore" type="float" value="-10.0" label="Minimum score to be considered for FDR calculation" help="A number lower than the lowest score will effectively disable this filter"/>
+    <param argument="-binsize" type="float" min="0.0" value="0.0001" label="Bin size for the cumulative histograms for score distributions" help="Should be about the same size as the smallest expected difference between scores. Smaller numbers will make XFDR more robust, but much slower. Negative numbers are not allowed. Should only be changed if the range of the main score changes or another score than the OpenPepXL score is used"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -114,16 +113,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_XFDR_1 -->
+  <tests>
+    <!-- TOPP_XFDR_1 -->
     <test expect_num_outputs="4">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="XFDR_test_in1.idXML"/>
-      <output name="out_idXML" file="XFDR_test_out1_temp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out1_temp.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out1_temp.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
+      <output name="out_idXML" value="XFDR_test_out1_temp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out_mzIdentML" value="XFDR_test_out1.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
+      <output name="out_xquest" value="XFDR_test_out1.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
       <param name="decoy_string" value="DECOY_"/>
       <param name="minborder" value="-50.0"/>
       <param name="maxborder" value="50.0"/>
@@ -139,6 +139,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_XFDR_2 -->
     <test expect_num_outputs="4">
@@ -147,9 +150,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="XFDR_test_in1.idXML"/>
-      <output name="out_idXML" file="XFDR_test_out2_temp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out2_temp.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out2_temp.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
+      <output name="out_idXML" value="XFDR_test_out2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out_mzIdentML" value="XFDR_test_out2.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
+      <output name="out_xquest" value="XFDR_test_out2.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
       <param name="decoy_string" value="DECOY_"/>
       <param name="minborder" value="-50.0"/>
       <param name="maxborder" value="50.0"/>
@@ -165,6 +168,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_XFDR_3 -->
     <test expect_num_outputs="4">
@@ -173,9 +179,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="XFDR_test_in2.xquest.xml"/>
-      <output name="out_idXML" file="XFDR_test_out3_temp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out3_temp.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out3_temp.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
+      <output name="out_idXML" value="XFDR_test_out3.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out_mzIdentML" value="XFDR_test_out3.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
+      <output name="out_xquest" value="XFDR_test_out3.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
       <param name="decoy_string" value="DECOY_"/>
       <param name="minborder" value="-50.0"/>
       <param name="maxborder" value="50.0"/>
@@ -191,6 +197,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_XFDR_4 -->
     <test expect_num_outputs="4">
@@ -199,9 +208,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="XFDR_test_in2.xquest.xml"/>
-      <output name="out_idXML" file="XFDR_test_out4_temp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out4_temp.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out4_temp.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
+      <output name="out_idXML" value="XFDR_test_out4.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out_mzIdentML" value="XFDR_test_out4.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
+      <output name="out_xquest" value="XFDR_test_out4.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
       <param name="decoy_string" value="DECOY_"/>
       <param name="minborder" value="-3.0"/>
       <param name="maxborder" value="3.0"/>
@@ -217,6 +226,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_XFDR_5 -->
     <test expect_num_outputs="4">
@@ -225,9 +237,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="XFDR_test_in3.xquest.xml"/>
-      <output name="out_idXML" file="XFDR_test_out5_temp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out5_temp.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out5_temp.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
+      <output name="out_idXML" value="XFDR_test_out5.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out_mzIdentML" value="XFDR_test_out5.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
+      <output name="out_xquest" value="XFDR_test_out5.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
       <param name="decoy_string" value="DECOY_"/>
       <param name="minborder" value="-3.0"/>
       <param name="maxborder" value="3.0"/>
@@ -243,6 +255,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_XFDR_6 -->
     <test expect_num_outputs="2">
@@ -251,7 +266,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="XFDR_test_in4.idXML"/>
-      <output name="out_idXML" file="XFDR_test_out6_temp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out_idXML" value="XFDR_test_out6.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="decoy_string" value="DECOY_"/>
       <param name="minborder" value="-50.0"/>
       <param name="maxborder" value="50.0"/>
@@ -267,6 +282,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_XFDR_7 -->
     <test expect_num_outputs="4">
@@ -275,9 +293,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="XFDR_test_in2.xquest.xml"/>
-      <output name="out_idXML" file="XFDR_test_out7_temp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out7_temp.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out7_temp.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
+      <output name="out_idXML" value="XFDR_test_out7.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out_mzIdentML" value="XFDR_test_out7.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
+      <output name="out_xquest" value="XFDR_test_out7.xquest.xml" compare="sim_size" delta_frac="0.7" ftype="xquest.xml"/>
       <param name="decoy_string" value="DECOY_"/>
       <param name="minborder" value="-50.0"/>
       <param name="maxborder" value="50.0"/>
@@ -293,11 +311,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Calculates false discovery rate estimates on crosslink identifications
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_XFDR.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_XFDR.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/XMLValidator.xml b/tools/openms/XMLValidator.xml
index a8b42a63f..2a398bde9 100644
--- a/tools/openms/XMLValidator.xml
+++ b/tools/openms/XMLValidator.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [[for Developers]]-->
 <tool id="XMLValidator" name="XMLValidator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Validates XML files against an XSD schema.</description>
+  <description>Validates XML files against an XSD schema</description>
   <macros>
     <token name="@EXECUTABLE@">XMLValidator</token>
     <import>macros.xml</import>
@@ -15,10 +14,10 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #if $schema:
   mkdir schema &&
-  ln -s '$schema' 'schema/${re.sub("[^\w\-_]", "_", $schema.element_identifier)}.$gxy2omsext($schema.ext)' &&
+  cp '$schema' 'schema/${re.sub("[^\w\-_]", "_", $schema.element_identifier)}.$gxy2omsext($schema.ext)' &&
 #end if
 
 ## Main program call
@@ -44,11 +43,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzdata,mzid,mzml,mzxml,pepxml,traml,xml" optional="false" label="file to validate" help=" select consensusxml,featurexml,idxml,mzdata,mzid,mzml,mzxml,pepxml,traml,xml data sets(s)"/>
-    <param argument="-schema" type="data" format="xml" optional="true" label="schema to validate against" help="If no schema is given, the file is validated against the latest schema of the file type select xml data sets(s)"/>
+    <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzdata,mzid,mzml,mzxml,pepxml,traml,xml" label="file to validate" help=" select consensusxml,featurexml,idxml,mzdata,mzid,mzml,mzxml,pepxml,traml,xml data sets(s)"/>
+    <param argument="-schema" type="data" format="xsd" optional="true" label="schema to validate against" help="If no schema is given, the file is validated against the latest schema of the file type select xsd data sets(s)"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -64,17 +63,32 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
-    <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
-       <assert_contents><has_text text="Success: the file is valid!"/></assert_contents>
-    </output>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- just chosen an arbitrary input and autgenerated output-->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
+      <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
+        <assert_contents>
+          <has_text text="Success: the file is valid!"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="1">
+      <!-- just chosen an arbitrary input and autgenerated output-->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
+      <param name="schema" ftype="xsd" location="https://raw.githubusercontent.com/HUPO-PSI/mzML/master/schema/schema_1.1/mzML1.1.0.xsd"/>
+      <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
+        <assert_contents>
+          <has_text text="Success: the file is valid!"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
   <help><![CDATA[Validates XML files against an XSD schema.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_XMLValidator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_XMLValidator.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/XTandemAdapter.xml b/tools/openms/XTandemAdapter.xml
index 246886a9e..ad112e6cb 100644
--- a/tools/openms/XTandemAdapter.xml
+++ b/tools/openms/XTandemAdapter.xml
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Identification]-->
+<!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
 <tool id="XTandemAdapter" name="XTandemAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Annotates MS/MS spectra using X! Tandem.</description>
+  <description>Annotates MS/MS spectra using X! Tandem</description>
   <macros>
     <token name="@EXECUTABLE@">XTandemAdapter</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
 #end if
@@ -23,10 +22,10 @@ ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($
   mkdir xml_out &&
 #end if
 mkdir database &&
-ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
 #if $default_config_file:
   mkdir default_config_file &&
-  ln -s '$default_config_file' 'default_config_file/${re.sub("[^\w\-_]", "_", $default_config_file.element_identifier)}.$gxy2omsext($default_config_file.ext)' &&
+  cp '$default_config_file' 'default_config_file/${re.sub("[^\w\-_]", "_", $default_config_file.element_identifier)}.$gxy2omsext($default_config_file.ext)' &&
 #end if
 
