This repository has moved to FragPipe
Please use the issue tracker in the new repository to ask questions/report issues/request new features. This repository is in a frozen state and won't be updated.
MSfragger GUI (now FragPipe)
This is a very basic Java GUI wrapper for MSFragger - ultrafast proteomic search engine.
It will help you launch MSFragger for Open and Closed searches and can also run post-processing of results with Peptide/Protein Prophets as well as generate tabular summary results using Philosopher.
Download precompiled binaries from the Releases section of this repository
- on Windows use one of the following:
- Use the Windows executable (.exe)
start javaw -jar MSfragger-GUI.jar
java -jar MSfragger-GUI.jar
- Linux/MacOS
- Run the shell script included in the release zip file
java -jar MSfragger-GUI.jar
Please cite the following paper:
Andy Kong, Felipe Leprevost, Dmitry Avtonomov, Dattatreya Mellacheruvu, Alexey Nesvizhskii. "MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics". Nat Meth, May 2017. DOI: 10.1038/nmeth.4256
Open the source project in NetBeans and do "Clean Build". You will get the jar in ./dist directory and a zip file with the current version in the file name and start scripts bundled.
The version of the build is stored in 2 separate places:
- MSFragger-GUI/src/umich/msfragger/Version.java
VERSION
static field
- MSFragger-GUI/src/umich/msfragger/gui/Bundle.properties
msfragger.gui.version
property Both need to be modified to the same value, otherwise you'll get a popup warning at the start of the application.