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 includes the Philosopher toolkit for downstream post-processing of MSFragger search results (PeptideProphet, iProphet, ProteinProphet), FDR filtering, label-based 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 TMT-Integrator for TMT/iTRAQ isobaric labeling-based quantification, IonQuant for label-free quantification with match-between-run (MBR) functionality, SpectraST and EasyPQP spectral library building modules, and DIA-Umpire SE module for direct analysis of data independent acquisition (DIA) data.

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Tutorials

• FragPipe setup
• Using FragPipe (most comprehensive tutorial covering all FragPipe modules)
• Built-in workflows
• Analyzing glycoproteomics data
• Converting LC/MS data files to mzML
• Setting up FragPipe on remote Linux server (with X forwarding)
• Using FragPipe for SILAC (or other MS1-labeled) data
• Running MSstats on TIMS-TOF data
• Importing results to Skyline

Documentation

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, Philosopher issue tracker, IonQuant issue tracker.

For other tools developed by Nesvizhskii lab, visit our website nesvilab.org

How to Run

• Windows:
  • Run the Windows executable (.exe) from the "bin" folder
  • 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:
  • Either run the FragPipe shell script from .zip distribution
    or execute the following command:
  • Or execute java -jar FragPipe-x.x.jar

Cite

• Kong, A. T., Leprevost, F. V., Avtonomov, D. M., Mellacheruvu, D., & Nesvizhskii, A. I. (2017). MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nature Methods, 14(5), 513-520.
• Yu, F., Teo, G. C., Kong, A. T., Haynes, S. E., Avtonomov, D. M., Geiszler, D. J., & Nesvizhskii, A. I. (2020). Identification of modified peptides using localization-aware open search. Nature Communications, 11(1), 1-9.
• Polasky, D. A., Yu, F., Teo, G. C., & Nesvizhskii, A. I. (2020). Fast and Comprehensive N-and O-glycoproteomics analysis with MSFragger-Glyco. Nature Methods, 17, 1125-1132.
• Chang, H. Y., Kong, A. T., da Veiga Leprevost, F., Avtonomov, D. M., Haynes, S. E., & Nesvizhskii, A. I. (2020). Crystal-C: A computational tool for refinement of open search results. Journal of Proteome Research, 19(6), 2511-2515.
• Geiszler, D. J., Kong, A. T., Avtonomov, D. M., Yu, F., da Veiga Leprevost, F., & Nesvizhskii, A. I. (2020). PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results. Molecular & Cellular Proteomics.
• da Veiga Leprevost, F., Haynes, S. E., Avtonomov, D. M., Chang, H. Y., Shanmugam, A. K., Mellacheruvu, D., Kong, A. T., & Nesvizhskii, A. I. (2020). Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nature Methods, 17(9), 869-870.
• Yu, F., Haynes, S. E., Teo, G. C., Avtonomov, D. M., Polasky, D. A., & Nesvizhskii, A. I. (2020). Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Molecular & Cellular Proteomics.
• Teo, G. C., Polasky, D. A., Yu, F., Nesvizhskii, A. I. (2020). A fast deisotoping algorithm and its implementation in the MSFragger search engine. Journal of Proteome Research.
• Tsou, C. C., Avtonomov, D., Larsen, B., Tucholska, M., Choi, H., Gingras, A. C., & Nesvizhskii, A. I. (2015). DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nature methods, 12(3), 258-264.

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/Bundle.properties
     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