Kojak

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

Highlights:

  • 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

Current Release

Version 2.0.0 alpha 8

Released on August 25 2021

Precompiled binaries provided for Windows and Linux. Free and open source, can be compiled on virtually any operating system including Windows, Linux, and MacOS.

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Documentation Updates

Jan 26 2022

A few new parameters have been added throughout Kojak 2.0 development. I've started updating the documentation to reflect ...

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Kojak Spectrum Viewer

Visualize MS/MS spectral results from Kojak. Multi-platform graphical user interface and publication quality exporter of cross-linked spectral images.

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Trans-Proteomic Pipeline

Multi-platform graphical interface for using Kojak, combined with downstream validation tools to estimate probabilities and FDR of Kojak results.

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ProXL: Protein XL Database

Analyze, visualize, and share your protein cross-linking data. Import Kojak results, combine multiple analyses, mine protein links, and produce 3D protein structure overlays.

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Kojak is published by the