From 04e4ffd50b1be71e3e764a2545503b1c30342df5 Mon Sep 17 00:00:00 2001 From: Reid Wagner Date: Tue, 7 May 2024 17:06:27 -0500 Subject: [PATCH] Final edits for release. --- tools/fragpipe/.shed.yml | 11 + tools/fragpipe/fragpipe.xml | 369 +++-- tools/fragpipe/genericize_db.py | 18 + tools/fragpipe/macros.xml | 1453 +++++++---------- tools/fragpipe/msfragger_macros.xml | 1070 ++++-------- .../test-data/default/outputs/workflow.txt | 308 ++++ tools/fragpipe/test-data/default/test.fasta | 72 + .../fragpipe/test-data/default/test.manifest | 2 + tools/fragpipe/test-data/default/test.mzML | 721 ++++++++ .../test-data/tmt11/outputs/workflow.txt | 309 ++++ .../fragpipe/test-data/tmt11/test.annotation | 11 + tools/fragpipe/test-data/tmt11/test.fasta | 193 +++ tools/fragpipe/test-data/tmt11/test.manifest | 1 + tools/fragpipe/test-data/tmt11/test.mzML | 716 ++++++++ tools/fragpipe/workflows/Default.workflow | 311 ++++ tools/fragpipe/workflows/LFQ-MBR.workflow | 312 ++++ .../workflows/Nonspecific-HLA.workflow | 312 ++++ tools/fragpipe/workflows/Open.workflow | 312 ++++ tools/fragpipe/workflows/TMT10.workflow | 312 ++++ tools/fragpipe/workflows/TMT11.workflow | 312 ++++ 20 files changed, 5363 insertions(+), 1762 deletions(-) create mode 100644 tools/fragpipe/.shed.yml create mode 100644 tools/fragpipe/genericize_db.py create mode 100644 tools/fragpipe/test-data/default/outputs/workflow.txt create mode 100644 tools/fragpipe/test-data/default/test.fasta create mode 100644 tools/fragpipe/test-data/default/test.manifest create mode 100644 tools/fragpipe/test-data/default/test.mzML create mode 100644 tools/fragpipe/test-data/tmt11/outputs/workflow.txt create mode 100644 tools/fragpipe/test-data/tmt11/test.annotation create mode 100644 tools/fragpipe/test-data/tmt11/test.fasta create mode 100644 tools/fragpipe/test-data/tmt11/test.manifest create mode 100644 tools/fragpipe/test-data/tmt11/test.mzML create mode 100755 tools/fragpipe/workflows/Default.workflow create mode 100755 tools/fragpipe/workflows/LFQ-MBR.workflow create mode 100755 tools/fragpipe/workflows/Nonspecific-HLA.workflow create mode 100755 tools/fragpipe/workflows/Open.workflow create mode 100755 tools/fragpipe/workflows/TMT10.workflow create mode 100755 tools/fragpipe/workflows/TMT11.workflow diff --git a/tools/fragpipe/.shed.yml b/tools/fragpipe/.shed.yml new file mode 100644 index 000000000..7009d37c3 --- /dev/null +++ b/tools/fragpipe/.shed.yml @@ -0,0 +1,11 @@ +owner: galaxyp +name: fragpipe +categories: +- Proteomics +description: Data analysis for mass spectrometry-based proteomics. +homepage_url: https://fragpipe.nesvilab.org/ +long_description: | + FragPipe is a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. + FragPipe uses MSFragger - an ultrafast proteomic search engine suitable for both conventional and “open” (wide precursor mass tolerance) peptide identification. +remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe +type: unrestricted diff --git a/tools/fragpipe/fragpipe.xml b/tools/fragpipe/fragpipe.xml index f4740af88..322f37c00 100644 --- a/tools/fragpipe/fragpipe.xml +++ b/tools/fragpipe/fragpipe.xml @@ -1,65 +1,103 @@ - - (BETA) data analysis for mass spectrometry-based proteomics + + Data analysis for mass spectrometry-based proteomics macros.xml fragpipe --help | grep 'FragPipe v' + + /psm.tsv to outputs/_psm.tsv - && ls -ltr `find * -type f` && cd outputs && ln -s log_*.txt log.txt - && for f in psm.tsv ion.tsv peptide.tsv protein.tsv; do n=0; for i in `find * -name \${f}`; do d=\${i%/*}; echo "\${n} \${d} \${i}"; if [[ \$n == 0 ]]; then awk 'NR==1{printf("Experiment\t%s\n",\$0);}' \$i > all_\${f}; fi; awk 'NR>1{printf("'"\${d}"'\t%s\n",\$0);}' \$i >> all_\${f}; t=`echo \${i} | tr '/' '.'`; mv \${i} \${t}; n=\$((n+1)); done; done - && ( if [[ -d tmt-report ]]; then for i in `find tmt-report -type f -name '*tsv'`; do cp \${i} \${i/_??.tsv/.tsv}; done; fi ) - && cd .. - && ls -ltr `find * -type f` - #else - ls -ltr `find * -type f` + #if $output_options and 'combined_outputs' in $output_options + && mkdir combined_outputs + && for f in combined*tsv; do [[ -e $\{f} || continue ]]; mv \${f} combined_outputs; done + #end if + && for f in psm.tsv ion.tsv peptide.tsv protein.tsv; do n=0; for i in `find * -name \${f}`; do d=\${i%/*}; echo "\${n} \${d} \${i}"; if [[ \$n == 0 ]]; then awk 'NR==1{printf("Experiment\t%s\n",\$0);}' \$i > concat_\${f}; fi; awk 'NR>1{printf("'"\${d}"'\t%s\n",\$0);}' \$i >> concat_\${f}; t=`echo \${i} | tr '/' '.'`; mv \${i} \${t}; n=\$((n+1)); done; done #end if ]]> + + + + + + + - - + + + + + + + + + + + + + + + + + + - - - - not workflow_only + + + workflow_only or (output_options and 'workflow' in output_options) + + + not workflow_only and output_options and 'log' in output_options + + + not workflow_only - + + not workflow_only and output_options and 'combined_outputs' in output_options + - - not workflow_only + + + + not workflow_only and concatenated_outputs in output_options - - not workflow_only + + not workflow_only and concatenated_outputs in output_options - --> - - not workflow_only + + not workflow_only and concatenated_outputs in output_options - - not workflow_only + + not workflow_only and concatenated_outputs in output_options - - not workflow_only + + + + (not workflow_only) and ('Open' in wf['workflow_name']) - - not workflow_only + + (not workflow_only) and ('Open' in wf['workflow_name']) - - - not workflow_only and scan['scans']['by_sample'] == 'yes' and len(scan['scans']) > 1 - - - not workflow_only and ('glyco' in wf['workflow_name'] or 'Open' in wf['workflow_name'] or 'Mass' in wf['workflow_name']) - - - not workflow_only and ('glyco' in wf['workflow_name'] or 'Open' in wf['workflow_name'] or 'Mass' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - - not workflow_only and ('TMT' in wf['workflow_name'] or 'TRAQ' in wf['workflow_name'] or 'SLC' in wf['workflow_name']) - - + + + (not workflow_only) and ('TMT' in wf['workflow_name']) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + generic|' to avoid being misinterpreted by Philosopher. +# + +import sys +import re + +input_db_file = sys.argv[1] +output_db_file = sys.argv[2] + +with open(input_db_file) as f: + input_db = f.readlines() + +subbed_lines = [re.sub(r'^>(?!sp\||tr\||db\||AP_|NP_|YP_|XP_|WP_|ENSP|UniRef|nxp|generic)', '>generic|', l) for l in input_db] + +with open(output_db_file, 'w') as f: + f.writelines(subbed_lines) diff --git a/tools/fragpipe/macros.xml b/tools/fragpipe/macros.xml index 0e0ca8a42..14811e56e 100644 --- a/tools/fragpipe/macros.xml +++ b/tools/fragpipe/macros.xml @@ -1,114 +1,89 @@ msfragger_macros.xml - 19.1 - dev8 + 20.0 + dev14 fragpipe - - - 10.1038/s41592-020-0912-y - 10.1038/nmeth.4256 - 10.1038/s41467-020-17921-y - 10.1038/s41592-020-0967-9 - 10.1021/acs.jproteome.0c00119 - 10.1074/mcp.TIR120.002216 - 10.1074/mcp.TIR120.002048 - 10.1016/j.mcpro.2021.100077 - 10.1021/acs.jproteome.0c00544 - 10.1038/nmeth.3255 - - - ['126', '127N', '127C', '128N', '128C', '129N', '129C', '130N', '130C', '131N', '131C', '132N', '132C', '133N', '133C', '134N', '134C', '135N'] - - + ['114', '115', '116', '117'] + ['113', '114', '115', '116', '117', '118', '119', '121'] - - - Only use letters, numbers, and chars: _- - [a-zA-Z0-9_-]+ - - - - - - - - - - - - - - - - - - - + - + - + - + - + + + + > fp.manifest && - #end for - #end for - #else - #set $scandir = $scan.scans.sample_name - #silent $i_names.append($scandir) - mkdir -p '$scandir' && - #for $sf in $scan.scans.inputs - #set $i_name = $ln_name($sf) - ln -s '$sf' '${scandir}/${i_name}' && - echo -e "\$CWD/${scandir}/${i_name}\t${scandir}\t\t${scan.scans.data_type}" >> fp.manifest && - #end for + #import os + #set CWD = os.getcwd() + CWD=`pwd | sed 's/\//\\\\\//g'` && + + mkdir -p scans && + #if $wf.workflow_name == "TMT10" or $wf.workflow_name == "TMT11" + cp -p '$wf.annotation' 'scans/annotation.txt' && #end if + + sed "s/^/\$CWD\/scans\//" $manifest > fp.manifest && + + #for $sf in $scan.inputs + #set $i_name = $ln_name($sf) + ln -s '$sf' 'scans/${i_name}' && + #end for + ]]> + - - + + + + + - - + + - - - -
- - -
- - - - + - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- -
- - - - - - +
- +
- - - +
- +
- - - - - - -
- -
- + + + +
- +
+ + + + + - - - - - - +
- +
- - - - - - - - - - - -
- -
- - -
- -
- - - - - - - - - - - - - -
- - -
- - - - - - - + + + + + + - -
- - -
- - - + + + - -
- - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + +
+ +
+ + + + + + + 0 #set $msfragger_dict['table.var-mods'] = '; '.join([$re.sub('^(.*,)(\d)$','\\1True,\\2',m) for m in $vmods]) -*# +#end if #for $k in $msfragger_dict.keys() #set $kv = $k + '=' + str($msfragger_dict[$k]) ## # $kv ## print this just for debugging #set $wfk = 'msfragger.' + $k #set $wfdict[$wfk] = str($msfragger_dict[$k]) #end for -#end if -#if $wf.workflow_name == 'history' -#pass -#elif $wf.workflow_name == 'Default' @VALIDATION@ -#elif $wf.workflow_name == 'Open' -@VALIDATION@ -#elif $wf.workflow_name == 'Mass-Offset-CommonPTMs' -@VALIDATION@ -#* Add these as they get worked on -#elif $wf.workflow_name == 'Nonspecific-HLA' -#elif $wf.workflow_name == 'Nonspecific-peptidome' -#elif $wf.workflow_name == 'DIA_DIA-Umpire_SpecLib_Quant' -#elif $wf.workflow_name == 'DIA_SpecLib_Quant' -#elif $wf.workflow_name == 'LFQ-MBR' -#elif $wf.workflow_name == 'LFQ-phospho' -#elif $wf.workflow_name == 'Labile_ADP-ribosylation' -#elif $wf.workflow_name == 'Labile_phospho' -#elif $wf.workflow_name == 'SILAC3-phospho' -#elif $wf.workflow_name == 'SILAC3' -#elif $wf.workflow_name == 'SLC-ABPP' -#elif $wf.workflow_name == 'TMT10-MS3-phospho' -#elif $wf.workflow_name == 'TMT10-MS3' -#elif $wf.workflow_name == 'TMT10-acetyl' -#elif $wf.workflow_name == 'TMT10-bridge' -#elif $wf.workflow_name == 'TMT10-phospho-bridge' -#elif $wf.workflow_name == 'TMT10-phospho' -#elif $wf.workflow_name == 'TMT10-ubiquitin' -#elif $wf.workflow_name == 'TMT10' -#elif $wf.workflow_name == 'TMT11' -#elif $wf.workflow_name == 'TMT16-MS3' -#elif $wf.workflow_name == 'TMT16-acetyl' -#elif $wf.workflow_name == 'TMT16-phospho' -#elif $wf.workflow_name == 'TMT16' -#elif $wf.workflow_name == 'XRNAX-MassOffset' -#elif $wf.workflow_name == 'glyco-N-HCD' -#elif $wf.workflow_name == 'glyco-N-Hybrid' -#elif $wf.workflow_name == 'glyco-N-LFQ' -#elif $wf.workflow_name == 'glyco-N-TMT' -#elif $wf.workflow_name == 'glyco-N-open-HCD' -#elif $wf.workflow_name == 'glyco-N-open-Hybrid' -#elif $wf.workflow_name == 'glyco-O-HCD' -#elif $wf.workflow_name == 'glyco-O-Hybrid' -#elif $wf.workflow_name == 'glyco-O-open-HCD' -#elif $wf.workflow_name == 'glyco-O-open-Hybrid' -#elif $wf.workflow_name == 'iTRAQ4' -#elif $wf.workflow_name == 'ipIAA-ABPP' -#elif $wf.workflow_name == 'isoDTB-ABPP' -#elif $wf.workflow_name == 'isoTOP-ABPP' -*# -#end if +@PTM_SHEPHERD@ +@LABEL_FREE_QUANTIFICATION@ + #for $comment in $comments $comment #end for + +## Populate the workflow with configuration dictionary entries populated by tool params. #for $k in sorted($wfdict.keys()) #set $kv = $k + '=' + str($wfdict[$k]) $kv @@ -450,46 +298,59 @@ $kv #slurp]]> + fp.workflow; +sed "s#^database.db-path.*#\database.db-path=\$DB#" $workflow_configfile > fp.workflow; ]]> - - - - - - - - - - - - - - - - - - - -
- - -
- + -
+
- - +
- -
+ + + + + + + + + +
+ + +
+ + + + + + + + + + +
@@ -499,10 +360,78 @@ sed "s#^database.db-path.*#\database.db-path=\$DB#" $workflow_configfile > fp.wo + + + + + + +
- -
+ + + + + + + + + + + + + + +
+ + + + + + +
+ + + + + + + + + + +
@@ -511,7 +440,9 @@ sed "s#^database.db-path.*#\database.db-path=\$DB#" $workflow_configfile > fp.wo + @@ -520,14 +451,17 @@ sed "s#^database.db-path.*#\database.db-path=\$DB#" $workflow_configfile > fp.wo + - + + @@ -535,45 +469,27 @@ sed "s#^database.db-path.*#\database.db-path=\$DB#" $workflow_configfile > fp.wo
- + - + +
@@ -581,10 +497,8 @@ sed "s#^database.db-path.*#\database.db-path=\$DB#" $workflow_configfile > fp.wo - -
+ +
@@ -592,32 +506,30 @@ ptmshepherd.output_extended - - - + -
-
+
- - - + + + - - - + + + - + - - + +
-
- + - +
+ -->
+ + - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - -
- - - - - - - - -
- -
- - - - - + @RE_AA@,@RE_FLOAT@ + @RE_EXCLUDEMOD@(;\s*@RE_EXCLUDEMOD@)* + -
+
@@ -941,26 +674,21 @@ Protein Inference: # ProteinProphet v5.2 -
+
- - + + - - - - - - - + + -
+
-
+
@@ -969,51 +697,68 @@ Protein Inference: # ProteinProphet v5.2
-
+
-
- - - - - - - - - - - - - - - - - + + + + - - - - -
-
- - + +
+ + + + + +
+ + +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ + ^\s*@RE_EXCLUDEMODS@\s*$ - - + +
-
+
@@ -1021,6 +766,8 @@ Protein Inference: # ProteinProphet v5.2
+ + - - - - + + +
@@ -1143,24 +897,16 @@ Protein Inference: # ProteinProphet v5.2 -
+
- - - - - - - - ^\d? + ^TMT-\d? - - + Virtual or specify a Reference sample tag: pool or Bridge - - - + + + @@ -1170,25 +916,35 @@ Protein Inference: # ProteinProphet v5.2 + - - - - - - - - - - - site localization confidence thresholdr: -1 for global, 0 for search engine determined, above 0 for probability - - + + + + + + + + + + + + + + + + + + site localization confidence thresholdr: -1 for global, 0 for search engine determined, above 0 for probability + + + + @@ -1198,18 +954,21 @@ Protein Inference: # ProteinProphet v5.2 - - - + - - + + - + + ^(none|[a-zA-Z]+\|)$ + @@ -1230,14 +989,11 @@ Protein Inference: # ProteinProphet v5.2 - - - + @@ -1251,141 +1007,148 @@ Protein Inference: # ProteinProphet v5.2
+ + - -
- - - - - - - - - -
- - - - - - - -
- - -
