Hello Delphine, Sorry about the delay. I have compiled a linux version of PTMProphetParser and placed it in my Dropbox for your testing purposes, please see: https://dl.dropboxusercontent.com/u/21286225/PTMProphetParser
If you haven't compiled your own version from the latest source, this may be an alternative, although it may fail due to system dependencies. Let me know how it goes. Thank you, -David On Mon, Jun 8, 2015 at 2:30 AM, delphine wood <[email protected]> wrote: > Hi David, > > We will try to compile the PTMProphet code from the svn repository: could > you tell me how to access this repository please? > > Thanks. > > Delphine > > 2015-06-05 21:48 GMT+02:00 David Shteynberg < > [email protected]>: > >> Hi Delphine, >> >> Unfortunately, with the version of PTMProphet you have this will not be >> for you to process this type of data. For linux processing, you will need >> to compile and use the latest PTMProphet code from the SVN repository, as >> it is not available as a release yet. Alternatively, you can install the >> windows version of the code on another machine, migrate your results and >> run the binary I sent a link for that includes the latest PTMProphet code. >> Our build manager has recently switched jobs so the building of the >> software and the releases have been lagging behind the development at the >> moment. >> >> Thanks for you patience, >> >> -David >> >> >> >> On Fri, May 22, 2015 at 5:54 AM, Delphine <[email protected]> wrote: >> >>> Hello, >>> >>> I recently asked a question about mods error for the methylation >>> identifications with PTMprophet ( >>> https://mail.google.com/mail/u/0/#14d15557e5baa348_group_thread_1). You >>> helped me to partially solve the problem. Now I have to identify >>> methylation, di-methylations and tri-methylations on the same data. I >>> modified the interrogation parameter files: >>> -comet: >>> variable_mod01 = 15.9949 M 0 3 -1 0 >>> variable_mod02 = 14.015650 K 0 3 -1 0 >>> variable_mod03 = 28.031300 K 0 3 -1 0 >>> variable_mod04 = 42.046950 K 0 3 -1 0 >>> -xtandem: >>> <note type="input" label="residue, modification mass">57.021464@C</note> >>> >>> <note type="input" label="residue, potential modification >>> mass">15.994915@M,14.015650@K,28.03130@K,42.046950@K</note> >>> >>> >>> I combine the identification results with iprophet (file joined) and >>> tried to use PTMprophet on this file. >>> >>> Here is the command line: >>> >>> * cd /opt/tpp/data/327_05_01_1704_multimethylations; >>> /opt/tpp/bin/PTMProphetParser K,14.0156,K,28.03130,K,42.046950,M,15.9949 >>> MZTOL=0.2 >>> /opt/tpp/data/327_05_01_1704_multimethylations/327_05_01_014_150417_01_MTCS_0_D_interact.iproph.pep.xml >>> 327_05_01_014_150417_01_MTCS_0_D_interact.ptm.pep.xml * >>> Here is the error: >>> >>> >>> INFO: Writing file 327_05_01_014_150417_01_MTCS_0_D_interact.ptm.pep.xml ... >>> INFO: Reading file >>> /opt/tpp/data/327_05_01_1704_multimethylations/327_05_01_014_150417_01_MTCS_0_D_interact.iproph.pep.xml >>> ...WARNING: Illegal peptide with unknown mod: DGDPLEK[156]WARNING: Illegal >>> peptide with unknown mod: NLM[147]TGMKWARNING: Illegal peptide with unknown >>> mod: NLMTGM[147]KWARNING: Illegal peptide with unknown mod: >>> K[156]AGESHRWARNING: Illegal peptide with unknown mod: IITNLSK[156]WARNING: >>> Illegal peptide with unknown mod: AM[147]NVNPK[156]WARNING: Illegal peptide >>> with unknown mod: C[160]PGELPRWARNING: Illegal peptide with unknown mod: >>> LTPSM[147]LRWARNING: Illegal peptide with unknown mod: >>> VTAAMGK[156]KWARNING: Illegal peptide with unknown mod: >>> VTAAMGKK[156]WARNING: Illegal peptide with unknown mod: >>> M[147]ANEVIK[142]WARNING: Illegal peptide with unknown mod: >>> M[147]ALTQVRWARNING: Illegal peptide with unknown mod: >>> M[147]ADAK[156]QKWARNING: Illegal peptide with unknown mod: >>> M[147]ADAKQK[156]WARNING: Illegal peptide with unknown mod: >>> AM[147]EAELK[156]WARNING: Illegal peptide with unknown mod: >>> K[142]ANSMVKWARNING: Illegal peptide with unknown mod: >>> K[142]ANSM[147]VK[156]WARNING: Illegal peptide with unknown mod: >>> K[156]ANSM[147]VK[142]WARNING: Illegal peptide with unknown mod: >>> KANSMVK[142]WARNING: Illegal peptide with unknown mod: >>> K[142]VPSAPPKWARNING: Illegal peptide with unknown mod: >>> KVPSAPPK[142]WARNING: Illegal peptide with unknown mod: >>> AEHSELK[156]WARNING: Illegal peptide with unknown mod: AEHSELK[156]WARNING: >>> Illegal peptide with unknown mod: VASPK[156]ANKWARNING: Illegal peptide >>> with unknown mod: VASPKANK[156]WARNING: Illegal peptide with unknown mod: >>> AVDQRNK[142]WARNING: Illegal peptide with unknown mod: LATWK[156]PLWARNING: >>> Illegal peptide with unknown mod: AMAEWVK[156]WARNING: Illegal peptide with >>> unknown mod: DSFDIIK[156]WARNING: Illegal peptide with unknown mod: >>> VPPHM[147]LRWARNING: Illegal peptide with unknown mod: LPKAEDRWARNING: >>> Illegal peptide with unknown mod: LKDSLPRWARNING: Illegal peptide with >>> unknown mod: KEVPLSRWARNING: Illegal peptide with unknown mod: >>> AM[147]LAM[147]FK[156]WARNING: Illegal peptide with unknown mod: >>> QAVGPEDK[156]WARNING: Illegal peptide with unknown mod: AM[147]LEVHK[156] >>> WARNING: Unrecognized mod on peptide: DILTQLK[170]WARNING: Cannot >>> initialize for sequence: DILTQLK[170], unknown mods may exist in spectrum >>> 327_05_01_014_150417_01.15465.15465.2WARNING: Illegal peptide with unknown >>> mod: SSVC[160]IC[160]K[156] >>> Segmentation fault >>> >>> *Command FAILED* >>> >>> RETURN CODE:35584 >>> >>> >>> >>> Do you have any idea to solve this problem? What I am doing wrong? >>> >>> Thanks for your help >>> >>> Delphine >>> >>> -- >>> 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 a topic in the >> Google Groups "spctools-discuss" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/spctools-discuss/D3doJvfIepc/unsubscribe >> . >> To unsubscribe from this group and all its topics, 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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