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Ultra fast and comprehensive peptide identification in mass spectrometry–based proteomics
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MSFragger is an ultrafast database search tool for peptide identifications in mass spectrometry-based proteomics. MSFragger has demonstrated excellent performance across a wide range of datasets and applications. The speed of MSFragger makes it particularly suitable for the analysis of large datasets (including timsTOF data), for enzyme unconstrained searches, and for ‘open’ database searches (with the precursor mass tolerance set to hundreds of Daltons) for identification of modified peptides.

MSFragger is implemented in the cross-platform Java programming language, and is available as a standalone JAR file. It is compatible with standard open file formats for mass spectrometry data (mzXML/mzML). It writes output in either tabular or pepXML formats, making it fully compatible with downstream data analysis pipelines such as Trans-Proteomic Pipeline and Philosopher.

Download MSFragger

If you never downloaded MSFragger before, please complete steps 1-3. To upgrade to the most recent version from a previosly downloaded version (JAR file), skip to step 3.

  1. Complete the license agreement form.
  2. Download the initial release of MSFragger software using instructions received by email.
  3. Once you obtained the MSFragger software, the latest version of the software can be downloaded (under the same license terms as the original version) using the Upgrade site.

Running MSFragger

The easiest way to run MSFragger/Philosopher tools is using FragPipe GUI. FragPipe also includes additional tools such as DIA-Umpire SE module for DIA data, and SpectraST-based spectral library building module.

For command-line option to run MSFragger/Philosopher tools see Tutorial.

Release Notes

The latest version of MSFragger was released on 2019-05-23. Check here for the full list of MSFragger versions and changes.


For documentation on MSFragger itself (hardware requirements, search parameters, etc.), see MSFragger Documentation Wiki page.

Questions and Technical Support

Please post all questions/bug reports regarding MSFragger itself on the MSFragger GitHub page, or if more appropriate on FragPipe page or Philsopher page.

Requests for Collaboration

If you would like to propose a new collaboration that can take advantage of MSFragger and related tools, please contact us directly.

How to Cite

Kong AT, Leprevost FV, Avtonomov DM, Mellacheruvu D, Nesvizhskii AI. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics. Nature Methods 14:513–520 (2017). Manuscript.

For other tools developed by Nesvizhskii lab, go to our website

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