+ + +MSFragger is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: http://msfragger-upgrader.nesvilab.org/upgrader/MSFragger-LICENSE.pdf. This license provides with non-exclusive, non-transferable right to use MSFragger solely for academic research, non-commercial or educational purposes. I agree to be subject to the terms and conditions of this license. I understand that to use MSFragger for other purposes requires a commercial license from the University of Michigan Office of Tech Transfer. + + +IonQuant is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: https://msfragger.arsci.com/ionquant/IonQuant%20Academic%20Use%20License%2005162022.pdf + + +I agree to the terms of Thermo (c) Raw File Reader License Agreement: http://msfragger-upgrader.nesvilab.org/upgrader/RawFileRdr_License_Agreement_RevA.pdf + + +I agree to the terms of Bruker SDK library distribution conditions: http://msfragger-upgrader.nesvilab.org/upgrader/redist.txt + + +@MSFRAGGER_LICENSE_AGREEMENT@ +@IONQUANT_LICENSE_AGREEMENT@ +@THERMO_RAW_READER_LICENSE_AGREEMENT@ +@BRUKER_LICENSE_AGREEMENT@ + + + + + + value == True +
+@IONQUANT_LICENSE_AGREEMENT@ +

+@THERMO_RAW_READER_LICENSE_AGREEMENT@ +

+@BRUKER_LICENSE_AGREEMENT@ + ]]> + - + + + 10.1038/s41592-020-0912-y + 10.1038/nmeth.4256 + 10.1038/s41467-020-17921-y + 10.1038/s41592-020-0967-9 + 10.1021/acs.jproteome.0c00119 + 10.1074/mcp.TIR120.002216 + 10.1074/mcp.TIR120.002048 + 10.1016/j.mcpro.2021.100077 + 10.1021/acs.jproteome.0c00544 + 10.1038/nmeth.3255 + + + diff --git a/tools/fragpipe/msfragger_macros.xml b/tools/fragpipe/msfragger_macros.xml index 9f7334e1e..8501a9340 100644 --- a/tools/fragpipe/msfragger_macros.xml +++ b/tools/fragpipe/msfragger_macros.xml @@ -1,12 +1,6 @@ - 3.5 - - - - - - + #import re #def identifier_or_name($input1) @@ -20,7 +14,7 @@ #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fas|fasta|imzml|mzml|mzxml|raw)$','', $re.sub('.*/','', $name1.rstrip('.gz')))) #return $name_clean #end def -#def ln_name($ds) +#def ln_name($ds) #set $ext = '' #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml') #set $ext = ".mzML" @@ -33,54 +27,24 @@ #else if $ds.is_of_type('fasta') #set $ext = ".fasta" #end if - #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext) + #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext) #return $name #end def #set $i_names = [] #set $db_name = None + [a-zA-Z][a-zA-Z0-9_-]* - - - - - - - - - - #for $si in $i_names - '$si' - #end for - - - - - - - #set $db_name = $ln_name($database_name) - - - - - + + @@ -90,8 +54,9 @@ + - + @@ -101,64 +66,22 @@ + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - - - - - - - - - - - + + @@ -167,19 +90,9 @@ + - - - - - - - - - - - - + @@ -189,164 +102,13 @@ + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #slurp -## Search Tolerances - -#if $prefix.search_tolerances.precursor.precursor_mass_units == 'Da' - #set $msfragger_dict['precursor_mass_units'] = 0 -#elif $prefix.search_tolerances.precursor.precursor_mass_units == 'ppm' - #set $msfragger_dict['precursor_mass_units'] = 1 -#end if -#if $prefix.search_tolerances.precursor.precursor_mass_units != 'default' - #if $prefix.search_tolerances.precursor.precursor_mass_lower is not None - #set $msfragger_dict['precursor_mass_lower'] = $prefix.search_tolerances.precursor.precursor_mass_lower - #end if - #if $prefix.search_tolerances.precursor.precursor_mass_upper is not None - #set $msfragger_dict['precursor_mass_upper'] = $prefix.search_tolerances.precursor.precursor_mass_upper - #end if -#end if - -#if $prefix.search_tolerances.precursor_true.precursor_true_units == 'Da' - #set $msfragger_dict['precursor_true_units'] = 0 -#elif $prefix.search_tolerances.precursor_true.precursor_true_units == 'ppm' - #set $msfragger_dict['precursor_true_units'] = 1 -#end if -#if $prefix.search_tolerances.precursor_true.precursor_true_units != 'default' - #if str($prefix.search_tolerances.precursor_true.precursor_true_tolerance).strip() - #set $msfragger_dict['precursor_true_tolerance'] = $prefix.search_tolerances.precursor_true.precursor_true_tolerance - #end if -#end if - -#if $prefix.search_tolerances.fragment.fragment_mass_units == 'Da' - #set $msfragger_dict['fragment_mass_units'] = 0 -#elif $prefix.search_tolerances.fragment.fragment_mass_units == 'ppm' - #set $msfragger_dict['fragment_mass_units'] = 1 -#end if -#if $prefix.search_tolerances.fragment.fragment_mass_units != 'default' - #if $prefix.search_tolerances.fragment.fragment_mass_tolerance is not None - #set $msfragger_dict['fragment_mass_tolerance'] = $prefix.search_tolerances.fragment.fragment_mass_tolerance - #end if -#end if - -#if $prefix.search_tolerances.isotope_error is not None - #set $msfragger_dict['isotope_error'] = $prefix.search_tolerances.isotope_error -#end if -#if $prefix.search_tolerances.data_type is not None - #set $msfragger_dict['data_type'] = $prefix.search_tolerances.data_type -#end if -#if $prefix.search_tolerances.calibrate_mass is not None - #set $msfragger_dict['calibrate_mass'] = $prefix.search_tolerances.calibrate_mass -#end if - -## digest parameters -##enzyme_1 -#if $prefix.digestion.digest.search_enzyme_name is not None - #set $msfragger_dict['search_enzyme_name_1'] = $prefix.digestion.digest.search_enzyme_name - #set $msfragger_dict['misc.fragger.enzyme-dropdown-1'] = $prefix.digestion.digest.search_enzyme_name -#end if -#if $prefix.digestion.digest.search_enzyme_cut is not None - #set $msfragger_dict['search_enzyme_cut_1'] = $prefix.digestion.digest.search_enzyme_cut -#end if -#if $prefix.digestion.digest.search_enzyme_nocut is not None - #set $msfragger_dict['search_enzyme_nocut_1'] = $prefix.digestion.digest.search_enzyme_nocut -#end if -#if $prefix.digestion.allowed_missed_cleavage is not None - #set $msfragger_dict['allowed_missed_cleavage_1'] = $prefix.digestion.allowed_missed_cleavage -#end if -#if $prefix.digestion.search_enzyme_sense is not None - #set $msfragger_dict['search_enzyme_sense_1'] = $prefix.digestion.search_enzyme_sense -#end if -##enzyme_2 -#if $prefix.digestion.enzyme2.digest2 == 'yes' - #if $prefix.digestion.enzyme2.digest.search_enzyme_name is not None - #set $msfragger_dict['search_enzyme_name_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_name - #set $msfragger_dict['misc.fragger.enzyme-dropdown-2'] = $prefix.digestion.enzyme2.digest.search_enzyme_name - #end if - #if $prefix.digestion.enzyme2.digest.search_enzyme_cut is not None - #set $msfragger_dict['search_enzyme_cut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_cut - #end if - #if $prefix.digestion.enzyme2.digest.search_enzyme_nocut is not None - #set $msfragger_dict['search_enzyme_nocut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_nocut - #end if - #if $prefix.digestion.enzyme2.allowed_missed_cleavage is not None - #set $msfragger_dict['allowed_missed_cleavage_2'] = $prefix.digestion.enzyme2.allowed_missed_cleavage - #end if - #if $prefix.digestion.enzyme2.search_enzyme_sense is not None - #set $msfragger_dict['search_enzyme_sense_2'] = $prefix.digestion.enzyme2.search_enzyme_sense - #end if -#else - #set $msfragger_dict['search_enzyme_sense_2'] = 'C' -#end if -#if $prefix.digestion.num_enzyme_termini is not None - #set $msfragger_dict['num_enzyme_termini'] = $prefix.digestion.num_enzyme_termini -#end if -#if $prefix.digestion.digest_min_length is not None - #set $msfragger_dict['digest_min_length'] = $prefix.digestion.digest_min_length -#end if -#if $prefix.digestion.digest_max_length is not None - #set $msfragger_dict['digest_max_length'] = $prefix.digestion.digest_max_length -#end if -#if $prefix.digestion.digest_mass_range_min is not None - #set $msfragger_dict['misc.fragger.digest-mass-lo'] = $prefix.digestion.digest_mass_range_min - ## #set $msfragger_dict['digest_mass_range'] = $prefix.digestion.digest_mass_range_min -#end if -#if $prefix.digestion.digest_mass_range_min is not None - #set $msfragger_dict['misc.fragger.digest-mass-hi'] = $prefix.digestion.digest_mass_range_max - ## #set $msfragger_dict['digest_mass_range'] = $prefix.digestion.digest_mass_range_max -#end if -#slurp - - #slurp - -#slurp - - +
@@ -362,9 +124,8 @@ - - - + + @@ -376,11 +137,11 @@ - - @@ -397,13 +158,12 @@ help="Fragment mass tolerance (window is +/- this value) Default: 20"/> - - + - + Isotope correction for MS/MS events triggered on isotopic peaks. 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. @@ -418,25 +178,65 @@ Isotope correction for MS/MS events triggered on isotopic peaks. Should be set t - - - - -
- + - +## Search Tolerances + +#if $prefix.search_tolerances.precursor.precursor_mass_units == 'Da' + #set $msfragger_dict['precursor_mass_units'] = 0 +#elif $prefix.search_tolerances.precursor.precursor_mass_units == 'ppm' + #set $msfragger_dict['precursor_mass_units'] = 1 +#end if +#if $prefix.search_tolerances.precursor.precursor_mass_units != 'default' + #if $prefix.search_tolerances.precursor.precursor_mass_lower != '' + #set $msfragger_dict['precursor_mass_lower'] = $prefix.search_tolerances.precursor.precursor_mass_lower + #end if + #if $prefix.search_tolerances.precursor.precursor_mass_upper != '' + #set $msfragger_dict['precursor_mass_upper'] = $prefix.search_tolerances.precursor.precursor_mass_upper + #end if +#end if + +#if $prefix.search_tolerances.precursor_true.precursor_true_units == 'Da' + #set $msfragger_dict['precursor_true_units'] = 0 +#elif $prefix.search_tolerances.precursor_true.precursor_true_units == 'ppm' + #set $msfragger_dict['precursor_true_units'] = 1 +#end if +#if $prefix.search_tolerances.precursor_true.precursor_true_units != 'default' + #if $prefix.search_tolerances.precursor_true.precursor_true_tolerance != '' + #set $msfragger_dict['precursor_true_tolerance'] = $prefix.search_tolerances.precursor_true.precursor_true_tolerance + #end if +#end if + +#if $prefix.search_tolerances.fragment.fragment_mass_units == 'Da' + #set $msfragger_dict['fragment_mass_units'] = 0 +#elif $prefix.search_tolerances.fragment.fragment_mass_units == 'ppm' + #set $msfragger_dict['fragment_mass_units'] = 1 +#end if +#if $prefix.search_tolerances.fragment.fragment_mass_units != 'default' + #if $prefix.search_tolerances.fragment.fragment_mass_tolerance != '' + #set $msfragger_dict['fragment_mass_tolerance'] = $prefix.search_tolerances.fragment.fragment_mass_tolerance + #end if +#end if + +#if $prefix.search_tolerances.isotope_error != 'None' + #set $msfragger_dict['isotope_error'] = $prefix.search_tolerances.isotope_error +#end if +#if $prefix.search_tolerances.calibrate_mass != 'None' + #set $msfragger_dict['calibrate_mass'] = $prefix.search_tolerances.calibrate_mass +#end if +#slurp - - - + @@ -514,7 +314,7 @@ Isotope correction for MS/MS events triggered on isotopic peaks. Should be set t - @@ -540,9 +340,9 @@ Isotope correction for MS/MS events triggered on isotopic peaks. Should be set t - - @@ -551,11 +351,53 @@ Isotope correction for MS/MS events triggered on isotopic peaks. Should be set t
- +## digest parameters +##enzyme_1 +#set $msfragger_dict['search_enzyme_name_1'] = $prefix.digestion.digest.search_enzyme_name +#set $msfragger_dict['misc.fragger.enzyme-dropdown-1'] = $prefix.digestion.digest.search_enzyme_name +#set $msfragger_dict['search_enzyme_cut_1'] = $prefix.digestion.digest.search_enzyme_cut +#set $msfragger_dict['search_enzyme_nocut_1'] = $prefix.digestion.digest.search_enzyme_nocut +#if $prefix.digestion.allowed_missed_cleavage != '' + #set $msfragger_dict['allowed_missed_cleavage_1'] = $prefix.digestion.allowed_missed_cleavage +#end if +#if $prefix.digestion.search_enzyme_sense != 'None' + #set $msfragger_dict['search_enzyme_sense_1'] = $prefix.digestion.search_enzyme_sense +#end if +##enzyme_2 +#if $prefix.digestion.enzyme2.digest2 == 'yes' + #set $msfragger_dict['search_enzyme_name_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_name + #set $msfragger_dict['misc.fragger.enzyme-dropdown-2'] = $prefix.digestion.enzyme2.digest.search_enzyme_name + #set $msfragger_dict['search_enzyme_cut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_cut + #set $msfragger_dict['search_enzyme_nocut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_nocut + #if $prefix.digestion.enzyme2.allowed_missed_cleavage != '' + #set $msfragger_dict['allowed_missed_cleavage_2'] = $prefix.digestion.enzyme2.allowed_missed_cleavage + #end if + #if $prefix.digestion.enzyme2.search_enzyme_sense != 'None' + #set $msfragger_dict['search_enzyme_sense_2'] = $prefix.digestion.enzyme2.search_enzyme_sense + #end if +#else + #set $msfragger_dict['search_enzyme_sense_2'] = 'C' +#end if +#if $prefix.digestion.num_enzyme_termini != 'None' + #set $msfragger_dict['num_enzyme_termini'] = $prefix.digestion.num_enzyme_termini +#end if +#if $prefix.digestion.digest_min_length != '' + #set $msfragger_dict['digest_min_length'] = $prefix.digestion.digest_min_length +#end if +#if $prefix.digestion.digest_max_length != '' + #set $msfragger_dict['digest_max_length'] = $prefix.digestion.digest_max_length +#end if +#if $prefix.digestion.digest_mass_range_min != '' + #set $msfragger_dict['misc.fragger.digest-mass-lo'] = $prefix.digestion.digest_mass_range_min +#end if +#if $prefix.digestion.digest_mass_range_min != '' + #set $msfragger_dict['misc.fragger.digest-mass-hi'] = $prefix.digestion.digest_mass_range_max +#end if +#slurp - + @@ -565,30 +407,24 @@ Isotope correction for MS/MS events triggered on isotopic peaks. Should be set t [+-]?\d+(\.\d*)? - ([A-Z]+|(c[A-Z*])+|(n[A-Z*])+|\[^|\]^) + ([A-Z]+|(c[A-Z*])+|(n[\^A-Z*])+|\[\^|\]) @RE_FLOAT@,@RE_AA@,\d @RE_MOD@(;\s*@RE_MOD@)*
- - - - - @@ -617,19 +450,14 @@ Example (M oxidation and N-terminal acetylation): - -
