Announcing Crux version 4.0 Inbox

[William S Noble]

The Crux development team is pleased to announce the release of version 4.0 of the Crux tandem mass spectrometry analysis toolkit.  This version includes the following major enhancements:

• Added the Kojak module for searching for cross-linked peptides. The methodology is described in Hoopmann et al. Journal of Proteome Research, 2015.
• Added the Tailor PSM score calibration method to Tide-search as an option. The methodology is described in Sulimov and Kertesz-Farkas. Journal of Proteome Research, 2020.
• Updated Param-Medic to enable inference of the presence of various types of modifications, including stable-isotope and isobaric labeling and tandem mass tags as well as the enrichment of phosphorylated peptides. The methodology is described in May et al. Journal of Proteome Research, 2019.
• Updated Crux to use Comet 2019.05.
• Removed the following Crux commands: search-for-xlinks, xlink-assign-ions, xlink-score-spectrum, barista, q-ranker, extract-columns, extract-rows, stat-column, sort-by-column.

A number of minor enhancements and fixes are also included, as listed in the release notes.  Source code as well as binaries for Linux, MacOS and native Windows are available from the Crux web page:

http://crux.ms/

Please address questions to the Crux users list, crux-us...@googlegroups.com.