Hi, I am using PTMprophet to localize the set of modifications (i.e. mass shifts) identified by running an open search with MSfragger, but I have some doubt regarding the interpretation of the output. In particular, MSfragger identified this peptide *GG(ox)MNGASPPTSQK* with a mass shift of 0.9869 Da, which match to the following modification according to Unimod 0.9840:Deamidated (Deamidation), 0.9840:Asn->Asp (Asn->Asp substitution), 0.9840:Gln->Glu (Gln->Glu substitution).
Of these 3 only the first 2 are possible (there is no Q in the sequence, so there cannot be any Gln->Glu substitution). Now, the output of PTMprophet is as follows: *G(0.000)G(0.000)M(0.000)N(0.000)G(0.000)A(0.000)S(0.000)P(0.000)P(0.000)T(0.000)S(0.000)Q(0.000)K(0.000)* Is a probability always 0 somehow an expected behavior? How do I interpret this? Am I right to say that the 0.9869 Da shift cannot be localized to any residues? My concerns comes from the fact that even if the mod cannot be localized, I would have expected to get a probability of (~0.008, i.e. 100/length of the peptides) for each residues... -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
