Hello Piero, It appears that the version of PTMProphet in Philosopher is a bit out of date. The latest TPP version is 5.1.0, and PTMProphet has been updated with bugfixes and new features in the meantime. I have run my latest PTMProphet code (targeted for the 5.2.0 version of TPP) on your data. For the PSMs matching this peptide I cannot replicate the issue you've reported. Instead, PTMProphet seems to be positioning the mass modification on the Asparagine in your peptide as you should see in the following result file:
https://www.dropbox.com/s/z3xf379ulljr3rr/01928_GA1_P020123_S00_R01_R1.PTMPro.pep.xml?dl=0 Thanks for your interest in PTMProphet. Cheers! -David On Fri, May 18, 2018 at 8:40 AM, Piero Giansanti <[email protected]> wrote: > 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 <[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. > -- 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.
