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 2

Released on December 20 2019

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

Get It Now » Quick Start Guide »

Read the Latest News

The Next Alpha Release

Dec 20 2019

This update adds a major new feature, decoy database generation. Previously, it was up to the user to supply decoys of their choice ...

Read More »

Kojak Spectrum Viewer

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

View details »

Trans-Proteomic Pipeline

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

View details »

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.

View details »

Kojak is published by the