PTM prophet unknown mod
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Delphine
Apr 29, 2015, 11:16:21 AM4/29/15
to spctools...@googlegroups.com
Hello,
And here is the error message:
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
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]EPPR WARNING: Illegal peptide with unknown mod: ALK[142]EPPR WARNING: Illegal peptide with unknown mod: ALK[142]EPPR WARNING: Illegal peptide with unknown mod: K[142]EGVK[142]PR WARNING: 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]PHPPKR WARNING: Illegal peptide with unknown mod: KPHPPK[142]R WARNING: Illegal peptide with unknown mod: DADFNGTK[142] WARNING: Illegal peptide with unknown mod: LYSC[160]TPR WARNING: Illegal peptide with unknown mod: KAVVVC[160]PK WARNING: Illegal peptide with unknown mod: KTPMC[160]EK WARNING: Illegal peptide with unknown mod: LAALAEALK[142] WARNING: Illegal peptide with unknown mod: VK[142]THLFR WARNING: Illegal peptide with unknown mod: MEFLKQK WARNING: Illegal peptide with unknown mod: MDK[142]TFER WARNING: Illegal peptide with unknown mod: GAGMSFSRK WARNING: Illegal peptide with unknown mod: ALLVYC[160]VK WARNING: Illegal peptide with unknown mod: ALLVYC[160]VK WARNING: Illegal peptide with unknown mod: VFISC[160]K[142]VQ WARNING: Illegal peptide with unknown mod: VMLYPSRI WARNING: Illegal peptide with unknown mod: MC[160]GDC[160]VEK WARNING: Illegal peptide with unknown mod: LSLHLSPIK[142] WARNING: Illegal peptide with unknown mod: MSVNISTAGK WARNING: Illegal peptide with unknown mod: NLMANRPAK[142] WARNING: Illegal peptide with unknown mod: TAMLLALQR WARNING: Illegal peptide with unknown mod: LSSC[160]KPPKK WARNING: Illegal peptide with unknown mod: K[142]QLYPFFK WARNING: Illegal peptide with unknown mod: KQLYPFFK[142] WARNING: Illegal peptide with unknown mod: TK[142]LNYNPPK WARNING: Illegal peptide with unknown mod: TKLNYNPPK[142] WARNING: Illegal peptide with unknown mod: IIK[142]ALDLPAK WARNING: Illegal peptide with unknown mod: IIKALDLPAK[142] WARNING: Illegal peptide with unknown mod: VK[142]PNVAVLSR WARNING: Illegal peptide with unknown mod: ASSLPSSAPAVK[142] WARNING: Illegal peptide with unknown mod: SLASSAQPGLGK[142] WARNING: Illegal peptide with unknown mod: AEMEELMEK WARNING: Illegal peptide with unknown mod: NDC[160]TTQSNVK WARNING: 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]RPDEMLLPK WARNING: Illegal peptide with unknown mod: KRPDEMLLPK[142] WARNING: Illegal peptide with unknown mod: LAERPNIKMR WARNING: Illegal peptide with unknown mod: K[142]ITGEIMHALK WARNING: Illegal peptide with unknown mod: KITGEIMHALK[142] WARNING: Illegal peptide with unknown mod: NVQTPQC[160]K[142]LR WARNING: 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: KAGTVMFEYGMR WARNING: Illegal peptide with unknown mod: REENQNEVNMK WARNING: Illegal peptide with unknown mod: K[142]NSGC[160]TEVC[160]HTR WARNING: Illegal peptide with unknown mod: QILLLLPVMINMLK[142] WARNING: Illegal peptide with unknown mod: QILLLLPVMINMLK[142] WARNING: Illegal peptide with unknown mod: LQGEGLSVAGIVC[160]HVGK WARNING: 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: AVATGKMDENQFVAVTSTNAAK WARNING: Illegal peptide with unknown mod: LPMASSMEHGK[142]DLPSVQLLMK[142] WARNING: Illegal peptide with unknown mod: MQILTPPLQSSVELVADPETR WARNING: Illegal peptide with unknown mod: LTPTEIVLILPMPEQRNSLTAK[142] WARNING: Illegal peptide with unknown mod: QKLC[160]YVSQGNASFTYGYEYLGC[160]TSR WARNING: 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]GNFQLQGTMLSDGQGFTQDDVQAAEVTYGAMAR