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A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
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Latest commit cc95215 Jan 10, 2020

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FragPipe is a Java Graphical User Interface (GUI) for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. It is powered by MSFragger - an ultrafast proteomic search engine suitable for both conventional and "open" (wide precursor mass tolerance) peptide identification. FragPipe also includes the Philosopher toolkit for downstream post-processing of MSFragger search results (PeptideProphet, iProphet, ProteinProphet), FDR filtering, label-free quantification, and multi-experiment summary report generation. Crystal-C and PTM-Shepherd are included to aid interpretation of open search results. Also included in FragPipe binary are SpectraST-based spectral library building module, and DIA-Umpire SE module for direct analysis of data independent acquisition (DIA) data.


Find the latest release here & see the tutorials below.



Complete MSFragger documentation can be found on the MSFragger wiki. For documentation on the Philosopher toolkit see the Philosopher wiki.

Questions and Technical Support

See the MSFragger wiki and FAQ. View previous questions/bug reports in the FragPipe issue tracker. Please post any new questions/bug reports regarding FragPipe itself here as well. For questions specific to individual components of FragPipe you can also use MSFragger issue tracker and Philosopher issue tracker.

For other tools developed by Nesvizhskii lab, visit our website


  • Windows:
    • Run the Windows executable (.exe)
    • Or start the FragPipe.bat from the .zip distribution
      or execute one of the following commands:
    • start javaw -jar FragPipe-x.x.jar
    • java -jar FragPipe-x.x.jar
  • Linux/Mac:
    • Either run the FragPipe shell script from .zip distribution
      or execute the following command:
    • Or execute java -jar FragPipe-x.x.jar

Citing the work

Please refer to 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

Building from scratch

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

    • File: MSFragger-GUI/src/umich/msfragger/gui/
      Property: msfragger.gui.version
    • File: MSFragger-GUI/build.gradle
      Property: version
  2. Build:
    You don't need to have Gradle installed. Gradle wrapper included in this repository will be used. From the root directory of the repository issue the following commands:

    cd ./MSFragger-GUI
    ./gradlew prepareReleaseNoExe
  3. Inspect the output in MSFragger-GUI/build/github-release directory.

  4. If you want .exe file for Windows, then you have to build on Windows with Launch4j installed.

    ./gradlew prepareReleaseWithExe


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