Comet 2026.02 rev. 2 is now available

[Jimmy Eng]

Comet 2026.02 rev. 2 is now available.
Release notes:  https://uwpr.github.io/Comet/releases/release_202602.html
Download link:  https://github.com/UWPR/Comet/releases

This is a maintenance release for a bug fix associated with fragment ion index searches.  There was a bug associated with how variable mods were handled.  The release notes has some details on what the issue was.  To give you an idea on the impact, here's a IMAC enriched sample searching with variable mods Ox-Met and phosphorylation against a human target-decoy database.  Values under each release column is the # PSMs at a 1% FDR cutoff based on Comet's E-value.  You can see that the new release gives about ~4% more PSMs compared to the previous release.

There's also a significant change in peptide index searches. Those now use the same .idx format as the fragment ion index.  The peptide index memory use is reduced significantly (one example search went from using ~10.5 GB pre-change down to ~6.5 GB).  An "index_search_type" parameter was introduced to control what type of index search gets performed since the .idx format is unified.