Hi Jesse, I am not certain I fully understand the issue, but it sounds to me like you have multiple searches and should therefore have multiple pepXML files (from you heavy and light). I would suggest you modify your pipeline slightly by analyzing the heavy and the light searches separately and combining them only after PTMProphet has processed the results. Is this feasible?
Thanks, -David On Mon, Dec 15, 2014 at 2:28 PM, Jesse <[email protected]> wrote: > > David, > > I think I need to have some modifications added to the TPP code for > PTMprophet to work. I trying to combine two database searches that specify > either fixed light lysine or fixed heavy lysine (+8.0142), both with > variable modification of diGlycine (+114.0429). Therefore, lysine in my > datasets is found modified with +8.0142, +114.0429, or +122.0572. If you > add these to TPP, will I be able to combine these searches and validate the > mods with PTMprophet? > > Any help would be appreciated. > > Thank you, > Jesse > > On 8/12/2014 1:16 PM, David Shteynberg wrote: > >> 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. >>> >> > > -- > Jesse Meyer > Graduate Student > Department of Chemistry and Biochemistry > University of California, San Diego > La Jolla, CA 92092 > > > --- > This email is free from viruses and malware because avast! Antivirus > protection is active. > http://www.avast.com > > -- > 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.
