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compomics / psm_utils

Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
https://psm-utils.readthedocs.io
Apache License 2.0
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pepXML or mzIdentML from Comet #86

Closed jke000 closed 4 months ago

jke000 commented 5 months ago

Hi Ralf. A user posted an issue on the Comet repository about pushing Comet's output through MS2Rescore. The post was with respect to changing Comet's output to be compatible with MS2Rescore. But after downloading MS2Rescore myself, it seems like one of Comet's pepXML or mzid outputs might have a chance of working. So I just tried a simple analysis and get these errors below using either the pepXML or mzid files as input. The zip file has the two identification files as well as the target+decoy yeast fasta. I'm less confident of Comet's mzid output as I don't use that format but Comet's pepXML output has been used for ages. Let me know if there's any hope of processing Comet's output through your tool. If not, I'll break the bad news to the user. Thanks!

pepXML log: image

mzid log: image

comet_example.zip

RalfG commented 4 months ago

Hi Jimmy,

Thanks for the detailed report and example files! We'll take a look at it. I think support for both should be feasible, but we'll start with pepXML.

Best, Ralf

RalfG commented 4 months ago

Hi @jke000,

Both pepXML and mzIdentML files from Comet should now be working with psm_utils 0.9.1, and by extent in MS²Rescore.

Best, Ralf

jke000 commented 3 months ago

I'll go let the researcher know of this, thanks Ralf.