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Question about PTMs in input sequence #2

Closed JannikSchneider12 closed 8 months ago

JannikSchneider12 commented 8 months ago

Hello everyone,

I want to use the model to rescore my peptide identifications. However the sequences contain also some PTMs in the form of the mass inside the string, e.g. "M+15.995VSDLAGEGVC+57.021K". Should I remove every modification for a correct rescoring or can I just pass them?

Thanks for your time and help

andradesalazar commented 8 months ago

Hi @JannikSchneider12,

thanks for reaching out. Spectralis is currently able to score peptides containing methionine oxidation (Mox) and carbamidomethyl (C) was specified as a fixed modification. That means your example sequence should be rescored without problems. For this, you would need to parse the residues M+15.995 and C+57.021 to the ProForma syntax, i.e. "M[UNIMOD:35]" and "C[UNIMOD:4]": "M[UNIMOD:35]VSDLAGEGVC[UNIMOD:4]". That should hopefully work.

Best, Daniela