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.