 ## Main program call
@@ -70,25 +69,25 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     <configfile name="hardcoded_json"><![CDATA[{"xtandem_executable": "xtandem", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file containing MS2 spectra" help=" select mzml data sets(s)"/>
-    <param argument="-database" type="data" format="fasta" optional="false" label="FASTA file or pro file" help="Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir' select fasta data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Input file containing MS2 spectra" help=" select mzml data sets(s)"/>
+    <param argument="-database" type="data" format="fasta" label="FASTA file or pro file" help="Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir' select fasta data sets(s)"/>
     <param argument="-default_config_file" type="data" format="xml" optional="true" label="Default X" help="Tandem configuration file. All parameters of this adapter take precedence over the file - use it for parameters not available here. A template file can be found at 'OpenMS/share/CHEMISTRY/XTandem_default_config.xml' select xml data sets(s)"/>
     <param argument="-ignore_adapter_param" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this to use the configuration given in 'default_config_file' exclusively, ignoring other parameters (apart from 'in', 'out', 'database', 'xtandem_executable') set via this adapte" help=""/>
-    <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor mass tolerance" help=""/>
-    <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.3" label="Fragment mass erro" help=""/>
-    <param argument="-precursor_error_units" type="select" optional="true" label="Parent monoisotopic mass error units" help="">
+    <param argument="-precursor_mass_tolerance" type="float" value="10.0" label="Precursor mass tolerance" help=""/>
+    <param argument="-fragment_mass_tolerance" type="float" value="0.3" label="Fragment mass erro" help=""/>
+    <param argument="-precursor_error_units" type="select" label="Parent monoisotopic mass error units" help="">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
       <expand macro="list_string_san" name="precursor_error_units"/>
     </param>
-    <param argument="-fragment_error_units" type="select" optional="true" label="Fragment monoisotopic mass error units" help="">
+    <param argument="-fragment_error_units" type="select" label="Fragment monoisotopic mass error units" help="">
       <option value="ppm">ppm</option>
       <option value="Da" selected="true">Da</option>
       <expand macro="list_string_san" name="fragment_error_units"/>
     </param>
-    <param argument="-max_precursor_charge" type="integer" optional="true" min="0" value="4" label="Maximum precursor charge ('0' to use X" help="Tandem default)"/>
+    <param argument="-max_precursor_charge" type="integer" min="0" value="4" label="Maximum precursor charge ('0' to use X" help="Tandem default)"/>
     <param argument="-no_isotope_error" type="boolean" truevalue="true" falsevalue="false" checked="false" label="By default, misassignment to the first and second isotopic 13C peak are also considered" help="Set this flag to disable"/>
-    <param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
+    <param argument="-fixed_modifications" type="select" multiple="true" optional="false" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
       <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
       <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
       <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -98,6 +97,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="2-succinyl (C)">2-succinyl (C)</option>
       <option value="2HPG (R)">2HPG (R)</option>
       <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+      <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+      <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+      <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+      <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
       <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
       <option value="3sulfo (N-term)">3sulfo (N-term)</option>
       <option value="4-ONE (C)">4-ONE (C)</option>
@@ -187,6 +190,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
       <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
       <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+      <option value="Andro-H2O (C)">Andro-H2O (C)</option>
       <option value="Archaeol (C)">Archaeol (C)</option>
       <option value="Arg (N-term)">Arg (N-term)</option>
       <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -290,6 +294,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
       <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
       <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+      <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
       <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
       <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
       <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -322,7 +327,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="BITC (N-term)">BITC (N-term)</option>
       <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
       <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-      <option value="Bodipy (C)">Bodipy (C)</option>
       <option value="Brij35 (N-term)">Brij35 (N-term)</option>
       <option value="Brij58 (N-term)">Brij58 (N-term)</option>
       <option value="Bromo (F)">Bromo (F)</option>
@@ -754,9 +758,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Dehydrated (T)">Dehydrated (T)</option>
       <option value="Dehydrated (Y)">Dehydrated (Y)</option>
       <option value="Dehydro (C)">Dehydro (C)</option>
+      <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
       <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-      <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
       <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
       <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -766,7 +770,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
       <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
       <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-      <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
       <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
       <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -778,6 +781,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
       <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
       <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+      <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
       <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
       <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -1350,7 +1354,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Ethanolyl (C)">Ethanolyl (C)</option>
       <option value="Ethanolyl (K)">Ethanolyl (K)</option>
       <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-      <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
       <option value="Ethyl (C-term)">Ethyl (C-term)</option>
       <option value="Ethyl (D)">Ethyl (D)</option>
       <option value="Ethyl (E)">Ethyl (E)</option>
@@ -1444,6 +1447,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
       <option value="Glu (E)">Glu (E)</option>
       <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+      <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
       <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
       <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
       <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -1458,7 +1462,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
       <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
       <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
       <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -1482,6 +1485,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gly (K)">Gly (K)</option>
       <option value="Gly (S)">Gly (S)</option>
       <option value="Gly (T)">Gly (T)</option>
+      <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
       <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
       <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
       <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -1872,6 +1876,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
       <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
       <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+      <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
       <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
       <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
       <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -1883,6 +1888,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
       <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
       <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+      <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+      <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+      <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
       <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
       <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
       <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -1938,6 +1946,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
       <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
       <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+      <option value="His+O(2) (H)">His+O(2) (H)</option>
       <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
       <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
       <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -2075,11 +2084,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+      <option value="Kdo (S)">Kdo (S)</option>
+      <option value="Kdo (T)">Kdo (T)</option>
       <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
       <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
       <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
       <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
       <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+      <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
       <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
       <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
       <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -2164,13 +2176,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
       <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
       <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+      <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
       <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
       <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
       <option value="Lipoyl (K)">Lipoyl (K)</option>
       <option value="LRGG (K)">LRGG (K)</option>
       <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
       <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+      <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
       <option value="Lys (N-term)">Lys (N-term)</option>
+      <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
       <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
       <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
       <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -2205,6 +2220,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Malonyl (C)">Malonyl (C)</option>
       <option value="Malonyl (K)">Malonyl (K)</option>
       <option value="Malonyl (S)">Malonyl (S)</option>
+      <option value="MBS+peptide (C)">MBS+peptide (C)</option>
       <option value="MDCC (C)">MDCC (C)</option>
       <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
       <option value="Menadione (C)">Menadione (C)</option>
@@ -2216,6 +2232,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="MesitylOxide (H)">MesitylOxide (H)</option>
       <option value="MesitylOxide (K)">MesitylOxide (K)</option>
       <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+      <option value="Met+O(2) (H)">Met+O(2) (H)</option>
       <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
       <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
       <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -2399,7 +2416,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
       <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
       <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-      <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
       <option value="NP40 (N-term)">NP40 (N-term)</option>
       <option value="NQIGG (K)">NQIGG (K)</option>
       <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -2487,6 +2503,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
       <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
       <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+      <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+      <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+      <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+      <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
       <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
       <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
       <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -2501,6 +2521,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phospho (Y)">Phospho (Y)</option>
       <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
       <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+      <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
       <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
       <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
       <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -2532,6 +2553,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
       <option value="Piperidine (K)">Piperidine (K)</option>
       <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+      <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
       <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
       <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
       <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -2609,18 +2631,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="QTGG (K)">QTGG (K)</option>
       <option value="Quinone (W)">Quinone (W)</option>
       <option value="Quinone (Y)">Quinone (Y)</option>
+      <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+      <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+      <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+      <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+      <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+      <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+      <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+      <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+      <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+      <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+      <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+      <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+      <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+      <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+      <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+      <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+      <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+      <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+      <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+      <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
       <option value="Retinylidene (K)">Retinylidene (K)</option>
       <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
       <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
       <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-      <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-      <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-      <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-      <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-      <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-      <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-      <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-      <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
       <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
       <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
       <option value="Saligenin (H)">Saligenin (H)</option>
@@ -2648,6 +2682,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="shTMT (K)">shTMT (K)</option>
       <option value="shTMT (N-term)">shTMT (N-term)</option>
       <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+      <option value="shTMTpro (K)">shTMTpro (K)</option>
+      <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+      <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
       <option value="SMA (K)">SMA (K)</option>
       <option value="SMA (N-term)">SMA (N-term)</option>
       <option value="spermidine (Q)">spermidine (Q)</option>
@@ -2823,7 +2860,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
       <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
       <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-      <option value="Ub-amide (C)">Ub-amide (C)</option>
       <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
       <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
       <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -3018,7 +3054,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="ZQG (K)">ZQG (K)</option>
       <expand macro="list_string_san" name="fixed_modifications"/>
     </param>
-    <param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
+    <param argument="-variable_modifications" type="select" multiple="true" optional="false" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
       <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
       <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
       <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
@@ -3028,6 +3064,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="2-succinyl (C)">2-succinyl (C)</option>
       <option value="2HPG (R)">2HPG (R)</option>
       <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option>
+      <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option>
+      <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option>
+      <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option>
+      <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option>
       <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option>
       <option value="3sulfo (N-term)">3sulfo (N-term)</option>
       <option value="4-ONE (C)">4-ONE (C)</option>
@@ -3117,6 +3157,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option>
       <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option>
       <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option>
+      <option value="Andro-H2O (C)">Andro-H2O (C)</option>
       <option value="Archaeol (C)">Archaeol (C)</option>
       <option value="Arg (N-term)">Arg (N-term)</option>
       <option value="Arg-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -3220,6 +3261,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option>
       <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option>
       <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option>
+      <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option>
       <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option>
       <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option>
       <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option>
@@ -3252,7 +3294,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="BITC (N-term)">BITC (N-term)</option>
       <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option>
       <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option>
-      <option value="Bodipy (C)">Bodipy (C)</option>
       <option value="Brij35 (N-term)">Brij35 (N-term)</option>
       <option value="Brij58 (N-term)">Brij58 (N-term)</option>
       <option value="Bromo (F)">Bromo (F)</option>
@@ -3684,9 +3725,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Dehydrated (T)">Dehydrated (T)</option>
       <option value="Dehydrated (Y)">Dehydrated (Y)</option>
       <option value="Dehydro (C)">Dehydro (C)</option>
+      <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option>
       <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option>
-      <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option>
       <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option>
       <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option>
       <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option>
@@ -3696,7 +3737,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option>
       <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option>
       <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option>
-      <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option>
       <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option>
       <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option>
@@ -3708,6 +3748,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option>
       <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option>
       <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option>
+      <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option>
       <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option>
       <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option>
       <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option>
@@ -4280,7 +4321,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Ethanolyl (C)">Ethanolyl (C)</option>
       <option value="Ethanolyl (K)">Ethanolyl (K)</option>
       <option value="Ethanolyl (R)">Ethanolyl (R)</option>
-      <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option>
       <option value="Ethyl (C-term)">Ethyl (C-term)</option>
       <option value="Ethyl (D)">Ethyl (D)</option>
       <option value="Ethyl (E)">Ethyl (E)</option>
@@ -4374,6 +4414,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gln-&gt;Xle (Q)">Gln-&gt;Xle (Q)</option>
       <option value="Glu (E)">Glu (E)</option>
       <option value="Glu (Protein C-term)">Glu (Protein C-term)</option>
+      <option value="Glu+O(2) (H)">Glu+O(2) (H)</option>
       <option value="Glu-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
       <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
       <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
@@ -4388,7 +4429,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
       <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-      <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
       <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
       <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
       <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
@@ -4412,6 +4452,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Gly (K)">Gly (K)</option>
       <option value="Gly (S)">Gly (S)</option>
       <option value="Gly (T)">Gly (T)</option>
+      <option value="Gly+O(2) (H)">Gly+O(2) (H)</option>
       <option value="Gly-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
       <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
       <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
@@ -4802,6 +4843,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option>
       <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option>
       <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option>
+      <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option>
       <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option>
       <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option>
       <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option>
@@ -4813,6 +4855,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option>
       <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option>
       <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option>
+      <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option>
+      <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option>
+      <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option>
       <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option>
       <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option>
       <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option>
@@ -4868,6 +4913,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="HexNAc(4) (T)">HexNAc(4) (T)</option>
       <option value="HexNAc(5) (S)">HexNAc(5) (S)</option>
       <option value="HexNAc(5) (T)">HexNAc(5) (T)</option>
+      <option value="His+O(2) (H)">His+O(2) (H)</option>
       <option value="His-&gt;Ala (H)">His-&gt;Ala (H)</option>
       <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
       <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
@@ -5005,11 +5051,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option>
       <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option>
+      <option value="Kdo (S)">Kdo (S)</option>
+      <option value="Kdo (T)">Kdo (T)</option>
       <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option>
       <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option>
       <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option>
       <option value="Label:13C(3) (A)">Label:13C(3) (A)</option>
       <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option>
+      <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option>
       <option value="Label:13C(4) (M)">Label:13C(4) (M)</option>
       <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option>
       <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option>
@@ -5094,13 +5143,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="LG-lactam-K (K)">LG-lactam-K (K)</option>
       <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option>
       <option value="LG-lactam-R (R)">LG-lactam-R (R)</option>
+      <option value="LG-pyrrole (C)">LG-pyrrole (C)</option>
       <option value="LG-pyrrole (K)">LG-pyrrole (K)</option>
       <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option>
       <option value="Lipoyl (K)">Lipoyl (K)</option>
       <option value="LRGG (K)">LRGG (K)</option>
       <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option>
       <option value="LRGG+methyl (K)">LRGG+methyl (K)</option>
+      <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option>
       <option value="Lys (N-term)">Lys (N-term)</option>
+      <option value="Lys+O(2) (H)">Lys+O(2) (H)</option>
       <option value="Lys-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
       <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
       <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
@@ -5135,6 +5187,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Malonyl (C)">Malonyl (C)</option>
       <option value="Malonyl (K)">Malonyl (K)</option>
       <option value="Malonyl (S)">Malonyl (S)</option>
+      <option value="MBS+peptide (C)">MBS+peptide (C)</option>
       <option value="MDCC (C)">MDCC (C)</option>
       <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option>
       <option value="Menadione (C)">Menadione (C)</option>
@@ -5146,6 +5199,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="MesitylOxide (H)">MesitylOxide (H)</option>
       <option value="MesitylOxide (K)">MesitylOxide (K)</option>
       <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option>
+      <option value="Met+O(2) (H)">Met+O(2) (H)</option>
       <option value="Met-&gt;Aha (M)">Met-&gt;Aha (M)</option>
       <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
       <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
@@ -5329,7 +5383,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option>
       <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option>
       <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option>
-      <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option>
       <option value="NP40 (N-term)">NP40 (N-term)</option>
       <option value="NQIGG (K)">NQIGG (K)</option>
       <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option>
@@ -5417,6 +5470,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
       <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
       <option value="Phe-&gt;Xle (F)">Phe-&gt;Xle (F)</option>
+      <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option>
+      <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option>
+      <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option>
+      <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option>
       <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option>
       <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option>
       <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option>
@@ -5431,6 +5488,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phospho (Y)">Phospho (Y)</option>
       <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option>
       <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option>
+      <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option>
       <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option>
       <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option>
       <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option>
@@ -5462,6 +5520,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Phytochromobilin (C)">Phytochromobilin (C)</option>
       <option value="Piperidine (K)">Piperidine (K)</option>
       <option value="Piperidine (N-term)">Piperidine (N-term)</option>
+      <option value="Pro+O(2) (H)">Pro+O(2) (H)</option>
       <option value="Pro-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
       <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
       <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
@@ -5539,18 +5598,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="QTGG (K)">QTGG (K)</option>
       <option value="Quinone (W)">Quinone (W)</option>
       <option value="Quinone (Y)">Quinone (Y)</option>
+      <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option>
+      <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option>
+      <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option>
+      <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option>
+      <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option>
+      <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option>
+      <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option>
+      <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option>
+      <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option>
+      <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option>
+      <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option>
+      <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option>
+      <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option>
+      <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option>
+      <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option>
+      <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option>
+      <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option>
+      <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option>
+      <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option>
+      <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option>
       <option value="Retinylidene (K)">Retinylidene (K)</option>
       <option value="RNPXL (N-term K)">RNPXL (N-term K)</option>
       <option value="RNPXL (N-term R)">RNPXL (N-term R)</option>
       <option value="RNPXlink1 (C)">RNPXlink1 (C)</option>
-      <option value="RNPXlink2 (F)">RNPXlink2 (F)</option>
-      <option value="RNPXlink2 (K)">RNPXlink2 (K)</option>
-      <option value="RNPXlink2 (L)">RNPXlink2 (L)</option>
-      <option value="RNPXlink3 (C)">RNPXlink3 (C)</option>
-      <option value="RNPXlink3 (F)">RNPXlink3 (F)</option>
-      <option value="RNPXlink4 (C)">RNPXlink4 (C)</option>
-      <option value="RNPXlink5 (F)">RNPXlink5 (F)</option>
-      <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option>
       <option value="s-GlcNAc (S)">s-GlcNAc (S)</option>
       <option value="s-GlcNAc (T)">s-GlcNAc (T)</option>
       <option value="Saligenin (H)">Saligenin (H)</option>
@@ -5578,6 +5649,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="shTMT (K)">shTMT (K)</option>
       <option value="shTMT (N-term)">shTMT (N-term)</option>
       <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option>
+      <option value="shTMTpro (K)">shTMTpro (K)</option>
+      <option value="shTMTpro (N-term)">shTMTpro (N-term)</option>
+      <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option>
       <option value="SMA (K)">SMA (K)</option>
       <option value="SMA (N-term)">SMA (N-term)</option>
       <option value="spermidine (Q)">spermidine (Q)</option>
@@ -5753,7 +5827,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
       <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
       <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;Xle (Y)</option>
-      <option value="Ub-amide (C)">Ub-amide (C)</option>
       <option value="Ub-Br2 (C)">Ub-Br2 (C)</option>
       <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option>
       <option value="Ub-VME (C)">Ub-VME (C)</option>
@@ -5948,53 +6021,54 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <option value="ZQG (K)">ZQG (K)</option>
       <expand macro="list_string_san" name="variable_modifications"/>
     </param>
-    <param argument="-minimum_fragment_mz" type="float" optional="true" value="150.0" label="Minimum fragment m/z" help=""/>
-    <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
-      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
-      <option value="CNBr">CNBr</option>
-      <option value="Formic_acid">Formic_acid</option>
-      <option value="Trypsin" selected="true">Trypsin</option>
-      <option value="unspecific cleavage">unspecific cleavage</option>
-      <option value="Lys-C">Lys-C</option>
-      <option value="Lys-N">Lys-N</option>
-      <option value="Lys-C/P">Lys-C/P</option>
-      <option value="PepsinA">PepsinA</option>
+    <param argument="-minimum_fragment_mz" type="float" value="150.0" label="Minimum fragment m/z" help=""/>
+    <param argument="-enzyme" type="select" label="The enzyme used for peptide digestion" help="">
       <option value="TrypChymo">TrypChymo</option>
       <option value="Trypsin/P">Trypsin/P</option>
       <option value="V8-DE">V8-DE</option>
-      <option value="Asp-N/B">Asp-N/B</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="Chymotrypsin">Chymotrypsin</option>
-      <option value="Arg-C/P">Arg-C/P</option>
-      <option value="Arg-C">Arg-C</option>
       <option value="V8-E">V8-E</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
       <option value="leukocyte elastase">leukocyte elastase</option>
       <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="Arg-C">Arg-C</option>
+      <option value="Arg-C/P">Arg-C/P</option>
+      <option value="no cleavage">no cleavage</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
       <option value="Alpha-lytic protease">Alpha-lytic protease</option>
       <option value="2-iodobenzoate">2-iodobenzoate</option>
+      <option value="Lys-C">Lys-C</option>
+      <option value="Lys-N">Lys-N</option>
+      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+      <option value="CNBr">CNBr</option>
+      <option value="Formic_acid">Formic_acid</option>
       <option value="Asp-N">Asp-N</option>
+      <option value="Asp-N/B">Asp-N/B</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
+      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="PepsinA">PepsinA</option>
       <expand macro="list_string_san" name="enzyme"/>
     </param>
-    <param argument="-missed_cleavages" type="integer" optional="true" value="1" label="Number of possible cleavage sites missed by the enzyme" help=""/>
+    <param argument="-missed_cleavages" type="integer" value="1" label="Number of possible cleavage sites missed by the enzyme" help=""/>
     <param argument="-semi_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require only peptide end to have a valid cleavage site, not both" help=""/>
-    <param argument="-output_results" type="select" optional="true" label="Which hits should be reported" help="All, valid ones (passing the E-Value threshold), or stochastic (failing the threshold)">
+    <param argument="-output_results" type="select" label="Which hits should be reported" help="All, valid ones (passing the E-Value threshold), or stochastic (failing the threshold)">
       <option value="all" selected="true">all</option>
       <option value="valid">valid</option>
       <option value="stochastic">stochastic</option>
       <expand macro="list_string_san" name="output_results"/>
     </param>
-    <param argument="-max_valid_expect" type="float" optional="true" value="0.1" label="Maximal E-Value of a hit to be reported (only evaluated if 'output_result' is 'valid' or 'stochastic')" help=""/>
+    <param argument="-max_valid_expect" type="float" value="0.1" label="Maximal E-Value of a hit to be reported (only evaluated if 'output_result' is 'valid' or 'stochastic')" help=""/>
     <param argument="-reindex" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Recalculate peptide to protein association using OpenMS" help="Annotates target-decoy information"/>
     <section name="PeptideIndexing" title="" help="" expanded="false">
       <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
         <expand macro="list_string_san" name="decoy_string"/>
       </param>
-      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="true" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
+      <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
         <option value="prefix" selected="true">prefix</option>
         <option value="suffix">suffix</option>
         <expand macro="list_string_san" name="decoy_string_position"/>
       </param>
-      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="true" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
+      <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
         <option value="error">error</option>
         <option value="warn" selected="true">warn</option>
         <option value="silent">silent</option>
@@ -6003,54 +6077,55 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
       <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
       <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
-      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="true" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
+      <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
         <option value="error" selected="true">error</option>
         <option value="warn">warn</option>
         <option value="remove">remove</option>
         <expand macro="list_string_san" name="unmatched_action"/>
       </param>
-      <param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
-      <param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
+      <param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
+      <param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
       <param name="IL_equivalent" argument="-PeptideIndexing:IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/>
+      <param name="allow_nterm_protein_cleavage" argument="-PeptideIndexing:allow_nterm_protein_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Allow the protein N-terminus amino acid to clip" help=""/>
       <section name="enzyme" title="" help="" expanded="false">
-        <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" optional="true" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
+        <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
           <option value="auto" selected="true">auto</option>
-          <option value="Chymotrypsin/P">Chymotrypsin/P</option>
-          <option value="CNBr">CNBr</option>
-          <option value="Formic_acid">Formic_acid</option>
-          <option value="Trypsin">Trypsin</option>
-          <option value="Lys-C/P">Lys-C/P</option>
-          <option value="PepsinA">PepsinA</option>
-          <option value="Alpha-lytic protease">Alpha-lytic protease</option>
           <option value="2-iodobenzoate">2-iodobenzoate</option>
           <option value="iodosobenzoate">iodosobenzoate</option>
           <option value="staphylococcal protease/D">staphylococcal protease/D</option>
           <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
-          <option value="Lys-C">Lys-C</option>
-          <option value="Lys-N">Lys-N</option>
-          <option value="Arg-C">Arg-C</option>
-          <option value="leukocyte elastase">leukocyte elastase</option>
+          <option value="Glu-C+P">Glu-C+P</option>
+          <option value="Chymotrypsin">Chymotrypsin</option>
+          <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+          <option value="CNBr">CNBr</option>
+          <option value="Trypsin">Trypsin</option>
+          <option value="unspecific cleavage">unspecific cleavage</option>
           <option value="proline endopeptidase">proline endopeptidase</option>
           <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-          <option value="V8-DE">V8-DE</option>
-          <option value="V8-E">V8-E</option>
-          <option value="Arg-C/P">Arg-C/P</option>
-          <option value="Asp-N">Asp-N</option>
+          <option value="Alpha-lytic protease">Alpha-lytic protease</option>
           <option value="TrypChymo">TrypChymo</option>
           <option value="Trypsin/P">Trypsin/P</option>
-          <option value="Glu-C+P">Glu-C+P</option>
+          <option value="Lys-C/P">Lys-C/P</option>
+          <option value="PepsinA">PepsinA</option>
           <option value="PepsinA + P">PepsinA + P</option>
           <option value="cyanogen-bromide">cyanogen-bromide</option>
           <option value="Clostripain/P">Clostripain/P</option>
           <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
           <option value="no cleavage">no cleavage</option>
-          <option value="unspecific cleavage">unspecific cleavage</option>
+          <option value="Asp-N">Asp-N</option>
           <option value="Asp-N/B">Asp-N/B</option>
           <option value="Asp-N_ambic">Asp-N_ambic</option>
-          <option value="Chymotrypsin">Chymotrypsin</option>
+          <option value="Arg-C">Arg-C</option>
+          <option value="Arg-C/P">Arg-C/P</option>
+          <option value="V8-DE">V8-DE</option>
+          <option value="V8-E">V8-E</option>
+          <option value="leukocyte elastase">leukocyte elastase</option>
+          <option value="Formic_acid">Formic_acid</option>
+          <option value="Lys-C">Lys-C</option>
+          <option value="Lys-N">Lys-N</option>
           <expand macro="list_string_san" name="name"/>
         </param>
-        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="true" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
+        <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
           <option value="auto" selected="true">auto</option>
           <option value="full">full</option>
           <option value="semi">semi</option>
@@ -6061,7 +6136,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -6085,14 +6160,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_XTandemAdapter_1 -->
+  <tests>
+    <!-- TOPP_XTandemAdapter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="spectra.mzML"/>
-      <output name="out" file="XTandemAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="XTandemAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="database" value="proteins.fasta"/>
       <param name="default_config_file" value="CHEMISTRY/XTandem_default_config.xml"/>
       <param name="ignore_adapter_param" value="false"/>
@@ -6102,7 +6178,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="fragment_error_units" value="Da"/>
       <param name="max_precursor_charge" value="0"/>
       <param name="no_isotope_error" value="false"/>
-      <param name="fixed_modifications"/>
       <param name="variable_modifications" value="Oxidation (M)"/>
       <param name="minimum_fragment_mz" value="150.0"/>
       <param name="enzyme" value="Trypsin"/>
@@ -6122,6 +6197,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="aaa_max" value="3"/>
         <param name="mismatches_max" value="0"/>
         <param name="IL_equivalent" value="false"/>
+        <param name="allow_nterm_protein_cleavage" value="true"/>
         <section name="enzyme">
           <param name="name" value="auto"/>
           <param name="specificity" value="auto"/>
@@ -6133,6 +6209,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_XTandemAdapter_2 -->
     <test expect_num_outputs="2">
@@ -6141,7 +6220,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="spectra.mzML"/>
-      <output name="out" file="XTandemAdapter_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="XTandemAdapter_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="database" value="proteins.fasta"/>
       <param name="default_config_file" value="CHEMISTRY/XTandem_default_config.xml"/>
       <param name="ignore_adapter_param" value="false"/>
@@ -6151,7 +6230,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="fragment_error_units" value="Da"/>
       <param name="max_precursor_charge" value="0"/>
       <param name="no_isotope_error" value="false"/>
-      <param name="fixed_modifications"/>
       <param name="variable_modifications" value="Oxidation (M)"/>
       <param name="minimum_fragment_mz" value="150.0"/>
       <param name="enzyme" value="Trypsin"/>
@@ -6171,6 +6249,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="aaa_max" value="3"/>
         <param name="mismatches_max" value="0"/>
         <param name="IL_equivalent" value="false"/>
+        <param name="allow_nterm_protein_cleavage" value="true"/>
         <section name="enzyme">
           <param name="name" value="auto"/>
           <param name="specificity" value="auto"/>
@@ -6182,6 +6261,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_XTandemAdapter_3 -->
     <test expect_num_outputs="2">
@@ -6190,7 +6272,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="test" value="true"/>
       </section>
       <param name="in" value="spectra.mzML"/>
-      <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="XTandemAdapter_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="database" value="proteinslong.fasta"/>
       <param name="default_config_file" value="CHEMISTRY/XTandem_default_config.xml"/>
       <param name="ignore_adapter_param" value="false"/>
@@ -6200,7 +6282,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <param name="fragment_error_units" value="Da"/>
       <param name="max_precursor_charge" value="0"/>
       <param name="no_isotope_error" value="false"/>
-      <param name="fixed_modifications"/>
       <param name="variable_modifications" value="Oxidation (M)"/>
       <param name="minimum_fragment_mz" value="150.0"/>
       <param name="enzyme" value="Trypsin"/>
@@ -6220,6 +6301,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
         <param name="aaa_max" value="3"/>
         <param name="mismatches_max" value="0"/>
         <param name="IL_equivalent" value="false"/>
+        <param name="allow_nterm_protein_cleavage" value="true"/>
         <section name="enzyme">
           <param name="name" value="auto"/>
           <param name="specificity" value="auto"/>
@@ -6231,11 +6313,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Annotates MS/MS spectra using X! Tandem.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_XTandemAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_XTandemAdapter.html]]></help>
   <expand macro="references"/>
 </tool>
diff --git a/tools/openms/aux/OMSSAAdapter.patch b/tools/openms/aux/OMSSAAdapter.patch
deleted file mode 100644
index af26c3f6f..000000000
--- a/tools/openms/aux/OMSSAAdapter.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- OMSSAAdapter.xml	2020-06-16 15:51:40.315400730 +0200
-+++ /tmp/OMSSAAdapter.xml	2020-06-16 15:50:23.536086074 +0200
-@@ -22,6 +22,7 @@
- mkdir database &&
- ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
- 
-+makeblastdb -dbtype prot -blastdb_version 4 -in 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
- ## Main program call
- 
- set -o pipefail &&
diff --git a/tools/openms/aux/PepNovoAdapter.patch b/tools/openms/aux/PepNovoAdapter.patch
deleted file mode 100644
index c4bd9eccd..000000000
--- a/tools/openms/aux/PepNovoAdapter.patch
+++ /dev/null
@@ -1,35 +0,0 @@
---- PepNovoAdapter.xml.orig	2022-03-17 17:05:19.818694614 +0100
-+++ PepNovoAdapter.xml	2022-03-17 17:06:06.570692873 +0100
-@@ -42,8 +42,13 @@
-   </configfiles>
-   <inputs>
-     <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
--    <param argument="-model_directory" type="text" optional="false" value="" label="Name of the directory where the model files are kept" help="">
--      <expand macro="list_string_san" name="model_directory"/>
-+    <param name="model_directory" argument="-model_directory" type="select" optional="false" label="Name of the directory where the model files are kept" help="">
-+      <options from_data_table="pepnovo_models">
-+        <column name="name" index="0"/>
-+        <column name="value" index="2"/>
-+        <filter type="unique_value" name="unique_set" column="0"/>
-+        <validator type="no_options" message="No model directory available"/>
-+      </options>
-     </param>
-     <param argument="-correct_pm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find optimal precursor mass and charge values" help=""/>
-     <param argument="-use_spectrum_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct charge" help=""/>
-@@ -51,8 +56,14 @@
-     <param argument="-no_quality_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not remove low quality spectra" help=""/>
-     <param argument="-fragment_tolerance" type="float" optional="true" value="-1.0" label="The fragment tolerance (between 0 and 0.75 Da" help="Set to -1.0 to use model's default setting)"/>
-     <param argument="-pm_tolerance" type="float" optional="true" value="-1.0" label="The precursor mass tolerance (between 0 and 5.0 Da" help="Set to -1.0 to use model's default setting)"/>
--    <param argument="-model" type="text" optional="true" value="CID_IT_TRYP" label="Name of the model that should be used" help="">
--      <expand macro="list_string_san" name="model"/>
-+    <param name="model" argument="-model" type="select" label="Name of the model that should be used" help="">
-+      <options from_data_table="pepnovo_models">
-+        <column name="name" index="1"/>
-+        <column name="value" index="1"/>
-+        <filter type="param_value" ref="model_directory" column="2"/>
-+        <filter type="unique_value" column="1"/>
-+        <validator type="no_options" message="No model available"/>
-+      </options>
-     </param>
-     <param argument="-digest" type="select" optional="true" label="Enzyme used for digestion (default TRYPSIN)" help="">
-       <option value="TRYPSIN" selected="true">TRYPSIN</option>
diff --git a/tools/openms/aux/filetypes.txt b/tools/openms/aux/filetypes.txt
index 55564eec9..6512eb347 100644
--- a/tools/openms/aux/filetypes.txt
+++ b/tools/openms/aux/filetypes.txt
@@ -81,7 +81,8 @@ xls           tsv
 XML           xml
 xml           xml
 xquest.xml    xquest.xml
-xsd           xml
+xsd           xsd
 