WARNING: Illegal peptide with unknown mod: EESLHSILAGSDMTVSQILLTQHGIPVMNLSDGK[142] WARNING: Illegal peptide with unknown mod: DPPAQC[160]SAGPVGDDMFHWQATIMGPISNYMLDN WARNING: Illegal peptide with unknown mod: LYC[160]NGDGEWMVPIGRC[160]TC[160]K[142]PGYEPENSVAC[160]K WARNING: Illegal peptide with unknown mod: LYC[160]NGDGEWMVPIGRC[160]TC[160]KPGYEPENSVAC[160]K[142] WARNING: Illegal peptide with unknown mod: ASVDSGNEDIIEALISLFYGVMTPMLNPLIYSLR WARNING: Illegal peptide with unknown mod: MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGK WARNING: Illegal peptide with unknown mod: GFPSQC[160]YSAQTLPELC[160]SPQDELDFLMEALIISK WARNING: Illegal peptide with unknown mod: LYTMDGITVTVADLFFAGTETTSTTLRYGLLILMK[142] WARNING: Illegal peptide with unknown mod: FVHKSFVEVNEEGTEAAAASSC[160]FVVAEC[160]C[160]MESGPR WARNING: Illegal peptide with unknown mod: GPLLAQEMPTVSVLEYALPQRPPQGPEDDRDLSER WARNING: Illegal peptide with unknown mod: GGEC[160]HGMDAEQEMR WARNING: Illegal peptide with unknown mod: WAAVMVPSGEEQR WARNING: Illegal peptide with unknown mod: MTSMMC[160]TVMLK[142]T WARNING: Illegal peptide with unknown mod: MSFSEMNR WARNING: Illegal peptide with unknown mod: MSFAGTVAWMAPEVIR WARNING: Illegal peptide with unknown mod: GSQDFSFREIMGSR WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: EMSEEMDK[142] WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: MVLLAGTGPEGGGAR WARNING: Illegal peptide with unknown mod: QDFNMMEQRK[142] WARNING: Illegal peptide with unknown mod: MEAMGEWNPNVK WARNING: Illegal peptide with unknown mod: AVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: TK[142]EMDVYGITDK WARNING: Illegal peptide with unknown mod: TKEMDVYGITDK[142] WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: VMAMAIDYR WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: AVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: AVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: IKFEMEQNLR WARNING: Illegal peptide with unknown mod: MNGLRNK WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: AVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: AVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: AVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: VMLYPSR WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: VMLYPSR WARNING: Illegal peptide with unknown mod: KLIMEAMK WARNING: Illegal peptide with unknown mod: MC[160]GDC[160]VEK WARNING: Illegal peptide with unknown mod: SESMDYSR WARNING: Illegal peptide with unknown mod: GMPGGRNLYK WARNING: Illegal peptide with unknown mod: AVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: MNAFYDAQVEFVK WARNING: Illegal peptide with unknown mod: IITVMSMGMK WARNING: Illegal peptide with unknown mod: LNIFDMMAVTK WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: DVDNAYMIK WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: MNWENESSPK WARNING: Illegal peptide with unknown mod: LNIFDMMAVTK WARNING: Illegal peptide with unknown mod: YYADGEDAYAMK WARNING: Illegal peptide with unknown mod: APAMFNIR WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: APAMFNIR WARNING: Illegal peptide with unknown mod: GFMVQTGDPTGTGR WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: MTLDDFR WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: QVLDNLTMEK WARNING: Illegal peptide with unknown mod: QVLDNLTMEK WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: QVLDNLTMEK WARNING: Illegal peptide with unknown mod: NTPGFMYK[142] WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: