Hello David, I am using PTMprophet via philosopher, and from the xml output it seems it is this version TPP v5.0.1 Post-Typhoon dev, Build 201706282113-exported (Linux-x86_64)
Regarding the settings, I am using --massdiffmode --mztol 0.01. The mass tolerance is not exactly the one used for the database search (20 ppm), but it should be somehow close to it. Here https://ufile.io/wiqqb the mzML, pepXML and the output I generated. Thanks On Friday, May 18, 2018 at 4:21:27 PM UTC+2, David Shteynberg wrote: > > 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 <p.gians...@gmail.com > <javascript:>> 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 spctools-discu...@googlegroups.com <javascript:>. >> To post to this group, send email to spctools...@googlegroups.com >> <javascript:>. >> 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
