quantms First Tasks for of improvements of OpenMS and quantms

This issue is to control some important tasks that should be done in OpenMS core related to the current pipeline:

[x] Support for common enzymes (commonly found in datasets annotated in quantms) in the main search engines SAGE, COMET and MSGF+. These are the enzymes: asp-n, lys-n, arg-c, chymotrypsin, lys-c/p, lys-c, trypsin/p, glutamyl endopeptidase, trypsin, leukocyte elastase. The first iteration of this issue started here #354.
[ ] Update the following tools to the latest versions: MSGF+, COMET, SAGE and Percolator.
[ ] Extend support for all tools to accept and produce .idXML and concensusXML in compressed mode gz. This is important because the intermediate files would be good to have then compressed.

After this is implemented, we should extend quantms to support compressed files, and the new search engine versions and test with other enzymes.

Jul 31 '24 10:07 ypriverol

sage is currently updated by a student:

Sep 18 '24 11:09 timosachsenberg

Should we then, @timosachsenberg work in MSGF+, COMET and Percolator-reset? @MaLLLiYA

Sep 18 '24 12:09 ypriverol

@MaLLLiYA did you update percolator-reset or only the search engines?

Mar 10 '25 07:03 ypriverol