Hello Delphine,
I ran the new version, which gives more information. The problem here is
that MASCOT generated and reported massed in the pepXML file are not close
enough to the PTMProphet computed masses. The error is small <0.01 for K
methylation and is likely related to the masses used internally in MASCOT
being different from those used internally by the other search engines you
applied.
If you can send me the dat file I can dig deeper into the MASCOT issue.
Thanks,
-David
Here are the new warnings:
*EXECUTING: cd c:/Inetpub/wwwroot/ISB/data/Delphine&&
c:\Inetpub\tpp-bin\PTMProphetParser
CQ,-17.0265,M,15.995,K,14.0156,E,-18.0106,n,42.0106 MZTOL=0.2
c:/Inetpub/wwwroot/ISB/data/Delphine/327_05_01_020_150417_01_MTCS_0_D_interact.iproph.pep.xml
interact.ptm.pep.xml *
INFO: Writing file interact.ptm.pep.xml ...
INFO: Reading file
c:/Inetpub/wwwroot/ISB/data/Delphine/327_05_01_020_150417_01_MTCS_0_D_interact.iproph.pep.xml
...WARNING: Illegal peptide found in pepXML with non-matching mass:
GTAGK[142]VIK[142]
Neutral Mass (from pepXML) = 800.52
Neutral Computed Mass for Evaluation = 800.512WARNING: Illegal
peptide found in pepXML with non-matching mass: ILVAIM[147]K[142]
Neutral Mass (from pepXML) = 816.522
Neutral Computed Mass for Evaluation = 816.514WARNING: Illegal
peptide found in pepXML with non-matching mass: VTNLHVK[142]
Neutral Mass (from pepXML) = 823.499
Neutral Computed Mass for Evaluation = 823.492WARNING: Illegal
peptide found in pepXML with non-matching mass: ALK[142]EPPR
Neutral Mass (from pepXML) = 823.499
Neutral Computed Mass for Evaluation = 823.492WARNING: Illegal
peptide found in pepXML with non-matching mass: ALK[142]EPPR
Neutral Mass (from pepXML) = 823.499
Neutral Computed Mass for Evaluation = 823.492WARNING: Illegal
peptide found in pepXML with non-matching mass: ALK[142]EPPR
Neutral Mass (from pepXML) = 823.499
Neutral Computed Mass for Evaluation = 823.492WARNING: Illegal
peptide found in pepXML with non-matching mass: K[142]EGVK[142]PR
Neutral Mass (from pepXML) = 840.526
Neutral Computed Mass for Evaluation = 840.518WARNING: Illegal
peptide found in pepXML with non-matching mass: VLEPENK[142]
Neutral Mass (from pepXML) = 841.462
Neutral Computed Mass for Evaluation = 841.455WARNING: Illegal
peptide found in pepXML with non-matching mass: VLNILEK[142]
Neutral Mass (from pepXML) = 841.535
Neutral Computed Mass for Evaluation = 841.527WARNING: Illegal
peptide found in pepXML with non-matching mass: WLVVPDK[142]
Neutral Mass (from pepXML) = 869.509
Neutral Computed Mass for Evaluation = 869.501WARNING: Illegal
peptide found in pepXML with non-matching mass: LLLTTPAK[142]
Neutral Mass (from pepXML) = 869.566
Neutral Computed Mass for Evaluation = 869.559WARNING: Illegal
peptide found in pepXML with non-matching mass: K[142]PHPPKR
Neutral Mass (from pepXML) = 872.542
Neutral Computed Mass for Evaluation = 872.534WARNING: Illegal
peptide found in pepXML with non-matching mass: KPHPPK[142]R
Neutral Mass (from pepXML) = 872.542
Neutral Computed Mass for Evaluation = 872.534WARNING: Illegal
peptide found in pepXML with non-matching mass: DADFNGTK[142]
Neutral Mass (from pepXML) = 880.4
Neutral Computed Mass for Evaluation = 880.393WARNING: Illegal
peptide found in pepXML with non-matching mass: LYSC[160]TPR
Neutral Mass (from pepXML) = 895.43
Neutral Computed Mass for Evaluation = 895.422WARNING: Illegal
peptide found in pepXML with non-matching mass: KAVVVC[160]PK
Neutral Mass (from pepXML) = 899.534
Neutral Computed Mass for Evaluation = 899.526WARNING: Illegal
peptide found in pepXML with non-matching mass: KTPM[147]C[160]EK
Neutral Mass (from pepXML) = 908.417
Neutral Computed Mass for Evaluation = 908.41WARNING: Illegal peptide
found in pepXML with non-matching mass: LAALAEALK[142]
Neutral Mass (from pepXML) = 912.572
Neutral Computed Mass for Evaluation = 912.564WARNING: Illegal
peptide found in pepXML with non-matching mass: VK[142]THLFR
Neutral Mass (from pepXML) = 913.558
Neutral Computed Mass for Evaluation = 913.55WARNING: Illegal peptide
