New Release is Alpha 16
April 11, 2022
This release has a critical fix for an intermittent crash in some data files. This release also contains minor speed improvements.
Alpha 13 Released
April 1, 2022
This update has two major overhauls. First, file loading is now multithreaded and pipelined to process the MS1 and MS2 spectra while they are being read from disk. This dramatically speeds up the spectral preprocessing stages of Kojak. It doesn’t affect the peptide search space, so the most noticeable speed improvements are with large files that have small search spaces.
The second major overhaul is to better organize the text output from Kojak. Previously PSMs were reported in the order in which the threads completed them. Now they are organized in the same order regardless of when computation time is completed. This includes sorting multiple PSMs within the same spectrum that have the same score (i.e. ties). This saves users from having to sort their results when repeating an analysis to look for differences.
As a minor note, the default/sample configuration files has been updated to reflect the latest parameter changes and generalized settings. Most noteworthy is the recommended bin size for orbitrap MS2 spectra is now 0.01.
January 26, 2022
A few new parameters have been added throughout Kojak 2.0 development. I’ve started updating the documentation to reflect these new parameters. aa_mass and results_path are now included in the documentation, and are very useful in both customizing the cross-linking analysis and organizing the results.