 # TODO needs to be implemented, needs to be below xml in order that Galaxy->OMS mapping gives xml
 # cachedMzML    xml
+zip           zip
\ No newline at end of file
diff --git a/tools/openms/generate.sh b/tools/openms/aux/generate.sh
similarity index 76%
rename from tools/openms/generate.sh
rename to tools/openms/aux/generate.sh
index ae2b38b91..1d0487333 100755
--- a/tools/openms/generate.sh
+++ b/tools/openms/aux/generate.sh
@@ -1,15 +1,15 @@
 #!/usr/bin/env bash
 
-VERSION=2.8
+# set -x
+
+VERSION=3.1
 FILETYPES="aux/filetypes.txt"
-# TODO make 21.01
 PROFILE="21.05"
 ## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g')
 
-export tmp=$(mktemp -d)
-# export tmp="/tmp/openms-stuff/"
-
-export CTDCONVERTER="$tmp/CTDConverter"
+# export tmp=$(mktemp -d)
+export tmp="/tmp/openms-stuff/"
+# export CTDCONVERTER="$tmp/CTDConverter"
 ###############################################################################
 ## reset old data
 ###############################################################################
@@ -60,20 +60,12 @@ find . -maxdepth 0 -name "[A-Z]*xml" -delete
 source $(dirname $(which conda))/../etc/profile.d/conda.sh
 conda activate OpenMS$VERSION-env
 CTDConverter galaxy -i ctd/*ctd -o ./ -s aux/tools_blacklist.txt -f "$FILETYPES" \
-	-m macros.xml -t tool.conf  -p aux/hardcoded_params.json \
+	-m macros.xml -p aux/hardcoded_params.json \
 	--test-macros macros_autotest.xml --test-macros-prefix autotest_  --test-macros aux/macros_test.xml --test-macros-prefix manutest_ \
 	--tool-version $VERSION --tool-profile $PROFILE --bump-file aux/bump.json > convert.out 2> convert.err
 if [[ "$?" -ne "0" ]]; then >&2 echo 'CTD -> XML conversion failed'; >&2 echo -e "stderr:\n$(cat convert.err)"; fi
 conda deactivate
 
->&2 echo "apply patches"
-patch PepNovoAdapter.xml < aux/PepNovoAdapter.patch
-patch OMSSAAdapter.xml < aux/OMSSAAdapter.patch
-
-# https://github.com/OpenMS/OpenMS/pull/4984
-sed -i -e 's@http://www.openms.de/doxygen/nightly/html/@http://www.openms.de/doxygen/release/2.8.0/html/@' ./*xml
-
-# TODO should be fixed in >2.8 https://github.com/OpenMS/OpenMS/pull/6018
-sed -i -e 's@https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking_with_openms@https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-openms@' ./*xml
+sed -i -e 's@http://www.openms.de/doxygen/nightly/html/@https://openms.de/doxygen/release/'$VERSION'.0/html/@' ./*xml
 
-rm -rf macros_autotest.xml macros_discarded_auto.xml prepare_test_data.sh ctd
\ No newline at end of file
+# rm -rf macros_autotest.xml macros_discarded_auto.xml prepare_test_data.sh ctd
\ No newline at end of file
diff --git a/tools/openms/aux/hardcoded_params.json b/tools/openms/aux/hardcoded_params.json
index 177bf754d..0c4b36f90 100644
--- a/tools/openms/aux/hardcoded_params.json
+++ b/tools/openms/aux/hardcoded_params.json
@@ -2,7 +2,7 @@
 	"#": "blacklist parameters",
 
 	"version": [{"value": "@"}],
-	"#": "DO NOT blacklist of hide -force https://github.com/OpenMS/OpenMS/issues/5921",
+	"#": "DO NOT blacklist or hide -force https://github.com/OpenMS/OpenMS/issues/5921",
 	"debug": [{"value": "@"}],
 	"algorithm:debug": [{"value": "@"}],
 	"java_memory": [{"value": "@"}],
@@ -23,9 +23,9 @@
 
 	"#": "TODO not usable in 2.5 https://github.com/OpenMS/OpenMS/issues/4456, corresponding test currently disabled",
     	"consensus_out": [{"value": "@", "tools": ["MaRaClusterAdapter"]}],
-	"#": "TODO would need treatment as prefix-output",
+	"#": "could be treated as prefix-output, but likely not needed",
 	"output_directory": [{"value": "@", "tools": ["MaRaClusterAdapter"]}],
-
+	
 	"#": "hardcode parameter values",
 
 	"comet_version": [{
@@ -52,15 +52,15 @@
 	"myrimatch_executable": [{
 		"value":"myrimatch"
 	}],
-	"omssa_executable": [{
-		"value":"$(dirname $(realpath $(which omssacl)))/omssacl"
-	}],
 	"ThermoRaw_executable": [{
 		"value": "ThermoRawFileParser.exe", 
 		"tools": ["FileConverter"]
 	}],
-	"pepnovo_executable": [{
-		"value":"pepnovo"
+	"sage_executable": [{
+		"value":"sage"
+	}],
+	"sirius_executable": [{
+		"value":"$(which sirius)"
 	}],
 	"percolator_executable": [{
 		"value":"percolator"
@@ -81,9 +81,6 @@
 		}, {
 			"value": "/home/berntm/Downloads/novor/lib/novor.jar",
 			"tools": ["NovorAdapter"]
-		}, {
-			"value":"$(which sirius)",
-			"tools": ["SiriusAdapter", "AssayGeneratorMetabo"]
 		}, {
 			"value":"spectrast",
 			"tools": ["SpectraSTSearchAdapter"]
@@ -126,15 +123,6 @@
 	"out_workspace_directory": [{
 		"value": "__SIRIUS_WORKSPACE__"
 	}],
-	"#": "MSSimulator model files need to be hardcoded or changed to input-file https://github.com/OpenMS/OpenMS/issues/4641",
-	"algorithm:MSSim:RT:HPLC:model_file": [{
-		"value": "SIMULATION/RTPredict.model",
-		"tools": ["MSSimulator"]
-	}],
-	"algorithm:MSSim:Detectability:dt_model_file": [{
-		"value": "SIMULATION/DTPredict.model",
-		"tools": ["MSSimulator"]
-	}],
 
 	"#": "hardcode the outer loop threads for OpenSwathWorkflow",
 	"outer_loop_threads": [{
@@ -157,7 +145,8 @@
 	"#": "test is not a hardcoded value since we need to set it in the tool tests", 
 	"test": [{
 		"CTD:type": "text",
-		"XML:type": "hidden"
+		"XML:type": "hidden",
+		"XML:optional": "true"
 	}],
 
 	"#": "overwrite CTD attributes of some parameters (some are not possible, e.g. type)",
@@ -169,23 +158,29 @@
 	}],
 
 	"#": "FileInfo, MapStatistics, SequenceCoverageCalculator wo -out just writes to stdout. not wanted here",
-	"#": "MzMLSplitter output prefix https://github.com/OpenMS/OpenMS/pull/5912",
-	"#": "IDRipper output prefix https://github.com/OpenMS/OpenMS/pull/5873",
+	"#": "IDRipper, MzMLSplitter output prefix can not properly get the ext from the corresponding input (needs https://github.com/galaxyproject/galaxy/pull/11754 and changes in the CTDConverter)",
 	"out": [{
 	 	"CTD:required": true,
 		"tools": ["FileInfo", "MapStatistics", "SequenceCoverageCalculator"]
 	}, {
-		"CTD:type": "output-prefix", 
-		"CTD:required": true,
 		"CTD:restrictions": "mzml",
+	 	"CTD:required": true,
 		"tools": ["MzMLSplitter"]
 	}, {
-		"CTD:type": "output-prefix", 
-		"CTD:required": true,
 		"CTD:restrictions": "idXML",
+		"CTD:required": true,
 		"tools": ["IDRipper"]
 	}],
 
+	"#": "The file splitter needs to split files ;) I guess the default is `.` which does not help here",
+	"#": "Analogous to out for MzMlSplitter and IDRipper we need to hardcode the format",
+	"outputDirectory": [{
+		"CTD:restrictions": "mzml",
+		"CTD:required": true,
+		"tools": ["OpenSwathFileSplitter"]
+	
+	}],
+
 	"#": "Try to remove xml data type whereever possible",
 	"#": "XTandem Adapter output is called .xml in OMS which is to unspecific -> use Galaxy's bioml",
 	"xml_out": [{
@@ -196,7 +191,6 @@
 	"#": "IDFileConverter remove xml",
 	"#": "OpenSwathWorkflow make in single file input and all outputs non-optional",
     "#": "XFDR does not need xml .. redundant with xquest.xml TODO check if list is up to date with each new release",
-	"#": "SeedListGenerator: remove consensusXML https://github.com/OpenMS/OpenMS/issues/4404 .. ",
 	"in": [{
 		"CTD:restrictions": "oms,idXML,mzid,fasta,pepXML,protXML,mascotXML,omssaXML,psms,tsv,xquest.xml",
 		"tools": ["IDFileConverter"]
@@ -206,9 +200,6 @@
 	}, {
 		"CTD:restrictions": "idXML,mzid,xquest.xml",
 		"tools": ["XFDR"]
-	}, {
-		"CTD:restrictions": "mzML,idXML,featureXML",
-		"tools": ["SeedListGenerator"]
 	}],
 
 	"#": "IDMapper has in and spectra:in params, in is used in out as format_source",
@@ -218,40 +209,13 @@
 		"tools": ["IDMapper"]
 	}],
 
-	"#": "hardcoding prefix parameters which are not yet available in OMS but in CTDOpts https://github.com/OpenMS/OpenMS/pull/5912",
-	"#": "output-prefix",
-	"outputDirectory": [{
-		"CTD:type": "output-prefix", 
-		"CTD:advanced": false,
-		"CTD:required": true,
-		"CTD:restrictions": "mzml",
-		"tools": ["OpenSwathFileSplitter"]
-	}],
-
-	"#": "OpenSwathDIAPreScoring: https://github.com/OpenMS/OpenMS/pull/4443",
-        "#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release",
+	"#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release",
 	"output_files": [{
-		"CTD:required": true,
-		"tools": ["OpenSwathDIAPreScoring"]
-	}, {
 		"CTD:restrictions": "txt,tsv,pep.xml,pepXML,html",
 		"tools": ["SpectraSTSearchAdapter"]
 	