EGMLMMMSPSPR WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MK WARNING: Illegal peptide with unknown mod: K[142]ALMPPVK WARNING: Illegal peptide with unknown mod: KALMPPVK[142] WARNING: Illegal peptide with unknown mod: K[142]PVMPK[142]K WARNING: 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]K WARNING: 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]SDDVLHDLGQK WARNING: Illegal peptide with unknown mod: VTMQKSDDVLHDLGQK[142] WARNING: Illegal peptide with unknown mod: VMLYPSRI WARNING: Illegal peptide with unknown mod: VMLYPSRI WARNING: Illegal peptide with unknown mod: VMLYPSRI WARNING: Illegal peptide with unknown mod: VMLYPSRI WARNING: Illegal peptide with unknown mod: MAGGLFAVSKK WARNING: Illegal peptide with unknown mod: IGQQLGMTFISVGHR WARNING: Illegal peptide with unknown mod: VMLYPSRI WARNING: Illegal peptide with unknown mod: VMLYPSRI WARNING: Illegal peptide with unknown mod: K[142]PVMPK[142]K WARNING: 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: VMLYPSRI WARNING: Illegal peptide with unknown mod: LEVVAIFGSVQMAMSRIINLHHHR WARNING: Illegal peptide with unknown mod: GLIFYDTKVTVMNR WARNING: Illegal peptide with unknown mod: LK[142]LSHLVQYEELPDYIMVMVANK[142] WARNING: Illegal peptide with unknown mod: AVLVDLEPGTMDSVR WARNING: Illegal peptide with unknown mod: AVLVDLEPGTMDSVR WARNING: 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
David Shteynberg
Apr 29, 2015, 1:30:26 PM4/29/15
to spctools-discuss
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
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delphine wood
Apr 30, 2015, 5:18:41 AM4/30/15
to David.Sh...@systemsbiology.org, spctools...@googlegroups.com
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]EPPR WARNING: Illegal peptide with unknown mod: ALK[142]EPPR WARNING: Illegal peptide with unknown mod: ALK[142]EPPR WARNING: Illegal peptide with unknown mod: K[142]EGVK[142]PR WARNING: 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]PHPPKR WARNING: Illegal peptide with unknown mod: KPHPPK[142]R WARNING: Illegal peptide with unknown mod: DADFNGTK[142] WARNING: Illegal peptide with unknown mod: LYSC[160]TPR WARNING: Illegal peptide with unknown mod: KAVVVC[160]PK
WARNING: Illegal peptide with unknown mod: KTPM[147]C[160]EK
WARNING: Illegal peptide with unknown mod: LAALAEALK[142] WARNING: Illegal peptide with unknown mod: VK[142]THLFR
WARNING: Illegal peptide with unknown mod: M[147]EFLKQK WARNING: Illegal peptide with unknown mod: M[147]DK[142]TFER WARNING: Illegal peptide with unknown mod: GAGM[147]SFSRK
WARNING: Illegal peptide with unknown mod: ALLVYC[160]VK WARNING: Illegal peptide with unknown mod: ALLVYC[160]VK WARNING: Illegal peptide with unknown mod: VFISC[160]K[142]VQ
WARNING: Illegal peptide with unknown mod: VM[147]LYPSRI WARNING: Illegal peptide with unknown mod: M[147]C[160]GDC[160]VEK
WARNING: Illegal peptide with unknown mod: LSLHLSPIK[142]
WARNING: Illegal peptide with unknown mod: M[147]SVNISTAGK
WARNING: Illegal peptide with unknown mod: NLMANRPAK[142]
WARNING: Illegal peptide with unknown mod: TAM[147]LLALQR
WARNING: Illegal peptide with unknown mod: LSSC[160]KPPKK WARNING: Illegal peptide with unknown mod: K[142]QLYPFFK WARNING: Illegal peptide with unknown mod: KQLYPFFK[142] WARNING: Illegal peptide with unknown mod: TK[142]LNYNPPK WARNING: Illegal peptide with unknown mod: TKLNYNPPK[142] WARNING: Illegal peptide with unknown mod: IIK[142]ALDLPAK WARNING: Illegal peptide with unknown mod: IIKALDLPAK[142] WARNING: Illegal peptide with unknown mod: VK[142]PNVAVLSR WARNING: 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]EK
