Hello Delphine, I have discovered the bug in Mascot2XML that was getting the masses wrong in the pepXML. You will need to reconvert from the dat file and rerun the PeptideProphet Mascot analysis followed by iProphet analysis followed by PTMProphet.
The corrected Mascol2XML binary for windows can be downloaded here for now: https://dl.dropboxusercontent.com/u/21286225/Mascot2XML.exe The updated version of PTMProphetParser for windows can be found here for now: https://dl.dropboxusercontent.com/u/21286225/PTMProphetParser.exe Backup and replace the copies you have in C:\Inetpub\tpp-bin with these copies if you want to test it out. Thanks, -David On Fri, May 1, 2015 at 11:27 AM, David Shteynberg < [email protected]> wrote: > Hello Delphine, > > I ran the new version, which gives more information. The problem here is > that MASCOT generated and reported massed in the pepXML file are not close > enough to the PTMProphet computed masses. The error is small <0.01 for K > methylation and is likely related to the masses used internally in MASCOT > being different from those used internally by the other search engines you > applied. > > If you can send me the dat file I can dig deeper into the MASCOT issue. > > Thanks, > -David > > Here are the new warnings: > > *EXECUTING: cd c:/Inetpub/wwwroot/ISB/data/Delphine&& > c:\Inetpub\tpp-bin\PTMProphetParser > CQ,-17.0265,M,15.995,K,14.0156,E,-18.0106,n,42.0106 MZTOL=0.2 > c:/Inetpub/wwwroot/ISB/data/Delphine/327_05_01_020_150417_01_MTCS_0_D_interact.iproph.pep.xml > interact.ptm.pep.xml * > > INFO: Writing file interact.ptm.pep.xml ... > INFO: Reading file > c:/Inetpub/wwwroot/ISB/data/Delphine/327_05_01_020_150417_01_MTCS_0_D_interact.iproph.pep.xml > ...WARNING: Illegal peptide found in pepXML with non-matching mass: > GTAGK[142]VIK[142] > Neutral Mass (from pepXML) = 800.52 > Neutral Computed Mass for Evaluation = 800.512WARNING: Illegal peptide > found in pepXML with non-matching mass: ILVAIM[147]K[142] > Neutral Mass (from pepXML) = 816.522 > Neutral Computed Mass for Evaluation = 816.514WARNING: Illegal peptide > found in pepXML with non-matching mass: VTNLHVK[142] > Neutral Mass (from pepXML) = 823.499 > Neutral Computed Mass for Evaluation = 823.492WARNING: Illegal peptide > found in pepXML with non-matching mass: ALK[142]EPPR > Neutral Mass (from pepXML) = 823.499 > Neutral Computed Mass for Evaluation = 823.492WARNING: Illegal peptide > found in pepXML with non-matching mass: ALK[142]EPPR > Neutral Mass (from pepXML) = 823.499 > Neutral Computed Mass for Evaluation = 823.492WARNING: Illegal peptide > found in pepXML with non-matching mass: ALK[142]EPPR > Neutral Mass (from pepXML) = 823.499 > Neutral Computed Mass for Evaluation = 823.492WARNING: Illegal peptide > found in pepXML with non-matching mass: K[142]EGVK[142]PR > Neutral Mass (from pepXML) = 840.526 > Neutral Computed Mass for Evaluation = 840.518WARNING: Illegal peptide > found in pepXML with non-matching mass: VLEPENK[142] > Neutral Mass (from pepXML) = 841.462 > Neutral Computed Mass for Evaluation = 841.455WARNING: Illegal peptide > found in pepXML with non-matching mass: VLNILEK[142] > Neutral Mass (from pepXML) = 841.535 > Neutral Computed Mass for Evaluation = 841.527WARNING: Illegal peptide > found in pepXML with non-matching mass: WLVVPDK[142] > Neutral Mass (from pepXML) = 869.509 > Neutral Computed Mass for Evaluation = 869.501WARNING: Illegal peptide > found in pepXML with non-matching mass: LLLTTPAK[142] > Neutral Mass (from pepXML) = 869.566 > Neutral Computed Mass for Evaluation = 869.559WARNING: Illegal peptide > found in pepXML with non-matching mass: K[142]PHPPKR > Neutral Mass (from pepXML) = 872.542 > Neutral Computed Mass for Evaluation = 872.534WARNING: Illegal peptide > found in pepXML with non-matching mass: KPHPPK[142]R > Neutral Mass (from pepXML) = 872.542 > Neutral Computed Mass for Evaluation = 872.534WARNING: Illegal peptide > found in pepXML with non-matching mass: DADFNGTK[142] > Neutral Mass (from pepXML) = 880.4 > Neutral Computed Mass for Evaluation = 880.393WARNING: Illegal peptide > found in pepXML with non-matching mass: LYSC[160]TPR > Neutral Mass (from pepXML) = 895.43 > Neutral Computed Mass for Evaluation = 895.422WARNING: Illegal peptide > found in pepXML with non-matching mass: KAVVVC[160]PK > Neutral Mass (from pepXML) = 899.534 > Neutral Computed Mass for Evaluation = 899.526WARNING: Illegal peptide > found in pepXML with non-matching mass: KTPM[147]C[160]EK > Neutral Mass (from pepXML) = 908.417 > Neutral Computed Mass for Evaluation = 908.41WARNING: Illegal peptide > found in pepXML with non-matching mass: LAALAEALK[142] > Neutral Mass (from pepXML) = 912.572 > Neutral Computed Mass for Evaluation = 912.564WARNING: Illegal peptide > found in pepXML with