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.
Find the latest FragPipe release here & see the setup tutorial below.
- FragPipe setup
- Basic FragPipe use
- Converting LC/MS data files to mzML
- Running MSstats on timsTOF data
Complete MSFragger documentation can be found on the MSFragger Documentation Wiki page.
For documentation on the Philosopher toolkit see the Philosopher site.
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 nesvilab.org
- 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
- Either run the
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
-
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
- File:
-
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
-
Inspect the output in
MSFragger-GUI/build/github-release
directory. -
If you want .exe file for Windows, then you have to build on Windows with Launch4j installed.
./gradlew prepareReleaseWithExe