#slurp ## Variable Modification Parameters -#if $prefix.variable_modification.clip_nTerm_M - #set $msfragger_dict['clip_nTerm_M'] = $prefix.variable_modification.clip_nTerm_M -#end if -#if $prefix.variable_modification.max_variable_mods_per_peptide +#if $prefix.variable_modification.max_variable_mods_per_peptide != '' #set $msfragger_dict['max_variable_mods_per_peptide'] = $prefix.variable_modification.max_variable_mods_per_peptide #end if ##maximum of 7 mods - amino acid codes, * for any amino acid, [ and ] specifies protein termini, n and c specifies peptide termini @@ -639,38 +467,36 @@ Example (M oxidation and N-terminal acetylation): ##variable_mod_03=-17.0265 nQnC ##variable_mod_04=-18.0106 nE ## -#if $prefix.variable_modification.use_all_mods_in_first_search +#if $prefix.variable_modification.use_all_mods_in_first_search != 'None' #set $msfragger_dict['use_all_mods_in_first_search'] = $prefix.variable_modification.use_all_mods_in_first_search #end if -#if $prefix.variable_modification.allow_multiple_variable_mods_on_residue - #set $msfragger_dict['allow_multiple_variable_mods_on_residue'] = $prefix.variable_modification.allow_multiple_variable_mods_on_residue +#if $prefix.variable_modification.clip_nTerm_M != 'None' + #set $msfragger_dict['clip_nTerm_M'] = $prefix.variable_modification.clip_nTerm_M #end if -#if $prefix.variable_modification.max_variable_mods_per_mod is not None - #set $msfragger_dict['max_variable_mods_per_mod'] = $prefix.variable_modification.max_variable_mods_per_mod +#if $prefix.variable_modification.allow_multiple_variable_mods_on_residue != 'None' + #set $msfragger_dict['allow_multiple_variable_mods_on_residue'] = $prefix.variable_modification.allow_multiple_variable_mods_on_residue #end if -#if $prefix.variable_modification.max_variable_mods_combinations is not None +#if $prefix.variable_modification.max_variable_mods_combinations != "None" #set $msfragger_dict['max_variable_mods_combinations'] = $prefix.variable_modification.max_variable_mods_combinations #end if -#set $vmods =[] -#if $prefix.variable_modification.variable_mods_select - ## $prefix.variable_modification.variable_mods_select +#set $vmods = [] +#if $prefix.variable_modification.variable_mods_select != 'None' #set $vmods = [x.replace(' ',',') for x in str($prefix.variable_modification.variable_mods_select).split(',')] #end if -#if $prefix.variable_modification.variable_mods - ## $prefix.variable_modification.variable_mods +#if $prefix.variable_modification.variable_mods != '' #set $vmods += [x.strip() for x in str($prefix.variable_modification.variable_mods).split(';')] #end if #slurp
- - - - @@ -728,110 +554,110 @@ Example (M oxidation and N-terminal acetylation): #slurp #set $fmods = {} -#if $prefix.static_modification.add_Cterm_peptide is not None +#if $prefix.static_modification.add_Cterm_peptide != '' #set $fmods['Cterm_peptide'] = $prefix.static_modification.add_Cterm_peptide #end if -#if $prefix.static_modification.add_Nterm_peptide is not None +#if $prefix.static_modification.add_Nterm_peptide != '' #set $fmods['Nterm_peptide'] = $prefix.static_modification.add_Nterm_peptide #end if -#if $prefix.static_modification.add_Cterm_protein is not None +#if $prefix.static_modification.add_Cterm_protein != '' #set $fmods['Cterm_protein'] = $prefix.static_modification.add_Cterm_protein #end if -#if $prefix.static_modification.add_Nterm_protein is not None +#if $prefix.static_modification.add_Nterm_protein != '' #set $fmods['Nterm_protein'] = $prefix.static_modification.add_Nterm_protein #end if -#if $prefix.static_modification.add_G_glycine is not None +#if $prefix.static_modification.add_G_glycine != '' #set $fmods['G_glycine'] = $prefix.static_modification.add_G_glycine #end if -#if $prefix.static_modification.add_A_alanine is not None +#if $prefix.static_modification.add_A_alanine != '' #set $fmods['A_alanine'] = $prefix.static_modification.add_A_alanine #end if -#if $prefix.static_modification.add_S_serine is not None +#if $prefix.static_modification.add_S_serine != '' #set $fmods['S_serine'] = $prefix.static_modification.add_S_serine #end if -#if $prefix.static_modification.add_P_proline is not None +#if $prefix.static_modification.add_P_proline != '' #set $fmods['P_proline'] = $prefix.static_modification.add_P_proline #end if -#if $prefix.static_modification.add_V_valine is not None +#if $prefix.static_modification.add_V_valine != '' #set $fmods['V_valine'] = $prefix.static_modification.add_V_valine #end if -#if $prefix.static_modification.add_T_threonine is not None +#if $prefix.static_modification.add_T_threonine != '' #set $fmods['T_threonine'] = $prefix.static_modification.add_T_threonine #end if -#if $prefix.static_modification.add_C_cysteine is not None +#if $prefix.static_modification.add_C_cysteine != '' #set $fmods['C_cysteine'] = $prefix.static_modification.add_C_cysteine #end if -#if $prefix.static_modification.add_L_leucine is not None +#if $prefix.static_modification.add_L_leucine != '' #set $fmods['L_leucine'] = $prefix.static_modification.add_L_leucine #end if -#if $prefix.static_modification.add_I_isoleucine is not None +#if $prefix.static_modification.add_I_isoleucine != '' #set $fmods['I_isoleucine'] = $prefix.static_modification.add_I_isoleucine #end if -#if $prefix.static_modification.add_N_asparagine is not None +#if $prefix.static_modification.add_N_asparagine != '' #set $fmods['N_asparagine'] = $prefix.static_modification.add_N_asparagine #end if -#if $prefix.static_modification.add_D_aspartic_acid is not None +#if $prefix.static_modification.add_D_aspartic_acid != '' #set $fmods['D_aspartic_acid'] = $prefix.static_modification.add_D_aspartic_acid #end if -#if $prefix.static_modification.add_Q_glutamine is not None +#if $prefix.static_modification.add_Q_glutamine != '' #set $fmods['Q_glutamine'] = $prefix.static_modification.add_Q_glutamine #end if -#if $prefix.static_modification.add_K_lysine is not None +#if $prefix.static_modification.add_K_lysine != '' #set $fmods['K_lysine'] = $prefix.static_modification.add_K_lysine #end if -#if $prefix.static_modification.add_E_glutamic_acid is not None +#if $prefix.static_modification.add_E_glutamic_acid != '' #set $fmods['E_glutamic_acid'] = $prefix.static_modification.add_E_glutamic_acid #end if -#if $prefix.static_modification.add_M_methionine is not None +#if $prefix.static_modification.add_M_methionine != '' #set $fmods['M_methionine'] = $prefix.static_modification.add_M_methionine #end if -#if $prefix.static_modification.add_H_histidine is not None +#if $prefix.static_modification.add_H_histidine != '' #set $fmods['H_histidine'] = $prefix.static_modification.add_H_histidine #end if -#if $prefix.static_modification.add_F_phenylalanine is not None +#if $prefix.static_modification.add_F_phenylalanine != '' #set $fmods['F_phenylalanine'] = $prefix.static_modification.add_F_phenylalanine #end if -#if $prefix.static_modification.add_R_arginine is not None +#if $prefix.static_modification.add_R_arginine != '' #set $fmods['R_arginine'] = $prefix.static_modification.add_R_arginine #end if -#if $prefix.static_modification.add_Y_tyrosine is not None +#if $prefix.static_modification.add_Y_tyrosine != '' #set $fmods['Y_tyrosine'] = $prefix.static_modification.add_Y_tyrosine #end if -#if $prefix.static_modification.add_W_tryptophan is not None +#if $prefix.static_modification.add_W_tryptophan != '' #set $fmods['W_tryptophan'] = $prefix.static_modification.add_W_tryptophan #end if #* -#if $prefix.static_modification.add_B_user_amino_acid is not None +#if $prefix.static_modification.add_B_user_amino_acid != '' #set $fmods['B_user_amino_acid'] = $prefix.static_modification.add_B_user_amino_acid #end if -#if $prefix.static_modification.add_J_user_amino_acid is not None +#if $prefix.static_modification.add_J_user_amino_acid != '' #set $fmods['J_user_amino_acid'] = $prefix.static_modification.add_J_user_amino_acid #end if -#if $prefix.static_modification.add_O_user_amino_acid is not None +#if $prefix.static_modification.add_O_user_amino_acid != '' #set $fmods['O_user_amino_acid'] = $prefix.static_modification.add_O_user_amino_acid #end if -#if $prefix.static_modification.add_U_user_amino_acid is not None +#if $prefix.static_modification.add_U_user_amino_acid != '' #set $fmods['U_user_amino_acid'] = $prefix.static_modification.add_U_user_amino_acid #end if -#if $prefix.static_modification.add_X_user_amino_acid is not None +#if $prefix.static_modification.add_X_user_amino_acid != '' #set $fmods['X_user_amino_acid'] = $prefix.static_modification.add_X_user_amino_acid #end if -#if $prefix.static_modification.add_Z_user_amino_acid is not None +#if $prefix.static_modification.add_Z_user_amino_acid != '' #set $fmods['Z_user_amino_acid'] = $prefix.static_modification.add_Z_user_amino_acid #end if *# #slurp - +
- - - - - + + + + + @@ -878,54 +706,54 @@ Example (M oxidation and N-terminal acetylation): #slurp ## spectral processing -#if $prefix.spectrum_processing.precursor_mass_mode +#if $prefix.spectrum_processing.precursor_mass_mode != 'None' #set $msfragger_dict['precursor_mass_mode'] = $prefix.spectrum_processing.precursor_mass_mode #end if -#if str($prefix.spectrum_processing.minimum_peaks).strip() +#if $prefix.spectrum_processing.minimum_peaks != '' #set $msfragger_dict['minimum_peaks'] = $prefix.spectrum_processing.minimum_peaks #end if -#if str($prefix.spectrum_processing.use_topN_peaks).strip() +#if $prefix.spectrum_processing.use_topN_peaks != '' #set $msfragger_dict['use_topN_peaks'] = $prefix.spectrum_processing.use_topN_peaks #end if -#if str($prefix.spectrum_processing.minimum_ratio).strip() +#if $prefix.spectrum_processing.minimum_ratio != '' #set $msfragger_dict['minimum_ratio'] = $prefix.spectrum_processing.minimum_ratio #end if #if $prefix.spectrum_processing.precursor.override_charge != 'default' #set $msfragger_dict['override_charge'] = $prefix.spectrum_processing.precursor.override_charge #end if #if $prefix.spectrum_processing.precursor.override_charge == 'true' - #if $prefix.spectrum_processing.precursor.precursor_charge_min is not None + #if $prefix.spectrum_processing.precursor.precursor_charge_min != '' #set $msfragger_dict['misc.fragger.precursor-charge-lo'] = $prefix.spectrum_processing.precursor.precursor_charge_min #end if - #if $prefix.spectrum_processing.precursor.precursor_charge_max is not None + #if $prefix.spectrum_processing.precursor.precursor_charge_max != '' #set $msfragger_dict['misc.fragger.precursor-charge-hi'] = $prefix.spectrum_processing.precursor.precursor_charge_max #end if #end if -#if $prefix.spectrum_processing.clear.clear_mz_range_min is not None +#if $prefix.spectrum_processing.clear.clear_mz_range_min != '' #set $msfragger_dict['misc.fragger.clear-mz-lo'] = $prefix.spectrum_processing.clear.clear_mz_range_min #end if -#if $prefix.spectrum_processing.clear.clear_mz_range_max is not None +#if $prefix.spectrum_processing.clear.clear_mz_range_max != '' #set $msfragger_dict['misc.fragger.clear-mz-hi'] = $prefix.spectrum_processing.clear.clear_mz_range_max #end if -#if $prefix.spectrum_processing.remove_precursor_peak +#if $prefix.spectrum_processing.remove_precursor_peak != 'None' #set $msfragger_dict['remove_precursor_peak'] = $prefix.spectrum_processing.remove_precursor_peak #end if -#if $prefix.spectrum_processing.remove_precursor_range_min is not None +#if $prefix.spectrum_processing.remove_precursor_range_min != '' #set $msfragger_dict['misc.fragger.remove-precursor-range-lo'] = $prefix.spectrum_processing.remove_precursor_range_min -#end if -#if $prefix.spectrum_processing.remove_precursor_range_max is not None +#end if +#if $prefix.spectrum_processing.remove_precursor_range_max != '' #set $msfragger_dict['misc.fragger.remove-precursor-range-hi'] = $prefix.spectrum_processing.remove_precursor_range_max -#end if +#end if -#if $prefix.spectrum_processing.intensity_transform is not None +#if $prefix.spectrum_processing.intensity_transform != 'None' #set $msfragger_dict['intensity_transform'] = $prefix.spectrum_processing.intensity_transform #end if -#if $prefix.spectrum_processing.check_spectral_files is not None - #set $msfragger_dict['check_spectral_files'] = $prefix.spectrum_processing.check_spectral_files -#end if +#set $msfragger_dict['check_spectral_files'] = $prefix.spectrum_processing.check_spectral_files +#set $msfragger_dict['require_precursor'] = $prefix.spectrum_processing.require_precursor +#set $msfragger_dict['reuse_dia_fragment_peaks'] = $prefix.spectrum_processing.reuse_dia_fragment_peaks -#if $prefix.spectrum_processing.activation_types is not None +#if $prefix.spectrum_processing.activation_types != 'None' #set $msfragger_dict['activation_types'] = $prefix.spectrum_processing.activation_types #end if #slurp @@ -937,10 +765,10 @@ Example (M oxidation and N-terminal acetylation): - - Track top N unmodified peptide results separately from main results internally for boosting features. + Track top N unmodified peptide results separately from main results internally for boosting features. Should be set to a number greater than output_report_topN if zero bin boosting is desired. Default: 0 @@ -951,69 +779,59 @@ Example (M oxidation and N-terminal acetylation): - - Useful for recovery of modified peptides near C-terminal in open search. + Useful for recovery of modified peptides near C-terminal in open search. Should be set to 0 (disabled) otherwise. Default: 0 -
#slurp ##open search parameters -#if $prefix.open_search.mass_diff_to_variable_mod is not None +#if $prefix.open_search.mass_diff_to_variable_mod != 'None' #set $msfragger_dict['mass_diff_to_variable_mod'] = $prefix.open_search.mass_diff_to_variable_mod #end if -#if str($prefix.open_search.track_zero_topN).strip() +#if $prefix.open_search.track_zero_topN != '' #set $msfragger_dict['track_zero_topN'] = $prefix.open_search.track_zero_topN #end if -#if str($prefix.open_search.zero_bin_accept_expect).strip() +#if $prefix.open_search.zero_bin_accept_expect != '' #set $msfragger_dict['zero_bin_accept_expect'] = $prefix.open_search.zero_bin_accept_expect #end if -#if str($prefix.open_search.zero_bin_mult_expect).strip() +#if $prefix.open_search.zero_bin_mult_expect != '' #set $msfragger_dict['zero_bin_mult_expect'] = $prefix.open_search.zero_bin_mult_expect #end if -#if str($prefix.open_search.add_topN_complementary).strip() +#if $prefix.open_search.add_topN_complementary != '' #set $msfragger_dict['add_topN_complementary'] = $prefix.open_search.add_topN_complementary #end if -#if $prefix.open_search.localize_delta_mass is not None - #set $msfragger_dict['localize_delta_mass'] = $prefix.open_search.localize_delta_mass -#end if -## TEST THIS +#set $msfragger_dict['localize_delta_mass'] = $prefix.open_search.localize_delta_mass #set $msfragger_dict['delta_mass_exclude_ranges'] = '(' + ','.join([str($prefix.open_search.delta_mass_exclude_ranges_min),str($prefix.open_search.delta_mass_exclude_ranges_max)]) + ')' #slurp
