You need to only enter the variable mods for PTMProphet. However, mods that are unknown will not be recognized without a change to the code. A future version of PTMProphet will hopefully correct these issues.
-David On Tue, Aug 12, 2014 at 11:59 AM, Jesse Meyer <[email protected]> wrote: > 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. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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