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pFindStudio / pGlyco3

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Incorrect amino acid in result #20

Closed elcientifico closed 1 year ago

elcientifico commented 1 year ago

I've been using pGlyco3 for some searches and I've noticed that it will substitute J for N . For example, I will run a search with only one protein that has a sequence 'MNDT' and the result will say that the peptide sequence for this protein is 'MJDT'. In the PeptideMH column with will report the mass for 'MNDT' + 1: 480.158

Perhaps this has something to do with the mass of Isoleucine and Leucine being 1 less than for N.

jalew188 commented 1 year ago

Peptide MH refers to the mass of peptide plus a proton

elcientifico commented 1 year ago

Thanks. That's what I noted in the original comment (mass of MNDT + 1). The issue is that in the results pGlyco3 changes the N to a J even though the PeptideMH will match the expected value for MNDT.

If the PeptideMH value is the mass of 'MNDT' + 1 (proton mass), why does pGlyco3 say that the sequence is MJDT ? the MJDT PeptideMH is smaller than MNDT PeptideMH

jalew188 commented 1 year ago

Ahh, we replaced all N by J with motif N-X-S/T/C.