 	}],
-
-	"#": "hardcode some options as boolean (i.e. set restrictions) obsolete for >2.8 https://github.com/OpenMS/OpenMS/pull/5965",
-	"algorithm:MetaboliteFeatureDeconvolution:use_minority_bound": [{
-		"CTD:restrictions": "true,false",
-		"tools": ["MetaboliteAdductDecharger"]
-	}],
-	"algorithm:MetaboliteFeatureDeconvolution:negative_mode": [{
-		"CTD:restrictions": "true,false",
-		"tools": ["MetaboliteAdductDecharger"]
-	}],
-	"algorithm:FeatureDeconvolution:negative_mode": [{
-		"CTD:restrictions": "true,false",
-		"tools": ["Decharger"]
-	}],
+	
 	"algorithm:tryptic_only": [{
 		"CTD:restrictions": "true,false",
 		"tools": ["CompNovo", "CompNovoCID"]
@@ -268,10 +232,6 @@
 		"CTD:restrictions": "true,false",
 		"tools": ["AccurateMassSearch"]
 	}],
-	"algorithm:Preprocessing:store_peptide_sequences": [{
-		"CTD:restrictions": "true,false",
-		"tools": ["PrecursorIonSelector"]
-	}],
 	"algorithm:write_log_messages": [{
 		"CTD:restrictions": "true,false",
 		"tools": ["NoiseFilterGaussian"]
diff --git a/tools/openms/aux/macros_test.xml b/tools/openms/aux/macros_test.xml
index f8e98e3ed..2690650fb 100644
--- a/tools/openms/aux/macros_test.xml
+++ b/tools/openms/aux/macros_test.xml
@@ -36,13 +36,6 @@
     <output name="html" ftype="html" value="CVInspector.html"/>
   </test>
 </xml>
-<xml name="manutest_DeMeanderize">
-  <test expect_num_outputs="1"><!-- test with the output of a MSsimulator output generated by a test below -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="MSsimulator_MALDI.mzml"/>
-	<output name="out" ftype="mzml" value="DeMeanderize.mzml"/>
-  </test>
-</xml>
 <xml name="manutest_Digestor">
   <test expect_num_outputs="1"><!-- just using some random fasta, in contrast to DigestorMotif idXML/fasta output possible, testing for the non-default fasta option -->
     <param name="adv_opts|test" value="true"/>
@@ -69,16 +62,6 @@
     <output name="out" value="FeatureFinderIsotopeWavelet.featureXML" compare="sim_size"/>
   </test>
 </xml>
-<xml name="manutest_FFEval">
-  <test expect_num_outputs="2"><!-- comparing an arbitarty FeatureFinder output with itself -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" value="FeatureFinderCentroided_1_output.featureXML"/>
-    <param name="truth" value="FeatureFinderCentroided_1_output.featureXML"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_FLAG,out_roc_FLAG"/>
-    <output name="out" value="FFEval.featureXML" compare="sim_size"/>
-	<output name="out_roc" value="FFEval_roc.csv" ftype="csv"/>
-  </test>
-</xml>
 <xml name="manutest_IDExtractor">
   <test expect_num_outputs="1"><!--  -->
     <param name="adv_opts|test" value="true"/>
@@ -276,15 +259,6 @@
       </output>
     </test>
 </xml>
-
-<xml name="manutest_LabeledEval">
-  <test expect_num_outputs="1"><!-- comparing an arbitarty featureXML that has a corresponding consensusXML -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/>
-    <param name="truth" value="FeatureLinkerLabeled_1_output.consensusXML"/>
-    <output name="stdout" value="LabeledEval.txt" compare="sim_size"/>
-  </test>
-</xml>
 <xml name="manutest_MapStatistics">
   <test expect_num_outputs="1"><!-- test with a featureXML input  -->
     <param name="adv_opts|test" value="true"/>
@@ -309,28 +283,9 @@
 <xml name="manutest_MRMPairFinder">
   <!-- TODO no idea about a useful input for pair_in -->
 </xml>
-<xml name="manutest_MSSimulator">
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
-    <output name="out" ftype="mzml" value="MSsimulator.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/>
-    <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/>
-    <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/>
-  </test>
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter generate MALDI output for use in the test for DeMeanderize -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
-    <output name="out" ftype="mzml" value="MSsimulator_MALDI.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/>
-    <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/>
-    <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/>
-    <param name="algorithm|MSSim|Global|ionization_type" value="MALDI"/>
-  </test>
-</xml>
 <xml name="manutest_OpenSwathDIAPreScoring">
   <!-- data from a test that included all the needed test files -->
-  <test>
+  <test expect_num_outputs="1">
     <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
     <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
     <output_collection name="output_files" count="1">
@@ -338,7 +293,7 @@
     </output_collection>
   </test>
   <!-- test with two inputs (actually the same file .. symlinked) -->
-  <test>
+  <test expect_num_outputs="1">
     <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
     <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/>
     <output_collection name="output_files" count="2">
@@ -354,21 +309,6 @@
     <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/>
   </test>
 </xml>
-<xml name="manutest_PepNovoAdapter">
-  <test expect_num_outputs="1"><!-- adapted from (dysfunctional) OMS 3rdParty tests (but model selection
-             unclear https://github.com/OpenMS/OpenMS/issues/4719)-->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="PepNovo_1.mzML"/>
-    <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/>
-    <param name="model" value="LTQ_COMP"/>
-  </test>
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="PepNovo_1.mzML"/>
-    <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/>
-    <param name="model" value="LTQ_COMP"/>
-  </test>
-</xml>
 <xml name="manutest_PhosphoScoring">
   <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
     <param name="adv_opts|test" value="true"/>
@@ -377,33 +317,6 @@
     <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/>
   </test>
 </xml>
-<!-- TODO PSMFeatureExtractor should have auto tests with >2.8 https://github.com/OpenMS/OpenMS/pull/5087 -->
-<xml name="manutest_PSMFeatureExtractor">
-  <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="adv_opts|skip_db_check" value="true"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
-    <param name="multiple_search_engines" value="true"/>
-    <param name="out_type" value="idxml"/>
-    <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="500"/>
-  </test>
-  <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="adv_opts|skip_db_check" value="true"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
-    <param name="multiple_search_engines" value="true"/>
-    <param name="out_type" value="mzid"/>
-    <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/>
-  </test>
-  <!-- test for the batch conditional crated for data parameters with multiple="true" -->
-  <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in_select" value="yes"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
-    <param name="out_type" value="idxml"/>
-    <output name="out" ftype="idxml" value="PSMFeatureExtractor_3.idXML" compare="sim_size" delta="500"/>
-  </test>
-</xml>
 <xml name="manutest_QCCalculator">
   <test expect_num_outputs="1"><!-- took test data from another test w mzML input -->
     <param name="adv_opts|test" value="true"/>
@@ -469,14 +382,7 @@
     <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/>
   </test>
 </xml>
-<xml name="manutest_RTEvaluation">
-  <!-- just chosen an arbitrary input and autgenerated output-->
-  <test expect_num_outputs="1">
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/>
-    <output name="out" ftype="tabular" value="RTEvaluation.tsv"/>
-  </test>
-</xml>
+
 <xml name="manutest_SemanticValidator">
   <test expect_num_outputs="1"><!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output-->
     <param name="adv_opts|test" value="true"/>
@@ -551,27 +457,30 @@
   <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
     <param name="adv_opts|test" value="true"/>
     <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/>
+    <section name="algorithm">
+      <section name="average_gaussian">
+        <param name="ms_level" value="2"/>
+      </section>
+    </section>
     <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/>
   </test>
 </xml>
-<xml name="manutest_SvmTheoreticalSpectrumGeneratorTrainer">
-<!-- -TODO model_output_file creates multiple files-->
-</xml>
-<xml name="manutest_TransformationEvaluation">
+<xml name="manutest_XMLValidator">
   <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
     <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="trafoxml" value="FileInfo_16_input.trafoXML"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
-    <output name="out" ftype="trafoxml" value="TransformationEvaluation.trafoXML" compare="sim_size" delta="100000000"/>
+    <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
+    <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
+       <assert_contents><has_text text="Success: the file is valid!"/></assert_contents>
+    </output>
   </test>
-</xml>
-<xml name="manutest_XMLValidator">
   <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
     <param name="adv_opts|test" value="true"/>
     <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
+    <param name="schema" ftype="xsd" location="https://raw.githubusercontent.com/HUPO-PSI/mzML/master/schema/schema_1.1/mzML1.1.0.xsd"/>
     <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
        <assert_contents><has_text text="Success: the file is valid!"/></assert_contents>
     </output>
   </test>
 </xml>
-<xml name="manutest_MetaboliteAdductDecharger"/><xml name="manutest_IDMapper"/><xml name="manutest_ProteinQuantifier"/><xml name="manutest_PeakPickerIterative"/><xml name="manutest_FeatureLinkerUnlabeledQT"/><xml name="manutest_TICCalculator"/><xml name="manutest_IDFilter"/><xml name="manutest_IDPosteriorErrorProbability"/><xml name="manutest_FeatureFinderIdentification"/><xml name="manutest_XFDR"/><xml name="manutest_OpenSwathWorkflow"/><xml name="manutest_MassCalculator"/><xml name="manutest_IDFileConverter"/><xml name="manutest_MultiplexResolver"/><xml name="manutest_AssayGeneratorMetabo"/><xml name="manutest_MassTraceExtractor"/><xml name="manutest_SiriusAdapter"/><xml name="manutest_IDMerger"/><xml name="manutest_MSstatsConverter"/><xml name="manutest_FileMerger"/><xml name="manutest_Decharger"/><xml name="manutest_PTPredict"/><xml name="manutest_XTandemAdapter"/><xml name="manutest_FeatureFinderMetabo"/><xml name="manutest_CruxAdapter"/><xml name="manutest_OpenSwathConfidenceScoring"/><xml name="manutest_PrecursorIonSelector"/><xml name="manutest_ConsensusMapNormalizer"/><xml name="manutest_RTPredict"/><xml name="manutest_PercolatorAdapter"/><xml name="manutest_ProteinInference"/><xml name="manutest_OpenSwathDecoyGenerator"/><xml name="manutest_TextExporter"/><xml name="manutest_FeatureFinderCentroided"/><xml name="manutest_DecoyDatabase"/><xml name="manutest_SpectraFilterWindowMower"/><xml name="manutest_NoiseFilterGaussian"/><xml name="manutest_MaRaClusterAdapter"/><xml name="manutest_ConsensusID"/><xml name="manutest_FileFilter"/><xml name="manutest_InclusionExclusionListCreator"/><xml name="manutest_FeatureLinkerUnlabeledKD"/><xml name="manutest_NovorAdapter"/><xml name="manutest_OpenPepXL"/><xml name="manutest_FalseDiscoveryRate"/><xml name="manutest_OpenPepXLLF"/><xml name="manutest_SpecLibSearcher"/><xml name="manutest_IDConflictResolver"/><xml name="manutest_MRMMapper"/><xml name="manutest_OMSSAAdapter"/><xml name="manutest_ExternalCalibration"/><xml name="manutest_PeakPickerHiRes"/><xml name="manutest_MascotAdapter"/><xml name="manutest_FeatureFinderMultiplex"/><xml name="manutest_MetaProSIP"/><xml name="manutest_FuzzyDiff"/><xml name="manutest_TargetedFileConverter"/><xml name="manutest_MapAlignerIdentification"/><xml name="manutest_IDRTCalibration"/><xml name="manutest_MRMTransitionGroupPicker"/><xml name="manutest_RTModel"/><xml name="manutest_OpenSwathAssayGenerator"/><xml name="manutest_IDSplitter"/><xml name="manutest_OpenSwathMzMLFileCacher"/><xml name="manutest_HighResPrecursorMassCorrector"/><xml name="manutest_OpenSwathChromatogramExtractor"/><xml name="manutest_OpenSwathAnalyzer"/><xml name="manutest_FeatureLinkerUnlabeled"/><xml name="manutest_CompNovoCID"/><xml name="manutest_DTAExtractor"/><xml name="manutest_FileInfo"/><xml name="manutest_MapAlignerSpectrum"/><xml name="manutest_IsobaricAnalyzer"/><xml name="manutest_LowMemPeakPickerHiRes"/><xml name="manutest_MyriMatchAdapter"/><xml name="manutest_InternalCalibration"/><xml name="manutest_TOFCalibration"/><xml name="manutest_MSGFPlusAdapter"/><xml name="manutest_PTModel"/><xml name="manutest_InspectAdapter"/><xml name="manutest_SpectraFilterSqrtMower"/><xml name="manutest_SimpleSearchEngine"/><xml name="manutest_PeakPickerWavelet"/><xml name="manutest_MapNormalizer"/><xml name="manutest_IDScoreSwitcher"/><xml name="manutest_FeatureLinkerLabeled"/><xml name="manutest_MapRTTransformer"/><xml name="manutest_RNPxlSearch"/><xml name="manutest_PrecursorMassCorrector"/><xml name="manutest_MapAlignerPoseClustering"/><xml name="manutest_MzTabExporter"/><xml name="manutest_BaselineFilter"/><xml name="manutest_FeatureFinderMRM"/><xml name="manutest_MascotAdapterOnline"/><xml name="manutest_DatabaseFilter"/><xml name="manutest_ProteinResolver"/><xml name="manutest_OpenSwathFeatureXMLToTSV"/><xml name="manutest_FidoAdapter"/><xml name="manutest_AccurateMassSearch"/><xml name="manutest_CompNovo"/><xml name="manutest_LowMemPeakPickerHiResRandomAccess"/><xml name="manutest_OpenSwathRTNormalizer"/><xml name="manutest_PeptideIndexer"/><xml name="manutest_CometAdapter"/><xml name="manutest_NoiseFilterSGolay"/><xml name="manutest_SpectraSTSearchAdapter"/><xml name="manutest_FeatureFinder"/><xml name="manutest_LuciphorAdapter"/><xml name="manutest_GNPSExport"/><xml name="manutest_Epifany"/><xml name="manutest_NucleicAcidSearchEngine"/><xml name="manutest_QualityControl"/><xml name="manutest_FeatureFinderMetaboIdent"/><xml name="manutest_RNAMassCalculator"/><xml name="manutest_MapAlignerTreeGuided"/><xml name="manutest_IDMassAccuracy"/><xml name="manutest_ProteomicsLFQ"/><xml name="manutest_IDDecoyProbability"/><xml name="manutest_DigestorMotif"/><xml name="manutest_DatabaseSuitability"/><xml name="manutest_StaticModification"/><xml name="manutest_TriqlerConverter"/><xml name="manutest_OpenMSDatabasesInfo"/><xml name="manutest_MSFraggerAdapter"/></macros>
+<xml name="manutest_PSMFeatureExtractor"/>
+<xml name="manutest_MetaboliteAdductDecharger"/><xml name="manutest_IDMapper"/><xml name="manutest_ProteinQuantifier"/><xml name="manutest_PeakPickerIterative"/><xml name="manutest_FeatureLinkerUnlabeledQT"/><xml name="manutest_TICCalculator"/><xml name="manutest_IDFilter"/><xml name="manutest_IDPosteriorErrorProbability"/><xml name="manutest_FeatureFinderIdentification"/><xml name="manutest_XFDR"/><xml name="manutest_OpenSwathWorkflow"/><xml name="manutest_MassCalculator"/><xml name="manutest_IDFileConverter"/><xml name="manutest_MultiplexResolver"/><xml name="manutest_AssayGeneratorMetabo"/><xml name="manutest_MassTraceExtractor"/><xml name="manutest_SiriusAdapter"/><xml name="manutest_IDMerger"/><xml name="manutest_MSstatsConverter"/><xml name="manutest_FileMerger"/><xml name="manutest_Decharger"/><xml name="manutest_XTandemAdapter"/><xml name="manutest_FeatureFinderMetabo"/><xml name="manutest_OpenSwathConfidenceScoring"/><xml name="manutest_ConsensusMapNormalizer"/><xml name="manutest_PercolatorAdapter"/><xml name="manutest_ProteinInference"/><xml name="manutest_OpenSwathDecoyGenerator"/><xml name="manutest_TextExporter"/><xml name="manutest_FeatureFinderCentroided"/><xml name="manutest_DecoyDatabase"/><xml name="manutest_SpectraFilterWindowMower"/><xml name="manutest_NoiseFilterGaussian"/><xml name="manutest_MaRaClusterAdapter"/><xml name="manutest_ConsensusID"/><xml name="manutest_FileFilter"/><xml name="manutest_FeatureLinkerUnlabeledKD"/><xml name="manutest_NovorAdapter"/><xml name="manutest_OpenPepXL"/><xml name="manutest_FalseDiscoveryRate"/><xml name="manutest_OpenPepXLLF"/><xml name="manutest_SpecLibSearcher"/><xml name="manutest_IDConflictResolver"/><xml name="manutest_MRMMapper"/><xml name="manutest_ExternalCalibration"/><xml name="manutest_PeakPickerHiRes"/><xml name="manutest_MascotAdapter"/><xml name="manutest_FeatureFinderMultiplex"/><xml name="manutest_MetaProSIP"/><xml name="manutest_FuzzyDiff"/><xml name="manutest_TargetedFileConverter"/><xml name="manutest_MapAlignerIdentification"/><xml name="manutest_IDRTCalibration"/><xml name="manutest_MRMTransitionGroupPicker"/><xml name="manutest_OpenSwathAssayGenerator"/><xml name="manutest_IDSplitter"/><xml name="manutest_OpenSwathMzMLFileCacher"/><xml name="manutest_HighResPrecursorMassCorrector"/><xml name="manutest_OpenSwathChromatogramExtractor"/><xml name="manutest_OpenSwathAnalyzer"/><xml name="manutest_FeatureLinkerUnlabeled"/><xml name="manutest_DTAExtractor"/><xml name="manutest_FileInfo"/><xml name="manutest_MapAlignerSpectrum"/><xml name="manutest_IsobaricAnalyzer"/><xml name="manutest_InternalCalibration"/><xml name="manutest_TOFCalibration"/><xml name="manutest_MSGFPlusAdapter"/><xml name="manutest_SpectraFilterSqrtMower"/><xml name="manutest_SimpleSearchEngine"/><xml name="manutest_PeakPickerWavelet"/><xml name="manutest_MapNormalizer"/><xml name="manutest_IDScoreSwitcher"/><xml name="manutest_FeatureLinkerLabeled"/><xml name="manutest_MapRTTransformer"/><xml name="manutest_RNPxlSearch"/><xml name="manutest_PrecursorMassCorrector"/><xml name="manutest_MapAlignerPoseClustering"/><xml name="manutest_MzTabExporter"/><xml name="manutest_BaselineFilter"/><xml name="manutest_FeatureFinderMRM"/><xml name="manutest_MascotAdapterOnline"/><xml name="manutest_DatabaseFilter"/><xml name="manutest_ProteinResolver"/><xml name="manutest_OpenSwathFeatureXMLToTSV"/><xml name="manutest_AccurateMassSearch"/><xml name="manutest_OpenSwathRTNormalizer"/><xml name="manutest_PeptideIndexer"/><xml name="manutest_CometAdapter"/><xml name="manutest_NoiseFilterSGolay"/><xml name="manutest_SpectraSTSearchAdapter"/><xml name="manutest_LuciphorAdapter"/><xml name="manutest_GNPSExport"/><xml name="manutest_Epifany"/><xml name="manutest_NucleicAcidSearchEngine"/><xml name="manutest_QualityControl"/><xml name="manutest_FeatureFinderMetaboIdent"/><xml name="manutest_RNAMassCalculator"/><xml name="manutest_MapAlignerTreeGuided"/><xml name="manutest_IDMassAccuracy"/><xml name="manutest_ProteomicsLFQ"/><xml name="manutest_IDDecoyProbability"/><xml name="manutest_DigestorMotif"/><xml name="manutest_DatabaseSuitability"/><xml name="manutest_StaticModification"/><xml name="manutest_TriqlerConverter"/><xml name="manutest_OpenMSDatabasesInfo"/><xml name="manutest_MSFraggerAdapter"/><xml name="manutest_FLASHDeconv"/><xml name="manutest_JSONExporter"/><xml name="manutest_SageAdapter"/><xml name="manutest_OpenMSInfo"/><xml name="manutest_DeMeanderize"/></macros>
diff --git a/tools/openms/aux/tools_blacklist.txt b/tools/openms/aux/tools_blacklist.txt
index 6cf0cefbe..ccb9bffce 100644
--- a/tools/openms/aux/tools_blacklist.txt
+++ b/tools/openms/aux/tools_blacklist.txt
@@ -1,18 +1,18 @@
-# seems not possible for 2.5 https://github.com/OpenMS/OpenMS/issues/4426
-# DigestorMotif
+
+# Stack smashing problem in bioconda build https://github.com/OpenMS/OpenMS/issues/7149
+Decharger
+MetaboliteAdductDecharger
+
+# would need the executable in conda https://github.com/bioconda/bioconda-recipes/pull/19219 or https://github.com/bioconda/bioconda-recipes/pull/21472
+MaRaClusterAdapter
+
+# FlashDeconv needs tests and use output prefix
+# https://github.com/OpenMS/OpenMS/pull/7160
+FLASHDeconv
 
 # deprecated https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/UTILS_IDDecoyProbability.html
 # https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/a16242.html
 IDDecoyProbability
 
