Kojak Release Notes

Added support for mzMLb files.
Added split_pepxml parameter to segregate single, loop, and cross-links into separate PepXML files.
Fixed bug in exporting mzIdentML after reading Thermo RAW files.
Fixed infinite loop caused by Hardklor precursor analysis (thank you, Lutz Fischer).

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.

Alternative two-pass search algorithm. More efficient, alters top_count parameter usage.
Added 15N-labeled homomultimer analysis.
Added detailed diagnostics features for advanced users.

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.

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

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.

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.

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.

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).