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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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PTM information is lost in pin and pout #81

Closed caetera closed 11 months ago

caetera commented 1 year ago

Hi,

it looks like the PTM information is lost in the PIN file produced by ms2rescore. PEPREC has a column with PTMS, but the PIN contains already just plain (stripped) peptide sequences and so does (obviously) the output. I wonder, is there any reason to strip the PTMs from the sequences or is it just a bug?

I believe PIN preserves SpecId from PEPREC, and, thus, one can "restore" PTMs if necessary, but I believe it would be much better if PTMs will be preserved in the output by default.

ArthurDeclercq commented 1 year ago

Hi @caetera,

It is indeed inconvenient that all the PTM information is lost in the pin and pout file by MS²Rescore. We will fix this bug in the next update of MS²Rescore!

Thank you for bringing this to our attention!

Cheers, Arthur

RalfG commented 11 months ago

Hi @caetera, Happy to say that this is now fixed in v3.0 of MS²Rescore.