-# personal communication with author V. Bafna: 
-# "InsPect is no longer maintained as there are many better tools including MS-GF+"
-InspectAdapter
-
 # https://github.com/OpenMS/OpenMS/issues/4550#issuecomment-594065727
 ProteomicsLFQ
-
-# https://github.com/OpenMS/OpenMS/issues/4401
-InclusionExclusionListCreator
-RTPredict
-PTPredict
diff --git a/tools/openms/fill_ctd_clargs.py b/tools/openms/fill_ctd_clargs.py
deleted file mode 100644
index f36e0ee86..000000000
--- a/tools/openms/fill_ctd_clargs.py
+++ /dev/null
@@ -1,70 +0,0 @@
-#!/usr/bin/env python3
-
-import operator
-from argparse import ArgumentParser
-from functools import reduce  # forward compatibility for Python 3
-from io import StringIO
-
-from CTDopts.CTDopts import (
-    _Null,
-    CTDModel,
-    ModelTypeError,
-    Parameters
-)
-
-
-def getFromDict(dataDict, mapList):
-    return reduce(operator.getitem, mapList, dataDict)
-
-
-def setInDict(dataDict, mapList, value):
-    getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value
-
-
-if __name__ == "__main__":
-    # note add_help=False since otherwise arguments starting with -h will
-    # trigger an error (despite allow_abbreviate)
-    parser = ArgumentParser(prog="fill_ctd_clargs",
-                            description="fill command line arguments"
-                            "into a CTD file and write the CTD file to stdout",
-                            add_help=False, allow_abbrev=False)
-    parser.add_argument("--ini_file", dest="ini_file", help="input ini file",
-                        metavar='INI', default=None, required=True)
-    parser.add_argument("--ctd_file", dest="ctd_file", help="input ctd file"
-                        "if given then optional parameters from the ini file"
-                        "will be filled with the defaults from this CTD file",
-                        metavar='CTD', default=None, required=False)
-    args, cliargs = parser.parse_known_args()
-
-    # load CTDModel
-    ini_model = None
-    try:
-        ini_model = CTDModel(from_file=args.ini_file)
-    except ModelTypeError:
-        pass
-    try:
-        ini_model = Parameters(from_file=args.ini_file)
-    except ModelTypeError:
-        pass
-    assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ini_file)
-
-    # get a dictionary of the ctd arguments where the values of the parameters
-    # given on the command line are overwritten
-    ini_values = ini_model.parse_cl_args(cl_args=cliargs, ignore_required=True)
-
-    if args.ctd_file:
-        ctd_model = CTDModel(from_file=args.ctd_file)
-        ctd_values = ctd_model.get_defaults()
-        for param in ini_model.get_parameters():
-            if not param.required and (param.default is None or type(param.default) is _Null):
-                lineage = param.get_lineage(name_only=True)
-                try:
-                    default = getFromDict(ctd_values, lineage)
-                except KeyError:
-                    continue
-                setInDict(ini_values, lineage, default)
-
-    # write the ctd with the values taken from the dictionary
-    out = StringIO()
-    ctd_tree = ini_model.write_ctd(out, ini_values)
-    print(out.getvalue())
diff --git a/tools/openms/generate-foo.sh b/tools/openms/generate-foo.sh
deleted file mode 100644
index 6a6a5ed91..000000000
--- a/tools/openms/generate-foo.sh
+++ /dev/null
@@ -1,215 +0,0 @@
-#!/usr/bin/env bash
-
-# parse test definitions from OpenMS sources for a tool with a given id
-function get_tests2 {
-    id=$1
-    >&2 echo "generate tests for $id"
-    echo '<xml name="autotest_'"$id"'">'
-
-    # get the tests from the CMakeLists.txt
-    # 1st remove some tests
-    # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399
-    # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt
-    # - several tools with duplicated input (leads to conflict when linking)
-    # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)
-    # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)
-    # - some input files are originally in a subdir (degenerated cases/), but not in test-data
-    # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet)
-    # - SiriusAdapter_4 depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010
-    # - SiriusAdapter_10 should work in >2.8 https://github.com/OpenMS/OpenMS/issues/5869
-    CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake  |
-        sed 's@${DATA_DIR_SHARE}/@@g' |
-        grep -v 'OpenSwathMzMLFileCacher .*-convert_back' |
-        sed 's/${TMP_RIP_PATH}/""/' |
-        grep -v "MaRaClusterAdapter.*-consensus_out"|
-        grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " |
-        sed 's@degenerate_cases/@@g' |
-        egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' |
-        sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' |
-        grep -v '"TOPP_SiriusAdapter_10"')
-
-    # 1st part is a dirty hack to join lines containing a single function call, e.g.
-    # addtest(....
-    #         ....)
-    echo "$CMAKE" | sed 's/#.*//; s/^\s*//; s/\s*$//' | grep -v "^#" | grep -v "^$"  | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | 
-        grep -iE "add_test\(\"(TOPP|UTILS)_.*/$id " | egrep -v "_prepare\"|_convert|WRITEINI|WRITECTD|INVALIDVALUE"  | while read -r line
-    do
-        line=$(echo "$line" | sed 's/add_test("\([^"]\+\)"/\1/; s/)$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g')
-        # >&2 echo $line
-        test_id=$(echo "$line" | cut -d" " -f 1)
-        tool_id=$(echo "$line" | cut -d" " -f 2)
-        # >&2 echo "test_id $test_id"
-        if [[ $test_id =~ _out_?[0-9]? ]]; then
-            >&2 echo "    skip $test_id $line"
-            continue
-        fi
-        if [[ ${id,,} != ${tool_id,,} ]]; then
-            >&2 echo "    skip $test_id ($id != $tool_id) $line"
-            continue
-        fi
-
-        #remove tests with set_tests_properties(....PROPERTIES WILL_FAIL 1)
-        if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
-            >&2 echo "    skip failing "$test_id
-            continue
-        fi
-        tes="  <test>\n"
-        line=$(fix_tmp_files "$line")
-        line=$(unique_files "$line")
-        # >&2 echo LINE $line
-        #if there is an ini file then we use this to generate the test
-        #otherwise the ctd file is used
-        #other command line parameters are inserted later into this xml
-        if grep -lq "\-ini" <<<"$line"; then
-            ini=$(echo $line | sed 's/.*-ini \([^ ]\+\).*/\1/')
-            ini="test-data/$ini"
-        else
-            ini="ctd/$tool_id.ctd"
-        fi
-        # >&2 echo "========================================================"
-        # >&2 echo "USING ini $ini"
-        cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//')
-
-        ctdtmp=$(mktemp)
-        # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"])
-        # >&2 echo "python3 fill_ctd_clargs.py --ini_file $ini $cli" 
-        eval "python3 fill_ctd_clargs.py --ini_file $ini $cli" > "$ctdtmp"
-        # >&2 echo $ctdtmp
-        # >&2 cat $ctdtmp
-        testtmp=$(mktemp)
-        # >&2 echo CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7"
-        CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" > /dev/null
-        echo "<!-- $test_id -->"
-        cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/'
-
-        rm "$ctdtmp" "$testtmp"
-
-        #> /dev/null
-
-        #rm $testtmp
-    done 
-    echo '</xml>'
-}
-
-#some tests use the same file twice which does not work in planemo tests
-#hence we create symlinks for each file used twice
-function unique_files {
-    line=$@
-    for arg in $@
-    do
-        if [[ ! -f "test-data/$arg" ]]; then
-            continue
-        fi
-        cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n'))
-        while [[ $cnt -gt 1 ]]; do
-            new_arg=$(echo $arg | sed "s/\(.*\)\./\1_$cnt./")
-            ln -fs $arg test-data/$new_arg
-            line=$(echo $line | sed "s/\($arg.*\)$arg/\1$new_arg/")
-            cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n'))
-        done
-    done
-
-    echo $line
-}
-
-# options of out_type selects need to be fixed to Galaxy data types
-function fix_out_type {
-    grep "^$1" "$2" | awk '{print $2}'
-}
-
-#OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file.
-#problem: the extension of the tmp files is unusable for test generation.
-#unfortunately the extensions used in the DIFF lines are not always usable for the CLI
-#(e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt)
-#this function replaces the tmp file by the expected file. 
-function fix_tmp_files {
-    # >&2 echo "FIX $line"
-    ret=""
-    for a in $@; do
-        # >&2 echo "    a "$a
-        if [[ ! $a =~ .tmp$ ]] && [[ ! $a =~ _tmp_ ]]; then
-            ret="$ret $a"
-            continue
-        fi
-        diff_line=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a")
-        # >&2 echo "    diff_line "$diff_line
-        in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$diff_line)
-        # >&2 echo "    in1 "$in1
-        if [[  "$a" != "$in1" ]]; then
-            ret="$ret $a"
-            continue
-        fi
-        in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$diff_line)
-        in2=$(basename $in2 | sed 's/)$//')
-        # >&2 echo "    in2 "$in2
-        if [[ -f "test-data/$in2" ]]; then
-            ln -fs "$in1" "test-data/$in2"
-            ret="$ret $in2"
-        else
-            ret="$ret $a"
-        fi
-    done
-#    >&2 echo "--> $ret"
-    echo "$ret"
-}
-
-function link_tmp_files {
-    # note this also considers commented lines (starting with a #)
-    # because of tests where the diff command is commented and we
-    # still want to use the extension of these files
-    cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/^\s*//; s/\s*$//' | grep -v "^$"  | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep "\${DIFF}" | while read -r line
-    do
-        in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$line)
-        in1=$(basename $in1 | sed 's/)$//')
-        in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$line)
-        in2=$(basename $in2 | sed 's/)$//')
-        if [[ "$in1" == "$in2" ]]; then
-            >&2 echo "not linking equal $in1 $in2"
-            continue
-        fi
-        ln -f -s $in1 test-data/$in2
-    done
-    
-    find test-data/ -name "*.tmp" -print0 | 
-    while IFS= read -r -d '' i; do 
-        if [ ! -e test-data/$(basename $i .tmp) ]; then
-            ln -s $(basename $i) test-data/$(basename $i .tmp)
-        else
-            ln -fs $(basename $i) test-data/$(basename $i .tmp)
-        fi
-    done
-}
-
-
-
-# parse data preparation calls from OpenMS sources for a tool with a given id
-function prepare_test_data {
-#     id=$1
-# | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?"
-
-    # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010
-    cat $OPENMSGIT/src/tests/topp/CMakeLists.txt  $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' | grep -v "^$"  | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | 
-        sed 's/degenerate_cases\///' | 
-        egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | 
-        grep add_test | 
-        egrep "TOPP|UTILS" |
-        sed 's@${DATA_DIR_SHARE}/@@g;'|
-        sed 's@${TMP_RIP_PATH}@./@g'|
-        sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| 
-	sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' |
-    while read line
-    do
-        test_id=$(echo "$line" | sed 's/add_test(//; s/"//g;  s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1)
-
-        if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
-            >&2 echo "    skip failing "$test_id
-            continue
-        fi
-
-        line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-)
-        # line="$(fix_tmp_files $line)"
-        echo 'echo executing "'$test_id'"'
-	echo "$line > $test_id.stdout 2> $test_id.stderr"
-        echo "if [[ \"\$?\" -ne \"0\" ]]; then >&2 echo '$test_id failed'; >&2 echo -e \"stderr:\n\$(cat $test_id.stderr | sed 's/^/    /')\"; echo -e \"stdout:\n\$(cat $test_id.stdout)\";fi"    
-    done
-}
diff --git a/tools/openms/get_tests.py b/tools/openms/get_tests.py
new file mode 100755
index 000000000..6fb8a74f1
--- /dev/null
+++ b/tools/openms/get_tests.py
@@ -0,0 +1,344 @@
+#!/usr/bin/env python
+
+import argparse
+import os.path
+import re
+import shlex
+import sys
+import tempfile
+from typing import (
+    Dict,
+    List,
+    Optional,
+    TextIO,
+    Tuple,
+)
+
+from ctdconverter.common.utils import (
+    ParameterHardcoder,
+    parse_hardcoded_parameters,
+    parse_input_ctds,
+)
+from ctdconverter.galaxy.converter import convert_models
+from CTDopts.CTDopts import (
+    CTDModel,
+    ModelTypeError,
+    Parameters,
+)
+
+SKIP_LIST = [
+    r"_prepare\"",
+    r"_convert",
+    r"WRITEINI",
+    r"WRITECTD",
+    r"INVALIDVALUE",
+    r"\.ini\.json",
+    r"OpenSwathMzMLFileCacher .*-convert_back",  # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399
+    r"MaRaClusterAdapter.*-consensus_out",  # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)
+    r"FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta ",  # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)
+    r'^(TOPP_OpenSwathAnalyzer_test_3|TOPP_OpenSwathAnalyzer_test_4)$',  # no  suppert for cached mzML
+    r'TOPP_SiriusAdapter_[0-9]+$',  # Do not test SiriusAdapter https://github.com/OpenMS/OpenMS/issues/7000 .. will be removed anyway
+    r'TOPP_AssayGeneratorMetabo_(7|8|9|10|11|12|13|14|15|16|17|18)$'  # Skip AssayGeneratorMetabo tests using Sirius  https://github.com/OpenMS/OpenMS/issues/7150 (will be replaced by two tools)
+]
+
+
+def get_failing_tests(cmake: List[str]) -> List[str]:
+    failing_tests = []
+    re_fail = re.compile(r"set_tests_properties\(\"([^\"]+)\" PROPERTIES WILL_FAIL 1\)")
+
+    for cmake in args.cmake:
+        with open(cmake) as cmake_fh:
+            for line in cmake_fh:
+                match = re_fail.search(line)
+                if match:
+                    failing_tests.append(match.group(1))
+    return failing_tests
+
+
+def fix_tmp_files(line: str, diff_pairs: Dict[str, str]) -> str:
+    """
+    OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file.
+    problem: the extension of the tmp files is unusable for test generation.
+    unfortunately the extensions used in the DIFF lines are not always usable for the CLI
+    (e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt)
+    this function replaces the tmp file by the expected file.
+    """
+    cmd = shlex.split(line)
+    for i, e in enumerate(cmd):
+        if e in diff_pairs:
+            dst = os.path.join("test-data", diff_pairs[e])
+            if os.path.exists(dst):
+                os.unlink(dst)
+            sys.stderr.write(f"symlink {e} {dst}\n")
+            os.symlink(e, dst)
+            cmd[i] = diff_pairs[e]
+    return shlex.join(cmd)
+
+
+def get_ini(line: str, tool_id: str) -> Tuple[str, str]:
+    """
+    if there is an ini file then we use this to generate the test
+    otherwise the ctd file is used
+    other command line parameters are inserted later into this xml
+    """
+    cmd = shlex.split(line)
+    ini = None
+    for i, e in enumerate(cmd):
+        if e == "-ini":
+            ini = cmd[i + 1]
+            cmd = cmd[:i] + cmd[i + 2:]
+    if ini:
+        return os.path.join("test-data", ini), shlex.join(cmd)
+    else:
+        return os.path.join("ctd", f"{tool_id}.ctd"), line
+
+
+def unique_files(line: str):
+    """
+    some tests use the same file twice which does not work in planemo tests
+    hence we create symlinks for each file used twice
+    """
+    cmd = shlex.split(line)
+    # print(f"{cmd}")
+    files = {}
+    # determine the list of indexes where each file argument (anything appearing in test-data/) appears
+    for idx, e in enumerate(cmd):
+        p = os.path.join("test-data", e)
+        if not os.path.exists(p) and not os.path.islink(p):
+            continue
+        try:
+            files[e].append(idx)
+        except KeyError:
+            files[e] = [idx]
+    # print(f"{files=}")
+    for f in files:
+        if len(files[f]) < 2:
+            continue
+        for i, idx in enumerate(files[f]):
+            f_parts = f.split(".")
+            f_parts[0] = f"{f_parts[0]}_{i}"
+            new_f = ".".join(f_parts)
+            # if os.path.exists(os.path.join("test-data", new_f)):
+            #     os.unlink(os.path.join("test-data", new_f))
+            sys.stderr.write(
+                f'\tsymlink {os.path.join("test-data", new_f)} {f}\n'
+            )
+            try:
+                os.symlink(f, os.path.join("test-data", new_f))
+            except FileExistsError:
+                pass
+            cmd[idx] = new_f
+    return shlex.join(cmd)
+
+
+def fill_ctd_clargs(ini: str, line: str, ctd_tmp: TextIO) -> None:
+    cmd = shlex.split(line)
+
+    # load CTDModel
+    ini_model = None
+    try:
+        ini_model = CTDModel(from_file=ini)
+    except ModelTypeError:
+        pass
+    try:
+        ini_model = Parameters(from_file=ini)
+    except ModelTypeError:
+        pass
+    assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (
+        args.ini_file
+    )
+
+    # get a dictionary of the ctd arguments where the values of the parameters
+    # given on the command line are overwritten
+    ini_values = ini_model.parse_cl_args(cl_args=cmd, ignore_required=True)
+    ini_model.write_ctd(ctd_tmp, ini_values)
+
+
+def process_test_line(
+    id: str,
+    line: str,
+    failing_tests: List[str],
+    skip_list: List[str],
+    diff_pairs: Dict[str, str],
+) -> Optional[str]:
+
+    re_test_id = re.compile(r"add_test\(\"([^\"]+)\" ([^ ]+) (.*)")
+    re_id_out_test = re.compile(r"_out_?[0-9]?")
+
+    # TODO auto extract from  set(OLD_OSW_PARAM ... lin
+    line = line.replace(
+        "${OLD_OSW_PARAM}",
+        " -test -mz_extraction_window 0.05 -mz_extraction_window_unit Th -ms1_isotopes 0 -Scoring:TransitionGroupPicker:compute_peak_quality -Scoring:Scores:use_ms1_mi false -Scoring:Scores:use_mi_score false",
+    )
+
+    line = line.replace("${TOPP_BIN_PATH}/", "")
+    line = line.replace("${DATA_DIR_TOPP}/", "")
+    line = line.replace("THIRDPARTY/", "")
+    line = line.replace("${DATA_DIR_SHARE}/", "")
+    # IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differently
+    line = line.replace("${TMP_RIP_PATH}/", "")
+    # some input files are originally in a subdir (degenerated cases/), but not in test-data
+    line = line.replace("degenerate_cases/", "")
+    # determine the test and tool ids and remove the 1) add_test("TESTID" 2) trailing )
+    match = re_test_id.match(line)
+    if not match:
+        sys.exit(f"Ill formated test line {line}\n")
+    test_id = match.group(1)
+    tool_id = match.group(2)
+
+    line = f"{match.group(2)} {match.group(3)}"
+
+    if test_id in failing_tests:
+        sys.stderr.write(f"    skip failing {test_id} {line}\n")
+        return
+
+    if id != tool_id:
+        sys.stderr.write(f"    skip {test_id} ({id} != {tool_id}) {line}\n")
+        return
+
+    if re_id_out_test.search(test_id):
+        sys.stderr.write(f"    skip {test_id} {line}\n")
+        return
+
+    for skip in skip_list:
+        if re.search(skip, line):
+            return
+        if re.search(skip, test_id):
+            return
+
+    line = fix_tmp_files(line, diff_pairs)
+    # print(f"fix {line=}")
+    line = unique_files(line)
+    # print(f"unq {line=}")
+    ini, line = get_ini(line, tool_id)
+
+    from dataclasses import dataclass, field
+
+    @dataclass
+    class CTDConverterArgs:
+        input_files: list
+        output_destination: str
+        default_executable_path: Optional[str] = None
+        hardcoded_parameters: Optional[str] = None
+        parameter_hardcoder: Optional[ParameterHardcoder] = None
+        xsd_location: Optional[str] = None
+        formats_file: Optional[str] = None
+        add_to_command_line: str = ""
+        required_tools_file: Optional[str] = None
+        skip_tools_file: Optional[str] = None
+        macros_files: Optional[List[str]] = field(default_factory=list)
+        test_macros_files: Optional[List[str]] = field(default_factory=list)
+        test_macros_prefix: Optional[List[str]] = field(default_factory=list)
+        test_test: bool = False
+        test_only: bool = False
+        test_unsniffable: Optional[List[str]] = field(default_factory=list)
+        test_condition: Optional[List[str]] = ("compare=sim_size", "delta_frac=0.05")
+        tool_version: str = None
+        tool_profile: str = None
+        bump_file: str = None
+
+    # create an ini/ctd file where the values are equal to the arguments from the command line
+    # and transform it to xml
+    test = [f"<!-- {test_id} -->\n"]
+    with tempfile.NamedTemporaryFile(
+        mode="w+", delete_on_close=False
+    ) as ctd_tmp, tempfile.NamedTemporaryFile(
+        mode="w+", delete_on_close=False
+    ) as xml_tmp:
+        fill_ctd_clargs(ini, line, ctd_tmp)
+        ctd_tmp.close()
+        xml_tmp.close()
+        parsed_ctd = parse_input_ctds(None, [ctd_tmp.name], xml_tmp.name, "xml")
+        ctd_args = CTDConverterArgs(
+            input_files=[ctd_tmp.name],
+            output_destination=xml_tmp.name,
+            macros_files=["macros.xml"],
+            skip_tools_file="aux/tools_blacklist.txt",
+            formats_file="aux/filetypes.txt",
+            # tool_conf_destination = "tool.conf",
+            hardcoded_parameters="aux/hardcoded_params.json",
+            tool_version="3.1",
+            test_only=True,
+            test_unsniffable=[
+                "csv",
+                "tsv",
+                "txt",
+                "dta",
+                "dta2d",
+                "edta",
+                "mrm",
+                "splib",
+            ],
+            test_condition=["compare=sim_size", "delta_frac=0.7"],
+        )
+        ctd_args.parameter_hardcoder = parse_hardcoded_parameters(
+            ctd_args.hardcoded_parameters
+        )
+        convert_models(ctd_args, parsed_ctd)
+        xml_tmp = open(xml_tmp.name, "r")
+        for l in xml_tmp:
+            test.append(l)
+
+    return "".join(test)
+
+
+parser = argparse.ArgumentParser(description="Create Galaxy tests for a OpenMS tools")
+parser.add_argument("--id", dest="id", help="tool id")
+parser.add_argument("--cmake", nargs="+", help="OpenMS test CMake files")
+args = parser.parse_args()
+sys.stderr.write(f"generate tests for {args.id}\n")
+
+re_comment = re.compile("#.*")
+re_empty_prefix = re.compile(r"^\s*")
+re_empty_suffix = re.compile(r"\s*$")
+re_add_test = re.compile(r"add_test\(\"(TOPP|UTILS)_.*/" + args.id)
+re_diff = re.compile(r"\$\{DIFF\}.* -in1 ([^ ]+) -in2 ([^ ]+)")
+failing_tests = get_failing_tests(args.cmake)
+tests = []
+
+# process the given CMake files and compile lists of
+# - test lines .. essentially add_test(...)
+# - and pairs of files that are diffed
+jline = ""
+test_lines = []
+diff_pairs = {}
+for cmake in args.cmake:
+    with open(cmake) as cmake_fh:
+        for line in cmake_fh:
+            # remove comments, empty prefixes and suffixes
+            line = re_comment.sub("", line)
+            line = re_empty_prefix.sub("", line)
+            line = re_empty_suffix.sub("", line)
+            # skip empty lines
+            if line == "":
+                continue
+
+            # join test statements that are split over multiple lines
+            if line.endswith(")"):
+                jline += " " + line[:-1]
+            else:
+                jline = line
+                continue
+            line, jline = jline.strip(), ""
+            match = re_diff.search(line)
+            if match:
+                in1 = match.group(1).split("/")[-1]
+                in2 = match.group(2).split("/")[-1]
+                if in1 != in2:
+                    diff_pairs[in1] = in2
+            elif re_add_test.match(line):
+                test_lines.append(line)
+
+for line in test_lines:
+    test = process_test_line(args.id, line, failing_tests, SKIP_LIST, diff_pairs)
+    if test:
+        tests.append(test)
+
+tests = "\n".join(tests)
+print(
+    f"""
+<xml name="autotest_{args.id}">
+{tests}
+</xml>
+"""
+)
diff --git a/tools/openms/macros.xml b/tools/openms/macros.xml
index a9a73ab19..546df4e19 100644
--- a/tools/openms/macros.xml
+++ b/tools/openms/macros.xml
@@ -3,19 +3,19 @@
      You can edit this file to add your own macros, if you so desire, or you can
      add additional macro files using the m/macros parameter -->
 <macros>
-  <token name="@TOOL_VERSION@">2.8</token>
+  <token name="@TOOL_VERSION@">3.1</token>
   <token name="@VERSION_SUFFIX@">0</token>
+  <token name="@TEST_DATA_LOCATION@"/>
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@TOOL_VERSION@">openms</requirement>
       <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement>
       <!-- omssa (which has been excluded from 3rdparty) and makeblastdb for OMSSAAdapter -->
-      <requirement type="package" version="2.1.9">omssa</requirement>
-      <requirement type="package" version="2.13.0">blast</requirement>
+      <requirement type="package" version="2.14.1">blast</requirement>
       <!--<requirement type="package" version="5.0.0">tpp</requirement>-->
       <!-- for realpath (used e.g. in LuciphorAdapter) -->
 	  <!--<requirement type="package" version="8.25">coreutils</requirement>-->
-	  <requirement type="package" version="1.4">ctdopts</requirement>
+	  <requirement type="package" version="1.5">ctdopts</requirement>
       <yield/>
     </requirements>
   </xml>
@@ -26,6 +26,8 @@
       <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>
       <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/>
       <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/>
+      <regex match="OMSSA ran out of RAM" level="fatal_oom" description="Could not allocate memory"/>
+      <regex match="comet' crashed hard (segfault-like). Please check the log." level="fatal_oom" description="Could not allocate memory"/>
     </stdio>
   </xml>
   <xml name="references">
@@ -113,11 +115,11 @@
   </token>
 
