New Release is Alpha 22

August 19, 2022

There were numerous small updates since the last release, but I will highlight only a few. First, cleavable crosslinkers are now better supported with the xl_cleavage_product_mass parameter. Yes, it is yet another parameter for defining crosslinkers. To make everyone’s life easier, I’ve added a macro to the default configuration file that lets you select all the features for a given crosslinker with a single parameter, predefined_crosslink. If this parameter is defined, it will automatically set all the necessary parameters for a given crosslinker without having to define cross_link, mono_link, etc. And to help everyone keep up-to-date with the latest parameters, you can now get a default parameter set directly from the commandline by executing:

kojak --config

from your command line. This will create a kojak_default_params.conf file which will have all the latest parameters for the current version. Just rename it (otherwise the next time you run this command, it will be overwritten) and edit it for your analysis.

Other updates include fixes for Percolator support and reconfiguration of default and suggested parameters.

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.

Documentation Updates

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.