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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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Filtering of PSMs from MaxQuant Search #74

Closed jamc1996 closed 11 months ago

jamc1996 commented 2 years ago

Hello,

I noticed that MS2Rescore filters PSMs with duplicate scan IDs from MaxQuant search results as "non-rank 1 PSMs" but to my understanding MaxQuant reports multiple PSMs for chimeric spectra and so filtering these PSMs seems incorrect. Is it possible to configure MS2Rescore to avoid this?

Just wanted to clarify this, thank you for your help.

Best wishes, John.

RalfG commented 2 years ago

Hi John,

Unfortunately, it is an implementation limitation of MS²PIP to only process a single peptide per spectrum in the MGF file. Nevertheless, we are currently working on a major refactoring of the MS²Rescore code, so we may be able to fix this issue in the process.

Best, Ralf

RalfG commented 11 months ago

Closing in favor of #83 (same feature request).

Multi-rank rescoring is now implicitly supported in MS²Rescore v3.0.