 <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o)
-    #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'}
+    #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xsd', 'zip': 'zip'}
     #return m[o]
 #end def
 #def gxy2omsext(g)
-    #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'}
+    #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml', 'xsd': 'xsd', 'zip': 'zip'}
     #return m[g]
 #end def
 ]]></token></macros>
diff --git a/tools/openms/prepare_test_data_manual.sh b/tools/openms/prepare_test_data_manual.sh
index 90fcb2e4a..35845ed05 100755
--- a/tools/openms/prepare_test_data_manual.sh
+++ b/tools/openms/prepare_test_data_manual.sh
@@ -1,8 +1,3 @@
-MSSimulator -test -in DecoyDatabase_1.fasta -out MSsimulator.mzml -algorithm:RandomNumberGenerators:biological reproducible -algorithm:RandomNumberGenerators:technical reproducible > MSSimulator_1.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'MSSimulator_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
-MSSimulator -test -in DecoyDatabase_1.fasta -out MSsimulator_MALDI.mzml -algorithm:RandomNumberGenerators:biological reproducible -algorithm:RandomNumberGenerators:technical reproducible -algorithm:MSSim:Global:ionization_type MALDI > MSSimulator_2.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'MSSimulator_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
 ClusterMassTracesByPrecursor -test -in_ms1 ConsensusMapNormalizer_input.consensusXML -in_swath ConsensusMapNormalizer_input.consensusXML -out ClusterMassTracesByPrecursor.mzml > ClusterMassTracesByPrecursor.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'ClusterMassTracesByPrecursor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
@@ -13,8 +8,7 @@ if [[ "$?" -ne "0" ]]; then >&2 echo 'ClusterMassTraces failed'; >&2 echo -e "st
 CVInspector -test -cv_files CHEMISTRY/XLMOD.obo -cv_names XLMOD -mapping_file MAPPING/ms-mapping.xml -html CVInspector.html > CVInspector.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'CVInspector failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
-DeMeanderize -test -in MSsimulator_MALDI.mzml -out DeMeanderize.mzml > DeMeanderize.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'DeMeanderize failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
+# TODO DeMeanderize
 
 # TODO DigestorMotif
 
@@ -30,26 +24,17 @@ FeatureFinderIsotopeWavelet -test -in FeatureFinderCentroided_1_input.mzML -out
 if [[ "$?" -ne "0" ]]; then >&2 echo 'FeatureFinderIsotopeWavelet failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
 
-FFEval -test -in  FeatureFinderCentroided_1_output.featureXML -truth  FeatureFinderCentroided_1_output.featureXML -out  FFEval.featureXML -out_roc FFEval_roc.csv  > FFEval.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'FFEval failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
 # TODO? deprecated IDDecoyProbability
 
 IDExtractor -test -in MSGFPlusAdapter_1_out.idXML -best_hits -number_of_peptides  1 -out  IDExtractor.idXML   > IDExtractor.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'IDExtractor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
-LabeledEval -test -in  FeatureLinkerLabeled_1_input.featureXML -truth  FeatureLinkerLabeled_1_output.consensusXML> LabeledEval.txt > LabeledEval.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'LabeledEval failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
 MapStatistics -test -in SiriusAdapter_3_input.featureXML -out MapStatistics.txt > MapStatistics_1.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'MapStatistics_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
 MapStatistics -test -in ConsensusXMLFile_1.consensusXML -out MapStatistics2.txt > MapStatistics_2.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'MapStatistics_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
-MetaboliteAdductDecharger -test -in Decharger_input.featureXML -out_cm MetaboliteAdductDecharger_cm.consensusXML -out_fm MetaboliteAdductDecharger_fm.featureXML -outpairs MetaboliteAdductDecharger_pairs.consensusXML > MetaboliteAdductDecharger.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'MetaboliteAdductDecharger failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
 MetaboliteSpectralMatcher -test -in spectra.mzML -database MetaboliteSpectralDB.mzML -out MetaboliteSpectralMatcher.mzTab > MetaboliteSpectralMatcher.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'MetaboliteSpectralMatcher failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
@@ -68,20 +53,6 @@ if [[ "$?" -ne "0" ]]; then >&2 echo 'OpenSwathDIAPreScoring failed'; >&2 echo -
 OpenSwathRewriteToFeatureXML -featureXML OpenSwathFeatureXMLToTSV_input.featureXML -out OpenSwathRewriteToFeatureXML.featureXML > OpenSwathRewriteToFeatureXML.stdout 2> stderr
 # if [[ "$?" -ne "0" ]]; then >&2 echo 'OpenSwathRewriteToFeatureXML failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
-# adapted from the commented tests in OpenMS TODO may be removed later https://github.com/OpenMS/OpenMS/issues/4719
-FileConverter -in PepNovo.mzXML -out PepNovo_1.mzML > /dev/null 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'FileConverter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
-PepNovoAdapter -ini PepNovoAdapter_1_parameters.ini -in PepNovo_1.mzML -out PepNovoAdapter_3_output.idXML -model_directory pepnovo_models/ -pepnovo_executable pepnovo > PepNovo_1.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
-FileConverter -in PepNovo.mzData -out PepNovo_4.mzML > /dev/null 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'FileConverter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-PepNovoAdapter -ini PepNovoAdapter_1_parameters.ini -in PepNovo_4.mzML -out PepNovoAdapter_4_output.idXML -model_directory pepnovo_models/ -pepnovo_executable pepnovo > PepNovo_1.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
-#PepNovoAdapter -ini PepNovoAdapter_5_parameters.ini -in PepNovoAdapter_5_output.pepnovo_out -out PepNovoAdapter_5_output.idXML -model_directory pepnovo_models/ 
-
 # TODO PhosphoScoring 
 PhosphoScoring -in spectra.mzML -id MSGFPlusAdapter_1_out1.tmp -out PhosphoScoring.idxml > PhosphoScoring.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
@@ -118,9 +89,6 @@ if [[ "$?" -ne "0" ]]; then >&2 echo 'RNADigestor failed'; >&2 echo -e "stderr:\
 RNPxlXICFilter -test -control FileFilter_1_input.mzML -treatment FileFilter_1_input.mzML -out RNPxlXICFilter.mzML > RNPxlXICFilter.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'RNPxlXICFilter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
-RTEvaluation -in PeptideIndexer_1.idXML -out RTEvaluation.tsv > RTEvaluation.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'RTEvaluation failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
 SemanticValidator -test -in FileFilter_1_input.mzML -mapping_file MAPPING/ms-mapping.xml > SemanticValidator.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'SemanticValidator failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
@@ -152,13 +120,8 @@ if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterScaler failed'; >&2 echo -e "
 SpectraFilterThresholdMower -test -in  SpectraFilterSqrtMower_1_input.mzML -out  SpectraFilterThresholdMower.mzML > SpectraFilterThresholdMower.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterThresholdMower failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
-SpectraMerger -test -in NovorAdapter_in.mzML -out SpectraMerger_1.mzML > SpectraMerger.stdout 2> stderr
+SpectraMerger -test -in NovorAdapter_in.mzML -out SpectraMerger_1.mzML -algorithm:average_gaussian:ms_level 2 > SpectraMerger.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraMerger failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
-# TODO SvmTheoreticalSpectrumGeneratorTrainer
-
-TransformationEvaluation -test -in FileInfo_16_input.trafoXML -out TransformationEvaluation.trafoXML > TransformationEvaluation.stdout 2> stderr
-if [[ "$?" -ne "0" ]]; then >&2 echo 'TransformationEvaluation failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-
 XMLValidator -test -in FileFilter_1_input.mzML > XMLValidator.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'XMLValidator failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
diff --git a/tools/openms/readme.md b/tools/openms/readme.md
index 012242379..b503a2224 100644
--- a/tools/openms/readme.md
+++ b/tools/openms/readme.md
@@ -11,7 +11,7 @@ More informations are available at:
  * https://www.openms.de/
 
 The wrappers for these tools and most of their tests are automatically
-generated using the `generate.sh` script. The generation of the tools is
+generated using the `./aux/generate.sh` script. The generation of the tools is
 based on the CTDConverter (https://github.com/WorkflowConversion/CTDConverter)
 which can be fine tuned via the `hardcoded_params.json` file. This file allows
 to blacklist and hardcode parameters and to modify or set arbitrary
@@ -129,15 +129,6 @@ More details can be found in the comments of the shell script.
 Open problems
 =============
 
-Some tools stall in CI testing using `--biocontainers` which is why the OpenMS
-tools are currently listed in `.tt_biocontainer_skip`. This is
-
-- AssayGeneratorMetabo and SiriusAdapter (both depend on sirius)
-- OMSSAAdapter
-
-Using `docker -t` seems to solve the problem (see
-https://github.com/galaxyproject/galaxy/issues/10153).
-
 Licence (MIT)
 =============
 
diff --git a/tools/openms/test-data.sh b/tools/openms/test-data.sh
index 7bb0c570e..78a4d2ac5 100755
--- a/tools/openms/test-data.sh
+++ b/tools/openms/test-data.sh
@@ -1,11 +1,10 @@
 #!/usr/bin/env bash
 
-VERSION=2.8
-FILETYPES="aux/filetypes.txt"
-CONDAPKG="https://anaconda.org/bioconda/openms/2.8.0/download/linux-64/openms-2.8.0-h7ca0330_0.tar.bz2"
+# set -x
 
-# import the magic
-. ./generate-foo.sh
+VERSION=3.1
+FILETYPES="aux/filetypes.txt"
+CONDAPKG="https://anaconda.org/bioconda/openms/3.1.0/download/linux-64/openms-3.1.0-h8964181_1.tar.bz2"
 
 # install conda
 if [ -z "$tmp" ]; then
@@ -45,17 +44,20 @@ eval "$(conda shell.bash hook)"
 
 echo "Clone OpenMS $VERSION sources"
 if [[ ! -d $OPENMSGIT ]]; then
-    # TODO >2.8 reenable original release branch .. also in else branch
-    # the plus branch contains commits from https://github.com/OpenMS/OpenMS/pull/5920 and https://github.com/OpenMS/OpenMS/pull/5917
-    # git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT
-    git clone -b release/$VERSION.0-plus https://github.com/bernt-matthias/OpenMS.git $OPENMSGIT
-    cd $OPENMSGIT
-    git submodule init
-    git submodule update
-    cd -
+    if [[ "$created" == "yes" ]]; then
+        GIT_DIR=$(mktemp -d --dry-run)
+        GIT_EXTRA_OPTS="--separate-git-dir=$GIT_DIR"
+    fi
+    git clone -b release/$VERSION.0 --depth 1 --recurse-submodules=THIRDPARTY --shallow-submodules $GIT_EXTRA_OPTS https://github.com/OpenMS/OpenMS.git $OPENMSGIT
+    ## save some space by just keeping the needed binaries
+    find $OPENMSGIT/THIRDPARTY/ -type f -not \( -name maracluster -o -name spectrast \) -delete
+    find $OPENMSGIT/THIRDPARTY/ -empty -type d -delete
+    if [[ "$created" == "yes" ]]; then
+        rm -rf $GIT_DIR
+    fi
 else
     cd $OPENMSGIT
-    git pull origin release/$VERSION.0-plus
+    git pull origin release/$VERSION.0
     cd -
 fi
 
@@ -65,7 +67,7 @@ echo "Create OpenMS $VERSION conda env"
 if conda env list | grep "$OPENMSENV"; then
     true
 else
-    conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION omssa=2.1.9 ctdopts=1.5 lxml
+    conda create -y --quiet --solver libmamba --override-channels --strict-channel-priority --channel conda-forge --channel bioconda -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.5 lxml
 # chmod -R u-w $OPENMSENV 
 fi
 ###############################################################################
@@ -101,33 +103,34 @@ cd -
 conda deactivate
 
 
-# ###############################################################################
-# ## copy all the test data files to test-data
-# ## most of it (outputs) will be overwritten later, but its needed for
-# ## prepare_test_data
-# ###############################################################################
+# # ###############################################################################
+# # ## copy all the test data files to test-data
+# # ## most of it (outputs) will be overwritten later, but its needed for
+# # ## prepare_test_data
+# # ###############################################################################
 echo "Get test data"
-find test-data -type f,l,d ! -name "*fa" ! -name "*loc" ! -name "test-data" -delete
+find test-data -type f,l,d ! -name "*fa" ! -name "*loc" ! -name "test-data" ! -name MetaboliteSpectralDB.mzML -delete
 
 cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/
 cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/
 cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/
 cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/
 if [ ! -f test-data/MetaboliteSpectralDB.mzML ]; then 
-    wget -nc https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML
+    wget -nc https://raw.githubusercontent.com/sneumann/OpenMS/master/share/OpenMS/CHEMISTRY/MetaboliteSpectralDB.mzML
+    # wget -nc https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML
     mv MetaboliteSpectralDB.mzML test-data/
 fi
 ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt
 ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv
 
-if [ ! -d test-data/pepnovo_models/ ]; then
-    mkdir -p /tmp/pepnovo
-    wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
-    unzip PepNovo.20120423.zip -d /tmp/pepnovo/
-    mv /tmp/pepnovo/Models test-data/pepnovo_models/
-    rm PepNovo.20120423.zip
-    rm -rf /tmp/pepnovo
-fi
+# if [ ! -d test-data/pepnovo_models/ ]; then
+#     mkdir -p /tmp/pepnovo
+#     wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
+#     unzip PepNovo.20120423.zip -d /tmp/pepnovo/
+#     mv /tmp/pepnovo/Models test-data/pepnovo_models/
+#     rm PepNovo.20120423.zip
+#     rm -rf /tmp/pepnovo
+# fi
 ###############################################################################
 ## generate ctd files using the binaries in the conda package 
 ###############################################################################
@@ -170,6 +173,47 @@ done
 ###############################################################################
 ## create script to create results for the tests and run it
 ###############################################################################
+# parse data preparation calls from OpenMS sources for a tool with a given id
+function prepare_test_data {
+#     id=$1
+# | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?"
+
+    OLD_OSW_PARAM=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt |sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' |awk '{printf("%s@NEWLINE@", $0)}' |  sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep OLD_OSW_PARAM | head -n 1 | sed 's/^[^"]\+//; s/)$//; s/"//g')
+    # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010
+    cat $OPENMSGIT/src/tests/topp/CMakeLists.txt  $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake |
+        sed "s/\${OLD_OSW_PARAM}/$OLD_OSW_PARAM/" |
+        grep -v "\.ini\.json" |
+        sed 's/.ini.json /ini /' | 
+        sed 's/#.*$//'| 
+        sed 's/^\s*//; s/\s*$//' | 
+        grep -v "^$"  | 
+        awk '{printf("%s@NEWLINE@", $0)}' | 
+        sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | 
+        sed 's/degenerate_cases\///' | 
+        egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | 
+        grep add_test | 
+        egrep "TOPP|UTILS" |
+        sed 's@${DATA_DIR_SHARE}/@@g;'|
+        sed 's@${TMP_RIP_PATH}@./@g'|
+        sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| 
+	sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' |
+    while read line
+    do
+        test_id=$(echo "$line" | sed 's/add_test(//; s/"//g;  s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1)
+
+        if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then
+            >&2 echo "    skip failing "$test_id
+            continue
+        fi
+
+        line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-)
+        # line="$(fix_tmp_files $line)"
+        echo 'echo executing "'$test_id'"'
+        echo "$line > $test_id.stdout 2> $test_id.stderr"
+        echo "if [[ \"\$?\" -ne \"0\" ]]; then >&2 echo '$test_id failed'; >&2 echo -e \"stderr:\n\$(cat $test_id.stderr | sed 's/^/    /')\"; echo -e \"stdout:\n\$(cat $test_id.stdout)\";fi"    
+    done
+}
+
 echo "Create test shell script"
 
 echo -n "" > prepare_test_data.sh
@@ -180,31 +224,19 @@ echo 'export FIDO_BINARY="Fido"' >> prepare_test_data.sh
 echo 'export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"' >> prepare_test_data.sh
 
 echo 'export MARACLUSTER_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"'>> prepare_test_data.sh
-echo 'export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar"'>> prepare_test_data.sh
+echo 'export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-3.5/MSFragger-3.5.jar"'>> prepare_test_data.sh
 echo 'export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"' >> prepare_test_data.sh
 echo 'export MYRIMATCH_BINARY="myrimatch"'>> prepare_test_data.sh
 echo 'export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"' >> prepare_test_data.sh
-echo 'export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"'>> prepare_test_data.sh
 echo 'export PERCOLATOR_BINARY="percolator"'>> prepare_test_data.sh
 echo 'export SIRIUS_BINARY="$(which sirius)"' >> prepare_test_data.sh
 echo 'export SPECTRAST_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/SpectraST/spectrast"' >> prepare_test_data.sh
 echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh
 echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh
+echo 'export SAGE_BINARY=sage' >> prepare_test_data.sh
 
 prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh
 
-## prepare_test_data > tmp_test_data.sh
-## # remove calls not needed for the tools listed in any .list file
-## echo LIST $LIST
-## if [ ! -z "$LIST" ]; then
-##     REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//')
-## else
-##     REX=".*"
-## fi
-## echo REX $REX
-## cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh
-## rm tmp_test_data.sh
-
 echo "Execute test shell script"
 chmod u+x prepare_test_data.sh
 cd ./test-data || exit
@@ -234,14 +266,11 @@ echo "<macros>" > "$autotests"
 for i in $(ls ctd/*ctd)
 do
     b=$(basename "$i" .ctd)
-    get_tests2 "$b" >> "$autotests"
+    ./get_tests.py --id "$b" --cmake "$OPENMSGIT"/src/tests/topp/CMakeLists.txt "$OPENMSGIT"/src/tests/topp/THIRDPARTY/third_party_tests.cmake >> "$autotests"
+    wc -l "$autotests"
 done
 echo "</macros>" >> "$autotests"
 
-# echo "Create test data links"
-# Breaks DecoyDatabase
-# link_tmp_files
-
 # tests for tools using output_prefix parameters can not be auto generated
 # hence we output the tests for manual curation in macros_test.xml
 # and remove them from the autotests
@@ -255,6 +284,7 @@ echo "</macros>" >> "$autotests"
 #
 # not able to specify composite test data  
 # -> SpectraSTSearchAdapter 
+echo "Discard some tests"
 if [[ ! -z "$1" ]]; then
     echo "" > macros_discarded_auto.xml
     for i in OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter
@@ -272,7 +302,7 @@ conda deactivate
 ## remove broken symlinks in test-data
 find test-data/ -xtype l -delete
 
-if [ ! -z "$created" ]; then
+if [[ "$created" == "yes" ]]; then
     echo "Removing temporary directory"
     rm -rf "$tmp"
 fi
diff --git a/tools/pepquery2/macros.xml b/tools/pepquery2/macros.xml
index 05458e4de..63b171c13 100644
--- a/tools/pepquery2/macros.xml
+++ b/tools/pepquery2/macros.xml
@@ -1,6 +1,6 @@
  <macros>
     <token name="@TOOL_VERSION@">2.0.2</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1101/gr.235028.118</citation>
@@ -20,7 +20,7 @@
     #end if
 #end def
 #def clean($name1)
-    #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fas|fasta|imzml|mzml|mzxml|mgf|raw)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
+    #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fas|fasta|imzml|mzml|mzxml|mgf)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
     #return $name_clean
 #end def
 #def ln_name($ds)
@@ -31,8 +31,6 @@
         #set $ext = ".mzXML"
     #else if $ds.is_of_type('mgf')
         #set $ext = ".mgf"
-    #else if $ds.is_of_type('thermo.raw')
-        #set $ext = ".raw"
     #else if $ds.is_of_type('fasta')
         #set $ext = ".fasta"
     #end if
diff --git a/tools/pepquery2/pepquery2.xml b/tools/pepquery2/pepquery2.xml
index 45fa85492..2ee023578 100644
--- a/tools/pepquery2/pepquery2.xml
+++ b/tools/pepquery2/pepquery2.xml
@@ -33,6 +33,9 @@
 ## PepQuery command
 pepquery 
   -Xmx\$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]g
+#if $digestion.enzyme == '0'
+  -XX:ThreadStackSize=2048
+#end if
 #if $validation.task_type == "known"
   -s 2 $validation.decoy
 #else
@@ -156,7 +159,7 @@ pepquery
             </param>
             <when value="novel"/> 
             <when value="known"> 
-                 <param name="decoy" argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/>
+                 <param argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/>
             </when>
         </conditional>
         <section name="req_inputs" title="Input Data" expanded="true">
@@ -254,7 +257,7 @@ pepquery
                     <option value="public">public proteomics data repositories</option>
                 </param>
                 <when value="history">
-                    <param name="spectrum_files" argument="-ms" type="data" format="mgf,mzml,mzxml,thermo.raw" label="Spectrum File" help="Spectrum file used for identification, formats: MGF,mzML,mzXML,Thermo RAW" />
+                    <param name="spectrum_files" argument="-ms" type="data" format="mgf,mzml,mzxml" label="Spectrum File" help="Spectrum file used for identification, formats: MGF,mzML,mzXML" />
                 </when>
                 <when value="indexed">
                     <param name="index" argument="-ms" type="data" format="txt" label="PepQuery Index" help="" />
@@ -273,7 +276,7 @@ pepquery
                 </when>
             </conditional>
 