found in pepXML with non-matching mass: M[147]EFLKQK
Neutral Mass (from pepXML) = 938.497
Neutral Computed Mass for Evaluation = 938.49WARNING: Illegal peptide
found in pepXML with non-matching mass: M[147]DK[142]TFER
Neutral Mass (from pepXML) = 955.451
Neutral Computed Mass for Evaluation = 955.443WARNING: Illegal
peptide found in pepXML with non-matching mass: GAGM[147]SFSRK
Neutral Mass (from pepXML) = 955.462
Neutral Computed Mass for Evaluation = 955.455WARNING: Illegal
peptide found in pepXML with non-matching mass: ALLVYC[160]VK
Neutral Mass (from pepXML) = 964.549
Neutral Computed Mass for Evaluation = 964.542WARNING: Illegal
peptide found in pepXML with non-matching mass: ALLVYC[160]VK
Neutral Mass (from pepXML) = 964.549
Neutral Computed Mass for Evaluation = 964.542WARNING: Illegal
peptide found in pepXML with non-matching mass: VFISC[160]K[142]VQ
Neutral Mass (from pepXML) = 993.54
Neutral Computed Mass for Evaluation = 993.532WARNING: Illegal
peptide found in pepXML with non-matching mass: VM[147]LYPSRI
Neutral Mass (from pepXML) = 993.539
Neutral Computed Mass for Evaluation = 993.532WARNING: Illegal
peptide found in pepXML with non-matching mass:
M[147]C[160]GDC[160]VEK
Neutral Mass (from pepXML) = 1013.37
Neutral Computed Mass for Evaluation = 1013.36WARNING: Illegal
peptide found in pepXML with non-matching mass: LSLHLSPIK[142]
Neutral Mass (from pepXML) = 1020.64
Neutral Computed Mass for Evaluation = 1020.63WARNING: Illegal
peptide found in pepXML with non-matching mass: M[147]SVNISTAGK
Neutral Mass (from pepXML) = 1022.51
Neutral Computed Mass for Evaluation = 1022.51WARNING: Illegal
peptide found in pepXML with non-matching mass: NLMANRPAK[142]
Neutral Mass (from pepXML) = 1027.57
Neutral Computed Mass for Evaluation = 1027.56WARNING: Illegal
peptide found in pepXML with non-matching mass: TAM[147]LLALQR
Neutral Mass (from pepXML) = 1031.59
Neutral Computed Mass for Evaluation = 1031.58WARNING: Illegal
peptide found in pepXML with non-matching mass: LSSC[160]KPPKK
Neutral Mass (from pepXML) = 1043.59
Neutral Computed Mass for Evaluation = 1043.58WARNING: Illegal
peptide found in pepXML with non-matching mass: K[142]QLYPFFK
Neutral Mass (from pepXML) = 1083.62
Neutral Computed Mass for Evaluation = 1083.61WARNING: Illegal
peptide found in pepXML with non-matching mass: KQLYPFFK[142]
Neutral Mass (from pepXML) = 1083.62
Neutral Computed Mass for Evaluation = 1083.61WARNING: Illegal
peptide found in pepXML with non-matching mass: TK[142]LNYNPPK
Neutral Mass (from pepXML) = 1087.61
Neutral Computed Mass for Evaluation = 1087.6WARNING: Illegal peptide
found in pepXML with non-matching mass: TKLNYNPPK[142]
Neutral Mass (from pepXML) = 1087.61
Neutral Computed Mass for Evaluation = 1087.6WARNING: Illegal peptide
found in pepXML with non-matching mass: IIK[142]ALDLPAK
Neutral Mass (from pepXML) = 1094.71
Neutral Computed Mass for Evaluation = 1094.71WARNING: Illegal
peptide found in pepXML with non-matching mass: IIKALDLPAK[142]
Neutral Mass (from pepXML) = 1094.71
Neutral Computed Mass for Evaluation = 1094.71WARNING: Illegal
peptide found in pepXML with non-matching mass: VK[142]PNVAVLSR
Neutral Mass (from pepXML) = 1095.68
Neutral Computed Mass for Evaluation = 1095.68WARNING: Illegal
peptide found in pepXML with non-matching mass: ASSLPSSAPAVK[142]
Neutral Mass (from pepXML) = 1127.63
Neutral Computed Mass for Evaluation = 1127.62WARNING: Illegal
peptide found in pepXML with non-matching mass: SLASSAQPGLGK[142]
Neutral Mass (from pepXML) = 1128.62
Neutral Computed Mass for Evaluation = 1128.61WARNING: Illegal
peptide found in pepXML with non-matching mass: AEM[147]EELM[147]EK
Neutral Mass (from pepXML) = 1140.48
Neutral Computed Mass for Evaluation = 1140.47WARNING: Illegal
peptide found in pepXML with non-matching mass: NDC[160]TTQSNVK
Neutral Mass (from pepXML) = 1165.51
Neutral Computed Mass for Evaluation = 1165.5WARNING: Illegal peptide
found in pepXML with non-matching mass: LNK[142]TPIPQTK[142]