- - - - - - + - - + - + - - + @@ -1023,40 +841,42 @@ Example (M oxidation and N-terminal acetylation):
#slurp -#* TODO -#if $prefix.modeling_output.output_report_topN is not None - #set $msfragger_dict['output_report_topN'] = $prefix.modeling_output.output_report_topN -#end if -#if $prefix.modeling_output.report_alternative_proteins is not None - #set $msfragger_dict['report_alternative_proteins'] = $prefix.modeling_output.report_alternative_proteins -#end if -#if prefix.modeling_output.output_max_expect is not None - #set $msfragger_dict['output_max_expect'] = $prefix.modeling_output.output_max_expect -#end if ##Peak matching -#if $prefix.modeling_output.min_fragments_modelling is not None +#if $prefix.modeling_output.min_fragments_modelling != '' #set $msfragger_dict['min_fragments_modelling'] = $prefix.modeling_output.min_fragments_modelling #end if -#if $prefix.modeling_output.min_matched_fragments is not None +#if $prefix.modeling_output.min_matched_fragments != '' #set $msfragger_dict['min_matched_fragments'] = $prefix.modeling_output.min_matched_fragments #end if -#if $prefix.modeling_output.max_fragment_charge is not None +#if $prefix.modeling_output.max_fragment_charge != '' #set $msfragger_dict['max_fragment_charge'] = $prefix.modeling_output.max_fragment_charge #end if -#set $msfragger_dict['deisotope'] = $prefix.modeling_output.deisotope +#if $prefix.modeling_output.deisotope != 'None' + #set $msfragger_dict['deisotope'] = $prefix.modeling_output.deisotope +#end if #set $msfragger_dict['deneutralloss'] = $prefix.modeling_output.deneutralloss -#set $msfragger_dict['fragment_ion_series'] = $prefix.modeling_output.fragment_ion_series -*# +#if $prefix.modeling_output.fragment_ion_series != 'None' + #set $msfragger_dict['fragment_ion_series'] = $prefix.modeling_output.fragment_ion_series +#end if #slurp + - +
- - - - + + + + + + + + + + + - + + @@ -1068,16 +888,19 @@ Example (M oxidation and N-terminal acetylation): #set $msfragger_dict['restrict_deltamass_to'] = $prefix.mass_offsets.restrict_deltamass_to #slurp - +
- - + + + @@ -1092,120 +915,92 @@ Example (M oxidation and N-terminal acetylation): - + + - +
#slurp #set $msfragger_dict['labile_search_mode'] = $prefix.glyco_labile.labile_search_mode #if $prefix.glyco_labile.labile_search_mode != 'off' #set $msfragger_dict['diagnostic_intensity_filter'] = $prefix.glyco_labile.diagnostic_intensity_filter + #set $msfragger_dict['min_sequence_matches'] = $prefix.glyco_labile.min_sequence_matches #set $msfragger_dict['diagnostic_fragments'] = $prefix.glyco_labile.diagnostic_fragments + +#if $prefix.glyco_labile.remainder_fragment_masses != '' #set $msfragger_dict['remainder_fragment_masses'] = $prefix.glyco_labile.remainder_fragment_masses +#end if #set $msfragger_dict['Y_type_masses'] = $prefix.glyco_labile.Y_type_masses #end if #slurp - - - - - - - - + + +
+ + + + + + + + + + + + + + + + + + + + +
- -#if 'mgf' in $output_format: -write_calibrated_mgf = 1 + + + +#set $msfragger_dict['output_format'] = $prefix.advanced_options.output_format.__str__.replace(',mgf','').replace(',','_') +#if $prefix.advanced_options.output_report_topN != '' + #set $msfragger_dict['output_report_topN'] = $prefix.advanced_options.output_report_topN +#end if +#set $msfragger_dict['report_alternative_proteins'] = $prefix.advanced_options.report_alternative_proteins +#if $prefix.advanced_options.output_max_expect != '' + #set $msfragger_dict['output_max_expect'] = $prefix.advanced_options.output_max_expect +#end if +#set $msfragger_dict['write_calibrated_mzml'] = $prefix.advanced_options.write_calibrated_mzml +#set $msfragger_dict['write_uncalibrated_mgf'] = $prefix.advanced_options.write_uncalibrated_mgf +#if $prefix.advanced_options.group_variable != 'None' + #set $msfragger_dict['group_variable'] = $prefix.advanced_options.group_variable #end if -output_file_extension = pepXML -output_format = $output_format.__str__.replace(',mgf','').replace(',','_') - #slurp -#import re -${indent}decoy_prefix${op} $decoy_prefix -@DEFAULT_CONFIG@ -## Variable Modification Parameters -@VARIABLE_MODIFICATION@ -@GLYCO_LABILE@ -@MASS_OFFSETS@ -@SPECTRUM_PROCESSING@ -@OPEN_SEARCH@ -@MODELING_OUTPUT@ -@STATIC_MODIFICATION@ -#slurp - + #slurp #import re #set $msfragger_dict = {} -@DEFAULT_DICT@ +@SEARCH_TOLERANCES@ ## Variable Modification Parameters sets $vmods @VARIABLE_MODIFICATION@ ## Static Modification Parameters sets $fmods @STATIC_MODIFICATION@ -#* -*# @GLYCO_LABILE@ @MASS_OFFSETS@ @SPECTRUM_PROCESSING@ @OPEN_SEARCH@ @MODELING_OUTPUT@ +@MSFRAGGER_ADVANCED_OPTIONS@ #slurp - -#set $prefix = $cfg -#if $prefix.default_config != 'history' -#set $indent = '' -#set $op = ' =' -@FRAGGER_PARAMS@ -#end if -@OUTPUT_FORMAT@ - - - $param_file && -#if $cfg.default_config == 'history': -grep -v '^database_name' '$cfg.msfragger_params' | grep -v '^output_format' >> $param_file && -echo "output_format = $output_format.__str__.replace(',mgf','').replace(',','_')" >> $param_file && -#else -cat $fragger_params >> '$param_file' && -#end if -]]> - - > "$logfile" -&& ls -ltr -#if 'pepxml' in $output_format: -&& cat *.pepXML > $output_pepxml -#end if -#if 'tsv' in $output_format: -&& cat *.tsv > $output_tsv -#end if -#if 'pin' in $output_format: -&& cat *.pin > $output_pin -#end if -## #if 'mgf' in $output_format: -## && cat *.mgf > $output_mgf -## #end if -]]> - - - scannum,precursor_neutral_mass,retention_time,charge,hit_rank,peptide,peptide_prev_aa,peptide_next_aa,protein,num_matched_ions,tot_num_ions,calc_neutral_pep_mass,massdiff,num_tol_term,num_missed_cleavages,modification_info,hyperscore,nextscore,expectscore,best_locs,score_without_delta_mass,best_score_with_delta_mass,second_best_score_with_delta_mass,delta_score,alternative_proteins - - SpecId,Label,ScanNr,ExpMass,retentiontime,rank,abs_ppm,isotope_errors,log10_evalue,hyperscore,delta_hyperscore,matched_ion_num,peptide_length,ntt,nmc,charge_1,charge_2,charge_3,charge_4,charge_5,charge_6,charge_7,Peptide,Proteins + 0/114.03169/193.99802/291.97492/406.00661 0 203.07937 406.15874 568.21156 730.26438 892.3172 349.137279 0 203.07937 406.15874 568.21156 730.26438 892.3172 349.137279 @@ -1220,7 +1015,7 @@ msfragger -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g fragger.params 0 203.07937 406.15874 568.21156 730.26438 349.137279 0 203.07937 406.15874 568.21156 730.26438 892.3172 349.137279 - + 0/541.06111 0/79.966331 -105.0248 -89.0299 -33.9877 -32.0085 -30.0106 -18.0106 -17.0265 -2.0157 -1.007825 -0.984 0 0.984 3.9949 12.0 13.9793 14.0157 15.9949 19.9898 21.969392 21.9819 23.95806 26.0157 27.9949 28.0313 28.990164 29.9742 31.972071 31.9898 37.9469 37.955882 42.0106 42.047 43.0058 43.9898 44.985078 47.9847 53.9193 57.0215 58.0055 61.9135 61.921774 68.026215 70.041865 71.0371 79.9568 79.9663 86.000394 100.016 114.042927 119.004099 128.095 146.0579 156.1011 162.0528 173.051 176.0321 178.0477 183.035399 189.046 203.0794 204.1878 210.1984 228.111 229.014009 238.2297 301.9865 340.1006 349.1373 365.1322 365.1322 406.1587 541.06111 @@ -1230,255 +1025,4 @@ msfragger -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g fragger.params 0 203.07937 349.137279 406.15874 552.216649 568.21156 714.269469 2026.68694 2188.73976 2350.79258 730.26438 876.322289 892.3172 1038.375109 1054.37002 1200.427929 1216.42284 1362.480749 1378.47566 1524.533569 1458.44199 1540.52848 1686.586389 1702.5813 1864.63412 1095.39657 1241.454479 1257.44939 1403.507299 1694.602716 1549.565208 1840.660625 1548.544807 1419.50221 1565.560119 1856.655536 2147.750952 1710.597627 1581.55503 1727.612939 2018.708356 1872.650447 1298.47594 1444.533849 1589.571357 1460.52876 1606.586669 1897.682086 1752.644578 1751.624177 1622.58158 1768.639489 2059.734906 2350.830322 1914.697398 2205.792815 2496.888231 2351.850724 2642.94614 1913.676997 2204.772413 1784.6344 1930.692309 2221.787726 2076.750218 2075.729817 1946.68722 2092.745129 2237.782637 1501.55531 1647.613219 1938.708636 1793.671128 1663.60813 1809.666039 2100.761456 2391.856872 1955.723948 1954.703547 2245.798963 1825.66095 1971.718859 2262.814276 2553.909692 2117.776768 2408.872185 2263.834677 2116.756367 2407.851783 1987.71377 2133.771679 2424.867096 2715.962512 3007.057929 2279.829588 2570.925005 2425.887497 2716.982914 3008.07833 3299.173747 2571.945406 2863.040823 2278.809187 2569.904603 2861.00002 2586.919916 2878.015332 2311.81941 2457.877319 2619.930139 1704.63468 1850.692589 2141.788006 2432.883422 1996.750498 1866.6875 2012.745409 2158.803318 2157.782917 2028.74032 2174.798229 2465.893646 2756.989062 3048.084479 2320.856138 2611.951555 2466.914047 2190.79314 2336.851049 2627.946466 2482.908958 2774.004375 3065.099791 2481.888557 2772.983973 3064.07939 2352.84596 2789.999286 3081.094702 2644.961778 2936.057195 2791.019687 3082.115104 2643.941377 2935.036793 3226.13221 3517.227626 2952.052106 2805.994197 2676.9516 3114.104926 3405.200342 1907.71405 2053.771959 2069.76687 2215.824779 2393.87251 2539.930419 2555.92533 2701.983239 3575.269489 2717.97815 2864.036059 3155.131476 4028.417725 3009.073567 2110.79342 2256.851329 2272.84624 2434.89906 2580.956969 2759.0047 2921.05752 3083.11034 3229.168249 3448.24253 2313.87279 2459.930699 2475.92561 2621.983519 2800.03125 2946.089159 3432.247619 0 146.0579 203.0794 349.1373 365.1322 406.1587 494.1748 511.1901 527.185 568.2116 609.2381 640.2327 656.2276 673.2429 689.2378 697.2541 698.2746 714.2695 730.2644 755.296 771.2909 786.2906 802.2855 812.3175 818.2804 835.2957 843.312 851.2907 859.307 876.3223 892.3172 917.3488 933.3438 974.3703 989.37 997.3486 1005.3649 1006.3853 1013.3435 1015.3969 1021.3598 1038.3751 1046.3914 1054.37 1079.4017 1095.3966 1136.4231 1151.4228 1159.4014 1183.4126 1192.4493 1200.4279 1216.4228 1218.4762 1224.4391 1241.4545 1257.4494 1282.481 1298.4759 1307.5127 1321.4542 1339.5025 1354.5021 1362.4807 1378.4757 1386.492 1395.5287 1403.5073 1444.5338 1460.5288 1501.5553 1524.5336 1532.5499 1540.5285 1548.5448 1557.5815 1565.5601 1573.5764 1574.5968 1589.5713 1606.5867 1622.5816 1647.6132 1663.6081 1686.5864 1704.6347 1727.6129 1752.6446 1768.6395 1825.6609 1831.6239 1866.6875 1905.6607 1913.677 1914.6974 1930.6923 1971.7189 1987.7138 2018.7083 2028.7403 2092.7451 2117.7768 2133.7717 2174.7982 2190.7931 2213.7714 2352.846 2393.8725 2498.9039 2555.9253 2701.9832 0 146.0579 203.0794 349.1373 365.1322 406.1587 494.1748 511.1901 527.185 568.2116 609.2381 640.2327 656.2276 673.2429 689.2378 697.2541 698.2746 714.2695 730.2644 755.296 771.2909 786.2906 802.2855 812.3175 818.2804 835.2957 843.312 851.2907 859.307 876.3223 892.3172 917.3488 933.3438 974.3703 989.37 997.3486 1005.3649 1006.3853 1013.3435 1015.3969 1021.3598 1038.3751 1046.3914 1054.37 1079.4017 1095.3966 1136.4231 1151.4228 1159.4014 1183.4126 1192.4493 1200.4279 1216.4228 1218.4762 1224.4391 1241.4545 1257.4494 1282.481 1298.4759 1307.5127 1321.4542 1339.5025 1354.5021 1362.4807 1378.4757 1386.492 1395.5287 1403.5073 1444.5338 1460.5288 1501.5553 1524.5336 1532.5499 1540.5285 1548.5448 1557.5815 1565.5601 1573.5764 1574.5968 1589.5713 1606.5867 1622.5816 1647.6132 1663.6081 1686.5864 1704.6347 1727.6129 1752.6446 1768.6395 1825.6609 1831.6239 1866.6875 1905.6607 1913.677 1914.6974 1930.6923 1971.7189 1987.7138 2018.7083 2028.7403 2092.7451 2117.7768 2133.7717 2174.7982 2190.7931 2213.7714 2352.846 2393.8725 2498.9039 2555.9253 2701.9832 - - - - -MSFragger is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software. -http://msfragger-upgrader.nesvilab.org/upgrader/MSFragger-LICENSE.pdf -This license provides with non-exclusive, non-transferable right to use MSFragger solely for academic research, non-commercial or educational purposes. I agree to be subject to the terms and conditions of this license. I understand that to use MSFragger for other purposes requires a commercial license from the University of Michigan Office of Tech Transfer. - - -I agree to the terms of Thermo (c) Raw File Reader License Agreement. -http://msfragger-upgrader.nesvilab.org/upgrader/RawFileRdr_License_Agreement_RevA.pdf - - -I agree to the terms of Bruker SDK library distribution conditions. -http://msfragger-upgrader.nesvilab.org/upgrader/redist.txt - - -@MSFRAGGER_LICENSE_AGREEMENT@ -@THERMO_RAW_READER_LICENSE_AGREEMENT@ -@BRUKER_LICENSE_AGREEMENT@ - - - - - @MSFRAGGER_LICENSE_AGREEMENT@ - - - -#if not $msfragger_license_agreements - echo "You must agree to the MSFragger license!"; exit 1; -#end if - - - doi:10.1038/nmeth.4256 - doi:10.1038/s41467-020-17921-y - doi:10.1038/s41592-020-0967-9 - diff --git a/tools/fragpipe/test-data/default/outputs/workflow.txt b/tools/fragpipe/test-data/default/outputs/workflow.txt new file mode 100644 index 000000000..53441d8cb --- /dev/null +++ b/tools/fragpipe/test-data/default/outputs/workflow.txt @@ -0,0 +1,308 @@ +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +diann.run-dia-nn=false +diann.run-dia-plex=false +diann.run-specific-protein-q-value=false +diann.unrelated-runs=false +diann.use-predicted-spectra=true +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=false +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.light= +ionquant.locprob=0.75 +ionquant.maxlfq=1 +ionquant.mbr=1 +ionquant.mbrimtol=0.05 +ionquant.mbrmincorr=0 +ionquant.mbrrttol=1 +ionquant.mbrtoprun=10 +ionquant.medium= +ionquant.minfreq=0 +ionquant.minions=2 +ionquant.minisotopes=2 +ionquant.minscans=3 +ionquant.mztol=10 +ionquant.normalization=1 +ionquant.peptidefdr=1 +ionquant.proteinfdr=1 +ionquant.requantify=1 +ionquant.rttol=0.4 +ionquant.run-ionquant=true +ionquant.tp=0 +ionquant.uniqueness=0 +ionquant.use-labeling=false +ionquant.use-lfq=true +ionquant.writeindex=0 +msbooster.predict-rt=true +msbooster.predict-spectra=true +msbooster.run-msbooster=false +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.deisotope=1 +msfragger.delta_mass_exclude_ranges=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=50 +msfragger.digest_min_length=7 +msfragger.fragment_ion_series=b,y +msfragger.fragment_mass_tolerance=20 +msfragger.fragment_mass_units=1 +msfragger.group_variable=0 +msfragger.intensity_transform=0 +msfragger.ion_series_definitions= +msfragger.isotope_error=0/1/2/3 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=0.0 +msfragger.misc.fragger.clear-mz-lo=0.0 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=500 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50.0 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses= +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore +peptide-prophet.combine-pepxml=false +peptide-prophet.run-peptide-prophet=false +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=true +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --picked --prot 0.01 +phi-report.pep-level-summary=false +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=true +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.05 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5 +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=false +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=true +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=00.2 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=00.1 +ptmshepherd.diagmine_fragMinSpecDiff=00.1 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_mode=false +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=00.2 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=true +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=true +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=false +ptmshepherd.spectra_maxfragcharge=2 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=false +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=10 +saintexpress.run-saint-express=false +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=ciRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=-1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=true +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-6 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=0 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=Bridge +tmtintegrator.run-tmtintegrator=false +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5 diff --git a/tools/fragpipe/test-data/default/test.fasta b/tools/fragpipe/test-data/default/test.fasta new file mode 100644 index 000000000..b2f43880e --- /dev/null +++ b/tools/fragpipe/test-data/default/test.fasta @@ -0,0 +1,72 @@ +>generic|U00096.3_prot_AAC76339.1_3292|30SribosomalsubunitproteinS3-Ecoli_MG1655 +MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP +AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI +TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA +DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK +>generic|OFI31430.1|phosphateacetyltransferase[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079] +MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRAGGDAPDQTTTIVRAN +STLPAAEPLKMSHVESLLSSNQKDVLMEEIIANYHANTKDAEVVLVEGLVPTRKHQFAQS +LNYEIAKTLNAEIVFVMSQGTDTPEQLNERIELTRSSFGGAKNTNITGVIINKLNAPVDE +QGRTRPDLSEIFDDSSKAQVIKIDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLNA +TIINEGDIKTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIG +ALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKV +QEYVANYVNAEWIESLTATSERSRRLSPPAFRYQLTELARKAGKRVVLPEGDEPRTVKAA +AICAERGIATCVLLGNPDEINRVAASQGVELGAGIEIVDPEVVRESYVARLVELRKSKGM +TEPVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVF +FMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSGAGSD +VEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGN +TTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQQQQ +>generic|OFI30005.1|serinehydroxymethyltransferase[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079] +MLKREMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYP +GKRYYGGCEYVDVVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLQPGDTVLGMN +LAQGGHLTHGSPVNFSGKLYNIVPYGIDESGKIDYDEMAKLAKEHKPKMIIGGFSAYSGV +VDWAKMREIADSIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLIL +AKGGDEELYKKLNSAVFPSAQGGPLMHVIAGKAVALKEAMEPEFKVYQQQVAKNAKAMVE +VFLNRGYKVVSGGTENHLFLLDLVDKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTS +GIRIGSPAVTRRGFKEAEVKELAGWMCDVLDNINDEATIERVKAKVLDICARFPVYA +>generic|OFI28972.1|translationelongationfactorTu,partial[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079] +MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARG +ITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI +LLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALE +GDAEWEAKIIELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVG +EEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIK +PHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMV +VTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVL +>generic|OFI28767.1|chitinase[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079] +MATSKLIQGDTITETTHAANGFDPATSDDKISYTSARVAKPVYNKYKNSTTKPKVFGYYT +DWSQYDSRLQGNMSQPGRGYDLTKVSPTAYDKLIFGFVGITGFRKIDTEDRDVVAEAAAL +CGKVKYEPTFLDPWGDFQSYINLGFDVSGWDVDPKTVTQSNAKGLLGALRDMQAKAKAAG +HTLALSMSIGGWSMSNGFHETAASDSSRKIFAKGVVKLFKQFPMFSEVDIDWEYPNNEGA +GNPFGPEDGANYALLIAELRKQLDSAGLSNVKISIAASAVTTIFDYAKVKDLMAAGLYGI +NLMTYDFFGTPWAETLGHHTNRKALEEGGWAVETIVDHLLAEGFSADRINIGYAGYTRNA +RQVEIESLSPLKGSYNPGSGPTTGSFESGTSEWYDVIYSYLDLENQKGRNGFNVYTDQVA +DADYLYSPESKLFLSLDTPRTVKAKGEYAAKLGLGGVFTWTIDQDNGVLVNAVREGLGYE +IESEVIDMEPFYFEGINVEKDEEQSDSDDAQKVNHAPKAAIELMVVGGSTVQLSGAGSSD +EDNDELSFSWGVPSQIDVADKTAEIIEVVVPEVSEKTAFQFTLFVRDCYNEPSSQQRFVL +TAVPALSQVQPEPEEEEEIIVPVPDEEEDTTPAEDDTPADDKTSPYAQWDASTVYGANWG +SFEIVSWKGHNYQVKWWSMGNQPDLNCGVGGAWTDLGAY +>generic|OFI28186.1|50SribosomalproteinL3[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079] +MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAVQVTTGAKKANRV +TKPEAGHFAKAGVEAGRGLWEFRLAEGEEYTVGQSISVELFADVKKVDVTGTSKGKGFAG +TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV +DAERNLLLVKGGVPGATGCDLIVKPAVKA +>generic|AL009126.3_prot_CAB11777.1_1|chromosomalreplicationinitiatorinformationalATPase-BSU +MENILDLWNQALAQIEKKLSKPSFETWMKSTKAHSLQGDTLTITAPNEFARDWLESRYLHLIADTIYELTGEELSIKFVIPQNQDVEDFMPKPQVKKAVKEDTSDFPQNMLNPKYTFDTFVIGSGNRFAHAASLAVAEAPAKAYNPLFIYGGVGLGKTHLMHAIGHYVIDHNPSAKVVYLSSEKFTNEFINSIRDNKAVDFRNRYRNVDVLLIDDIQFLAGKEQTQEEFFHTFNTLHEESKQIVISSDRPPKEIPTLEDRLRSRFEWGLITDITPPDLETRIAILRKKAKAEGLDIPNEVMLYIANQIDSNIRELEGALIRVVAYSSLINKDINADLAAEALKDIIPSSKPKVITIKEIQRVVGQQFNIKLEDFKAKKRTKSVAFPRQIAMYLSREMTDSSLPKIGEEFGGRDHTTVIHAHEKISKLLADDEQLQQHVKEIKEQLK +>generic|AL009126.3_prot_CAB11778.1_2|DNApolymeraseIII(betasubunit)-BSU +MKFTIQKDRLVESVQDVLKAVSSRTTIPILTGIKIVASDDGVSFTGSDSDISIESFIPKEEGDKEIVTIEQPGSIVLQARFFSEIVKKLPMATVEIEVQNQYLTIIRSGKAEFNLNGLDADEYPHLPQIEEHHAIQIPTDLLKNLIRQTVFAVSTSETRPILTGVNWKVEQSELLCTATDSHRLALRKAKLDIPEDRSYNVVIPGKSLTELSKILDDNQELVDIVITETQVLFKAKNVLFFSRLLDGNYPDTTSLIPQDSKTEIIVNTKEFLQAIDRASLLAREGRNNVVKLSAKPAESIEISSNSPEIGKVVEAIVADQIEGEELNISFSPKYMLDALKVLEGAEIRVSFTGAMRPFLIRTPNDETIVQLILPVRTY +>generic|AL009126.3_prot_CAB11779.1_3|RNAbindingproteininvolvedinribosomematuration-BSU +MANPISIDTEMITLGQFLKLADVIQSGGMAKWFLSEHEVLVNDEPDNRRGRKLYVGDVVEIEGFGSFQVVN +>generic|AL009126.3_prot_CAB11780.1_4|RecAfilament-DNAcomplexstabilisation,ssDNAanddsDNAbinding,ATPbinding-BSU +MYIQNLELTSYRNYDHAELQFENKVNVIIGENAQGKTNLMEAIYVLSMAKSHRTSNDKELIRWDKDYAKIEGRVMKQNGAIPMQLVISKKGKKGKVNHIEQQKLSQYVGALNTIMFAPEDLNLVKGSPQVRRRFLDMEIGQVSPVYLHDLSLYQKILSQRNHFLKQLQTRKQTDRTMLDVLTDQLVEVAAKVVVKRLQFTAQLEKWAQPIHAGISRGLEELTLKYHTALDVSDPLDLSKIGDSYQEAFSKLREKEIERGVTLSGPHRDDVLFYVNGRDVQTYGSQGQQRTTALSLKLAEIDLIHEEIGEYPILLLDDVLSELDDYRQSHLLHTIQGRVQTFVTTTSVDGIDHETLRQAGMFRVQNGALVK +>generic|AL009126.3_prot_CAB11781.2_5|regulatorofextracellularmatrixformation-BSU +MYIHLGDDFVVSTRDIVGIFDFKANMSPIVEEFLKKQKHKVVPSVNGTPKSIVVTVQNIYYSPLSSSTLKKRAQFMFEIDS +>generic|AL009126.3_prot_CAB11782.1_6|DNAgyrase(subunitB)-BSU +MEQQQNSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIHEKMGRPAVEVIMTVLHAGGKFDGSGYKVSGGLHGVGASVVNALSTELDVTVHRDGKIHRQTYKRGVPVTDLEIIGETDHTGTTTHFVPDPEIFSETTEYDYDLLANRVRELAFLTKGVNITIEDKREGQERKNEYHYEGGIKSYVEYLNRSKEVVHEEPIYIEGEKDGITVEVALQYNDSYTSNIYSFTNNINTYEGGTHEAGFKTGLTRVINDYARKKGLIKENDPNLSGDDVREGLTAIISIKHPDPQFEGQTKTKLGNSEARTITDTLFSTAMETFMLENPDAAKKIVDKGLMAARARMAAKKARELTRRKSALEISNLPGKLADCSSKDPSISELYIVEGDSAGGSAKQGRDRHFQAILPLRGKILNVEKARLDKILSNNEVRSMITALGTGIGEDFNLEKARYHKVVIMTDADVDGAHIRTLLLTFFYRYMRQIIENGYVYIAQPPLYKVQQGKRVEYAYNDKELEELLKTLPQTPKPGLQRYKGLGEMNATQLWETTMDPSSRTLLQVTLEDAMDADETFEMLMGDKVEPRRNFIEANARYVKNLDI +>generic|AL009126.3_prot_CAB11783.1_7|DNAgyrase(subunitA)-BSU +MSEQNTPQVREINISQEMRTSFLDYAMSVIVSRALPDVRDGLKPVHRRILYAMNDLGMTSDKPYKKSARIVGEVIGKYHPHGDSAVYESMVRMAQDFNYRYMLVDGHGNFGSVDGDSAAAMRYTEARMSKISMEILRDITKDTIDYQDNYDGSEREPVVMPSRFPNLLVNGAAGIAVGMATNIPPHQLGEIIDGVLAVSENPDITIPELMEVIPGPDFPTAGQILGRSGIRKAYESGRGSITIRAKAEIEQTSSGKERIIVTELPYQVNKAKLIEKIADLVRDKKIEGITDLRDESDRTGMRIVIEIRRDANANVILNNLYKQTALQTSFGINLLALVDGQPKVLTLKQCLEHYLDHQKVVIRRRTAYELRKAEARAHILEGLRVALDHLDAVISLIRNSQTAEIARTGLIEQFSLTEKQAQAILDMRLQRLTGLEREKIEEEYQSLVKLIAELKDILANEYKVLEIIREELTEIKERFNDERRTEIVTSGLETIEDEDLIERENIVVTLTHNGYVKRLPASTYRSQKRGGKGVQGMGTNEDDFVEHLISTSTHDTILFFSNKGKVYRAKGYEIPEYGRTAKGIPIINLLEVEKGEWINAIIPVTEFNAELYLFFTTKHGVSKRTSLSQFANIRNNGLIALSLREDDELMGVRLTDGTKQIIIGTKNGLLIRFPETDVREMGRTAAGVKGITLTDDDVVVGMEILEEESHVLIVTEKGYGKRTPAEEYRTQSRGGKGLKTAKITENNGQLVAVKATKGEEDLMIITASGVLIRMDINDISITGRVTQGVRLIRMAEEEHVATVALVEKNEEDENEEEQEEV +>generic|AL009126.3_prot_CAB11784.1_8|conservedproteinofunknownfunction-BSU 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+diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=false +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.light= +ionquant.locprob=0.75 +ionquant.maxlfq=1 +ionquant.mbr=0 +ionquant.mbrimtol=0.05 +ionquant.mbrmincorr=0 +ionquant.mbrrttol=1 +ionquant.mbrtoprun=10 +ionquant.medium= +ionquant.minfreq=0 +ionquant.minions=2 +ionquant.minisotopes=2 +ionquant.minscans=3 +ionquant.mztol=10 +ionquant.normalization=1 +ionquant.peptidefdr=1 +ionquant.proteinfdr=1 +ionquant.requantify=1 +ionquant.rttol=0.4 +ionquant.run-ionquant=true +ionquant.tp=0 +ionquant.uniqueness=0 +ionquant.use-labeling=false +ionquant.use-lfq=true +ionquant.writeindex=0 +msbooster.predict-rt=true +msbooster.predict-spectra=true +msbooster.run-msbooster=false +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.deisotope=1 +msfragger.delta_mass_exclude_ranges=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=50 +msfragger.digest_min_length=7 +msfragger.fragment_ion_series=b,y +msfragger.fragment_mass_tolerance=20 +msfragger.fragment_mass_units=1 +msfragger.group_variable=0 +msfragger.intensity_transform=0 +msfragger.ion_series_definitions= +msfragger.isotope_error=-1/0/1/2/3 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=131.5 +msfragger.misc.fragger.clear-mz-lo=125.5 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=200 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50.0 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses=-18.01056 79.96633 +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 229.16293,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 229.16293,n^,true,1; 229.16293,S,true,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore +peptide-prophet.combine-pepxml=false +peptide-prophet.run-peptide-prophet=false +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=true +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --picked --prot 0.01 +phi-report.pep-level-summary=false +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=false +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline= +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=true +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=false +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=00.2 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=00.1 +ptmshepherd.diagmine_fragMinSpecDiff=00.1 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_mode=false +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=00.2 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=false +ptmshepherd.spectra_maxfragcharge=2 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=false +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=3 +saintexpress.run-saint-express=true +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=noiRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=false +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-11 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0.9 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=1 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=Bridge +tmtintegrator.run-tmtintegrator=true +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.description=

Basic TMT 11-plex workflow, with identification and quantification from high mass accuracy MS2. Met oxidation, protein N-term Acetyl, n-term TMT, and TMT on S ("overlabeling") are specified as variable modifications. TMT-Integrator with virtual reference approach, median-centering normalization, data summarization at the gene level. If a reference/bridge sample is available, specify the corresponding channel/sample name tag in the annotation file(s) and in TMT-Integrator tab.

+workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5 diff --git a/tools/fragpipe/test-data/tmt11/test.annotation b/tools/fragpipe/test-data/tmt11/test.annotation new file mode 100644 index 000000000..2df9b7263 --- /dev/null +++ b/tools/fragpipe/test-data/tmt11/test.annotation @@ -0,0 +1,11 @@ +126 sample-01 +127N sample-02 +127C sample-03 +128N sample-04 +128C sample-05 +129N sample-06 +129C sample-07 +130N sample-08 +130C sample-09 +131N sample-10 +131C Bridge diff --git a/tools/fragpipe/test-data/tmt11/test.fasta b/tools/fragpipe/test-data/tmt11/test.fasta new file mode 100644 index 000000000..127e0e696 --- /dev/null +++ b/tools/fragpipe/test-data/tmt11/test.fasta @@ -0,0 +1,193 @@ +>sp|P22314|UBA1_HUMAN Ubiquitin-like modifier-activating enzyme 1 OS=Homo sapiens OX=9606 GN=UBA1 PE=1 SV=3 +MSSSPLSKKRRVSGPDPKPGSNCSPAQSVLSEVPSVPTNGMAKNGSEADIDEGLYSRQLY +VLGHEAMKRLQTSSVLVSGLRGLGVEIAKNIILGGVKAVTLHDQGTAQWADLSSQFYLRE +EDIGKNRAEVSQPRLAELNSYVPVTAYTGPLVEDFLSGFQVVVLTNTPLEDQLRVGEFCH +NRGIKLVVADTRGLFGQLFCDFGEEMILTDSNGEQPLSAMVSMVTKDNPGVVTCLDEARH +GFESGDFVSFSEVQGMVELNGNQPMEIKVLGPYTFSICDTSNFSDYIRGGIVSQVKVPKK +ISFKSLVASLAEPDFVVTDFAKFSRPAQLHIGFQALHQFCAQHGRPPRPRNEEDAAELVA +LAQAVNARALPAVQQNNLDEDLIRKLAYVAAGDLAPINAFIGGLAAQEVMKACSGKFMPI +MQWLYFDALECLPEDKEVLTEDKCLQRQNRYDGQVAVFGSDLQEKLGKQKYFLVGAGAIG +CELLKNFAMIGLGCGEGGEIIVTDMDTIEKSNLNRQFLFRPWDVTKLKSDTAAAAVRQMN +PHIRVTSHQNRVGPDTERIYDDDFFQNLDGVANALDNVDARMYMDRRCVYYRKPLLESGT +LGTKGNVQVVIPFLTESYSSSQDPPEKSIPICTLKNFPNAIEHTLQWARDEFEGLFKQPA +ENVNQYLTDPKFVERTLRLAGTQPLEVLEAVQRSLVLQRPQTWADCVTWACHHWHTQYSN +NIRQLLHNFPPDQLTSSGAPFWSGPKRCPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTG +SQDRAAVATFLQSVQVPEFTPKSGVKIHVSDQELQSANASVDDSRLEELKATLPSPDKLP +GFKMYPIDFEKDDDSNFHMDFIVAASNLRAENYDIPSADRHKSKLIAGKIIPAIATTTAA +VVGLVCLELYKVVQGHRQLDSYKNGFLNLALPFFGFSEPLAAPRHQYYNQEWTLWDRFEV +QGLQPNGEEMTLKQFLDYFKTEHKLEITMLSQGVSMLYSFFMPAAKLKERLDQPMTEIVS +RVSKRKLGRHVRALVLELCCNDESGEDVEVPYVRYTIR +>sp|P31151|S10A7_HUMAN Protein S100-A7 OS=Homo sapiens OX=9606 GN=S100A7 PE=1 SV=4 +MSNTQAERSIIGMIDMFHKYTRRDDKIEKPSLLTMMKENFPNFLSACDKKGTNYLADVFE +KKDKNEDKKIDFSEFLSLLGDIATDYHKQSHGAAPCSGGSQ +>sp|Q8TCU5|NMD3A_HUMAN Glutamate receptor ionotropic, NMDA 3A OS=Homo sapiens OX=9606 GN=GRIN3A PE=1 SV=2 +MRRLSLWWLLSRVCLLLPPPCALVLAGVPSSSSHPQPCQILKRIGHAVRVGAVHLQPWTT +APRAASRAPDDSRAGAQRDEPEPGTRRSPAPSPGARWLGSTLHGRGPPGSRKPGEGARAE +ALWPRDALLFAVDNLNRVEGLLPYNLSLEVVMAIEAGLGDLPLLPFSSPSSPWSSDPFSF +LQSVCHTVVVQGVSALLAFPQSQGEMMELDLVSLVLHIPVISIVRHEFPRESQNPLHLQL +SLENSLSSDADVTVSILTMNNWYNFSLLLCQEDWNITDFLLLTQNNSKFHLGSIINITAN +LPSTQDLLSFLQIQLESIKNSTPTVVMFGCDMESIRRIFEITTQFGVMPPELRWVLGDSQ +NVEELRTEGLPLGLIAHGKTTQSVFEHYVQDAMELVARAVATATMIQPELALIPSTMNCM +EVETTNLTSGQYLSRFLANTTFRGLSGSIRVKGSTIVSSENNFFIWNLQHDPMGKPMWTR +LGSWQGGKIVMDYGIWPEQAQRHKTHFQHPSKLHLRVVTLIEHPFVFTREVDDEGLCPAG +QLCLDPMTNDSSTLDSLFSSLHSSNDTVPIKFKKCCYGYCIDLLEKIAEDMNFDFDLYIV +GDGKYGAWKNGHWTGLVGDLLRGTAHMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTR +DTAAPIGAFMWPLHWTMWLGIFVALHITAVFLTLYEWKSPFGLTPKGRNRSKVFSFSSAL +NICYALLFGRTVAIKPPKCWTGRFLMNLWAIFCMFCLSTYTANLAAVMVGEKIYEELSGI +HDPKLHHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVEYLKNDPEKLD +AFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTANISELISQYKSHGFM +DMLHDKWYRVVPCGKRSFAVTETLQMGIKHFSGLFVLLCIGFGLSILTTIGEHIVYRLLL +PRIKNKSKLQYWLHTSQRLHRAINTSFIEEKQQHFKTKRVEKRSNVGPRQLTVWNTSNLS +HDNRRKYIFSDEEGQNQLGIRIHQDIPLPPRRRELPALRTTNGKADSLNVSRNSVMQELS +ELEKQIQVIRQELQLAVSRKTELEEYQRTSRTCES +>sp|Q9HC84|MUC5B_HUMAN Mucin-5B OS=Homo sapiens OX=9606 GN=MUC5B PE=1 SV=3 +MGAPSACRTLVLALAAMLVVPQAETQGPVEPSWENAGHTMDGGAPTSSPTRRVSFVPPVT +VFPSLSPLNPAHNGRVCSTWGDFHYKTFDGDVFRFPGLCNYVFSEHCRAAYEDFNVQLRR +GLVGSRPVVTRVVIKAQGLVLEASNGSVLINGQREELPYSRTGLLVEQSGDYIKVSIRLV +LTFLWNGEDSALLELDPKYANQTCGLCGDFNGLPAFNEFYAHNARLTPLQFGNLQKLDGP +TEQCPDPLPLPAGNCTDEEGICHRTLLGPAFAECHALVDSTAYLAACAQDLCRCPTCPCA +TFVEYSRQCAHAGGQPRNWRCPELCPRTCPLNMQHQECGSPCTDTCSNPQRAQLCEDHCV +DGCFCPPGTVLDDITHSGCLPLGQCPCTHGGRTYSPGTSFNTTCSSCTCSGGLWQCQDLP +CPGTCSVQGGAHISTYDEKLYDLHGDCSYVLSKKCADSSFTVLAELRKCGLTDNENCLKA +VTLSLDGGDTAIRVQADGGVFLNSIYTQLPLSAANITLFTPSSFFIVVQTGLGLQLLVQL +VPLMQVFVRLDPAHQGQMCGLCGNFNQNQADDFTALSGVVEATGAAFANTWKAQAACANA +RNSFEDPCSLSVENENYARHWCSRLTDPNSAFSRCHSIINPKPFHSNCMFDTCNCERSED +CLCAALSSYVHACAAKGVQLSDWRDGVCTKYMQNCPKSQRYAYVVDACQPTCRGLSEADV +TCSVSFVPVDGCTCPAGTFLNDAGACVPAQECPCYAHGTVLAPGEVVHDEGAVCSCTGGK +LSCLGASLQKSTGCAAPMVYLDCSNSSAGTPGAECLRSCHTLDVGCFSTHCVSGCVCPPG +LVSDGSGGCIAEEDCPCVHNEATYKPGETIRVDCNTCTCRNRRWECSHRLCLGTCVAYGD +GHFITFDGDRYSFEGSCEYILAQDYCGDNTTHGTFRIVTENIPCGTTGTTCSKAIKLFVE +SYELILQEGTFKAVARGPGGDPPYKIRYMGIFLVIETHGMAVSWDRKTSVFIRLHQDYKG +RVCGLCGNFDDNAINDFATRSRSVVGDALEFGNSWKLSPSCPDALAPKDPCTANPFRKSW +AQKQCSILHGPTFAACRSQVDSTKYYEACVNDACACDSGGDCECFCTAVAAYAQACHDAG +LCVSWRTPDTCPLFCDFYNPHGGCEWHYQPCGAPCLKTCRNPSGHCLVDLPGLEGCYPKC +PPSQPFFNEDQMKCVAQCGCYDKDGNYYDVGARVPTAENCQSCNCTPSGIQCAHSLEACT +CTYEDRTYSYQDVIYNTTDGLGACLIAICGSNGTIIRKAVACPGTPATTPFTFTTAWVPH +STTSPALPVSTVCVREVCRWSSWYNGHRPEPGLGGGDFETFENLRQRGYQVCPVLADIEC +RAAQLPDMPLEELGQQVDCDRMRGLMCANSQQSPPLCHDYELRVLCCEYVPCGPSPAPGT +SPQPSLSASTEPAVPTPTQTTATEKTTLWVTPSIRSTAALTSQTGSSSGPVTVTPSAPGT +TTCQPRCQWTEWFDEDYPKSEQLGGDVESYDKIRAAGGHLCQQPKDIECQAESFPNWTLA +QVGQKVHCDVHFGLVCRNWEQEGVFKMCYNYRIRVLCCSDDHCRGRATTPPPTTELETAT +TTTTQALFSTPQPTSSPGLTRAPPASTTAVPTLSEGLTSPRYTSTLGTATTGGPTTPAGS +TEPTVPGVATSTLPTRSALPGTTGSLGTWRPSQPPTLAPTTMATSRARPTGTASTASKEP +LTTSLAPTLTSELSTSQAETSTPRTETTMSPLTNTTTSQGTTRCQPKCEWTEWFDVDFPT +SGVAGGDMETFENIRAAGGKMCWAPKSIECRAENYPEVSIDQVGQVLTCSLETGLTCKNE +DQTGRFNMCFNYNVRVLCCDDYSHCPSTPATSSTATPSSTPGTTWILTKPTTTATTTAST +GSTATPTSTLRTAPPPKVLTTTATTPTVTSSKATPSSSPGTATALPALRSTATTPTATSV +TPIPSSSLGTTWTRLSQTTTPTATMSTATPSSTPETAHTSTVLTATATTTGATGSVATPS +STPGTAHTTKVPTTTTTGFTATPSSSPGTALTPPVWISTTTTPTTRGSTVTPSSIPGTTH +TATVLTTTTTTVATGSMATPSSSTQTSGTPPSLTTTATTITATGSTTNPSSTPGTTPIPP +VLTTTATTPAATSNTVTPSSALGTTHTPPVPNTMATTHGRSLPPSSPHTVRTAWTSATSG +ILGTTHITEPSTVTSHTLAATTGTTQHSTPALSSPHPSSRTTESPPSPGTTTPGHTTATS +RTTATATPSKTRTSTLLPSSPTSAPITTVVTMGCEPQCAWSEWLDYSYPMPGPSGGDFDT +YSNIRAAGGAVCEQPLGLECRAQAQPGVPLRELGQVVECSLDFGLVCRNREQVGKFKMCF +NYEIRVFCCNYGHCPSTPATSSTAMPSSTPGTTWILTELTTTATTTESTGSTATPSSTPG +TTWILTEPSTTATVTVPTGSTATASSTQATAGTPHVSTTATTPTVTSSKATPFSSPGTAT +ALPALRSTATTPTATSFTAIPSSSLGTTWTRLSQTTTPTATMSTATPSSTPETVHTSTVL +TTTATTTGATGSVATPSSTPGTAHTTKVLTTTTTGFTATPSSSPGTARTLPVWISTTTTP +TTRGSTVTPSSIPGTTHTPTVLTTTTTTVATGSMATPSSSTQTSGTPPSLTTTATTITAT +GSTTNPSSTPGTTPIPPVLTTTATTPAATSSTVTPSSALGTTHTPPVPNTTATTHGRSLS +PSSPHTVRTAWTSATSGTLGTTHITEPSTGTSHTPAATTGTTQHSTPALSSPHPSSRTTE +SPPSPGTTTPGHTRATSRTTATATPSKTRTSTLLPSSPTSAPITTVVTMGCEPQCAWSEW +LDYSYPMPGPSGGDFDTYSNIRAAGGAVCEQPLGLECRAQAQPGVPLRELGQVVECSLDF +GLVCRNREQVGKFKMCFNYEIRVFCCNYGHCPSTPATSSTATPSSTPGTTWILTEQTTAA +TTTATTGSTAIPSSTPGTAPPPKVLTSTATTPTATSSKATSSSSPRTATTLPVLTSTATK +STATSFTPIPSFTLGTTGTLPEQTTTPMATMSTIHPSSTPETTHTSTVLTTKATTTRATS +SMSTPSSTPGTTWILTELTTAATTTAATGPTATPSSTPGTTWILTEPSTTATVTVPTGST +ATASSTRATAGTLKVLTSTATTPTVISSRATPSSSPGTATALPALRSTATTPTATSVTAI +PSSSLGTAWTRLSQTTTPTATMSTATPSSTPETVHTSTVLTTTTTTTRATGSVATPSSTP +GTAHTTKVPTTTTTGFTATPSSSPGTALTPPVWISTTTTPTTRGSTVTPSSIPGTTHTAT +VLTTTTTTVATGSMATPSSSTQTSGTPPSLTTTATTITATGSTTNPSSTPGTTPIPPVLT +TTATTPAATSSTVTPSSALGTTHTPPVPNTTATTHGRSLPPSSPHTVRTAWTSATSGILG +TTHITEPSTVTSHTPAATTSTTQHSTPALSSPHPSSRTTESPPSPGTTTPGHTRGTSRTT +ATATPSKTRTSTLLPSSPTSAPITTVVTTGCEPQCAWSEWLDYSYPMPGPSGGDFDTYSN +IRAAGGAVCEQPLGLECRAQAQPGVPLRELGQVVECSLDFGLVCRNREQVGKFKMCFNYE +IRVFCCNYGHCPSTPATSSTATPSSTPGTTWILTKLTTTATTTESTGSTATPSSTPGTTW +ILTEPSTTATVTVPTGSTATASSTQATAGTPHVSTTATTPTVTSSKATPFSSPGTATALP +ALRSTATTPTATSFTAIPSSSLGTTWTRLSQTTTPTATMSTATPSSTPETAHTSTVLTTT +ATTTRATGSVATPSSTPGTAHTTKVPTTTTTGFTVTPSSSPGTARTPPVWISTTTTPTTS +GSTVTPSSVPGTTHTPTVLTTTTTTVATGSMATPSSSTQTSGTPPSLITTATTITATGST +TNPSSTPGTTPIPPVLTTTATTPAATSSTVTPSSALGTTHTPPVPNTTATTHGRSLSPSS +PHTVRTAWTSATSGTLGTTHITEPSTGTSHTPAATTGTTQHSTPALSSPHPSSRTTESPP +SPGTTTPGHTTATSRTTATATPSKTRTSTLLPSSPTSAPITTVVTTGCEPQCAWSEWLDY +SYPMPGPSGGDFDTYSNIRAAGGAVCEQPLGLECRAQAQPGVPLGELGQVVECSLDFGLV +CRNREQVGKFKMCFNYEIRVFCCNYGHCPSTPATSSTAMPSSTPGTTWILTELTTTATTT +ASTGSTATPSSTPGTAPPPKVLTSPATTPTATSSKATSSSSPRTATTLPVLTSTATKSTA +TSVTPIPSSTLGTTGTLPEQTTTPVATMSTIHPSSTPETTHTSTVLTTKATTTRATSSTS +TPSSTPGTTWILTELTTAATTTAATGPTATPSSTPGTTWILTELTTTATTTASTGSTATP +SSTPGTTWILTEPSTTATVTVPTGSTATASSTQATAGTPHVSTTATTPTVTSSKATPSSS +PGTATALPALRSTATTPTATSFTAIPSSSLGTTWTRLSQTTTPTATMSTATPSSTPETVH +TSTVLTATATTTGATGSVATPSSTPGTAHTTKVPTTTTTGFTATPSSSPGTALTPPVWIS +TTTTPTTTTPTTSGSTVTPSSIPGTTHTARVLTTTTTTVATGSMATPSSSTQTSGTPPSL +TTTATTITATGSTTNPSSTPGTTPITPVLTSTATTPAATSSKATSSSSPRTATTLPVLTS +TATKSTATSFTPIPSSTLWTTWTVPAQTTTPMSTMSTIHTSSTPETTHTSTVLTTTATMT +RATNSTATPSSTLGTTRILTELTTTATTTAATGSTATLSSTPGTTWILTEPSTIATVMVP +TGSTATASSTLGTAHTPKVVTTMATMPTATASTVPSSSTVGTTRTPAVLPSSLPTFSVST +VSSSVLTTLRPTGFPSSHFSTPCFCRAFGQFFSPGEVIYNKTDRAGCHFYAVCNQHCDID +RFQGACPTSPPPVSSAPLSSPSPAPGCDNAIPLRQVNETWTLENCTVARCVGDNRVVLLD +PKPVANVTCVNKHLPIKVSDPSQPCDFHYECECICSMWGGSHYSTFDGTSYTFRGNCTYV +LMREIHARFGNLSLYLDNHYCTASATAAAARCPRALSIHYKSMDIVLTVTMVHGKEEGLI +LFDQIPVSSGFSKNGVLVSVLGTTTMRVDIPALGVSVTFNGQVFQARLPYSLFHNNTEGQ +CGTCTNNQRDDCLQRDGTTAASCKDMAKTWLVPDSRKDGCWAPTGTPPTASPAAPVSSTP +TPTPCPPQPLCDLMLSQVFAECHNLVPPGPFFNACISDHCRGRLEVPCQSLEAYAELCRA +RGVCSDWRGATGGLCDLTCPPTKVYKPCGPIQPATCNSRNQSPQLEGMAEGCFCPEDQIL +FNAHMGICVQACPCVGPDGFPKFPGERWVSNCQSCVCDEGSVSVQCKPLPCDAQGQPPPC +NRPGFVTVTRPRAENPCCPETVCVCNTTTCPQSLPVCPPGQESICTQEEGDCCPTFRCRP +QLCSYNGTFYGVGATFPGALPCHMCTCLSGDTQDPTVQCQEDACNNTTCPQGFEYKRVAG +QCCGECVQTACLTPDGQPVQLNETWVNSHVDNCTVYLCEAEGGVHLLTPQPASCPDVSSC +RGSLRKTGCCYSCEEDSCQVRINTTILWHQGCETEVNITFCEGSCPGASKYSAEAQAMQH +QCTCCQERRVHEETVPLHCPNGSAILHTYTHVDECGCTPFCVPAPMAPPHTRGFPAQEAT +AV +>sp|Q9UBG3|CRNN_HUMAN Cornulin OS=Homo sapiens OX=9606 GN=CRNN PE=1 SV=1 +MPQLLQNINGIIEAFRRYARTEGNCTALTRGELKRLLEQEFADVIVKPHDPATVDEVLRL +LDEDHTGTVEFKEFLVLVFKVAQACFKTLSESAEGACGSQESGSLHSGASQELGEGQRSG +TEVGRAGKGQHYEGSSHRQSQQGSRGQNRPGVQTQGQATGSAWVSSYDRQAESQSQERIS +PQIQLSGQTEQTQKAGEGKRNQTTEMRPERQPQTREQDRAHQTGETVTGSGTQTQAGATQ +TVEQDSSHQTGRTSKQTQEATNDQNRGTETHGQGRSQTSQAVTGGHAQIQAGTHTQTPTQ +TVEQDSSHQTGSTSTQTQESTNGQNRGTEIHGQGRSQTSQAVTGGHTQIQAGSHTETVEQ +DRSQTVSHGGAREQGQTQTQPGSGQRWMQVSNPEAGETVPGGQAQTGASTESGRQEWSST +HPRRCVTEGQGDRQPTVVGEEWVDDHSRETVILRLDQGNLHTSVSSAQGQDAAQSEEKRG +ITARELYSYLRSTKP +>generic|con_K1C10_HUMAN|K1C10_HUMAN +MSVRYSSSKHYSSSRSGGGGGGGGCGGGGGVSSLRISSSKGSLGGGFSSGGFSGGSFSRG +SSGGGCFGGSSGGYGGLGGFGGGSFHGSYGSSSFGGSYGGSFGGGNFGGGSFGGGSFGGG +GFGGGGFGGGFGGGFGGDGGLLSGNEKVTMQNLNDRLASYLDKVRALEESNYELEGKIKE +WYEKHGNSHQGEPRDYSKYYKTIDDLKNQILNLTTDNANILLQIDNARLAADDFRLKYEN +EVALRQSVEADINGLRRVLDELTLTKADLEMQIESLTEELAYLKKNHEEEMKDLRNVSTG +DVNVEMNAAPGVDLTQLLNNMRSQYEQLAEQNRKDAEAWFNEKSKELTTEIDNNIEQISS +YKSEITELRRNVQALEIELQSQLALKQSLEASLAETEGRYCVQLSQIQAQISALEEQLQQ +IRAETECQNTEYQQLLDIKIRLENEIQTYRSLLEGEGSSGGGGRGGGSFGGGYGGGSSGG +GSSGGGYGGGHGGSSGGGYGGGSSGGGSSGGGYGGGSSSGGHGGGSSSGGHGGSSSGGYG +GGSSGGGGGGYGGGSSGGGSSSGGGYGGGSSSGGHKSSSSGSVGESSSKGPRY +>generic|con_K2C1_HUMAN|K2C1_HUMAN +SRQFSSRSGYRSGGGFSSGSAGIINYQRRTTSSSTRRSGGGGGRFSSCGGGGGSFGAGGG +FGSRSLVNLGGSKSISISVARGGGRGSGFGGGYGGGGFGGGGFGGGGFGGGGIGGGGFGG +FGSGGGGFGGGGFGGGGYGGGYGPVCPPGGIQEVTINQSLLQPLNVEIDPEIQKVKSRER +EQIKSLNNQFASFIDKVRFLEQQNQVLQTKWELLQQVDTSTRTHNLEPYFESFINNLRRR +VDQLKSDQSRLDSELKNMQDMVEDYRNKYEDEINKRTNAENEFVTIKKDVDGAYMTKVDL +QAKLDNLQQEIDFLTALYQAELSQMQTQISETNVILSMDNNRSLDLDSIIAEVKAQNEDI +AQKSKAEAESLYQSKYEELQITAGRHGDSVRNSKIEISELNRVIQRLRSEIDNVKKQISN +LQQSISDAEQRGENALKDAKNKLNDLEDALQQAKEDLARLLRDYQELMNTKLALDLEIAT +YRTLLEGEESRMSGECAPNVSVSVSTSHTTISGGGSRGGGGGGYGSGGSSYGSGGGSYGS +GGGGGGGRGSYGSGGSSYGSGGGSYGSGGGGGGHGSYGSGSSSGGYRGGSGGGGGGSSGG +RGSGGGSSGGSIGGRGSSSGGVKSSGGSSSVRFVSTTYSGVTR +>sp|A0A087X1C5|CP2D7_HUMAN Putative cytochrome P450 2D7 OS=Homo sapiens OX=9606 GN=CYP2D7 PE=5 SV=1 +MGLEALVPLAMIVAIFLLLVDLMHRHQRWAARYPPGPLPLPGLGNLLHVDFQNTPYCFDQLRRRFGDVFSLQLAWTPVVVLNGLAAVREAMVTRGEDTADRPPAPIYQVLGFGPRSQGVILSRYGPAWREQRRFSVSTLRNLGLGKKSLEQWVTEEAACLCAAFADQAGRPFRPNGLLDKAVSNVIASLTCGRRFEYDDPRFLRLLDLAQEGLKEESGFLREVLNAVPVLPHIPALAGKVLRFQKAFLTQLDELLTEHRMTWDPAQPPRDLTEAFLAKKEKAKGSPESSFNDENLRIVVGNLFLAGMVTTSTTLAWGLLLMILHLDVQRGRRVSPGCPIVGTHVCPVRVQQEIDDVIGQVRRPEMGDQAHMPCTTAVIHEVQHFGDIVPLGVTHMTSRDIEVQGFRIPKGTTLITNLSSVLKDEAVWKKPFRFHPEHFLDAQGHFVKPEAFLPFSAGRRACLGEPLARMELFLFFTSLLQHFSFSVAAGQPRPSHSRVVSFLVTPSPYELCAVPR +>sp|A0A0B4J2F0|PIOS1_HUMAN Protein PIGBOS1 OS=Homo sapiens OX=9606 GN=PIGBOS1 PE=1 SV=1 +MFRRLTFAQLLFATVLGIAGGVYIFQPVFEQYAKDQKELKEKMQLVQESEEKKS +>sp|A0A0B4J2F2|SIK1B_HUMAN Putative serine/threonine-protein kinase SIK1B OS=Homo sapiens OX=9606 GN=SIK1B PE=5 SV=1 +MVIMSEFSADPAGQGQGQQKPLRVGFYDIERTLGKGNFAVVKLARHRVTKTQVAIKIIDKTRLDSSNLEKIYREVQLMKLLNHPHIIKLYQVMETKDMLYIVTEFAKNGEMFDYLTSNGHLSENEARKKFWQILSAVEYCHDHHIVHRDLKTENLLLDGNMDIKLADFGFGNFYKSGEPLSTWCGSPPYAAPEVFEGKEYEGPQLDIWSLGVVLYVLVCGSLPFDGPNLPTLRQRVLEGRFRIPFFMSQDCESLIRRMLVVDPARRITIAQIRQHRWMRAEPCLPGPACPAFSAHSYTSNLGDYDEQALGIMQTLGVDRQRTVESLQNSSYNHFAAIYYLLLERLKEYRNAQCARPGPARQPRPRSSDLSGLEVPQEGLSTDPFRPALLCPQPQTLVQSVLQAEMDCELQSSLQWPLFFPVDASCSGVFRPRPVSPSSLLDTAISEEARQGPGLEEEQDTQESLPSSTGRRHTLAEVSTRLSPLTAPCIVVSPSTTASPAEGTSSDSCLTFSASKSPAGLSGTPATQGLLGACSPVRLASPFLGSQSATPVLQAQGGLGGAVLLPVSFQEGRRASDTSLTQGLKAFRQQLRKTTRTKGFLGLNKIKGLARQVCQVPASRASRGGLSPFHAPAQSPGLHGGAAGSREGWSLLEEVLEQQRLLQLQHHPAAAPGCSQAPQPAPAPFVIAPCDGPGAAPLPSTLLTSGLPLLPPPLLQTGASPVASAAQLLDTHLHIGTGPTALPAVPPPRLARLAPGCEPLGLLQGDCEMEDLMPCSLGTFVLVQ +>sp|A0A0C5B5G6|MOTSC_HUMAN Mitochondrial-derived peptide MOTS-c OS=Homo sapiens OX=9606 GN=MT-RNR1 PE=1 SV=1 +MRWQEMGYIFYPRKLR +>sp|A0A0K2S4Q6|CD3CH_HUMAN Protein CD300H OS=Homo sapiens OX=9606 GN=CD300H PE=1 SV=1 +MTQRAGAAMLPSALLLLCVPGCLTVSGPSTVMGAVGESLSVQCRYEEKYKTFNKYWCRQPCLPIWHEMVETGGSEGVVRSDQVIITDHPGDLTFTVTLENLTADDAGKYRCGIATILQEDGLSGFLPDPFFQVQVLVSSASSTENSVKTPASPTRPSQCQGSLPSSTCFLLLPLLKVPLLLSILGAILWVNRPWRTPWTES +>sp|A0A0U1RRE5|NBDY_HUMAN Negative regulator of P-body association OS=Homo sapiens OX=9606 GN=NBDY PE=1 SV=1 +MGDQPCASGRSTLPPGNAREAKPPKKRCLLAPRWDYPEGTPNGGSTTLPSAPPPASAGLKSHPPPPEK +>sp|A0A1B0GTW7|CIROP_HUMAN Ciliated left-right organizer metallopeptidase OS=Homo sapiens OX=9606 GN=CIROP PE=1 SV=1 +MLLLLLLLLLLPPLVLRVAASRCLHDETQKSVSLLRPPFSQLPSKSRSSSLTLPSSRDPQPLRIQSCYLGDHISDGAWDPEGEGMRGGSRALAAVREATQRIQAVLAVQGPLLLSRDPAQYCHAVWGDPDSPNYHRCSLLNPGYKGESCLGAKIPDTHLRGYALWPEQGPPQLVQPDGPGVQNTDFLLYVRVAHTSKCHQETVSLCCPGWSTAAQSQLTAALTSWAQRRGFVMLPRLCLKLLGSSNLPTLASQSIRITGPSVIAYAACCQLDSEDRPLAGTIVYCAQHLTSPSLSHSDIVMATLHELLHALGFSGQLFKKWRDCPSGFSVRENCSTRQLVTRQDEWGQLLLTTPAVSLSLAKHLGVSGASLGVPLEEEEGLLSSHWEARLLQGSLMTATFDGAQRTRLDPITLAAFKDSGWYQVNHSAAEELLWGQGSGPEFGLVTTCGTGSSDFFCTGSGLGCHYLHLDKGSCSSDPMLEGCRMYKPLANGSECWKKENGFPAGVDNPHGEIYHPQSRCFFANLTSQLLPGDKPRHPSLTPHLKEAELMGRCYLHQCTGRGAYKVQVEGSPWVPCLPGKVIQIPGYYGLLFCPRGRLCQTNEDINAVTSPPVSLSTPDPLFQLSLELAGPPGHSLGKEQQEGLAEAVLEALASKGGTGRCYFHGPSITTSLVFTVHMWKSPGCQGPSVATLHKALTLTLQKKPLEVYHGGANFTTQPSKLLVTSDHNPSMTHLRLSMGLCLMLLILVGVMGTTAYQKRATLPVRPSASYHSPELHSTRVPVRGIREV +>sp|A0AV02|S12A8_HUMAN Solute carrier family 12 member 8 OS=Homo sapiens OX=9606 GN=SLC12A8 PE=1 SV=4 +MTQMSQVQELFHEAAQQDALAQPQPWWKTQLFMWEPVLFGTWDGVFTSCMINIFGVVLFLRTGWLVGNTGVLLGMFLVSFVILVALVTVLSGIGVGERSSIGSGGVYSMISSVLGGQTGGTIGLLYVFGQCVAGAMYITGFAESISDLLGLGNIWAVRGISVAVLLALLGINLAGVKWIIRLQLLLLFLLAVSTLDFVVGSFTHLDPEHGFIGYSPELLQNNTLPDYSPGESFFTVFGVFFPAATGVMAGFNMGGDLREPAASIPLGSLAAVGISWFLYIIFVFLLGAICTREALRYDFLIAEKVSLMGFLFLLGLYISSLASCMGGLYGAPRILQCIAQEKVIPALACLGQGKGPNKTPVAAICLTSLVTMAFVFVGQVNVLAPIVTINFMLTYVAVDYSYFSLSMCSCSLTPVPEPVLREGAEGLHCSEHLLLEKAPSYGSEGPAQRVLEGTLLEFTKDMDQLLQLTRKLESSQPRQGEGNRTPESQKRKSKKATKQTLQDSFLLDLKSPPSFPVEISDRLPAASWEGQESCWNKQTSKSEGTQPEGTYGEQLVPELCNQSESSGEDFFLKSRLQEQDVWRRSTSFYTHMCNPWVSLLGAVGSLLIMFVIQWVYTLVNMGVAAIVYFYIGRASPGLHLGSASNFSFFRWMRSLLLPSCRSLRSPQEQIILAPSLAKVDMEMTQLTQENADFATRDRYHHSSLVNREQLMPHY +>sp|A0AV96|RBM47_HUMAN RNA-binding protein 47 OS=Homo sapiens OX=9606 GN=RBM47 PE=1 SV=2 +MTAEDSTAAMSSDSAAGSSAKVPEGVAGAPNEAALLALMERTGYSMVQENGQRKYGGPPPGWEGPHPQRGCEVFVGKIPRDVYEDELVPVFEAVGRIYELRLMMDFDGKNRGYAFVMYCHKHEAKRAVRELNNYEIRPGRLLGVCCSVDNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVKILYVRNLMIETTEDTIKKSFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTELEGSCLEVTLAKPVDKEQYSRYQKAARGGGAAEAAQQPSYVYSCDPYTLAYYGYPYNALIGPNRDYFVKAGSIRGRGRGAAGNRAPGPRGSYLGGYSAGRGIYSRYHEGKGKQQEKGYELVPNLEIPTVNPVAIKPGTVAIPAIGAQYSMFPAAPAPKMIEDGKIHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPTVSTPPPFQGRPITPVYTVAPNVQRIPTAGIYGASYVPFAAPATATIATLQKNAAAAAAMYGGYAGYIPQAFPAAAIQVPIPDVYQTY +>sp|A0AVF1|IFT56_HUMAN Intraflagellar transport protein 56 OS=Homo sapiens OX=9606 GN=TTC26 PE=1 SV=1 +MMLSRAKPAVGRGVQHTDKRKKKGRKIPKLEELLSKRDFTGAITLLEFKRHVGEEEEDTNLWIGYCAFHLGDYKRALEEYENATKEENCNSEVWVNLACTYFFLGMYKQAEAAGFKASKSRLQNRLLFHLAHKFNDEKKLMSFHQNLQDVTEDQLSLASIHYMRSHYQEAIDIYKRILLDNREYLALNVYVALCYYKLDYYDVSQEVLAVYLQQIPDSTIALNLKACNHFRLYNGRAAEAELKSLMDNASSSFEFAKELIRHNLVVFRGGEGALQVLPPLVDVIPEARLNLVIYYLRQDDVQEAYNLIKDLEPTTPQEYILKGVVNAALGQEMGSRDHMKIAQQFFQLVGGSASECDTIPGRQCMASCFFLLKQFDDVLIYLNSFKSYFYNDDIFNFNYAQAKAATGNTSEGEEAFLLIQSEKMKNDYIYLSWLARCYIMNKKPRLAWELYLKMETSGESFSLLQLIANDCYKMGQFYYSAKAFDVLERLDPNPEYWEGKRGACVGIFQMIIAGREPKETLREVLHLLRSTGNTQVEYMIRIMKKWAKENRVSI diff --git a/tools/fragpipe/test-data/tmt11/test.manifest b/tools/fragpipe/test-data/tmt11/test.manifest new file mode 100644 index 000000000..f72ac065f --- /dev/null +++ b/tools/fragpipe/test-data/tmt11/test.manifest @@ -0,0 +1 @@ +test1.mzML sample1 DDA diff --git a/tools/fragpipe/test-data/tmt11/test.mzML b/tools/fragpipe/test-data/tmt11/test.mzML new file mode 100644 index 000000000..6e3fcdded --- /dev/null +++ b/tools/fragpipe/test-data/tmt11/test.mzML @@ -0,0 +1,716 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + 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 + + + + + + + + + 4969 + 12006 + 19296 + 25382 + 33117 + 40521 + 47398 + 55783 + 64003 + 71458 + + + 394827517 + 5930f131cffee70a428e4f7db7248ce056e29e8a + diff --git a/tools/fragpipe/workflows/Default.workflow b/tools/fragpipe/workflows/Default.workflow new file mode 100755 index 000000000..e515f44cf --- /dev/null +++ b/tools/fragpipe/workflows/Default.workflow @@ -0,0 +1,311 @@ +# Workflow: Default + +crystalc.run-crystalc=false +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +diann.run-dia-nn=false +diann.run-dia-plex=false +diann.run-specific-protein-q-value=false +diann.unrelated-runs=false +diann.use-predicted-spectra=true +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=false +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.light= +ionquant.locprob=0.75 +ionquant.maxlfq=1 +ionquant.mbr=1 +ionquant.mbrimtol=0.05 +ionquant.mbrmincorr=0 +ionquant.mbrrttol=1 +ionquant.mbrtoprun=10 +ionquant.medium= +ionquant.minfreq=0 +ionquant.minions=2 +ionquant.minisotopes=2 +ionquant.minscans=3 +ionquant.mztol=10 +ionquant.normalization=1 +ionquant.peptidefdr=1 +ionquant.proteinfdr=1 +ionquant.requantify=1 +ionquant.rttol=0.4 +ionquant.run-ionquant=true +ionquant.tp=0 +ionquant.uniqueness=0 +ionquant.use-labeling=false +ionquant.use-lfq=true +ionquant.writeindex=0 +msbooster.predict-rt=true +msbooster.predict-spectra=true +msbooster.run-msbooster=true +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.deisotope=1 +msfragger.delta_mass_exclude_ranges=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=50 +msfragger.digest_min_length=7 +msfragger.fragment_ion_series=b,y +msfragger.fragment_mass_tolerance=20 +msfragger.fragment_mass_units=1 +msfragger.group_variable=0 +msfragger.intensity_transform=0 +msfragger.ion_series_definitions= +msfragger.isotope_error=0/1/2/3 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=0 +msfragger.misc.fragger.clear-mz-lo=0 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=500 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses= +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore +peptide-prophet.combine-pepxml=false +peptide-prophet.run-peptide-prophet=false +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=true +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --picked --prot 0.01 +phi-report.pep-level-summary=false +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=true +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5 +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=false +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=true +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=00.2 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=00.1 +ptmshepherd.diagmine_fragMinSpecDiff=00.1 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_mode=false +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=00.2 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=true +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=true +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=false +ptmshepherd.spectra_maxfragcharge=2 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=false +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=10 +saintexpress.run-saint-express=false +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=ciRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=-1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=true +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-6 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=0 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=Bridge +tmtintegrator.run-tmtintegrator=false +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5 diff --git a/tools/fragpipe/workflows/LFQ-MBR.workflow b/tools/fragpipe/workflows/LFQ-MBR.workflow new file mode 100755 index 000000000..9608fd842 --- /dev/null +++ b/tools/fragpipe/workflows/LFQ-MBR.workflow @@ -0,0 +1,312 @@ +# Workflow: LFQ-MBR + +crystalc.run-crystalc=false +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +diann.run-dia-nn=false +diann.run-dia-plex=false +diann.run-specific-protein-q-value=false +diann.unrelated-runs=false +diann.use-predicted-spectra=true +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=false +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.light= +ionquant.locprob=0.75 +ionquant.maxlfq=1 +ionquant.mbr=1 +ionquant.mbrimtol=0.05 +ionquant.mbrmincorr=0 +ionquant.mbrrttol=1 +ionquant.mbrtoprun=10 +ionquant.medium= +ionquant.minfreq=0 +ionquant.minions=2 +ionquant.minisotopes=2 +ionquant.minscans=3 +ionquant.mztol=10 +ionquant.normalization=1 +ionquant.peptidefdr=1 +ionquant.proteinfdr=1 +ionquant.requantify=1 +ionquant.rttol=0.4 +ionquant.run-ionquant=true +ionquant.tp=0 +ionquant.uniqueness=0 +ionquant.use-labeling=false +ionquant.use-lfq=true +ionquant.writeindex=0 +msbooster.predict-rt=true +msbooster.predict-spectra=true +msbooster.run-msbooster=true +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.deisotope=1 +msfragger.delta_mass_exclude_ranges=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=50 +msfragger.digest_min_length=7 +msfragger.fragment_ion_series=b,y +msfragger.fragment_mass_tolerance=20 +msfragger.fragment_mass_units=1 +msfragger.group_variable=0 +msfragger.intensity_transform=0 +msfragger.ion_series_definitions= +msfragger.isotope_error=0/1/2 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=0 +msfragger.misc.fragger.clear-mz-lo=0 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=500 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses= +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore +peptide-prophet.combine-pepxml=false +peptide-prophet.run-peptide-prophet=false +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=true +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --prot 0.01 +phi-report.pep-level-summary=false +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=false +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5 +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=false +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=true +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=00.2 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=00.1 +ptmshepherd.diagmine_fragMinSpecDiff=00.1 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_mode=false +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=00.2 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=false +ptmshepherd.spectra_maxfragcharge=2 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=true +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=10 +saintexpress.run-saint-express=false +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=noiRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=-1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=true +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-6 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=0 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=Bridge +tmtintegrator.run-tmtintegrator=false +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.description=Perform closed search, followed by label free quantification with match-between-runs using IonQuant. If using mzML files, need to choose the right MS data type (Regular MS vs IM-MS). Need to assign runs to experiments. +workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5 diff --git a/tools/fragpipe/workflows/Nonspecific-HLA.workflow b/tools/fragpipe/workflows/Nonspecific-HLA.workflow new file mode 100755 index 000000000..0a136198f --- /dev/null +++ b/tools/fragpipe/workflows/Nonspecific-HLA.workflow @@ -0,0 +1,312 @@ +# Workflow: Nonspecific-HLA + +crystalc.run-crystalc=false +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +diann.run-dia-nn=false +diann.run-dia-plex=false +diann.run-specific-protein-q-value=false +diann.unrelated-runs=false +diann.use-predicted-spectra=false +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=false +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.light= +ionquant.locprob=0.75 +ionquant.maxlfq=1 +ionquant.mbr=1 +ionquant.mbrimtol=0.05 +ionquant.mbrmincorr=0 +ionquant.mbrrttol=1 +ionquant.mbrtoprun=10 +ionquant.medium= +ionquant.minfreq=0 +ionquant.minions=2 +ionquant.minisotopes=2 +ionquant.minscans=3 +ionquant.mztol=10 +ionquant.normalization=1 +ionquant.peptidefdr=1 +ionquant.proteinfdr=1 +ionquant.requantify=1 +ionquant.rttol=0.4 +ionquant.run-ionquant=true +ionquant.tp=0 +ionquant.uniqueness=0 +ionquant.use-labeling=false +ionquant.use-lfq=true +ionquant.writeindex=0 +msbooster.predict-rt=true +msbooster.predict-spectra=true +msbooster.run-msbooster=true +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.deisotope=1 +msfragger.delta_mass_exclude_ranges=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=25 +msfragger.digest_min_length=7 +msfragger.fragment_ion_series=b,y +msfragger.fragment_mass_tolerance=20 +msfragger.fragment_mass_units=1 +msfragger.group_variable=0 +msfragger.intensity_transform=1 +msfragger.ion_series_definitions= +msfragger.isotope_error=0/1 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=5 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.00 +msfragger.misc.fragger.clear-mz-hi=0 +msfragger.misc.fragger.clear-mz-lo=0 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=200 +msfragger.misc.fragger.enzyme-dropdown-1=nonspecific +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=0 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=15 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses=-18.01056 79.96633 +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=- +msfragger.search_enzyme_cut_2=- +msfragger.search_enzyme_name_1=nonspecific +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),false,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,2; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQ,true,1; -18.0106,nE,true,1; 119.0041,C,true,1; 0.98402,N,false,1; 8.014199,K,false,1; 10.008269,R,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=300 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore +peptide-prophet.combine-pepxml=false +peptide-prophet.run-peptide-prophet=false +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=true +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --prot 1 +phi-report.pep-level-summary=true +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=true +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline= +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=false +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=true +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=00.2 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=00.1 +ptmshepherd.diagmine_fragMinSpecDiff=00.1 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_mode=false +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=00.2 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=false +ptmshepherd.spectra_maxfragcharge=2 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=false +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=10 +saintexpress.run-saint-express=false +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=noiRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=-1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=true +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-6 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=0 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=Bridge +tmtintegrator.run-tmtintegrator=false +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.description=