-            <param name="indexType" argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" >
+            <param argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" >
                 <option value="1">index (1-based) in MGF</option>
                 <option value="2">spectrum title in MGF</option>
             </param>
@@ -304,7 +307,7 @@ pepquery
 
              <param name="max_mods" argument="-maxVar" type="integer" label="Max Modifications" value="" min="0" max="10" optional="true" help="Max number of variable modifications  Default: 3" />
              <param name="unmodified" argument="-hc" type="boolean" truevalue="-hc" falsevalue="" checked="false" label="Use more stringent criterion for unrestricted modification searching" help="TRUE: score(UMS)>=score(targetPSM); FALSE: score(UMS)>score(targetPSM)" />
-             <param name="aa" argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." />
+             <param argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." />
         </section>
 
         <section name="digestion" title="Digestion" expanded="false">
@@ -366,7 +369,7 @@ pepquery
             <option value="ptm_detail.txt">ptm_detail.txt</option>
             <option value="ms_index">MS/MS Index</option>
         </param>
-        <param name="fast" argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." />
+        <param argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." />
     </inputs>
     <outputs>
         <data name="log_txt" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt">
@@ -677,6 +680,72 @@ pepquery
             </output>
         </test>
 
+        <!-- Test-5  Non-enzyme search -->
+        <test expect_num_outputs="2">
+            <conditional name="validation">
+                <param name="task_type" value="novel"/>
+            </conditional>
+            <section name="req_inputs">
+                <conditional name="input_type">
+                    <param name="input_type_selector" value="peptide"/>
+                    <conditional name="multiple">
+                        <param name="peptide_input_selector" value="single" />
+                        <param name="input" value="ELGSSDLTAR"/>
+                    </conditional>
+                </conditional>
+                <conditional name="db_type">
+                    <param name="db_type_selector" value="history" />
+                    <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
+                </conditional>
+                <conditional name="ms_dataset">
+                    <param name="ms_dataset_type" value="history"/>
+                    <param name="spectrum_files" ftype="mgf" value="iTRAQ_f4.mgf"/>
+                </conditional>
+                <param name="indexType" value="1"/>
+            </section>
+            <param name="parameter_set" value=""/>
+            <section name="modifications">
+                 <!-- 21: iTRAQ 4-plex of K [144.1020624208] -->
+                 <!-- 22: iTRAQ 4-plex of peptide N-term [144.1020624208] -->
+                 <param name="fixed_mod" value="1,21,22"/>
+                 <!-- 2: Oxidation of M [15.99491461956] -->
+                 <param name="var_mod" value="2"/>
+                 <param name="max_mods" value="3"/>
+                 <param name="unmodified" value="True"/>
+                 <param name="aa" value="False"/>
+            </section>
+            <section name="digestion">
+                <param name="enzyme" value="0"/>
+            </section>
+            <section name="ms_params">
+                <section name="tolerance_params">
+                    <param name="precursor_tolerance" value="10"/>
+                    <param name="precursor_unit" value="ppm"/>
+                    <param name="tolerance" value="0.6"/>
+                </section>
+                <section name="search">
+                    <param name="frag_method" value="1"/>
+                    <param name="scoring_method" value="1"/>
+                    <param name="extra_score_validation" value="False"/>
+                    <param name="min_charge" value="2"/>
+                    <param name="max_charge" value="3"/>
+                    <param name="min_peaks" value="10"/>
+                    <param name="isotope_error" value="0"/>
+                    <param name="min_score" value="12"/>
+                    <param name="min_length" value="7"/>
+                    <param name="max_length" value="45"/>
+                    <param name="num_random_peptides" value="1000"/>
+                </section>
+            </section>
+            <output name="psm_rank_txt">
+                <assert_contents>
+                    <has_text text="ELGSSDLTAR" />
+                    <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\[144.1\d+\]\t2\tiTRAQ_f4:3:2\t2\t1191.62\d+\t-3.04\d+\t-0.003\d+\t0.0\t1191.6\d+\t596.8\d+\t24.1\d+\t0\t13\t1\t995\t0.002\d+\t1\t0\tYes\t10.3\d+\t8.23\d+"/>
+                    <has_n_columns n="22" />
+                </assert_contents>
+            </output>
+        </test>
+
     </tests>
     <help><![CDATA[
 **PepQuery2**
diff --git a/tools/pepquery2/pepquery2_index.xml b/tools/pepquery2/pepquery2_index.xml
index d8e0e3c18..7d93574ff 100644
--- a/tools/pepquery2/pepquery2_index.xml
+++ b/tools/pepquery2/pepquery2_index.xml
@@ -12,7 +12,7 @@
 $index_spectrum_files($output.files_path, $inputs)
     ]]></command>
     <inputs>
-        <param name="inputs" argument="-i" type="data" format="mfg,mzml,mzxml" multiple="true" label="MS Spectrum files">
+        <param name="inputs" argument="-i" type="data" format="mgf,mzml,mzxml" multiple="true" label="MS Spectrum files">
         </param>
     </inputs>
     <outputs>
diff --git a/tools/pepquery2/pepquery2_show_sets.xml b/tools/pepquery2/pepquery2_show_sets.xml
index 74d927ddb..ca4e4283e 100644
--- a/tools/pepquery2/pepquery2_show_sets.xml
+++ b/tools/pepquery2/pepquery2_show_sets.xml
@@ -45,7 +45,7 @@ echo "PepQuery2 Show Sets $sets"
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <output name="pepquerydb">
                 <assert_contents>
                     <has_text text="CPTAC_PDA_Discovery_Study_Proteome_PDC000270" />
diff --git a/tools/qupath_roi_splitter/qupath_roi_splitter.py b/tools/qupath_roi_splitter/qupath_roi_splitter.py
index ba02875d2..9f727a039 100644
--- a/tools/qupath_roi_splitter/qupath_roi_splitter.py
+++ b/tools/qupath_roi_splitter/qupath_roi_splitter.py
@@ -6,12 +6,45 @@
 import pandas as pd
 
 
-def draw_poly(input_df, input_img, col=(0, 0, 0)):
+def draw_poly(input_df, input_img, col=(0, 0, 0), fill=False):
     s = np.array(input_df)
-    output_img = cv2.fillPoly(input_img, pts=np.int32([s]), color=col)
+    if fill:
+        output_img = cv2.fillPoly(input_img, pts=np.int32([s]), color=col)
+    else:
+        output_img = cv2.polylines(input_img, np.int32([s]), True, color=col, thickness=1)
     return output_img
 
 
+def draw_roi(input_roi, input_img, fill):
+    if len(input_roi["geometry"]["coordinates"]) == 1:
+        # Polygon w/o holes
+        input_img = draw_poly(input_roi["geometry"]["coordinates"][0], input_img, fill=fill)
+    else:
+        first_roi = True
+        for sub_roi in input_roi["geometry"]["coordinates"]:
+            # Polygon with holes
+            if not isinstance(sub_roi[0][0], list):
+                if first_roi:
+                    first_roi = False
+                    col = (0, 0, 0)
+                else:
+                    # holes in ROI
+                    col = (255, 255, 255) if not fill else (0, 0, 0)
+                input_img = draw_poly(sub_roi, input_img, col=col, fill=fill)
+            else:
+                # MultiPolygon with holes
+                for sub_coord in sub_roi:
+                    if first_roi:
+                        first_roi = False
+                        col = (0, 0, 0)
+                    else:
+                        # holes in ROI
+                        col = (255, 255, 255) if not fill else (0, 0, 0)
+                    input_img = draw_poly(sub_coord, input_img, col=col, fill=fill)
+
+    return input_img
+
+
 def split_qupath_roi(in_roi):
     with open(in_roi) as file:
         qupath_roi = geojson.load(file)
@@ -28,30 +61,13 @@ def split_qupath_roi(in_roi):
         img.fill(255)
 
         for i, roi in enumerate(qupath_roi["features"]):
-            if roi["properties"]["classification"]["name"] == cell_type:
-                if len(roi["geometry"]["coordinates"]) == 1:
-                    # Polygon w/o holes
-                    img = draw_poly(roi["geometry"]["coordinates"][0], img)
-                else:
-                    first_roi = True
-                    for sub_roi in roi["geometry"]["coordinates"]:
-                        # Polygon with holes
-                        if not isinstance(sub_roi[0][0], list):
-                            if first_roi:
-                                img = draw_poly(sub_roi, img)
-                                first_roi = False
-                            else:
-                                # holes in ROI
-                                img = draw_poly(sub_roi, img, col=(255, 255, 255))
-                        else:
-                            # MultiPolygon with holes
-                            for sub_coord in sub_roi:
-                                if first_roi:
-                                    img = draw_poly(sub_coord, img)
-                                    first_roi = False
-                                else:
-                                    # holes in ROI
-                                    img = draw_poly(sub_coord, img, col=(255, 255, 255))
+            if not args.all:
+                if "classification" not in roi["properties"]:
+                    continue
+                if roi["properties"]["classification"]["name"] == cell_type:
+                    img = draw_roi(roi, img, args.fill)
+            else:
+                img = draw_roi(roi, img, args.fill)
 
         # get all black pixel
         coords_arr = np.column_stack(np.where(img == (0, 0, 0)))
@@ -63,7 +79,10 @@ def split_qupath_roi(in_roi):
         coords_arr_xy = np.delete(coords_arr_xy, 2, axis=1)
 
         # to pandas and rename columns to x and y
-        coords_df = pd.DataFrame(coords_arr_xy, columns=['x', 'y'])
+        coords_df = pd.DataFrame(coords_arr_xy, columns=['y', 'x'])
+
+        # reorder columns
+        coords_df = coords_df[['x', 'y']]
 
         # drop duplicates
         coords_df = coords_df.drop_duplicates(
@@ -72,11 +91,18 @@ def split_qupath_roi(in_roi):
 
         coords_df.to_csv("{}_{}.txt".format(tma_name, cell_type), sep='\t', index=False)
 
+        # img save
+        if args.img:
+            cv2.imwrite("{}_{}.png".format(tma_name, cell_type), img)
+
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Split ROI coordinates of QuPath TMA annotation by cell type (classfication)")
     parser.add_argument("--qupath_roi", default=False, help="Input QuPath annotation (GeoJSON file)")
+    parser.add_argument("--fill", action="store_true", required=False, help="Fill pixels in ROIs")
     parser.add_argument('--version', action='version', version='%(prog)s 0.1.0')
+    parser.add_argument("--all", action="store_true", required=False, help="Extracts all ROIs")
+    parser.add_argument("--img", action="store_true", required=False, help="Generates image of ROIs")
     args = parser.parse_args()
 
     if args.qupath_roi:
diff --git a/tools/qupath_roi_splitter/qupath_roi_splitter.xml b/tools/qupath_roi_splitter/qupath_roi_splitter.xml
index 7dc186569..757dfc728 100644
--- a/tools/qupath_roi_splitter/qupath_roi_splitter.xml
+++ b/tools/qupath_roi_splitter/qupath_roi_splitter.xml
@@ -1,24 +1,42 @@
-<tool id="qupath_roi_splitter" name="QuPath ROI Splitter" version="0.1.0+galaxy1">
+<tool id="qupath_roi_splitter" name="QuPath ROI Splitter" version="@VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Split ROI coordinates of QuPath TMA annotation by cell type (classification)</description>
+    <macros>
+        <token name="@VERSION@">0.2.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
     <requirements>
         <requirement type="package" version="3.0.1">geojson</requirement>
         <requirement type="package" version="1.24.2">numpy</requirement>
         <requirement type="package" version="4.7.0">opencv</requirement>
-        <requirement type="package" version="2.0.0">pandas</requirement>        
+        <requirement type="package" version="2.0.0">pandas</requirement>
     </requirements>
      <command detect_errors="exit_code"><![CDATA[
         #for $input in $input_collection
-            python3 '$__tool_directory__/qupath_roi_splitter.py' --qupath_roi '$input' &&
+            python3 '$__tool_directory__/qupath_roi_splitter.py'
+                --qupath_roi '$input'
+                $optional.fill
+                $optional.all
+                $optional.img
+             &&
         #end for
-        mkdir out &&
-        mv *.txt out/
+        mkdir out
+        && mv *.txt out/
+        && mv *.png out/
     ]]></command>
     <inputs>
         <param name="input_collection" type="data_collection" format="geojson" label="Input QuPath annotation" help="Collection containing GeoJSON files"/>
+        <section name="optional" title="Optional">
+            <param name="fill" type="boolean" truevalue="--fill" falsevalue="" checked="false" label="Fill ROIs" help="Fill pixels in ROIs"/>
+            <param name="all" type="boolean" truevalue="--all" falsevalue="" checked="false" label="Extract all" help="Extracts all ROIs"/>
+            <param name="img" type="boolean" truevalue="--img" falsevalue="" checked="false" label="Generate image" help="Generates image from ROIs"/>
+        </section>
     </inputs>
     <outputs>
         <collection name="output_txts" type="list" label="${tool.name} on ${on_string}: ROI data">
-            <discover_datasets pattern="__name_and_ext__" directory="out" visible="false" format="txt"/>
+            <discover_datasets pattern="(?P&lt;name&gt;.*\.txt)" directory="out" visible="false" ext="txt"/>
+        </collection>
+        <collection name="output_imgs" type="list" label="${tool.name} on ${on_string}: Images of ROIs">
+            <discover_datasets pattern="(?P&lt;name&gt;.*\.png)" directory="out" visible="false" ext="png"/>
         </collection>
     </outputs>
     <tests>
@@ -29,8 +47,12 @@
                     <element name="annotations_TMA_F-5.geojson" value="annotations_TMA_F-5.geojson" />
                 </collection>
             </param>
+            <section name="optional">
+                <param name="fill" value="true"/>
+                <param name="img" value="true"/>
+            </section>
             <output_collection name="output_txts" type="list" count="4">
-                <element name="F-5_Stroma">
+                <element name="F-5_Stroma.txt">
                     <assert_contents>
                         <has_text text="x"/>
                         <has_text text="y"/>
@@ -39,6 +61,13 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <output_collection name="output_imgs" type="list" count="4">
+                <element name="E-5_Tumor.png">
+                    <assert_contents>
+                        <has_size value="1309478"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
         </test>
     </tests>
     <help><![CDATA[
@@ -52,4 +81,16 @@
 
