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 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