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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)

Release Downloads

FragPipe (previously - MSfragger GUI)

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

Referencing the work

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

To build

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.

Updating build version

The version of the build is stored in 2 separate places:

  • MSFragger-GUI/src/umich/msfragger/
    • VERSION static field
  • MSFragger-GUI/src/umich/msfragger/gui/
    • 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.