         https://github.com/npinter/ROIsplitter
     ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @misc{
+                toolsGalaxyP,
+                author = {Pinter, N, Föll, MC },
+                title = {Galaxy Proteomics Tools},
+                publisher = {GitHub}, journal = {GitHub repository},
+                year = {2024},
+                url = {https://github.com/galaxyproteomics/tools-galaxyp}
+            }
+        </citation>
+    </citations>
 </tool>
diff --git a/tools/unipept/unipept.xml b/tools/unipept/unipept.xml
index d0e5a7638..9744f0e73 100644
--- a/tools/unipept/unipept.xml
+++ b/tools/unipept/unipept.xml
@@ -1,4 +1,4 @@
-<tool id="unipept" name="Unipept" version="4.5.1">
+<tool id="unipept" name="Unipept" version="4.5.1" profile="22.05">
     <description>retrieve taxonomy for peptides</description>
     <macros>
         <xml name="equate_il">
@@ -17,10 +17,10 @@
             </param>
         </xml>
         <xml name="names">
-            <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names" >
+            <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names">
                 <help>return the names in complete taxonomic lineage</help>
             </param>
-            <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields" >
+            <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields">
                 <help>include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage</help>
             </param>
         </xml>
@@ -39,13 +39,13 @@
             </param>
         </xml>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">unipept</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="3">python</requirement>
     </requirements>
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-    <command><![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
       python '$__tool_directory__/unipept.py' 
       ## --url 'http://morty.ugent.be/api/v1' -g -M 1  
       --api=$unipept.api
@@ -106,142 +106,142 @@
       #end if
     ]]></command>
     <inputs>
-      <conditional name="unipept">
-          <param name="api" type="select" label="Unipept application" >
-              <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option>
-              <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option>
-              <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option>
-              <option value="pept2ec">pept2ec: Tryptic peptides and associated EC terms</option>
-              <option value="pept2go">pept2go: Tryptic peptides and associated GO terms</option>
-              <option value="pept2interpro">pept2interpro: Tryptic peptides and associated InterPro entries</option>
-              <option value="pept2funct">pept2funct: Tryptic peptides and associated EC and GO terms</option>
-              <option value="peptinfo">peptinfo: Tryptic peptides and associated EC and GO terms and lowest common ancestor taxonomy</option>
-          </param>
-          <when value="pept2lca">
-              <expand macro="equate_il" />
-              <expand macro="extra">
-                  <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help>
-              </expand>
-              <expand macro="names" />
-          </when>
-          <when value="pept2taxa">
-              <expand macro="equate_il" />
-              <expand macro="extra_true">
-                  <help>Return the complete lineage of each organism, and include ID fields.</help>
-              </expand>
-              <expand macro="names" />
-          </when>
-          <when value="pept2prot">
-              <expand macro="equate_il" />
-              <expand macro="extra">
-                  <help>Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids
+        <conditional name="unipept">
+            <param name="api" type="select" label="Unipept application">
+                <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option>
+                <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option>
+                <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option>
+                <option value="pept2ec">pept2ec: Tryptic peptides and associated EC terms</option>
+                <option value="pept2go">pept2go: Tryptic peptides and associated GO terms</option>
+                <option value="pept2interpro">pept2interpro: Tryptic peptides and associated InterPro entries</option>
+                <option value="pept2funct">pept2funct: Tryptic peptides and associated EC and GO terms</option>
+                <option value="peptinfo">peptinfo: Tryptic peptides and associated EC and GO terms and lowest common ancestor taxonomy</option>
+            </param>
+            <when value="pept2lca">
+                <expand macro="equate_il"/>
+                <expand macro="extra">
+                    <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help>
+                </expand>
+                <expand macro="names"/>
+            </when>
+            <when value="pept2taxa">
+                <expand macro="equate_il"/>
+                <expand macro="extra_true">
+                    <help>Return the complete lineage of each organism, and include ID fields.</help>
+                </expand>
+                <expand macro="names"/>
+            </when>
+            <when value="pept2prot">
+                <expand macro="equate_il"/>
+                <expand macro="extra">
+                    <help>Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids
                         WARNING: Huge perfomance penalty!  Only use for small number of peptides when the extra infomation is required.
                   </help>
-              </expand>
-          </when>
-          <when value="pept2ec">
-              <expand macro="equate_il" />
-              <expand macro="extra_true">
-                  <help>Return the name of the EC-number.
+                </expand>
+            </when>
+            <when value="pept2ec">
+                <expand macro="equate_il"/>
+                <expand macro="extra_true">
+                    <help>Return the name of the EC-number.
                   </help>
-              </expand>
-          </when>
-          <when value="pept2go">
-              <expand macro="equate_il" />
-              <expand macro="extra_true">
-                  <help>Return the name of the GO-term.
+                </expand>
+            </when>
+            <when value="pept2go">
+                <expand macro="equate_il"/>
+                <expand macro="extra_true">
+                    <help>Return the name of the GO-term.
                   </help>
-              </expand>
-              <expand macro="domains" />
-          </when>
-          <when value="pept2interpro">
-              <expand macro="equate_il" />
-              <expand macro="extra_true">
-                  <help>Return the name of the GO-term.
+                </expand>
+                <expand macro="domains"/>
+            </when>
+            <when value="pept2interpro">
+                <expand macro="equate_il"/>
+                <expand macro="extra_true">
+                    <help>Return the name of the GO-term.
                   </help>
-              </expand>
-              <expand macro="domains" />
-          </when>
-          <when value="pept2funct">
-              <expand macro="equate_il" />
-              <expand macro="extra_true">
-                  <help>Return the name of the  EC-number and GO-term.
+                </expand>
+                <expand macro="domains"/>
+            </when>
+            <when value="pept2funct">
+                <expand macro="equate_il"/>
+                <expand macro="extra_true">
+                    <help>Return the name of the  EC-number and GO-term.
                   </help>
-              </expand>
-              <expand macro="domains" />
-          </when>
-          <when value="peptinfo">
-              <expand macro="equate_il" />
-              <expand macro="extra_true">
-                  <help>Return the name of the  EC-number and GO-term.
+                </expand>
+                <expand macro="domains"/>
+            </when>
+            <when value="peptinfo">
+                <expand macro="equate_il"/>
+                <expand macro="extra_true">
+                    <help>Return the name of the  EC-number and GO-term.
                   </help>
-              </expand>
-              <expand macro="domains" />
-              <expand macro="names" />
-          </when>
-      </conditional>
-      <conditional name="peptide_src">
-        <param name="fmt" type="select" label="Peptides input format" >
-          <option value="proteomic">proteomics formats:  mzid, pepxml, fasta</option>
-          <option value="tabular">tabular</option>
-          <option value="fasta">fasta</option>
-          <option value="mzid">mzid</option>
-          <option value="pepxml">pepxml</option>
+                </expand>
+                <expand macro="domains"/>
+                <expand macro="names"/>
+            </when>
+        </conditional>
+        <conditional name="peptide_src">
+            <param name="fmt" type="select" label="Peptides input format">
+                <option value="proteomic">proteomics formats:  mzid, pepxml, fasta</option>
+                <option value="tabular">tabular</option>
+                <option value="fasta">fasta</option>
+                <option value="mzid">mzid</option>
+                <option value="pepxml">pepxml</option>
+            </param>
+            <when value="proteomic">
+                <param name="input" type="data" format="mzid,pepxml,fasta" label="Peptide Input"/>
+            </when>
+            <when value="tabular">
+                <param name="input_tsv" type="data" format="tabular" label="Tabular Input Containing Peptide column"/>
+                <param name="column" label="Select column with peptides" type="data_column" numerical="false" data_ref="input_tsv"/>
+            </when>
+            <when value="fasta">
+                <param name="input_fasta" type="data" format="fasta" label="Peptide Fasta Input"/>
+            </when>
+            <when value="mzid">
+                <param name="input_mzid" type="data" format="mzid" label="mzIndetML Input"/>
+            </when>
+            <when value="pepxml">
+                <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input"/>
+            </when>
+        </conditional>
+        <param name="peptide_match" type="select" label="Match input peptides by">
+            <option value="full">Match to the full input peptide</option>
+            <option value="best" selected="true">Best match to tryptic parts of the input peptide</option>
+            <option value="report">Best match to tryptic parts, add tryptic_match column</option>
+        </param>
+        <param name="unmatched_aa" type="select" label="Show tryptic_match as:">
+            <option value="default">List of matched tryptic parts</option>
+            <option value=".">peptide with unmatched AAs as .</option>
+            <option value="x">peptide with unmatched AAs as x</option>
         </param>
-        <when value="proteomic">
-          <param name="input" type="data" format="mzid,pepxml,fasta" label="Peptide Input" />
-        </when>
-        <when value="tabular">
-          <param name="input_tsv" type="data" format="tabular" label="Tabular Input Containing Peptide column" />
-          <param name="column" label="Select column with peptides" type="data_column" numerical="false" data_ref="input_tsv" />
-        </when>
-        <when value="fasta">
-          <param name="input_fasta" type="data" format="fasta" label="Peptide Fasta Input" />
-        </when>
-        <when value="mzid">
-          <param name="input_mzid" type="data" format="mzid" label="mzIndetML Input" />
-        </when>
-        <when value="pepxml">
-          <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input" />
-        </when>
-      </conditional>
-      <param name="peptide_match" type="select" label="Match input peptides by">
-          <option value="full">Match to the full input peptide</option>
-          <option value="best" selected="true">Best match to tryptic parts of the input peptide</option>
-          <option value="report">Best match to tryptic parts, add tryptic_match column</option>
-      </param> 
-      <param name="unmatched_aa" type="select" label="Show tryptic_match as:">
-          <option value="default">List of matched tryptic parts</option>
-          <option value=".">peptide with unmatched AAs as .</option>
-          <option value="x">peptide with unmatched AAs as x</option>
-      </param> 
-      <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
-       <option value="tsv" selected="true">Tabular with one line per peptide</option>
-       <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
-        <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
-        <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option>
-        <option value="ipr_tsv">Peptide InterPro entries in normalized tabular (for pept2interpro, pept2funct, and peptinfo)</option>
-        <option value="ec_tsv">Peptide EC terms in normalized tabular (for pept2ec, pept2funct, and peptinfo)</option>
-        <option value="ec_json">JSON EC Coverage Tree (for pept2ec, pep2funct, and peptinfo)</option>
-        <option value="unmatched">Unmatched peptides</option>
-      </param>
-      <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/>
+        <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
+            <option value="tsv" selected="true">Tabular with one line per peptide</option>
+            <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
+            <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
+            <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option>
+            <option value="ipr_tsv">Peptide InterPro entries in normalized tabular (for pept2interpro, pept2funct, and peptinfo)</option>
+            <option value="ec_tsv">Peptide EC terms in normalized tabular (for pept2ec, pept2funct, and peptinfo)</option>
+            <option value="ec_json">JSON EC Coverage Tree (for pept2ec, pep2funct, and peptinfo)</option>
+            <option value="unmatched">Unmatched peptides</option>
+        </param>
+        <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/>
     </inputs>
     <outputs>
-      <data name="output_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} Taxonomy json"> 
-        <filter>'json' in selected_outputs and unipept['api'] in ('pept2lca', 'pept2taxa', 'peptinfo')</filter>
-        <change_format>
-            <when input="api" value="pept2prot" format="json" />
-        </change_format>
-      </data> 
-      <data name="output_ec_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} EC json">
-        <filter>'ec_json' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
-      </data>
-      <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv"> 
-        <filter>'tsv' in selected_outputs</filter>
-        <actions>
-            <action name="comment_lines" type="metadata" default="1" />
-            <!--
+        <data name="output_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} Taxonomy json">
+            <filter>'json' in selected_outputs and unipept['api'] in ('pept2lca', 'pept2taxa', 'peptinfo')</filter>
+            <change_format>
+                <when input="api" value="pept2prot" format="json"/>
+            </change_format>
+        </data>
+        <data name="output_ec_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} EC json">
+            <filter>'ec_json' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
+        </data>
+        <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv">
+            <filter>'tsv' in selected_outputs</filter>
+            <actions>
+                <action name="comment_lines" type="metadata" default="1"/>
+                <!--
             <conditional name="unipept.api">
                 <when value="pept2funct">
                     <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names,go_terms,go_protein_counts,go_names" />
@@ -254,195 +254,194 @@
                 </when>
             </conditional>
             -->
-        </actions>
-      </data> 
-      <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv"> 
-        <filter>'csv' in selected_outputs</filter>
-      </data> 
-      <data name="output_ec_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} EC tsv"> 
-        <filter>'ec_tsv' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
-        <actions>
-            <action name="column_names" type="metadata" default="Peptide,Total Protein Count,EC Number,Protein Count,EC Name" />
-        </actions>
-      </data> 
-      <data name="output_go_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} GO tsv"> 
-        <filter>'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo')</filter>
-        <actions>
-            <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name" />
-        </actions>
-      </data> 
-      <data name="output_ipr_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} InterPro tsv"> 
-        <filter>'ipr_tsv' in selected_outputs and unipept['api'] in ('pept2interpro', 'pept2funct', 'peptinfo')</filter>
-        <actions>
-            <action name="column_names" type="metadata" default="Peptide,Total Protein Count,InterPro Code,Protein Count,InterPro Type,InterPro Name" />
-        </actions>
-      </data> 
-
-      <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched"> 
-        <filter>'unmatched' in selected_outputs</filter>
-        <actions>
-            <action name="column_names" type="metadata" default="Unmatched Peptide" />
-        </actions>
-      </data> 
+            </actions>
+        </data>
+        <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv">
+            <filter>'csv' in selected_outputs</filter>
+        </data>
+        <data name="output_ec_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} EC tsv">
+            <filter>'ec_tsv' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="Peptide,Total Protein Count,EC Number,Protein Count,EC Name"/>
+            </actions>
+        </data>
+        <data name="output_go_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} GO tsv">
+            <filter>'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo')</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name"/>
+            </actions>
+        </data>
+        <data name="output_ipr_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} InterPro tsv">
+            <filter>'ipr_tsv' in selected_outputs and unipept['api'] in ('pept2interpro', 'pept2funct', 'peptinfo')</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="Peptide,Total Protein Count,InterPro Code,Protein Count,InterPro Type,InterPro Name"/>
+            </actions>
+        </data>
+        <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched">
+            <filter>'unmatched' in selected_outputs</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="Unmatched Peptide"/>
+            </actions>
+        </data>
     </outputs>
     <tests>
-      <!-- Test-1 -->
-      <test>
-        <param name="api" value="pept2lca"/>
-        <param name="fmt" value="tabular"/>
-        <param name="input_tsv" value="tryptic.tsv"/>
-        <param name="column" value="2"/>
-        <param name="extra" value="True"/>
-        <param name="names" value="True"/>
-        <param name="selected_outputs" value="tsv,unmatched"/>
-        <output name="output_tsv">
-            <assert_contents>
-              <has_text text="Homininae" />
-            </assert_contents>
-        </output>
-        <output name="output_unmatched">
-            <assert_contents>
-              <has_text text="QTAMAV" />
-            </assert_contents>
-        </output>
-      </test>
-      <!-- Test-2 -->
-      <test>
-        <param name="api" value="pept2lca"/>
-        <param name="fmt" value="fasta"/>
-        <param name="input_fasta" value="peptide.fa"/>
-        <param name="equate_il" value="True"/>
-        <param name="extra" value="True"/>
-        <param name="names" value="True"/>
-        <param name="selected_outputs" value="json,tsv"/>
-        <output name="output_json">
-            <assert_contents>
-              <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV" />
-            </assert_contents>
-        </output>
-        <output name="output_tsv">
-            <assert_contents>
-              <has_text text="9606" />
-              <has_text text="9596" />
-            </assert_contents>
-        </output>
-      </test>
-      <!-- Test-3 -->
-      <test>
-        <param name="api" value="pept2taxa"/>
-        <param name="fmt" value="fasta"/>
-        <param name="input_fasta" value="peptide.fa"/>
-        <param name="equate_il" value="True"/>
-        <param name="extra" value="False"/>
-        <param name="names" value="False"/>
-        <param name="selected_outputs" value="tsv"/>
-        <output name="output_tsv">
-            <assert_contents>
-              <has_text text="sapiens" />
-              <has_text text="troglodytes" />
-            </assert_contents>
-        </output>
-      </test>
-      <!-- Test-4 -->
-      <test>
-        <param name="api" value="pept2funct"/>
-        <param name="fmt" value="tabular"/>
-        <param name="input_tsv" value="input.tsv"/>
-        <param name="column" value="2"/>
-        <param name="extra" value="True"/>
-        <param name="names" value="True"/>
-        <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
-        <output name="output_tsv">
-            <assert_contents>
-              <has_text text="GO:0004802" />
-              <has_text text="2.2.1.1" />
-              <has_text text="IPR005475" />
-            </assert_contents>
-        </output>
-        <output name="output_ec_tsv">
-            <assert_contents>
-              <has_text text="2.2.1.1" />
-            </assert_contents>
-        </output>
-        <output name="output_go_tsv">
-            <assert_contents>
-              <has_text text="GO:0004802" />
-            </assert_contents>
-        </output>
-        <output name="output_ipr_tsv">
-            <assert_contents>
-              <has_text text="IPR005475" />
-            </assert_contents>
-        </output>
-      </test>
-      <!-- Test-5 -->
-      <test>
-        <param name="api" value="pept2funct"/>
-        <param name="fmt" value="tabular"/>
-        <param name="input_tsv" value="input.tsv"/>
-        <param name="column" value="2"/>
-        <param name="extra" value="True"/>
-        <param name="names" value="True"/>
-        <param name="peptide_match" value="full"/>
-        <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
-        <output name="output_tsv">
-            <assert_contents>
-              <has_text text="GO:0004802" />
-              <has_text text="2.2.1.1" />
-              <has_text text="IPR005475" />
-              <has_text_matching expression="FAPLLEEYKAEDWVQK\t0" />
-            </assert_contents>
-        </output>
-        <output name="output_ec_tsv">
-            <assert_contents>
-              <has_text text="2.2.1.1" />
-            </assert_contents>
-        </output>
-        <output name="output_go_tsv">
-            <assert_contents>
-              <has_text text="GO:0004802" />
-            </assert_contents>
-        </output>
-        <output name="output_ipr_tsv">
-            <assert_contents>
-              <has_text text="IPR005475" />
-            </assert_contents>
-        </output>
-      </test>
-      <!-- Test-6 -->
-      <test>
-        <param name="api" value="pept2funct"/>
-        <param name="fmt" value="tabular"/>
-        <param name="input_tsv" value="input.tsv"/>
-        <param name="column" value="2"/>
-        <param name="extra" value="True"/>
-        <param name="names" value="True"/>
-        <param name="peptide_match" value="report"/>
-        <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
-        <output name="output_tsv">
-            <assert_contents>
-              <has_text text="GO:0004802" />
-              <has_text text="2.2.1.1" />
-              <has_text text="IPR005475" />
-              <has_text_matching expression="FAPLLEEYKAEDWVQK\tAEDWVQK\t1" />
-            </assert_contents>
-        </output>
-        <output name="output_ec_tsv">
-            <assert_contents>
-              <has_text text="2.2.1.1" />
-            </assert_contents>
-        </output>
-        <output name="output_go_tsv">
-            <assert_contents>
-              <has_text text="GO:0004802" />
-            </assert_contents>
-        </output>
-        <output name="output_ipr_tsv">
-            <assert_contents>
-              <has_text text="IPR005475" />
-            </assert_contents>
-        </output>
-      </test>
+        <!-- Test-1 -->
+        <test expect_num_outputs="2">
+            <param name="api" value="pept2lca"/>
+            <param name="fmt" value="tabular"/>
+            <param name="input_tsv" value="tryptic.tsv"/>
+            <param name="column" value="2"/>
+            <param name="extra" value="True"/>
+            <param name="names" value="True"/>
+            <param name="selected_outputs" value="tsv,unmatched"/>
+            <output name="output_tsv">
+                <assert_contents>
+                    <has_text text="Homininae"/>
+                </assert_contents>
+            </output>
+            <output name="output_unmatched">
+                <assert_contents>
+                    <has_text text="QTAMAV"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test-2 -->
+        <test expect_num_outputs="2">
+            <param name="api" value="pept2lca"/>
+            <param name="fmt" value="fasta"/>
+            <param name="input_fasta" value="peptide.fa"/>
+            <param name="equate_il" value="True"/>
+            <param name="extra" value="True"/>
+            <param name="names" value="True"/>
+            <param name="selected_outputs" value="json,tsv"/>
+            <output name="output_json">
+                <assert_contents>
+                    <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV"/>
+                </assert_contents>
+            </output>
+            <output name="output_tsv">
+                <assert_contents>
+                    <has_text text="9606"/>
+                    <has_text text="9596"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test-3 -->
+        <test expect_num_outputs="1">
+            <param name="api" value="pept2taxa"/>
+            <param name="fmt" value="fasta"/>
+            <param name="input_fasta" value="peptide.fa"/>
+            <param name="equate_il" value="True"/>
+            <param name="extra" value="False"/>
+            <param name="names" value="False"/>
+            <param name="selected_outputs" value="tsv"/>
+            <output name="output_tsv">
+                <assert_contents>
+                    <has_text text="sapiens"/>
+                    <has_text text="Cercocebus"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test-4 -->
+        <test expect_num_outputs="5">
+            <param name="api" value="pept2funct"/>
+            <param name="fmt" value="tabular"/>
+            <param name="input_tsv" value="input.tsv"/>
+            <param name="column" value="2"/>
+            <param name="extra" value="True"/>
+            <param name="names" value="True"/>
+            <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
+            <output name="output_tsv">
+                <assert_contents>
+                    <has_text text="GO:0004802"/>
+                    <has_text text="2.2.1.1"/>
+                    <has_text text="IPR005475"/>
+                </assert_contents>
+            </output>
+            <output name="output_ec_tsv">
+                <assert_contents>
+                    <has_text text="2.2.1.1"/>
+                </assert_contents>
+            </output>
+            <output name="output_go_tsv">
+                <assert_contents>
+                    <has_text text="GO:0004802"/>
+                </assert_contents>
+            </output>
+            <output name="output_ipr_tsv">
+                <assert_contents>
+                    <has_text text="IPR005475"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test-5 -->
+        <test expect_num_outputs="5">
+            <param name="api" value="pept2funct"/>
+            <param name="fmt" value="tabular"/>
+            <param name="input_tsv" value="input.tsv"/>
+            <param name="column" value="2"/>
+            <param name="extra" value="True"/>
+            <param name="names" value="True"/>
+            <param name="peptide_match" value="full"/>
+            <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
+            <output name="output_tsv">
+                <assert_contents>
+                    <has_text text="GO:0004802"/>
+                    <has_text text="2.2.1.1"/>
+                    <has_text text="IPR005475"/>
+                    <has_text_matching expression="FAPLLEEYKAEDWVQK\t0"/>
+                </assert_contents>
+            </output>
+            <output name="output_ec_tsv">
+                <assert_contents>
+                    <has_text text="2.2.1.1"/>
+                </assert_contents>
+            </output>
+            <output name="output_go_tsv">
+                <assert_contents>
+                    <has_text text="GO:0004802"/>
+                </assert_contents>
+            </output>
+            <output name="output_ipr_tsv">
+                <assert_contents>
+                    <has_text text="IPR005475"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test-6 -->
+        <test expect_num_outputs="5">
+            <param name="api" value="pept2funct"/>
+            <param name="fmt" value="tabular"/>
+            <param name="input_tsv" value="input.tsv"/>
+            <param name="column" value="2"/>
+            <param name="extra" value="True"/>
+            <param name="names" value="True"/>
+            <param name="peptide_match" value="report"/>
+            <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
+            <output name="output_tsv">
+                <assert_contents>
+                    <has_text text="GO:0004802"/>
+                    <has_text text="2.2.1.1"/>
+                    <has_text text="IPR005475"/>
+                    <has_text_matching expression="AAEGGLSR\tAAEGGLSR\t6"/>
+                </assert_contents>
+            </output>
+            <output name="output_ec_tsv">
+                <assert_contents>
+                    <has_text text="2.2.1.1"/>
+                </assert_contents>
+            </output>
+            <output name="output_go_tsv">
+                <assert_contents>
+                    <has_text text="GO:0004802"/>
+                </assert_contents>
+            </output>
+            <output name="output_ipr_tsv">
+                <assert_contents>
+                    <has_text text="IPR005475"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
     **Unipept** 
@@ -637,8 +636,7 @@
     DOI: 10.1002/pmic.201400361
 
     ]]></help>
-  <citations>
-    <citation type="doi">doi:10.1002/pmic.201400361</citation>
-  </citations>
-
+    <citations>
+        <citation type="doi">doi:10.1002/pmic.201400361</citation>
+    </citations>
 </tool>