WARNING: Illegal peptide with unknown mod: NDC[160]TTQSNVK WARNING: 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]RPDEMLLPK WARNING: Illegal peptide with unknown mod: KRPDEMLLPK[142]
WARNING: Illegal peptide with unknown mod: LAERPNIKM[147]R
WARNING: Illegal peptide with unknown mod: K[142]ITGEIMHALK WARNING: Illegal peptide with unknown mod: KITGEIMHALK[142] WARNING: Illegal peptide with unknown mod: NVQTPQC[160]K[142]LR WARNING: 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]FEYGMR WARNING: Illegal peptide with unknown mod: KAGTVMFEYGM[147]R WARNING: Illegal peptide with unknown mod: REENQNEVNM[147]K
WARNING: Illegal peptide with unknown mod: K[142]NSGC[160]TEVC[160]HTR
WARNING: 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]HVGK WARNING: 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]DENQFVAVTSTNAAK
WARNING: Illegal peptide with unknown mod: LPMASSMEHGK[142]DLPSVQLLMK[142]
WARNING: Illegal peptide with unknown mod: M[147]QILTPPLQSSVELVADPETR WARNING: Illegal peptide with unknown mod: LTPTEIVLILPM[147]PEQRNSLTAK[142]
WARNING: Illegal peptide with unknown mod: QKLC[160]YVSQGNASFTYGYEYLGC[160]TSR WARNING: 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]LSDGQGFTQDDVQAAEVTYGAMAR WARNING: Illegal peptide with unknown mod: K[142]GNFQLQGTMLSDGQGFTQDDVQAAEVTYGAM[147]AR WARNING: Illegal peptide with unknown mod: EESLHSILAGSDM[147]TVSQILLTQHGIPVM[147]NLSDGK[142] WARNING: Illegal peptide with unknown mod: DPPAQC[160]SAGPVGDDM[147]FHWQATIM[147]GPISNYMLDN WARNING: Illegal peptide with unknown mod: DPPAQC[160]SAGPVGDDM[147]FHWQATIMGPISNYM[147]LDN WARNING: Illegal peptide with unknown mod: DPPAQC[160]SAGPVGDDMFHWQATIM[147]GPISNYM[147]LDN WARNING: Illegal peptide with unknown mod: LYC[160]NGDGEWM[147]VPIGRC[160]TC[160]K[142]PGYEPENSVAC[160]K WARNING: 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]TPMLNPLIYSLR WARNING: Illegal peptide with unknown mod: ASVDSGNEDIIEALISLFYGVMTPM[147]LNPLIYSLR WARNING: Illegal peptide with unknown mod: M[147]GFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGK WARNING: Illegal peptide with unknown mod: MGFNRPSKIQENALPLM[147]LAEPPQNLIAQSQSGTGK WARNING: Illegal peptide with unknown mod: GFPSQC[160]YSAQTLPELC[160]SPQDELDFLM[147]EALIISK WARNING: 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]ESGPR WARNING: 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
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David Shteynberg
May 1, 2015, 2:28:00 PM5/1/15
to delphine wood, spctools-discuss
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
RETURN CODE:0
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 = 800.512 WARNING: Illegal peptide found in pepXML with non-matching mass: ILVAIM[147]K[142] Neutral Mass (from pepXML) = 816.522 Neutral Computed Mass for Evaluation = 816.514 WARNING: Illegal peptide found in pepXML with non-matching mass: VTNLHVK[142] Neutral Mass (from pepXML) = 823.499 Neutral Computed Mass for Evaluation = 823.492 WARNING: Illegal peptide found in pepXML with non-matching mass: ALK[142]EPPR Neutral Mass (from pepXML) = 823.499 Neutral Computed Mass for Evaluation = 823.492 WARNING: Illegal peptide found in pepXML with non-matching mass: ALK[142]EPPR Neutral Mass (from pepXML) = 823.499 Neutral Computed Mass for Evaluation = 823.492 WARNING: Illegal peptide found in pepXML with non-matching mass: ALK[142]EPPR