non-matching mass: VK[142]THLFR > Neutral Mass (from pepXML) = 913.558 > Neutral Computed Mass for Evaluation = 913.55WARNING: Illegal peptide > found in pepXML with non-matching mass: M[147]EFLKQK > Neutral Mass (from pepXML) = 938.497 > Neutral Computed Mass for Evaluation = 938.49WARNING: Illegal peptide > found in pepXML with non-matching mass: M[147]DK[142]TFER > Neutral Mass (from pepXML) = 955.451 > Neutral Computed Mass for Evaluation = 955.443WARNING: Illegal peptide > found in pepXML with non-matching mass: GAGM[147]SFSRK > Neutral Mass (from pepXML) = 955.462 > Neutral Computed Mass for Evaluation = 955.455WARNING: Illegal peptide > found in pepXML with non-matching mass: ALLVYC[160]VK > Neutral Mass (from pepXML) = 964.549 > Neutral Computed Mass for Evaluation = 964.542WARNING: Illegal peptide > found in pepXML with non-matching mass: ALLVYC[160]VK > Neutral Mass (from pepXML) = 964.549 > Neutral Computed Mass for Evaluation = 964.542WARNING: Illegal peptide > found in pepXML with non-matching mass: VFISC[160]K[142]VQ > Neutral Mass (from pepXML) = 993.54 > Neutral Computed Mass for Evaluation = 993.532WARNING: Illegal peptide > found in pepXML with non-matching mass: VM[147]LYPSRI > Neutral Mass (from pepXML) = 993.539 > Neutral Computed Mass for Evaluation = 993.532WARNING: Illegal peptide > found in pepXML with non-matching mass: M[147]C[160]GDC[160]VEK > Neutral Mass (from pepXML) = 1013.37 > Neutral Computed Mass for Evaluation = 1013.36WARNING: Illegal peptide > found in pepXML with non-matching mass: LSLHLSPIK[142] > Neutral Mass (from pepXML) = 1020.64 > Neutral Computed Mass for Evaluation = 1020.63WARNING: Illegal peptide > found in pepXML with non-matching mass: M[147]SVNISTAGK > Neutral Mass (from pepXML) = 1022.51 > Neutral Computed Mass for Evaluation = 1022.51WARNING: Illegal peptide > found in pepXML with non-matching mass: NLMANRPAK[142] > Neutral Mass (from pepXML) = 1027.57 > Neutral Computed Mass for Evaluation = 1027.56WARNING: Illegal peptide > found in pepXML with non-matching mass: TAM[147]LLALQR > Neutral Mass (from pepXML) = 1031.59 > Neutral Computed Mass for Evaluation = 1031.58WARNING: Illegal peptide > found in pepXML with non-matching mass: LSSC[160]KPPKK > Neutral Mass (from pepXML) = 1043.59 > Neutral Computed Mass for Evaluation = 1043.58WARNING: Illegal peptide > found in pepXML with non-matching mass: K[142]QLYPFFK > Neutral Mass (from pepXML) = 1083.62 > Neutral Computed Mass for Evaluation = 1083.61WARNING: Illegal peptide > found in pepXML with non-matching mass: KQLYPFFK[142] > Neutral Mass (from pepXML) = 1083.62 > Neutral Computed Mass for Evaluation = 1083.61WARNING: Illegal peptide > found in pepXML with non-matching mass: TK[142]LNYNPPK > Neutral Mass (from pepXML) = 1087.61 > Neutral Computed Mass for Evaluation = 1087.6WARNING: Illegal peptide > found in pepXML with non-matching mass: TKLNYNPPK[142] > Neutral Mass (from pepXML) = 1087.61 > Neutral Computed Mass for Evaluation = 1087.6WARNING: Illegal peptide > found in pepXML with non-matching mass: IIK[142]ALDLPAK > Neutral Mass (from pepXML) = 1094.71 > Neutral Computed Mass for Evaluation = 1094.71WARNING: Illegal peptide > found in pepXML with non-matching mass: IIKALDLPAK[142] > Neutral Mass (from pepXML) = 1094.71 > Neutral Computed Mass for Evaluation = 1094.71WARNING: Illegal peptide > found in pepXML with non-matching mass: VK[142]PNVAVLSR > Neutral Mass (from pepXML) = 1095.68 > Neutral Computed Mass for Evaluation = 1095.68WARNING: Illegal peptide > found in pepXML with non-matching mass: ASSLPSSAPAVK[142] > Neutral Mass (from pepXML) = 1127.63 > Neutral Computed Mass for Evaluation = 1127.62WARNING: Illegal peptide > found in pepXML with non-matching mass: SLASSAQPGLGK[142] > Neutral Mass (from pepXML) = 1128.62 > Neutral Computed Mass for Evaluation = 1128.61WARNING: Illegal peptide > found in pepXML with non-matching mass: AEM[147]EELM[147]EK > Neutral Mass (from pepXML) = 1140.48 > Neutral Computed Mass for Evaluation = 1140.47WARNING: Illegal peptide > found in pepXML with non-matching mass: NDC[160]TTQSNVK > Neutral Mass (from pepXML) = 1165.51 > Neutral Computed Mass for Evaluation = 1165.5WARNING: Illegal peptide > found in pepXML with non-matching mass: LNK[142]TPIPQTK[142] > Neutral Mass (from pepXML) = 1166.71 > Neutral Computed Mass for Evaluation = 1166.7WARNING: Illegal peptide > found in pepXML with non-matching mass: SSLLGTGITSPK[142] > Neutral Mass (from pepXML) = 1173.67 > Neutral Computed Mass for Evaluation = 1173.66WARNING: Illegal peptide > found in pepXML with non-matching mass: LIDLC[160]QPTQK[142] > Neutral Mass (from pepXML) = 1228.66 > Neutral Computed Mass for Evaluation = 1228.65WARNING: Illegal peptide > found in pepXML with non-matching mass: RNQDRPSLLK[142] > Neutral