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. 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