Sorry I got cut off. You can find the full parameter file I used here: https://dl.dropboxusercontent.com/u/21286225/tandem_params.xml
Next I had to modify PTMProphetParser.exe to be able to process this type of data. The updated binary can be found here: https://dl.dropboxusercontent.com/u/21286225/PTMProphetParser.exe After rerunning the search and xinteract with PeptideProphet and iProphet and verifying that I was getting good matches, I used the following settings for PTMProphetParsers: MZTOL=0.4 STY,79.966,M,15.995,nK,6.0318 I hope this helps you process your data on your own. If you still cannot get it to work based on this I can send you the actual pepXMl results as well. Thanks for continuing to use the TPP and for helping us improve the tools! -David On Tue, Aug 26, 2014 at 4:35 PM, David Shteynberg <[email protected]> wrote: > Dear Oded, > > Sorry it has taken me this long to work the bugs out in this analysis. > The first problem I found was with your search parameters. Instead > of using two different static mods on K and n-terminus (which is not > supported by TPP in a single search), I used a static mod in > combination with a variable mod so instead of: > <parameter name="residue, modification mass" > value="+57.021464@C,+28.031300@K,+28.031300@["/> > <parameter name="residue, modification mass 1" > value="+57.021464@C,+34.063117@K,+34.063117@["/> > <parameter name="residue, potential modification mass" > value="15.994915@M,79.966331@Y,79.966331@S,79.966331@T"/> > > we now have: > > > > > On Tue, Aug 12, 2014 at 1:19 PM, Jesse Meyer <[email protected]> wrote: >> Even though the cysteine mod is variable, I was able to successfully run >> PTMprophet by entering the cysteine mod as one of the PTMs for PTMprophet. >> Do you think this will cause problems? Also, what localization score should >> be used as a cutoff for correct localization? >> >> Thanks, >> 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 G. Meyer >> Ph. D. Candidate >> Department of Chemistry and Biochemistry >> University of California, San Diego >> [email protected] >> >> >> --- >> 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.
