Thank David. I will give a try. Oded On Wednesday, August 27, 2014 9:43:11 AM UTC+10, David Shteynberg wrote: > > 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] <javascript:>> 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] > <javascript:>> 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] > <javascript:>> > >>> 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] <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. > >> > >> > >> > >> -- > >> Jesse G. Meyer > >> Ph. D. Candidate > >> Department of Chemistry and Biochemistry > >> University of California, San Diego > >> [email protected] <javascript:> > >> > >> > >> --- > >> 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] <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. >
-- 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.
