Kojak Release Notes
Version 2.0.0 (all alpha releases) - December 2019-present
- Added support for mzIdentML output format.
- Added e-value computation for PSMs.
- Added on-the-fly decoy sequence generation.
- Added full report log generation to capture on-screen information for each run.
- Added new parameter: aa_mass to customize amino acid masses.
- Added new parameter: minimum_peptide_score as a filter prior to second pass analysis.
- Added new parameter: results_path to export results to a new location.
- Added new (possibly temporary) parameter: xl_cleavage_product_mass for cleavable crosslinkers.
- Added new parameter: predefined_crosslink to rapidly set all parameters for common crosslinkers.
- Pipelined file loading and spectral transformations for increased speed.
- Updated command-line interface for more streamlined information.
- Updated percolator output to use -log10(e-value).
- Updated percolator output to correctly specify charge state parameters.
- Updated percolator output to better resolve multiple interpretations of the same PSM.
- Updated percolator output to avoid redundant protein listings.
- Updated percolator output to use additional scoring parameters.
- Percolator output now properly labeled with .pin extension
- Optimizations for PeptideProphet and Trans-Proteomic Pipeline support.
- Optimizations to support Crux.
- Standardized text output for consistency.
- Fixes in parameter parsing to better catch errors.
- Fixed PSM output to place targets above decoys in cases where scores are tied.
Version 1.6.1 - December 1 2017
- Fixed critical bug in 15N labeling.
Version 1.6.0 - November 27 2017
- Alternative two-pass search algorithm. More efficient, alters top_count parameter usage.
- Added 15N-labeled homomultimer analysis.
- Added detailed diagnostics features for advanced users.
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 formatted
- 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).
- Added cross-linking of acyl groups.
- Fixed bug in labeling of Inter and Intra cross-linked Percolator files.
- Percolator results now divided into multiple files based on PSM type.
- Improved Kojak Xcorr algorithm to use less memory
- Faster Xcorr implementation over Version 1.0
- Support for multi-threaded systems