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 16

Released on April 11 2022

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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Read the Latest News

New Release is Alpha 16

Apr 11 2022

This release has a critical fix for an intermittent crash in some data files. This release also contains minor speed improvements. ...

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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