Nonspecific search, with recommended settings for HLA peptides. Peptide length 7-25. MSFragger search assumes cysteines were not alkylated (i.e. samples were not treated with iodoacetamide). Cysteinylation (C+119) is specified as variable modification. MSFragger rescoring with MSBooster. PSM validation with Percolator. Protein FDR filter is not applied, so each output file (PSM, ion, peptide) is filtered to 1% FDR at that level. If needed, extend to add label-free quantifcation (using IonQuant) or spectral library building with EasyPQP.

+workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5 diff --git a/tools/fragpipe/workflows/Open.workflow b/tools/fragpipe/workflows/Open.workflow new file mode 100755 index 000000000..8b19354b0 --- /dev/null +++ b/tools/fragpipe/workflows/Open.workflow @@ -0,0 +1,312 @@ +# Workflow: Open + +crystalc.run-crystalc=true +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +diann.run-dia-nn=false +diann.run-dia-plex=false +diann.run-specific-protein-q-value=false +diann.unrelated-runs=false +diann.use-predicted-spectra=true +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=true +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.light= +ionquant.locprob=0.75 +ionquant.maxlfq=1 +ionquant.mbr=0 +ionquant.mbrimtol=0.05 +ionquant.mbrmincorr=0 +ionquant.mbrrttol=1 +ionquant.mbrtoprun=10 +ionquant.medium= +ionquant.minfreq=0 +ionquant.minions=2 +ionquant.minisotopes=2 +ionquant.minscans=3 +ionquant.mztol=10 +ionquant.normalization=1 +ionquant.peptidefdr=1 +ionquant.proteinfdr=1 +ionquant.requantify=1 +ionquant.rttol=0.4 +ionquant.run-ionquant=false +ionquant.tp=0 +ionquant.uniqueness=0 +ionquant.use-labeling=false +ionquant.use-lfq=true +ionquant.writeindex=0 +msbooster.predict-rt=true +msbooster.predict-spectra=true +msbooster.run-msbooster=false +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.deisotope=1 +msfragger.delta_mass_exclude_ranges=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=50 +msfragger.digest_min_length=7 +msfragger.fragment_ion_series=b,y +msfragger.fragment_mass_tolerance=20 +msfragger.fragment_mass_units=1 +msfragger.group_variable=0 +msfragger.intensity_transform=0 +msfragger.ion_series_definitions= +msfragger.isotope_error=0 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=true +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=0 +msfragger.misc.fragger.clear-mz-lo=0 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=500 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-150 +msfragger.precursor_mass_mode=corrected +msfragger.precursor_mass_units=0 +msfragger.precursor_mass_upper=500 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses= +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 +peptide-prophet.combine-pepxml=true +peptide-prophet.run-peptide-prophet=true +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=false +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --prot 0.01 --mapmods +phi-report.pep-level-summary=false +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=true +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline= +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=false +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=true +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=25 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=12.5 +ptmshepherd.diagmine_fragMinSpecDiff=25 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_mode=false +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=25 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=true +ptmshepherd.spectra_maxfragcharge=1 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=false +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=10 +saintexpress.run-saint-express=false +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=ciRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=-1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=false +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-10 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=-1 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=-1 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=pool +tmtintegrator.run-tmtintegrator=false +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.description=

Open search workflow for PTM analysis. MSFragger localization-aware open search (LOS) algorithm, with deisotoping, mass calibration, parameter optimization, and monoisotope correction enabled. Mass range -150 to 500 Da. PeptideProphet with extended mass model. Crystal-C for artifact removal. Precursor ion quantification using Freequant. PTM-Shepherd for mass shift summarization. For faster run time, in MSFragger change the number of allowed missed cleavages to 1.

+workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5 diff --git a/tools/fragpipe/workflows/TMT10.workflow b/tools/fragpipe/workflows/TMT10.workflow new file mode 100755 index 000000000..ad80ddfb2 --- /dev/null +++ b/tools/fragpipe/workflows/TMT10.workflow @@ -0,0 +1,312 @@ +# Workflow: TMT10 + +crystalc.run-crystalc=false +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +diann.run-dia-nn=false +diann.run-dia-plex=false +diann.run-specific-protein-q-value=false +diann.unrelated-runs=false +diann.use-predicted-spectra=true +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=false +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.light= +ionquant.locprob=0.75 +ionquant.maxlfq=1 +ionquant.mbr=0 +ionquant.mbrimtol=0.05 +ionquant.mbrmincorr=0 +ionquant.mbrrttol=1 +ionquant.mbrtoprun=10 +ionquant.medium= +ionquant.minfreq=0 +ionquant.minions=2 +ionquant.minisotopes=2 +ionquant.minscans=3 +ionquant.mztol=10 +ionquant.normalization=1 +ionquant.peptidefdr=1 +ionquant.proteinfdr=1 +ionquant.requantify=1 +ionquant.rttol=0.4 +ionquant.run-ionquant=true +ionquant.tp=0 +ionquant.uniqueness=0 +ionquant.use-labeling=false +ionquant.use-lfq=true +ionquant.writeindex=0 +msbooster.predict-rt=true +msbooster.predict-spectra=true +msbooster.run-msbooster=true +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.deisotope=1 +msfragger.delta_mass_exclude_ranges=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=50 +msfragger.digest_min_length=7 +msfragger.fragment_ion_series=b,y +msfragger.fragment_mass_tolerance=20 +msfragger.fragment_mass_units=1 +msfragger.group_variable=0 +msfragger.intensity_transform=0 +msfragger.ion_series_definitions= +msfragger.isotope_error=-1/0/1/2/3 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=131.5 +msfragger.misc.fragger.clear-mz-lo=125.5 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=200 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses=-18.01056 79.96633 +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 229.16293,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 229.16293,n^,true,1; 229.16293,S,true,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore +peptide-prophet.combine-pepxml=false +peptide-prophet.run-peptide-prophet=false +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=true +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --picked --prot 0.01 +phi-report.pep-level-summary=false +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=false +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline= +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=true +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=false +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=00.2 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=00.1 +ptmshepherd.diagmine_fragMinSpecDiff=00.1 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_mode=false +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=00.2 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=false +ptmshepherd.spectra_maxfragcharge=2 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=false +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=3 +saintexpress.run-saint-express=true +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=noiRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=false +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-10 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0.9 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=1 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=Bridge +tmtintegrator.run-tmtintegrator=true +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.description=

Basic TMT 10-plex workflow, with identification and quantification from high mass accuracy MS2. Met oxidation, protein N-term Acetyl, n-term TMT, and TMT on S ("overlabeling") are specified as variable modifications. TMT-Integrator with virtual reference approach, median-centering normalization, data summarization at the gene level. If a reference/bridge sample is available, specify the corresponding channel/sample name tag in the annotation file(s) and in TMT-Integrator tab.

+workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5 diff --git a/tools/fragpipe/workflows/TMT11.workflow b/tools/fragpipe/workflows/TMT11.workflow new file mode 100755 index 000000000..0bd504d19 --- /dev/null +++ b/tools/fragpipe/workflows/TMT11.workflow @@ -0,0 +1,312 @@ +# Workflow: TMT11 + +crystalc.run-crystalc=false +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +diann.run-dia-nn=false +diann.run-dia-plex=false +diann.run-specific-protein-q-value=false +diann.unrelated-runs=false +diann.use-predicted-spectra=true +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=false +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.light= +ionquant.locprob=0.75 +ionquant.maxlfq=1 +ionquant.mbr=0 +ionquant.mbrimtol=0.05 +ionquant.mbrmincorr=0 +ionquant.mbrrttol=1 +ionquant.mbrtoprun=10 +ionquant.medium= +ionquant.minfreq=0 +ionquant.minions=2 +ionquant.minisotopes=2 +ionquant.minscans=3 +ionquant.mztol=10 +ionquant.normalization=1 +ionquant.peptidefdr=1 +ionquant.proteinfdr=1 +ionquant.requantify=1 +ionquant.rttol=0.4 +ionquant.run-ionquant=true +ionquant.tp=0 +ionquant.uniqueness=0 +ionquant.use-labeling=false +ionquant.use-lfq=true +ionquant.writeindex=0 +msbooster.predict-rt=true +msbooster.predict-spectra=true +msbooster.run-msbooster=true +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.add_topN_complementary=0 +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.deisotope=1 +msfragger.delta_mass_exclude_ranges=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=50 +msfragger.digest_min_length=7 +msfragger.fragment_ion_series=b,y +msfragger.fragment_mass_tolerance=20 +msfragger.fragment_mass_units=1 +msfragger.group_variable=0 +msfragger.intensity_transform=0 +msfragger.ion_series_definitions= +msfragger.isotope_error=-1/0/1/2/3 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=131.5 +msfragger.misc.fragger.clear-mz-lo=125.5 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=200 +msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin +msfragger.misc.fragger.enzyme-dropdown-2=null +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dia1=5 +msfragger.output_report_topN_dia2=3 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses=-18.01056 79.96633 +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=KR +msfragger.search_enzyme_cut_2= +msfragger.search_enzyme_name_1=stricttrypsin +msfragger.search_enzyme_name_2=null +msfragger.search_enzyme_nocut_1= +msfragger.search_enzyme_nocut_2= +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 229.16293,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 229.16293,n^,true,1; 229.16293,S,true,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore +peptide-prophet.combine-pepxml=false +peptide-prophet.run-peptide-prophet=false +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=true +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --picked --prot 0.01 +phi-report.pep-level-summary=false +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=false +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline= +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=true +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=false +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagextract_mode=false +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=00.2 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=00.1 +ptmshepherd.diagmine_fragMinSpecDiff=00.1 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_mode=false +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=00.2 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_mode=false +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=false +ptmshepherd.spectra_maxfragcharge=2 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=false +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=3 +saintexpress.run-saint-express=true +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=noiRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=false +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-11 +tmtintegrator.dont-run-fq-lq=false +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=0 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0.9 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=1 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=Bridge +tmtintegrator.run-tmtintegrator=true +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.description=

Basic TMT 11-plex workflow, with identification and quantification from high mass accuracy MS2. Met oxidation, protein N-term Acetyl, n-term TMT, and TMT on S ("overlabeling") are specified as variable modifications. TMT-Integrator with virtual reference approach, median-centering normalization, data summarization at the gene level. If a reference/bridge sample is available, specify the corresponding channel/sample name tag in the annotation file(s) and in TMT-Integrator tab.

+workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.saved-with-ver=20.0-build5