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UWPR / Comet

An tandem mass spectrometry (MS/MS) sequence database search tool.
https://uwpr.github.io/Comet/
Apache License 2.0
42 stars 13 forks source link

Time of peptide ID in mzid #65

Closed julianu closed 2 months ago

julianu commented 2 months ago

This is a very minor but: right now you export the time of the <SpectrumIdentificationResult> in mzid with the CVParam "retention time" (MS:1000894). The mzid-documentation recommends the usage of "scan start time" (MS:1000016), though. It's maybe not intuitive, but should be used like that.

Just wanted to mention it, as I stumbled across it :)

jke000 commented 2 months ago

Thanks Julian. I appreciate all feedback, good or bad, so keep these coming if you find any more! It's clear I know very little about the mzid format so I used the supplied mzid example files as templates when generating Comet's mzid output. I believe I simply copied the "retention time" param use from this mzIdentML v1.2 example file. I do now see on page 73 of the 1.2 release doc that it shows MS:1000016 as an example child term of Spectrum Identification Result. I just made this quick change with commit 091e269. I plan on making a maintenance release later today or tomorrow which will include these mzid corrections as well address the other bugs that have been reported with the most recent release.