Mass (from pepXML) = 1239.71 > Neutral Computed Mass for Evaluation = 1239.7WARNING: Illegal peptide > found in pepXML with non-matching mass: K[142]RPDEMLLPK > Neutral Mass (from pepXML) = 1239.71 > Neutral Computed Mass for Evaluation = 1239.7WARNING: Illegal peptide > found in pepXML with non-matching mass: KRPDEMLLPK[142] > Neutral Mass (from pepXML) = 1239.71 > Neutral Computed Mass for Evaluation = 1239.7WARNING: Illegal peptide > found in pepXML with non-matching mass: LAERPNIKM[147]R > Neutral Mass (from pepXML) = 1242.69 > Neutral Computed Mass for Evaluation = 1242.69WARNING: Illegal peptide > found in pepXML with non-matching mass: K[142]ITGEIMHALK > Neutral Mass (from pepXML) = 1253.72 > Neutral Computed Mass for Evaluation = 1253.72WARNING: Illegal peptide > found in pepXML with non-matching mass: KITGEIMHALK[142] > Neutral Mass (from pepXML) = 1253.72 > Neutral Computed Mass for Evaluation = 1253.72WARNING: Illegal peptide > found in pepXML with non-matching mass: NVQTPQC[160]K[142]LR > Neutral Mass (from pepXML) = 1256.67 > Neutral Computed Mass for Evaluation = 1256.67WARNING: Illegal peptide > found in pepXML with non-matching mass: VGAWGISGEPRK[142] > Neutral Mass (from pepXML) = 1269.69 > Neutral Computed Mass for Evaluation = 1269.68WARNING: Illegal peptide > found in pepXML with non-matching mass: DLLHPSPEEEK[142] > Neutral Mass (from pepXML) = 1306.65 > Neutral Computed Mass for Evaluation = 1306.64WARNING: Illegal peptide > found in pepXML with non-matching mass: GALGPGGPLGHPGEK[142] > Neutral Mass (from pepXML) = 1356.72 > Neutral Computed Mass for Evaluation = 1356.71WARNING: Illegal peptide > found in pepXML with non-matching mass: KAGTVM[147]FEYGMR > Neutral Mass (from pepXML) = 1404.66 > Neutral Computed Mass for Evaluation = 1404.65WARNING: Illegal peptide > found in pepXML with non-matching mass: KAGTVMFEYGM[147]R > Neutral Mass (from pepXML) = 1404.66 > Neutral Computed Mass for Evaluation = 1404.65WARNING: Illegal peptide > found in pepXML with non-matching mass: REENQNEVNM[147]K > Neutral Mass (from pepXML) = 1405.63 > Neutral Computed Mass for Evaluation = 1405.63WARNING: Illegal peptide > found in pepXML with non-matching mass: K[142]NSGC[160]TEVC[160]HTR > Neutral Mass (from pepXML) = 1461.65 > Neutral Computed Mass for Evaluation = 1461.65WARNING: Illegal peptide > found in pepXML with non-matching mass: QILLLLPVM[147]INM[147]LK[142] > Neutral Mass (from pepXML) = 1684.01 > Neutral Computed Mass for Evaluation = 1684WARNING: Illegal peptide > found in pepXML with non-matching mass: QILLLLPVM[147]INM[147]LK[142] > Neutral Mass (from pepXML) = 1684.01 > Neutral Computed Mass for Evaluation = 1684WARNING: Illegal peptide > found in pepXML with non-matching mass: LQGEGLSVAGIVC[160]HVGK > Neutral Mass (from pepXML) = 1722.92 > Neutral Computed Mass for Evaluation = 1722.91WARNING: Illegal peptide > found in pepXML with non-matching mass: SWAEAYK[142]DLENSDEFK[142] > Neutral Mass (from pepXML) = 1958.9 > Neutral Computed Mass for Evaluation = 1958.89WARNING: Illegal peptide > found in pepXML with non-matching mass: DLVSGGSNEGNGK[142]EDWAMK[142] > Neutral Mass (from pepXML) = 2020.92 > Neutral Computed Mass for Evaluation = 2020.92WARNING: Illegal peptide > found in pepXML with non-matching mass: AVATGKM[147]DENQFVAVTSTNAAK > Neutral Mass (from pepXML) = 2268.11 > Neutral Computed Mass for Evaluation = 2268.11WARNING: Illegal peptide > found in pepXML with non-matching mass: LPMASSMEHGK[142]DLPSVQLLMK[142] > Neutral Mass (from pepXML) = 2339.21 > Neutral Computed Mass for Evaluation = 2339.21WARNING: Illegal peptide > found in pepXML with non-matching mass: M[147]QILTPPLQSSVELVADPETR > Neutral Mass (from pepXML) = 2339.21 > Neutral Computed Mass for Evaluation = 2339.2WARNING: Illegal peptide > found in pepXML with non-matching mass: LTPTEIVLILPM[147]PEQRNSLTAK[142] > Neutral Mass (from pepXML) = 2493.4 > Neutral Computed Mass for Evaluation = 2493.39WARNING: Illegal peptide > found in pepXML with non-matching mass: QKLC[160]YVSQGNASFTYGYEYLGC[160]TSR > Neutral Mass (from pepXML) = 2951.33 > Neutral Computed Mass for Evaluation = 2951.32WARNING: Illegal peptide > found in pepXML with non-matching mass: DNEIQMDMTLGPIEEAYAILNRFEVEVTK[142] > Neutral Mass (from pepXML) = 3381.66 > Neutral Computed Mass for Evaluation = 3381.65WARNING: Illegal peptide > found in pepXML with non-matching mass: > QM[147]GQEIGNELDEQNEIIDDLANLVENTDEK[142] > Neutral Mass (from pepXML) = 3445.58 > Neutral Computed Mass for Evaluation = 3445.57WARNING: Illegal peptide > found in pepXML with non-matching mass: > HLVC[160]SFRLYPFTVHTVSPGNSHLALYQVFK[142] > Neutral Mass (from pepXML) = 3530.84 > Neutral Computed Mass for Evaluation = 3530.83WARNING: Illegal peptide > found in pepXML with non-matching mass: > EVK[142]VYLLTTSSAPYC[160]NAFQLLTVAPNHGISLK[142] > Neutral Mass (from pepXML) = 3561.9 > Neutral Computed Mass for Evaluation = 3561.89WARNING: Illegal peptide > found in pepXML with non-matching mass: > K[142]GNFQLQGTM[147]LSDGQGFTQDDVQAAEVTYGAMAR > Neutral Mass (from pepXML) = 3663.7 > Neutral Computed Mass for Evaluation = 3663.69WARNING: Illegal peptide > found in pepXML with non-matching mass: > K[142]GNFQLQGTMLSDGQGFTQDDVQAAEVTYGAM[147]AR > Neutral Mass (from pepXML) = 3663.7 > Neutral Computed Mass for Evaluation = 3663.69WARNING: Illegal peptide > found in pepXML with non-matching mass: > EESLHSILAGSDM[147]TVSQILLTQHGIPVM[147]NLSDGK[142] > Neutral Mass (from pepXML) = 3665.84 > Neutral Computed Mass for Evaluation = 3665.83WARNING: Illegal peptide > found in pepXML with non-matching mass: > DPPAQC[160]SAGPVGDDM[147]FHWQATIM[147]GPISNYMLDN > Neutral Mass (from pepXML) = 3666.56 > Neutral Computed Mass for Evaluation = 3666.55WARNING: Illegal peptide > found in pepXML with non-matching mass: > DPPAQC[160]SAGPVGDDM[147]FHWQATIMGPISNYM[147]LDN > Neutral Mass (from pepXML) = 3666.56 > Neutral Computed Mass for Evaluation = 3666.55WARNING: Illegal peptide > found in pepXML with non-matching mass: > DPPAQC[160]SAGPVGDDMFHWQATIM[147]GPISNYM[147]LDN > Neutral Mass (from pepXML) = 3666.56 > Neutral Computed Mass for Evaluation = 3666.55WARNING: Illegal peptide > found in pepXML with non-matching mass: > LYC[160]NGDGEWM[147]VPIGRC[160]TC[160]K[142]PGYEPENSVAC[160]K > Neutral Mass (from pepXML) = 3676.6 > Neutral Computed Mass for Evaluation = 3676.59WARNING: Illegal peptide > found in pepXML with non-matching mass: > LYC[160]NGDGEWM[147]VPIGRC[160]TC[160]KPGYEPENSVAC[160]K[142] > Neutral Mass (from pepXML) = 3676.6 > Neutral Computed Mass for Evaluation = 3676.59WARNING: Illegal peptide > found in pepXML with non-matching mass: > ASVDSGNEDIIEALISLFYGVM[147]TPMLNPLIYSLR > Neutral Mass (from pepXML) = 3756.91 > Neutral Computed Mass for Evaluation = 3756.9WARNING: Illegal peptide > found in pepXML with non-matching mass: > ASVDSGNEDIIEALISLFYGVMTPM[147]LNPLIYSLR > Neutral Mass (from pepXML) = 3756.91 > Neutral Computed Mass for Evaluation = 3756.9WARNING: Illegal peptide > found in pepXML with non-matching mass: > M[147]GFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGK > Neutral Mass (from pepXML) = 3780.94 > Neutral Computed Mass for Evaluation = 3780.93WARNING: Illegal peptide > found in pepXML with non-matching mass: > MGFNRPSKIQENALPLM[147]LAEPPQNLIAQSQSGTGK > Neutral Mass (from pepXML) = 3780.94 > Neutral Computed Mass for Evaluation = 3780.93WARNING: Illegal peptide > found in pepXML with non-matching mass: > GFPSQC[160]YSAQTLPELC[160]SPQDELDFLM[147]EALIISK > Neutral Mass (from pepXML) = 3802.79 > Neutral Computed Mass for Evaluation = 3802.78WARNING: Illegal peptide > found in pepXML with non-matching mass: > LYTM[147]DGITVTVADLFFAGTETTSTTLRYGLLILMK[142] > Neutral Mass (from pepXML) = 3885.03 > Neutral Computed Mass for Evaluation = 3885.02WARNING: Illegal peptide > found in pepXML with non-matching mass: > LYTMDGITVTVADLFFAGTETTSTTLRYGLLILM[147]K[142] > Neutral Mass (from pepXML) = 3885.03 > Neutral Computed Mass for Evaluation = 3885.02WARNING: Illegal peptide > found in pepXML with non-matching mass: > FVHKSFVEVNEEGTEAAAASSC[160]FVVAEC[160]C[160]M[147]ESGPR > Neutral Mass (from pepXML) = 3906.7 > Neutral Computed Mass for Evaluation = 3906.7WARNING: Illegal peptide > found in pepXML with non-matching mass: > GPLLAQEM[147]PTVSVLEYALPQRPPQGPEDDRDLSER > Neutral Mass (from pepXML) = 3918.95 > Neutral Computed Mass for Evaluation = 3918.94 > > *Command Successful* > RETURN CODE:0 > > > > > On Thu, Apr 30, 2015 at 2:18 AM, delphine wood <[email protected]> wrote: > >> Hi, >> >> I send you the mzxml file through wetransfer. >> I tried with this command >> * /opt/tpp/bin/PTMProphetParser STY,79.966,K,14.0156,M,15.995 MZTOL=0.2 >> /opt/tpp/data/327_05_01/327_05_01_020_150417_01_MTCS_0_D_interact.iproph.pep.xml >> interact.ptm.pep.xml * >> >> I got these warnings: >> >> INFO: Writing file interact.ptm.pep.xml ... >> INFO: Reading file >> /opt/tpp/data/327_05_01/327_05_01_020_150417_01_MTCS_0_D_interact.iproph.pep.xml >> ...WARNING: Illegal peptide with unknown mod: GTAGK[142]VIK[142]WARNING: >> Illegal peptide with unknown mod: ILVAIM[147]K[142]WARNING: Illegal peptide >> with unknown mod: VTNLHVK[142]WARNING: Illegal peptide with unknown mod: >> ALK[142]EPPRWARNING: Illegal peptide with unknown mod: ALK[142]EPPRWARNING: >> Illegal peptide with unknown mod: ALK[142]EPPRWARNING: Illegal peptide with >> unknown mod: K[142]EGVK[142]PRWARNING: Illegal peptide with unknown mod: >> VLEPENK[142]WARNING: Illegal peptide with unknown mod: VLNILEK[142]WARNING: >> Illegal peptide with unknown mod: WLVVPDK[142]WARNING: