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compomics / ms2rescore

Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
https://ms2rescore.readthedocs.io
Apache License 2.0
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Support different levels of confidence estimates when using mokapot #112

Open jonasscheid opened 7 months ago

jonasscheid commented 7 months ago

Currently PSMs are evaluated using psm-level FDR when using mokapot see here Peptide-level confidence estimates are also present in the object mokapot returns. Would be of interest to give the user the freedom to choose the FDR-level

RalfG commented 7 months ago

Agreed that this could be reported somehow. The main issue blocking this is that the (output) object in MSĀ²Rescore is the PSM list, which has only PSM-level entries. Would you repeat each peptide/protein-level q-value and PEP for each PSM linked to these? Remaining issue then is how to deal with PSMs linked to multiple protein groups. Or am I missing something? Ideas are very much welcome!

jonasscheid commented 7 months ago

Would you repeat each peptide/protein-level q-value and PEP for each PSM linked to these?

Yes I had that also in mind! But for peptides mapping to multiple proteins that is indeed a tricky one.. One ad-hoc idea I have for protein-level fdr is to store a dict of proteins with the confidence estimates in provenance_data, but then again provenance_data : dict[str, str] so that is currently not possible. Maybe only support peptide-level-fdr for now? šŸ¤”