Neutral Mass (from pepXML) = 823.499 Neutral Computed Mass for Evaluation = 823.492 WARNING: 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 = 840.518 WARNING: Illegal peptide found in pepXML with non-matching mass: VLEPENK[142] Neutral Mass (from pepXML) = 841.462 Neutral Computed Mass for Evaluation = 841.455 WARNING: Illegal peptide found in pepXML with non-matching mass: VLNILEK[142] Neutral Mass (from pepXML) = 841.535 Neutral Computed Mass for Evaluation = 841.527 WARNING: Illegal peptide found in pepXML with non-matching mass: WLVVPDK[142] Neutral Mass (from pepXML) = 869.509 Neutral Computed Mass for Evaluation = 869.501 WARNING: Illegal peptide found in pepXML with non-matching mass: LLLTTPAK[142] Neutral Mass (from pepXML) = 869.566 Neutral Computed Mass for Evaluation = 869.559 WARNING: Illegal peptide found in pepXML with non-matching mass: K[142]PHPPKR Neutral Mass (from pepXML) = 872.542 Neutral Computed Mass for Evaluation = 872.534 WARNING: Illegal peptide found in pepXML with non-matching mass: KPHPPK[142]R Neutral Mass (from pepXML) = 872.542 Neutral Computed Mass for Evaluation = 872.534 WARNING: Illegal peptide found in pepXML with non-matching mass: DADFNGTK[142] Neutral Mass (from pepXML) = 880.4 Neutral Computed Mass for Evaluation = 880.393 WARNING: Illegal peptide found in pepXML with non-matching mass: LYSC[160]TPR Neutral Mass (from pepXML) = 895.43 Neutral Computed Mass for Evaluation = 895.422 WARNING: Illegal peptide found in pepXML with non-matching mass: KAVVVC[160]PK Neutral Mass (from pepXML) = 899.534 Neutral Computed Mass for Evaluation = 899.526 WARNING: 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 = 908.41 WARNING: Illegal peptide found in pepXML with non-matching mass: LAALAEALK[142] Neutral Mass (from pepXML) = 912.572 Neutral Computed Mass for Evaluation = 912.564 WARNING: Illegal peptide found in pepXML with non-matching mass: VK[142]THLFR Neutral Mass (from pepXML) = 913.558 Neutral Computed Mass for Evaluation = 913.55 WARNING: Illegal peptide found in pepXML with non-matching mass: M[147]EFLKQK Neutral Mass (from pepXML) = 938.497 Neutral Computed Mass for Evaluation = 938.49 WARNING: 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 = 955.443 WARNING: Illegal peptide found in pepXML with non-matching mass: GAGM[147]SFSRK Neutral Mass (from pepXML) = 955.462 Neutral Computed Mass for Evaluation = 955.455 WARNING: Illegal peptide found in pepXML with non-matching mass: ALLVYC[160]VK Neutral Mass (from pepXML) = 964.549 Neutral Computed Mass for Evaluation = 964.542 WARNING: Illegal peptide found in pepXML with non-matching mass: ALLVYC[160]VK Neutral Mass (from pepXML) = 964.549 Neutral Computed Mass for Evaluation = 964.542 WARNING: 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 = 993.532 WARNING: Illegal peptide found in pepXML with non-matching mass: VM[147]LYPSRI Neutral Mass (from pepXML) = 993.539 Neutral Computed Mass for Evaluation = 993.532 WARNING: 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 = 1013.36 WARNING: Illegal peptide found in pepXML with non-matching mass: LSLHLSPIK[142] Neutral Mass (from pepXML) = 1020.64 Neutral Computed Mass for Evaluation = 1020.63 WARNING: Illegal peptide found in pepXML with non-matching mass: M[147]SVNISTAGK Neutral Mass (from pepXML) = 1022.51 Neutral Computed Mass for Evaluation = 1022.51 WARNING: Illegal peptide found in pepXML with non-matching mass: NLMANRPAK[142] Neutral Mass (from pepXML) = 1027.57 Neutral Computed