If you specify this mod also in the command it should process fine. Cheers, -David
On Wed, Jul 20, 2016 at 4:25 PM, Jesse <[email protected]> wrote: > The error in my above post is definitely due to allowing variable > deamidation and then tandem looking for pyro-glutamate at the same time. I > don't really need to search for deamidation, so I think I'm all good. > > Thanks again, > Jesse Meyer > > On Wednesday, July 20, 2016 at 3:25:38 PM UTC-7, Jesse wrote: > >> Hello David, >> >> Thanks for the quick reply as always. >> >> It runs fine for me with the MSGF+ results as you stated, but now neither >> the tandem or comet results run at all. Both give the following error: >> >> >> *EXECUTING: cd c:/Inetpub/wwwroot/ISB/data/allDIAv3& >> c:\Inetpub\tpp-bin\PTMProphetParser K,42.010565,M,15.994915,NQ,0.984016 >> MZTOL=0.1 >> c:/Inetpub/wwwroot/ISB/data/allDIAv3/interact-160611_0001_fulldia_1_q1.pep.xml >> interact.ptm.pep.xml * >> >> WARN: deprecated format used to specify modifications >> (K,42.010565,M,15.994915,NQ,0.984016). Please see usage statement for more >> information. >> INFO: Writing file interact.ptm.pep.xml ... >> INFO: Reading file >> c:/Inetpub/wwwroot/ISB/data/allDIAv3/interact-160611_0001_fulldia_1_q1.pep.xml >> ... >> to be setModByType: 112WARNING: Cannot initialize for sequence: >> Q[112]IN[115]QDAM[147]SMQQSSALR, unknown mods may exist in spectrum >> 160611_0001_fullDIA_1_Q1.01159.01159.2 >> >> *Command FAILED* >> RETURN CODE:65280 >> >> I think it might be related to having deamidation enabled with variable >> n-terminal pyroglutamate formation. >> >> Best, >> Jesse >> >> On Wednesday, July 20, 2016 at 1:45:10 PM UTC-7, David Shteynberg wrote: >> >> 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: EGML >> >> ... > > -- > 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.
