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] <javascript:>> > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > Visit this group at http://groups.google.com/group/spctools-discuss. > > For more options, visit https://groups.google.com/d/optout. >
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