Mass for Evaluation = 1027.56 WARNING: Illegal peptide found in pepXML with non-matching mass: TAM[147]LLALQR Neutral Mass (from pepXML) = 1031.59 Neutral Computed Mass for Evaluation = 1031.58 WARNING: Illegal peptide found in pepXML with non-matching mass: LSSC[160]KPPKK Neutral Mass (from pepXML) = 1043.59 Neutral Computed Mass for Evaluation = 1043.58 WARNING: Illegal peptide found in pepXML with non-matching mass: K[142]QLYPFFK Neutral Mass (from pepXML) = 1083.62 Neutral Computed Mass for Evaluation = 1083.61 WARNING: Illegal peptide found in pepXML with non-matching mass: KQLYPFFK[142] Neutral Mass (from pepXML) = 1083.62 Neutral Computed Mass for Evaluation = 1083.61 WARNING: Illegal peptide found in pepXML with non-matching mass: TK[142]LNYNPPK Neutral Mass (from pepXML) = 1087.61 Neutral Computed Mass for Evaluation = 1087.6 WARNING: Illegal peptide found in pepXML with non-matching mass: TKLNYNPPK[142] Neutral Mass (from pepXML) = 1087.61 Neutral Computed Mass for Evaluation = 1087.6 WARNING: Illegal peptide found in pepXML with non-matching mass: IIK[142]ALDLPAK Neutral Mass (from pepXML) = 1094.71 Neutral Computed Mass for Evaluation = 1094.71 WARNING: Illegal peptide found in pepXML with non-matching mass: IIKALDLPAK[142] Neutral Mass (from pepXML) = 1094.71 Neutral Computed Mass for Evaluation = 1094.71 WARNING: Illegal peptide found in pepXML with non-matching mass: VK[142]PNVAVLSR Neutral Mass (from pepXML) = 1095.68 Neutral Computed Mass for Evaluation = 1095.68 WARNING: Illegal peptide found in pepXML with non-matching mass: ASSLPSSAPAVK[142] Neutral Mass (from pepXML) = 1127.63 Neutral Computed Mass for Evaluation = 1127.62 WARNING: Illegal peptide found in pepXML with non-matching mass: SLASSAQPGLGK[142] Neutral Mass (from pepXML) = 1128.62 Neutral Computed Mass for Evaluation = 1128.61 WARNING: 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 = 1140.47 WARNING: Illegal peptide found in pepXML with non-matching mass: NDC[160]TTQSNVK Neutral Mass (from pepXML) = 1165.51 Neutral Computed Mass for Evaluation = 1165.5 WARNING: Illegal peptide found in pepXML with non-matching mass: LNK[142]TPIPQTK[142] Neutral Mass (from pepXML) = 1166.71 Neutral Computed Mass for Evaluation = 1166.7 WARNING: Illegal peptide found in pepXML with non-matching mass: SSLLGTGITSPK[142] Neutral Mass (from pepXML) = 1173.67 Neutral Computed Mass for Evaluation = 1173.66 WARNING: Illegal peptide found in pepXML with non-matching mass: LIDLC[160]QPTQK[142] Neutral Mass (from pepXML) = 1228.66 Neutral Computed Mass for Evaluation = 1228.65 WARNING: Illegal peptide found in pepXML with non-matching mass: RNQDRPSLLK[142] Neutral Mass (from pepXML) = 1239.71 Neutral Computed Mass for Evaluation = 1239.7 WARNING: Illegal peptide found in pepXML with non-matching mass: K[142]RPDEMLLPK Neutral Mass (from pepXML) = 1239.71 Neutral Computed Mass for Evaluation = 1239.7 WARNING: Illegal peptide found in pepXML with non-matching mass: KRPDEMLLPK[142] Neutral Mass (from pepXML) = 1239.71 Neutral Computed Mass for Evaluation = 1239.7 WARNING: Illegal peptide found in pepXML with non-matching mass: LAERPNIKM[147]R Neutral Mass (from pepXML) = 1242.69 Neutral Computed Mass for Evaluation = 1242.69 WARNING: Illegal peptide found in pepXML with non-matching mass: K[142]ITGEIMHALK Neutral Mass (from pepXML) = 1253.72 Neutral Computed Mass for Evaluation = 1253.72 WARNING: Illegal peptide found in pepXML with non-matching mass: KITGEIMHALK[142] Neutral Mass (from pepXML) = 