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A complete proteomics pipeline with MSFragger search engine at heart.

Release Downloads


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 Philosopher toolkit for downstream post-processing of MSFragger search results (PeptideProphet, iProphet, ProteinProphet), FDR filtering, label-free quantification, and multi-experiment summary report generation. 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.


Download precompiled binaries from the Releases section of this repository.

MSFragger binary needs to be downloaded separately, the user interface has a link to the download location. You can find detailed instructions on the MSFragger website.


A tutorial on converting LC/MS data files to the mzML format used by MSFragger can be found here. A tutorial for basic FragPipe use can be found here. We are currently working on creating additional tutorials for most commonly used workflows supported in FragPipe.

For MSFragger documentation (search parameters etc.) see MSFragger Documentation Wiki page.
For documentation on Philosopher toolkit see Philosopher site.

Questions and Technical Support

Please post all questions/bug reports regarding FragPipe itself in the FragPipe issue tracker.
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


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