Free, open-source application for identification of cross-linked peptides from mass spectra.


  • Use virtually any stable cross-linker chemistry
  • Analyze isotopically labeled or non-labeled data
  • Supports open data formats (including mzXML and mzML)
  • Pre-compiled binaries get you started quickly

New to Kojak?

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Current Release

Version 1.6.1

Released on December 1 2017. Get your copy from our Downloads page.


We are open to collaborations on the analysis of protein structures using cross-linking technology. Interested parties should contact Dr. Michael Hoopmann.

Update for TPP Users

Dec 1 2017

This update fixes an issue with validating PSMs that use 15N with PeptideProphet in TPP when using the browser front end. ...

Kojak is published by the