Hello Jesse, There have been many bug fixes and improvements made to PTMProphet since the last release. You can test out the new binary by replacing your PTMProphetParser.exe file in C:\Inetpu\tpp-bin with this pre-release version made for TPP 5: https://dl.dropboxusercontent.com/u/21286225/PTMProphetParser.exe
I ran it on your file without the WARNING messages as follows: PTMProphetParser.exe K:42.010565,M:15.994915,NQ:0.984016 MZTOL=0.055 interact-160611_0001_fulldia_1_q1_msgf.pep.xml msgf.test1.interact.ptm.pep.xml Let us know should other issues arise. Thank you, -David On Wed, Jul 20, 2016 at 12:22 PM, Jesse <[email protected]> wrote: > Hello David, > > I'm having a related issue. I'm searching with Comet, X!tandem, and > MSGF+, and results from MSGF+ or tandem that have been filtered with > peptide prophet using xinteract. When I run the following on files from > MSGF+ searches or X!tandem searches: > > *EXECUTING: cd c:/Inetpub/wwwroot/ISB/data/allDIAv3& > c:\Inetpub\tpp-bin\PTMProphetParser K,42.010565,M,15.994915,NQ,0.984016 > MZTOL=0.055 > c:/Inetpub/wwwroot/ISB/data/allDIAv3/interact-160611_0001_fulldia_1_q1_msgf.pep.xml > msgf.test1.interact.ptm.pep.xml * > > I get many errors in the form of (also see attached text logs): > > WARNING: Illegal peptide found in pepXML with non-matching mass: > QRHKQ[129]N[115]LYGDYAFDAN[115]R > Neutral Mass (from pepXML) = 2080.92 > Neutral Computed Mass for Evaluation = 2097.95 > PPM difference = 8182.22WARNING: Illegal peptide found in pepXML with > non-matching mass: M[147]TISFLLR > Neutral Mass (from pepXML) = 1037.56 > Neutral Computed Mass for Evaluation = 995.547 > PPM difference = 40489.9 > > However, these PTM prophet runs finish with error code = 0 and produce > pep.xml files that I can view and that have localization scores. Is this OK? > > More importantly, when I run the same command on the comet output, I get > nothing: > > *EXECUTING: cd > c:/Inetpub/wwwroot/ISB/data/allDIAv3& > c:\Inetpub\tpp-bin\PTMProphetParser K,42.010565,M,15.994915,NQ,0.984016 > MZTOL=0.055 > c:/Inetpub/wwwroot/ISB/data/allDIAv3/interact-160611_0001_fulldia_1_q1_c.pep.xml > comet.test1.interact.ptm.pep.xml > * > > INFO: Writing file comet.test1.interact.ptm.pep.xml ... > INFO: Reading file > c:/Inetpub/wwwroot/ISB/data/allDIAv3/interact-160611_0001_fulldia_1_q1_c.pep.xml > ... > *Command FAILED* > > RETURN CODE:65280 > I could omit the comet search results if you say that the PTMprophet results > for MSGF+ and X!tandem searches are OK despite the errors. > > Here is a link to all the relevant files on google drive: > > https://drive.google.com/folderview?id=0B4N83JlasjgsVVBBVDM0NGlCcTQ&usp=sharing > > Your help is appreciated. > > Best regards, > Jesse Meyer > > On Thursday, May 14, 2015 at 1:47:03 PM UTC-7, David Shteynberg wrote: >> >> 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 https://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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
