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A database search algorithm for solving cross-linked peptide mass spectra. Features, documentation, and additional tools can be found on the primary Kojak website:


Copyright 2014-2016, Michael R. Hoopmann, Institute for Systems Biology

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Kojak Release Notes

Version 1.6.1 - December 1 2017

  • Fixed bug with 15N protein reporting and the TPP.

Version 1.6.0 - November 27 2017

  • Added searches for 15N-labeled homomultimers.
  • Added ability to export results to target path.
  • Major change to search algorithm.
  • Changed function of top_count parameter to fit with the new search algorithm.
  • Updated diagnostic output information. Can also output diagnostics for all spectrum in one report.

Version 1.5.5 - May 4 2017

  • Fixed support for MGF files. These are now valid input.
  • Fixed bug when searching loop-links with multiple cross-linkers.
  • Added searches for n-terminal peptide modifications on linked first peptide amino acid (and c-terminal counterparts).
  • Added precursor_refinement parameter to toggle MS1 analysis on or off.

Version 1.5.4 - February 9 2017

  • Added new fixed and differential modification settings.
  • More accurate reporting of N-terminal and C-terminal mods in pepXML output.

Version 1.5.3 - November 11 2016

  • Fixed edge-case bug causing a segfault.

Version 1.5.2 - October 6 2016

  • Fixed buffer overrun when using the turbo_button.
  • Fixed incorrect position reporting of differential mods on the n- and c-termini of loop links.

Version 1.5.1 - August 19 2016

  • Fixed buffer corruption when using multiple threads.
  • Fixed data file path issues in pepXML output.

Version 1.5.0 - July 28 2016

  • Changed how cross-link and mono-link sites are defined in the parameters.
  • Fixed bug with modifications on protein termini with loop-links.
  • Disabled and deprecated use_comet_xcorr.
  • Added turbo_button and other speed improvements.
  • Added additional information (version number, parameters, etc.) to the pepXML output.
  • Updated threading code.

Version 1.4.3 - April 8 2016

  • Added output in pepXML format
  • Minor bug fixes

Version 1.4.2 - November 30 2015

  • Fixed c-terminus parsing bug in sequence database.
  • Fixed bug in enzyme digest/database parsing.
  • Improved scoring algorithm: no inflation of scores for shared fragment ions from two peptides.
  • Suppressed warning message when Thermo MSFileReader not installed/active.

Version 1.4.1 - September 11 2015

  • Fixed duplication when reporting enriched cross-link results.
  • Fixed bug when detecting enriched precursor ions.
  • Removed diagnostic message displayed if searching for non-covalent dimers.
  • Removed diagnostic message displayed if searching with enrichment.
  • Corrected improper values included in sample configuration file.

Version 1.4.0 - August 14 2015

  • Fixed bugs in Percolator-formatted results files.
  • Fixed duplication when reporting some results.
  • Fixed bug where precursor ions of zero intensity were identified.
  • Added additional ion-series to the analysis (a,b,c,x,y,z-dot).
  • Added batch analysis of multiple files from the command line.
  • Added toggle Percolator output with export_percolator parameter.
  • Improved parameter reading. Better error checking.
  • Deprecated output_file and percolator_file parameters.
  • Output file names derived from input file names.
  • Extended analysis to allow for ETD spectra.
  • Extended Percolator output to include retention time. Possibly temporary.

Version 1.3.6 - June 17 2015

  • Fixed bug where protein site of linkage was offset by 1.
  • Fixed bug where heterobifunctional cross-links were duplicated in the results.
  • Fixed bug when reporting negative cross-link masses.
  • Fixed buffer overrun when pairing peptide mass to spectrum mass range.
  • Added toggle for searching differential modifications on cross-linked peptides.
  • Added toggle for searching mono-linked sites on cross-linked peptides.
  • Improved precursor refinement algorithm.
  • Extended prefer_precursor_pred to supplement precursor info with Kojak determined precursors.
  • Extended diagnostics to support multiple spectra.

Version 1.3.5 - April 15 2015

  • Fixed bug in setting modifications to protein C-terminus.
  • Fixed Inter/Intra Percolator-formatted results for real this time.
  • Added amine+ reactive group for cross-linking (lysines and n-terminus, plus alternate sites of serine, threonine, and tyrosine).

Version 1.3.4

  • Added cross-linking of acyl groups.
  • Fixed bug in labeling of Inter and Intra cross-linked Percolator files.

Version 1.3.3

  • Percolator results now divided into multiple files based on PSM type.

Version 1.3.2

  • Improved Kojak Xcorr algorithm to use less memory
  • Faster Xcorr implementation over Version 1.0
  • Support for multi-threaded systems

Version 1.0

  • Initial Release