Illegal peptide with >> unknown mod: LLLTTPAK[142]WARNING: Illegal peptide with unknown mod: >> K[142]PHPPKRWARNING: Illegal peptide with unknown mod: KPHPPK[142]RWARNING: >> Illegal peptide with unknown mod: DADFNGTK[142]WARNING: Illegal peptide with >> unknown mod: LYSC[160]TPRWARNING: Illegal peptide with unknown mod: >> KAVVVC[160]PKWARNING: Illegal peptide with unknown mod: >> KTPM[147]C[160]EKWARNING: Illegal peptide with unknown mod: >> LAALAEALK[142]WARNING: Illegal peptide with unknown mod: >> VK[142]THLFRWARNING: Illegal peptide with unknown mod: M[147]EFLKQKWARNING: >> Illegal peptide with unknown mod: M[147]DK[142]TFERWARNING: Illegal peptide >> with unknown mod: GAGM[147]SFSRKWARNING: Illegal peptide with unknown mod: >> ALLVYC[160]VKWARNING: Illegal peptide with unknown mod: >> ALLVYC[160]VKWARNING: Illegal peptide with unknown mod: >> VFISC[160]K[142]VQWARNING: Illegal peptide with unknown mod: >> VM[147]LYPSRIWARNING: Illegal peptide with unknown mod: >> M[147]C[160]GDC[160]VEKWARNING: Illegal peptide with unknown mod: >> LSLHLSPIK[142]WARNING: Illegal peptide with unknown mod: >> M[147]SVNISTAGKWARNING: Illegal peptide with unknown mod: >> NLMANRPAK[142]WARNING: Illegal peptide with unknown mod: >> TAM[147]LLALQRWARNING: Illegal peptide with unknown mod: >> LSSC[160]KPPKKWARNING: Illegal peptide with unknown mod: >> K[142]QLYPFFKWARNING: Illegal peptide with unknown mod: >> KQLYPFFK[142]WARNING: Illegal peptide with unknown mod: >> TK[142]LNYNPPKWARNING: Illegal peptide with unknown mod: >> TKLNYNPPK[142]WARNING: Illegal peptide with unknown mod: >> IIK[142]ALDLPAKWARNING: Illegal peptide with unknown mod: >> IIKALDLPAK[142]WARNING: Illegal peptide with unknown mod: >> VK[142]PNVAVLSRWARNING: Illegal peptide with unknown mod: >> ASSLPSSAPAVK[142]WARNING: Illegal peptide with unknown mod: >> SLASSAQPGLGK[142]WARNING: Illegal peptide with unknown mod: >> AEM[147]EELM[147]EKWARNING: Illegal peptide with unknown mod: >> NDC[160]TTQSNVKWARNING: Illegal peptide with unknown mod: >> LNK[142]TPIPQTK[142]WARNING: Illegal peptide with unknown mod: >> SSLLGTGITSPK[142]WARNING: Illegal peptide with unknown mod: >> LIDLC[160]QPTQK[142]WARNING: Illegal peptide with unknown mod: >> RNQDRPSLLK[142]WARNING: Illegal peptide with unknown mod: >> K[142]RPDEMLLPKWARNING: Illegal peptide with unknown mod: >> KRPDEMLLPK[142]WARNING: Illegal peptide with unknown mod: >> LAERPNIKM[147]RWARNING: Illegal peptide with unknown mod: >> K[142]ITGEIMHALKWARNING: Illegal peptide with unknown mod: >> KITGEIMHALK[142]WARNING: Illegal peptide with unknown mod: >> NVQTPQC[160]K[142]LRWARNING: Illegal peptide with unknown mod: >> VGAWGISGEPRK[142]WARNING: Illegal peptide with unknown mod: >> DLLHPSPEEEK[142]WARNING: Illegal peptide with unknown mod: >> GALGPGGPLGHPGEK[142]WARNING: Illegal peptide with unknown mod: >> KAGTVM[147]FEYGMRWARNING: Illegal peptide with unknown mod: >> KAGTVMFEYGM[147]RWARNING: Illegal peptide with unknown mod: >> REENQNEVNM[147]KWARNING: Illegal peptide with unknown mod: >> K[142]NSGC[160]TEVC[160]HTRWARNING: Illegal peptide with unknown mod: >> QILLLLPVM[147]INM[147]LK[142]WARNING: Illegal peptide with unknown mod: >> QILLLLPVM[147]INM[147]LK[142]WARNING: Illegal peptide with unknown mod: >> LQGEGLSVAGIVC[160]HVGKWARNING: Illegal peptide with unknown mod: >> SWAEAYK[142]DLENSDEFK[142]WARNING: Illegal peptide with unknown mod: >> DLVSGGSNEGNGK[142]EDWAMK[142]WARNING: Illegal peptide with unknown mod: >> AVATGKM[147]DENQFVAVTSTNAAKWARNING: Illegal peptide with unknown mod: >> LPMASSMEHGK[142]DLPSVQLLMK[142]WARNING: Illegal peptide with unknown mod: >> M[147]QILTPPLQSSVELVADPETRWARNING: Illegal peptide with unknown mod: >> LTPTEIVLILPM[147]PEQRNSLTAK[142]WARNING: Illegal peptide with unknown mod: >> QKLC[160]YVSQGNASFTYGYEYLGC[160]TSRWARNING: Illegal peptide with unknown >> mod: DNEIQMDMTLGPIEEAYAILNRFEVEVTK[142]WARNING: Illegal peptide with unknown >> mod: QM[147]GQEIGNELDEQNEIIDDLANLVENTDEK[142]WARNING: Illegal peptide with >> unknown mod: HLVC[160]SFRLYPFTVHTVSPGNSHLALYQVFK[142]WARNING: Illegal >> peptide with unknown mod: >> EVK[142]VYLLTTSSAPYC[160]NAFQLLTVAPNHGISLK[142]WARNING: Illegal peptide with >> unknown mod: K[142]GNFQLQGTM[147]LSDGQGFTQDDVQAAEVTYGAMARWARNING: Illegal >> peptide with unknown mod: >> K[142]GNFQLQGTMLSDGQGFTQDDVQAAEVTYGAM[147]ARWARNING: Illegal peptide with >> unknown mod: EESLHSILAGSDM[147]TVSQILLTQHGIPVM[147]NLSDGK[142]WARNING: >> Illegal peptide with unknown mod: >> DPPAQC[160]SAGPVGDDM[147]FHWQATIM[147]GPISNYMLDNWARNING: Illegal peptide >> with unknown mod: DPPAQC[160]SAGPVGDDM[147]FHWQATIMGPISNYM[147]LDNWARNING: >> Illegal peptide with unknown mod: >> DPPAQC[160]SAGPVGDDMFHWQATIM[147]GPISNYM[147]LDNWARNING: Illegal peptide >> with unknown mod: >> LYC[160]NGDGEWM[147]VPIGRC[160]TC[160]K[142]PGYEPENSVAC[160]KWARNING: >> Illegal peptide with unknown mod: >> LYC[160]NGDGEWM[147]VPIGRC[160]TC[160]KPGYEPENSVAC[160]K[142]WARNING: >> Illegal peptide with unknown mod: >> ASVDSGNEDIIEALISLFYGVM[147]TPMLNPLIYSLRWARNING: Illegal peptide with unknown >> mod: ASVDSGNEDIIEALISLFYGVMTPM[147]LNPLIYSLRWARNING: Illegal peptide with >> unknown mod: M[147]GFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKWARNING: Illegal >> peptide with unknown mod: MGFNRPSKIQENALPLM[147]LAEPPQNLIAQSQSGTGKWARNING: >> Illegal peptide with unknown mod: >> GFPSQC[160]YSAQTLPELC[160]SPQDELDFLM[147]EALIISKWARNING: Illegal peptide >> with unknown mod: LYTM[147]DGITVTVADLFFAGTETTSTTLRYGLLILMK[142]WARNING: >> Illegal peptide with unknown mod: >> LYTMDGITVTVADLFFAGTETTSTTLRYGLLILM[147]K[142]WARNING: Illegal peptide with >> unknown mod: FVHKSFVEVNEEGTEAAAASSC[160]FVVAEC[160]C[160]M[147]ESGPRWARNING: >> Illegal peptide with unknown mod: GPLLAQEM[147]PTVSVLEYALPQRPPQGPEDDRDLSER >> Failed to open input file >> '/opt/tpp/data/327_05_01/spectrast/327_05_01_020_150417_01.mzXML'.ERROR: >> cannot read scan in data file >> /opt/tpp/data/327_05_01/spectrast/327_05_01_020_150417_01.mzXML exiting ... >> >> >> There is an error at the end. I don't understand why it is looking for >> the mzxml file in the spectrast folder... Thus I copied the mzxml file to >> the spectrast folder and it seems to work. >> Could you please check if the latest PTMprophet version gives the same >> warnings? >> >> Thanks for your help :-) >> >> Delphine >> >> 2015-04-29 19:30 GMT+02:00 David Shteynberg < >> [email protected]>: >> >>> Hi, >>> >>> There may be several things going on here, which will require a new copy >>> of PTMProphet for you to process the results. I think that you are using >>> an older version of PTMProphet which has seen recent improvements to cover >>> more PTM user cases. PTMProphet compares the internally calculated mass to >>> the search engine reported mass, these may not agree and cause this problem >>> for the K[142] peptides. The other peptides are M containing with oxidized >>> Methionine so you PTMProphet settings should include M,15.9949 to make >>> those go away. If you also send the mzXML file, I can try the latest code >>> on you data. >>> >>> >>> Thanks, >>> -David >>> >>> On Wed, Apr 29, 2015 at 8:16 AM, Delphine <[email protected]> wrote: >>> >>>> Hello, >>>> >>>> I'm trying to use ptmprophet to identify methylation on lysines. First >>>> I identify the peptides with comet, xtandem, spectraST and mascot. Here are >>>> the lines where the modification is discribed in the xtandem and comet >>>> parameter files I used: >>>> comet: variable_mod02 = 14.015650 K 0 3 -1 0 >>>> xtandem: <note type="input" label="residue, potential modification >>>> mass">15.994915@M,14.015650@K</note> >>>> >>>> I combine the 4 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; /opt/tpp/bin/PTMProphetParser K,14.0156 >>>> MZTOL=0.2 >>>> /opt/tpp/data/327_05_01/327_05_01_020_150417_01_MTCS_0_D_interact.iproph.pep.xml >>>> interact.ptm.pep.xml * >>>> >>>> And here is the error message: >>>> >>>> INFO: Writing file interact.ptm.pep.xml ... >>>> INFO: Reading file >>>> /opt/tpp/data/327_05_01/327_05_01_020_150417_01_MTCS_0_D_interact.iproph.pep.xml >>>> ...WARNING: Illegal peptide with unknown mod: GTAGK[142]VIK[142]WARNING: >>>> Illegal peptide with unknown mod: ILVAIMK[142]WARNING: Illegal peptide >>>> with unknown mod: VTNLHVK[142]WARNING: Illegal peptide with unknown mod: >>>> ALK[142]EPPRWARNING: Illegal peptide with unknown mod: >>>> ALK[142]EPPRWARNING: Illegal peptide with unknown mod: >>>> ALK[142]EPPRWARNING: Illegal peptide with unknown mod: >>>> K[142]EGVK[142]PRWARNING: Illegal peptide with unknown mod: >>>> VLEPENK[142]WARNING: Illegal peptide with unknown mod: >>>> VLNILEK[142]WARNING: Illegal peptide with unknown mod: >>>> WLVVPDK[142]WARNING: Illegal peptide with unknown mod: >>>> LLLTTPAK[142]WARNING: Illegal peptide with unknown mod: >>>> K[142]PHPPKRWARNING: Illegal peptide with unknown mod: >>>> KPHPPK[142]RWARNING: Illegal peptide with unknown mod: >>>> DADFNGTK[142]WARNING: Illegal peptide with unknown mod: >>>> LYSC[160]TPRWARNING: Illegal peptide with unknown mod: >>>> KAVVVC[160]PKWARNING: Illegal peptide with unknown mod: >>>> KTPMC[160]EKWARNING: Illegal peptide with unknown mod: >>>> LAALAEALK[142]WARNING: Illegal peptide with unknown mod: >>>> VK[142]THLFRWARNING: Illegal peptide with unknown mod: MEFLKQKWARNING: >>>> Illegal peptide with unknown mod: MDK[142]TFERWARNING: Illegal peptide >>>> with unknown mod: GAGMSFSRKWARNING: Illegal peptide with unknown mod: >>>> ALLVYC[160]VKWARNING: Illegal peptide with unknown mod: >>>> ALLVYC[160]VKWARNING: Illegal peptide with unknown mod: >>>> VFISC[160]K[142]VQWARNING: Illegal