1253.72 Neutral Computed Mass for Evaluation = 1253.72 WARNING: 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 = 1256.67 WARNING: Illegal peptide found in pepXML with non-matching mass: VGAWGISGEPRK[142] Neutral Mass (from pepXML) = 1269.69 Neutral Computed Mass for Evaluation = 1269.68 WARNING: Illegal peptide found in pepXML with non-matching mass: DLLHPSPEEEK[142] Neutral Mass (from pepXML) = 1306.65 Neutral Computed Mass for Evaluation = 1306.64 WARNING: Illegal peptide found in pepXML with non-matching mass: GALGPGGPLGHPGEK[142] Neutral Mass (from pepXML) = 1356.72 Neutral Computed Mass for Evaluation = 1356.71 WARNING: Illegal peptide found in pepXML with non-matching mass: KAGTVM[147]FEYGMR Neutral Mass (from pepXML) = 1404.66 Neutral Computed Mass for Evaluation = 1404.65 WARNING: Illegal peptide found in pepXML with non-matching mass: KAGTVMFEYGM[147]R Neutral Mass (from pepXML) = 1404.66 Neutral Computed Mass for Evaluation = 1404.65 WARNING: Illegal peptide found in pepXML with non-matching mass: REENQNEVNM[147]K Neutral Mass (from pepXML) = 1405.63 Neutral Computed Mass for Evaluation = 1405.63 WARNING: 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 = 1461.65 WARNING: 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 = 1684 WARNING: 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 = 1684 WARNING: Illegal peptide found in pepXML with non-matching mass: LQGEGLSVAGIVC[160]HVGK Neutral Mass (from pepXML) = 1722.92 Neutral Computed Mass for Evaluation = 1722.91 WARNING: Illegal peptide found in pepXML with non-matching mass: SWAEAYK[142]DLENSDEFK[142] Neutral Mass (from pepXML) = 1958.9 Neutral Computed Mass for Evaluation = 1958.89 WARNING: Illegal peptide found in pepXML with non-matching mass: DLVSGGSNEGNGK[142]EDWAMK[142] Neutral Mass (from pepXML) = 2020.92 Neutral Computed Mass for Evaluation = 2020.92 WARNING: Illegal peptide found in pepXML with non-matching mass: AVATGKM[147]DENQFVAVTSTNAAK Neutral Mass (from pepXML) = 2268.11 Neutral Computed Mass for Evaluation = 2268.11 WARNING: Illegal peptide found in pepXML with non-matching mass: LPMASSMEHGK[142]DLPSVQLLMK[142] Neutral Mass (from pepXML) = 2339.21 Neutral Computed Mass for Evaluation = 2339.21 WARNING: Illegal peptide found in pepXML with non-matching mass: M[147]QILTPPLQSSVELVADPETR Neutral Mass (from pepXML) = 2339.21 Neutral Computed Mass for Evaluation = 2339.2 WARNING: Illegal peptide found in pepXML with non-matching mass: LTPTEIVLILPM[147]PEQRNSLTAK[142] Neutral Mass (from pepXML) = 2493.4 Neutral Computed Mass for Evaluation = 2493.39 WARNING: 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 = 2951.32 WARNING: Illegal peptide found in pepXML with non-matching mass: DNEIQMDMTLGPIEEAYAILNRFEVEVTK[142] Neutral Mass (from pepXML) = 3381.66 Neutral Computed Mass for Evaluation = 3381.65 WARNING: Illegal peptide found in pepXML with non-matching mass: QM[147]GQEIGNELDEQNEIIDDLANLVENTDEK[142] Neutral Mass (from pepXML) = 3445.58 Neutral Computed Mass for Evaluation = 3445.57 WARNING: Illegal peptide found in pepXML with non-matching mass: HLVC[160]SFRLYPFTVHTVSPGNSHLALYQVFK[142] Neutral Mass (from pepXML) = 3530.84 Neutral Computed Mass for Evaluation = 3530.83 WARNING: 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 = 3561.89 WARNING: 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 = 3663.69 WARNING: 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 = 3663.69 WARNING: 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 = 