Hello Piero, Thank you for trying the software. This is indeed an unusual result. Can you tell me which version of PTMProphet you are using and how you are running the tool? Is it possible for you to post your pepXML file and data file online for me to download and test this particular ID?
Cheers, -David On Fri, May 18, 2018 at 1:53 AM, Piero Giansanti <[email protected]> wrote: > 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. > -- 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.