peptide with unknown mod: >>>> VMLYPSRIWARNING: Illegal peptide with unknown mod: >>>> MC[160]GDC[160]VEKWARNING: Illegal peptide with unknown mod: >>>> LSLHLSPIK[142]WARNING: Illegal peptide with unknown mod: >>>> MSVNISTAGKWARNING: Illegal peptide with unknown mod: >>>> NLMANRPAK[142]WARNING: Illegal peptide with unknown mod: TAMLLALQRWARNING: >>>> Illegal peptide with unknown mod: LSSC[160]KPPKKWARNING: Illegal peptide >>>> with unknown mod: K[142]QLYPFFKWARNING: Illegal peptide with unknown mod: >>>> KQLYPFFK[142]WARNING: Illegal peptide with unknown mod: >>>> TK[142]LNYNPPKWARNING: Illegal peptide with unknown mod: >>>> TKLNYNPPK[142]WARNING: Illegal peptide with unknown mod: >>>> IIK[142]ALDLPAKWARNING: Illegal peptide with unknown mod: >>>> IIKALDLPAK[142]WARNING: Illegal peptide with unknown mod: >>>> VK[142]PNVAVLSRWARNING: Illegal peptide with unknown mod: >>>> ASSLPSSAPAVK[142]WARNING: Illegal peptide with unknown mod: >>>> SLASSAQPGLGK[142]WARNING: Illegal peptide with unknown mod: >>>> AEMEELMEKWARNING: Illegal peptide with unknown mod: >>>> NDC[160]TTQSNVKWARNING: Illegal peptide with unknown mod: >>>> LNK[142]TPIPQTK[142]WARNING: Illegal peptide with unknown mod: >>>> SSLLGTGITSPK[142]WARNING: Illegal peptide with unknown mod: >>>> LIDLC[160]QPTQK[142]WARNING: Illegal peptide with unknown mod: >>>> RNQDRPSLLK[142]WARNING: Illegal peptide with unknown mod: >>>> K[142]RPDEMLLPKWARNING: Illegal peptide with unknown mod: >>>> KRPDEMLLPK[142]WARNING: Illegal peptide with unknown mod: >>>> LAERPNIKMRWARNING: Illegal peptide with unknown mod: >>>> K[142]ITGEIMHALKWARNING: Illegal peptide with unknown mod: >>>> KITGEIMHALK[142]WARNING: Illegal peptide with unknown mod: >>>> NVQTPQC[160]K[142]LRWARNING: Illegal peptide with unknown mod: >>>> VGAWGISGEPRK[142]WARNING: Illegal peptide with unknown mod: >>>> DLLHPSPEEEK[142]WARNING: Illegal peptide with unknown mod: >>>> GALGPGGPLGHPGEK[142]WARNING: Illegal peptide with unknown mod: >>>> KAGTVMFEYGMRWARNING: Illegal peptide with unknown mod: REENQNEVNMKWARNING: >>>> Illegal peptide with unknown mod: K[142]NSGC[160]TEVC[160]HTRWARNING: >>>> Illegal peptide with unknown mod: QILLLLPVMINMLK[142]WARNING: Illegal >>>> peptide with unknown mod: QILLLLPVMINMLK[142]WARNING: Illegal peptide with >>>> unknown mod: LQGEGLSVAGIVC[160]HVGKWARNING: Illegal peptide with unknown >>>> mod: SWAEAYK[142]DLENSDEFK[142]WARNING: Illegal peptide with unknown mod: >>>> DLVSGGSNEGNGK[142]EDWAMK[142]WARNING: Illegal peptide with unknown mod: >>>> AVATGKMDENQFVAVTSTNAAKWARNING: Illegal peptide with unknown mod: >>>> LPMASSMEHGK[142]DLPSVQLLMK[142]WARNING: Illegal peptide with unknown mod: >>>> MQILTPPLQSSVELVADPETRWARNING: Illegal peptide with unknown mod: >>>> LTPTEIVLILPMPEQRNSLTAK[142]WARNING: Illegal peptide with unknown mod: >>>> QKLC[160]YVSQGNASFTYGYEYLGC[160]TSRWARNING: Illegal peptide with unknown >>>> mod: DNEIQMDMTLGPIEEAYAILNRFEVEVTK[142]WARNING: Illegal peptide with >>>> unknown mod: QMGQEIGNELDEQNEIIDDLANLVENTDEK[142]WARNING: Illegal peptide >>>> with unknown mod: HLVC[160]SFRLYPFTVHTVSPGNSHLALYQVFK[142]WARNING: Illegal >>>> peptide with unknown mod: >>>> EVK[142]VYLLTTSSAPYC[160]NAFQLLTVAPNHGISLK[142]WARNING: Illegal peptide >>>> with unknown mod: K[142]GNFQLQGTMLSDGQGFTQDDVQAAEVTYGAMARWARNING: Illegal >>>> peptide with unknown mod: EESLHSILAGSDMTVSQILLTQHGIPVMNLSDGK[142]WARNING: >>>> Illegal peptide with unknown mod: >>>> DPPAQC[160]SAGPVGDDMFHWQATIMGPISNYMLDNWARNING: Illegal peptide with >>>> unknown mod: >>>> LYC[160]NGDGEWMVPIGRC[160]TC[160]K[142]PGYEPENSVAC[160]KWARNING: Illegal >>>> peptide with unknown mod: >>>> LYC[160]NGDGEWMVPIGRC[160]TC[160]KPGYEPENSVAC[160]K[142]WARNING: Illegal >>>> peptide with unknown mod: ASVDSGNEDIIEALISLFYGVMTPMLNPLIYSLRWARNING: >>>> Illegal peptide with unknown mod: >>>> MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKWARNING: Illegal peptide with unknown >>>> mod: GFPSQC[160]YSAQTLPELC[160]SPQDELDFLMEALIISKWARNING: Illegal peptide >>>> with unknown mod: LYTMDGITVTVADLFFAGTETTSTTLRYGLLILMK[142]WARNING: Illegal >>>> peptide with unknown mod: >>>> FVHKSFVEVNEEGTEAAAASSC[160]FVVAEC[160]C[160]MESGPRWARNING: Illegal peptide >>>> with unknown mod: GPLLAQEMPTVSVLEYALPQRPPQGPEDDRDLSERWARNING: Illegal >>>> peptide with unknown mod: GGEC[160]HGMDAEQEMRWARNING: Illegal peptide with >>>> unknown mod: WAAVMVPSGEEQRWARNING: Illegal peptide with unknown mod: >>>> MTSMMC[160]TVMLK[142]TWARNING: Illegal peptide with unknown mod: >>>> MSFSEMNRWARNING: Illegal peptide with unknown mod: >>>> MSFAGTVAWMAPEVIRWARNING: Illegal peptide with unknown mod: >>>> GSQDFSFREIMGSRWARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> EMSEEMDK[142]WARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> MVLLAGTGPEGGGARWARNING: Illegal peptide with unknown