I am also getting this error with a peptide containing a fixed modification of cysteine (N-ethylmaleimide +125.047679). I am running PTMprophet to localize a different variable modification on lysine. Do I need to enter all mods including fixed mods under PTMprophet in the Petunia GUI?
Thanks, Jesse On Saturday, July 12, 2014 7:13:57 AM UTC-7, [email protected] wrote: > > Sure. Let me know what you need and I will send you the data. > Best, > Oded > > On Saturday, July 12, 2014 5:11:39 AM UTC+10, David Shteynberg wrote: >> >> Hi Oded, >> >> >> It is likely there is an issue with PTMProphet that doesn't recognize >> the modifications in your dataset. If you can share a portion of your >> data for testing purposes I can help troubleshoot further. >> >> Thank you! >> -David >> >> On Tue, Jul 1, 2014 at 5:33 AM, Oded <[email protected]> wrote: >> > Hi all, >> > I am using TPP 4.7.1 on Win7 and currently trying to analyze data of >> > dimethylated phosphopeptides searched with X!tandem. >> > The searches were done by using 2 sets of fixed modifications for the >> Cys >> > alkylation plus light or heavy dimethylation on N-term and K with STY >> > phosphorylation, Met-Ox and protein N-term acetylation as set as >> variable >> > modifications. >> > When I try to run PTM prophet (following peptide prophet and iprophet >> runs) >> > I getting the following error: >> > >> > >> > EXECUTING: run_in >> c:/Inetpub/wwwroot/ISB/data/Oded/Enzo/Phospho_June2014; >> > c:\Inetpub\tpp-bin\PTMProphetParser >> > STY,79.966,C,57.021464,n,34.063117,K,34.063117,M,15.99 MZTOL=0.1 >> > >> c:/Inetpub/wwwroot/ISB/data/Oded/Enzo/Phospho_June2014/interactNative1.ipro.pep.xml >> >> >> > interactNative >> > INFO: Writing file interactNative1.ptm.pep.xml ... >> > INFO: Reading file >> > >> c:/Inetpub/wwwroot/ISB/data/Oded/Enzo/Phospho_June2014/interactNative1.ipro.pep.xml >> >> >> > ... >> > WARNING: Cannot initialize for sequence: n[71]M[147]KDEPRSTNLFMK, >> unknown >> > mods may exist in spectrum CHH20140618_M1HTiO2_100mM.03738.03738.2 >> > WARNING: Cannot initialize for sequence: n[35]K[162]S[167]PAAAR, >> unknown >> > mods may exist in spectrum CHH20140618_M1HTiO2_100mM.03900.03900.2 >> > WARNING: Cannot initialize for sequence: n[35]VPS[167]RHINIGR, unknown >> mods >> > may exist in spectrum CHH20140618_M1HTiO2_100mM.04358.04358.2 >> > WARNING: Cannot initialize for sequence: >> > n[35]EGEEPT[181]VYSDEEEPK[162]DESAR, unknown mods may exist in spectrum >> > CHH20140618_M1HTiO2_100mM.04499.04499.3 >> > WARNING: Cannot initialize for sequence: n[35]GTPGPAVR, unknown mods >> may >> > exist in spectrum CHH20140618_M1HTiO2_100mM.05584.05584.2 >> > WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162] >> > WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162] >> > WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162] >> > WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162] >> > WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162] >> > WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162] >> > {this appear 100-200 times} >> > >> > >> > >> > This application has requested the Runtime to terminate it in an >> unusual >> > way. >> > Please contact the application's support team for more information. >> > >> > command "c:\Inetpub\tpp-bin\PTMProphetParser >> > STY,79.966,C,57.021464,n,34.063117,K,34.063117,M,15.99 MZTOL=0.1 >> > >> c:/Inetpub/wwwroot/ISB/data/Oded/Enzo/Phospho_June2014/interactNative1.ipro.pep.xml >> >> >> > interactNative1.ptm.pep.xml" failed: No such process >> > >> > >> > I tried adding both heavy and light dimethylation (+28 and +34 on K and >> > N-term) just light and just heavy (as shown above), the the mass of the >> > DiMet N-term as it appear in the pepXML (+35 or +29) but the error is >> still >> > the same... >> > Is there a way to sort this? >> > Many thanks, >> > Oded >> > >> > -- >> > 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 http://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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