3665.83 WARNING: 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 = 3666.55 WARNING: 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 = 3666.55 WARNING: 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 = 3666.55 WARNING: 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 = 3676.59 WARNING: 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 = 3676.59 WARNING: Illegal peptide found in pepXML with non-matching mass: ASVDSGNEDIIEALISLFYGVM[147]TPMLNPLIYSLR Neutral Mass (from pepXML) = 3756.91 Neutral Computed Mass for Evaluation = 3756.9 WARNING: Illegal peptide found in pepXML with non-matching mass: ASVDSGNEDIIEALISLFYGVMTPM[147]LNPLIYSLR Neutral Mass (from pepXML) = 3756.91 Neutral Computed Mass for Evaluation = 3756.9 WARNING: Illegal peptide found in pepXML with non-matching mass: M[147]GFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGK Neutral Mass (from pepXML) = 3780.94 Neutral Computed Mass for Evaluation = 3780.93 WARNING: Illegal peptide found in pepXML with non-matching mass: MGFNRPSKIQENALPLM[147]LAEPPQNLIAQSQSGTGK Neutral Mass (from pepXML) = 3780.94 Neutral Computed Mass for Evaluation = 3780.93 WARNING: 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 = 3802.78 WARNING: Illegal peptide found in pepXML with non-matching mass: LYTM[147]DGITVTVADLFFAGTETTSTTLRYGLLILMK[142] Neutral Mass (from pepXML) = 3885.03 Neutral Computed Mass for Evaluation = 3885.02 WARNING: Illegal peptide found in pepXML with non-matching mass: LYTMDGITVTVADLFFAGTETTSTTLRYGLLILM[147]K[142] Neutral Mass (from pepXML) = 3885.03 Neutral Computed Mass for Evaluation = 3885.02 WARNING: 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 = 3906.7 WARNING: Illegal peptide found in pepXML with non-matching mass: GPLLAQEM[147]PTVSVLEYALPQRPPQGPEDDRDLSER Neutral Mass (from pepXML) = 3918.95 Neutral Computed Mass for Evaluation = 3918.94Command Successful
RETURN CODE:0
David Shteynberg
May 14, 2015, 4:47:03 PM5/14/15
to delphine wood, spctools-discuss
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:
The updated version of PTMProphetParser for windows can be found here for now:
Backup and replace the copies you have in C:\Inetpub\tpp-bin with these copies if you want to test it out.
Thanks,
-David
Jesse
Jul 20, 2016, 3:22:32 PM7/20/16
to spctools-discuss, woo...@gmail.com
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):
Jesse Meyer
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 = 8182.22 WARNING: 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 = 40489.9Best regards,
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.
Jesse Meyer
David Shteynberg
Jul 20, 2016, 4:45:10 PM7/20/16
to spctools-discuss
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
Visit this group at https://groups.google.com/group/spctools-discuss.
Jesse
Jul 20, 2016, 6:25:38 PM7/20/16
to spctools-discuss
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
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: 112
WARNING: 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
RETURN CODE:65280
I think it might be related to having deamidation enabled with variable n-terminal pyroglutamate formation.
Best,
Jesse
Best,
Jesse
...
Jesse
Jul 20, 2016, 7:25:55 PM7/20/16
to spctools-discuss
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
...
David Shteynberg
Jul 20, 2016, 7:56:09 PM7/20/16
to spctools-discuss
If you specify this mod also in the command it should process fine.
Cheers,
-David
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