mod: >>>> QDFNMMEQRK[142]WARNING: Illegal peptide with unknown mod: >>>> MEAMGEWNPNVKWARNING: Illegal peptide with unknown mod: >>>> AVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> TK[142]EMDVYGITDKWARNING: Illegal peptide with unknown mod: >>>> TKEMDVYGITDK[142]WARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> VMAMAIDYRWARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> AVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> AVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> IKFEMEQNLRWARNING: Illegal peptide with unknown mod: MNGLRNKWARNING: >>>> Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MKWARNING: Illegal >>>> peptide with unknown mod: AVGIWHC[160]GSC[160]MKWARNING: Illegal peptide >>>> with unknown mod: AVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with >>>> unknown mod: AVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown >>>> mod: RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> VMLYPSRWARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> VMLYPSRWARNING: Illegal peptide with unknown mod: KLIMEAMKWARNING: Illegal >>>> peptide with unknown mod: MC[160]GDC[160]VEKWARNING: Illegal peptide with >>>> unknown mod: SESMDYSRWARNING: Illegal peptide with unknown mod: >>>> GMPGGRNLYKWARNING: Illegal peptide with unknown mod: >>>> AVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> MNAFYDAQVEFVKWARNING: Illegal peptide with unknown mod: IITVMSMGMKWARNING: >>>> Illegal peptide with unknown mod: LNIFDMMAVTKWARNING: Illegal peptide with >>>> unknown mod: RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown >>>> mod: DVDNAYMIKWARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> MNWENESSPKWARNING: Illegal peptide with unknown mod: LNIFDMMAVTKWARNING: >>>> Illegal peptide with unknown mod: YYADGEDAYAMKWARNING: Illegal peptide >>>> with unknown mod: APAMFNIRWARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> APAMFNIRWARNING: Illegal peptide with unknown mod: GFMVQTGDPTGTGRWARNING: >>>> Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MKWARNING: Illegal >>>> peptide with unknown mod: MTLDDFRWARNING: Illegal peptide with unknown >>>> mod: RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> QVLDNLTMEKWARNING: Illegal peptide with unknown mod: QVLDNLTMEKWARNING: >>>> Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MKWARNING: Illegal >>>> peptide with unknown mod: RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide >>>> with unknown mod: QVLDNLTMEKWARNING: Illegal peptide with unknown mod: >>>> NTPGFMYK[142]WARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> EGMLMMMSPSPRWARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod: >>>> K[142]ALMPPVKWARNING: Illegal peptide with unknown mod: >>>> KALMPPVK[142]WARNING: Illegal peptide with unknown mod: >>>> K[142]PVMPK[142]KWARNING: Illegal peptide with unknown mod: >>>> K[142]PVMPKK[142]WARNING: Illegal peptide with unknown mod: >>>> KPVMPK[142]K[142]WARNING: Illegal peptide with unknown mod: >>>> K[142]PVMPK[142]KWARNING: Illegal peptide with unknown mod: >>>> K[142]PVMPKK[142]WARNING: Illegal peptide with unknown mod: >>>> KPVMPK[142]K[142]WARNING: Illegal peptide with unknown mod: >>>> VTMQK[142]SDDVLHDLGQKWARNING: Illegal peptide with unknown mod: >>>> VTMQKSDDVLHDLGQK[142]WARNING: Illegal peptide with unknown mod: >>>> VMLYPSRIWARNING: Illegal peptide with unknown mod: VMLYPSRIWARNING: >>>> Illegal peptide with unknown mod: VMLYPSRIWARNING: Illegal peptide with >>>> unknown mod: VMLYPSRIWARNING: Illegal peptide with unknown mod: >>>> MAGGLFAVSKKWARNING: Illegal peptide with unknown mod: >>>> IGQQLGMTFISVGHRWARNING: Illegal peptide with unknown mod: VMLYPSRIWARNING: >>>> Illegal peptide with unknown mod: VMLYPSRIWARNING: Illegal peptide with >>>> unknown mod: K[142]PVMPK[142]KWARNING: Illegal peptide with unknown mod: >>>> K[142]PVMPKK[142]WARNING: Illegal peptide with unknown mod: >>>> KPVMPK[142]K[142]WARNING: Illegal peptide with unknown mod: >>>> VMLYPSRIWARNING: Illegal peptide with unknown mod: >>>> LEVVAIFGSVQMAMSRIINLHHHRWARNING: Illegal peptide with unknown mod: >>>> GLIFYDTKVTVMNRWARNING: Illegal peptide with unknown mod: >>>> LK[142]LSHLVQYEELPDYIMVMVANK[142]WARNING: Illegal peptide with unknown >>>> mod: AVLVDLEPGTMDSVRWARNING: Illegal peptide with unknown mod: >>>> AVLVDLEPGTMDSVRWARNING: Illegal peptide with unknown mod: TMADQQARR >>>> WARNING: Unrecognized mod on peptide: TVVGQITVDM[147]WARNING: Cannot >>>> initialize for sequence: TVVGQITVDM[147], unknown mods may exist in >>>> spectrum 327_05_01_020_150417_01.05584.05584.2 >>>> Segmentation fault >>>> >>>> >>>> I am not very familliar with the search of PTM.... >>>> Thanks in advance 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/Af65TfANAl0/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.