Neutral Mass (from pepXML) = 1166.71
Neutral Computed Mass for Evaluation = 1166.7WARNING: Illegal peptide
found in pepXML with non-matching mass: SSLLGTGITSPK[142]
Neutral Mass (from pepXML) = 1173.67
Neutral Computed Mass for Evaluation = 1173.66WARNING: Illegal
peptide found in pepXML with non-matching mass: LIDLC[160]QPTQK[142]
Neutral Mass (from pepXML) = 1228.66
Neutral Computed Mass for Evaluation = 1228.65WARNING: Illegal
peptide found in pepXML with non-matching mass: RNQDRPSLLK[142]
Neutral Mass (from pepXML) = 1239.71
Neutral Computed Mass for Evaluation = 1239.7WARNING: Illegal peptide
found in pepXML with non-matching mass: K[142]RPDEMLLPK
Neutral Mass (from pepXML) = 1239.71
Neutral Computed Mass for Evaluation = 1239.7WARNING: Illegal peptide
found in pepXML with non-matching mass: KRPDEMLLPK[142]
Neutral Mass (from pepXML) = 1239.71
Neutral Computed Mass for Evaluation = 1239.7WARNING: Illegal peptide
found in pepXML with non-matching mass: LAERPNIKM[147]R
Neutral Mass (from pepXML) = 1242.69
Neutral Computed Mass for Evaluation = 1242.69WARNING: Illegal
peptide found in pepXML with non-matching mass: K[142]ITGEIMHALK
Neutral Mass (from pepXML) = 1253.72
Neutral Computed Mass for Evaluation = 1253.72WARNING: Illegal
peptide found in pepXML with non-matching mass: KITGEIMHALK[142]
Neutral Mass (from pepXML) = 1253.72
Neutral Computed Mass for Evaluation = 1253.72WARNING: Illegal
peptide found in pepXML with non-matching mass: NVQTPQC[160]K[142]LR
Neutral Mass (from pepXML) = 1256.67
Neutral Computed Mass for Evaluation = 1256.67WARNING: Illegal
peptide found in pepXML with non-matching mass: VGAWGISGEPRK[142]
Neutral Mass (from pepXML) = 1269.69
Neutral Computed Mass for Evaluation = 1269.68WARNING: Illegal
peptide found in pepXML with non-matching mass: DLLHPSPEEEK[142]
Neutral Mass (from pepXML) = 1306.65
Neutral Computed Mass for Evaluation = 1306.64WARNING: Illegal
peptide found in pepXML with non-matching mass: GALGPGGPLGHPGEK[142]
Neutral Mass (from pepXML) = 1356.72
Neutral Computed Mass for Evaluation = 1356.71WARNING: Illegal
peptide found in pepXML with non-matching mass: KAGTVM[147]FEYGMR
Neutral Mass (from pepXML) = 1404.66
Neutral Computed Mass for Evaluation = 1404.65WARNING: Illegal
peptide found in pepXML with non-matching mass: KAGTVMFEYGM[147]R
Neutral Mass (from pepXML) = 1404.66
Neutral Computed Mass for Evaluation = 1404.65WARNING: Illegal
peptide found in pepXML with non-matching mass: REENQNEVNM[147]K
Neutral Mass (from pepXML) = 1405.63
Neutral Computed Mass for Evaluation = 1405.63WARNING: Illegal
peptide found in pepXML with non-matching mass:
K[142]NSGC[160]TEVC[160]HTR
Neutral Mass (from pepXML) = 1461.65
Neutral Computed Mass for Evaluation = 1461.65WARNING: Illegal
peptide found in pepXML with non-matching mass:
QILLLLPVM[147]INM[147]LK[142]
Neutral Mass (from pepXML) = 1684.01
Neutral Computed Mass for Evaluation = 1684WARNING: Illegal peptide
found in pepXML with non-matching mass: QILLLLPVM[147]INM[147]LK[142]
Neutral Mass (from pepXML) = 1684.01
Neutral Computed Mass for Evaluation = 1684WARNING: Illegal peptide
found in pepXML with non-matching mass: LQGEGLSVAGIVC[160]HVGK
Neutral Mass (from pepXML) = 1722.92
Neutral Computed Mass for Evaluation = 1722.91WARNING: Illegal
peptide found in pepXML with non-matching mass:
SWAEAYK[142]DLENSDEFK[142]
Neutral Mass (from pepXML) = 1958.9
Neutral Computed Mass for Evaluation = 1958.89WARNING: Illegal
peptide found in pepXML with non-matching mass:
DLVSGGSNEGNGK[142]EDWAMK[142]
Neutral Mass (from pepXML) = 2020.92
Neutral Computed Mass for Evaluation = 2020.92WARNING: Illegal
peptide found in pepXML with non-matching mass:
AVATGKM[147]DENQFVAVTSTNAAK
Neutral Mass (from pepXML) = 2268.11
Neutral Computed Mass for Evaluation = 2268.11WARNING: Illegal
peptide found in pepXML with non-matching mass:
LPMASSMEHGK[142]DLPSVQLLMK[142]
Neutral Mass (from pepXML) = 2339.21
Neutral Computed Mass for Evaluation = 2339.21WARNING: Illegal
peptide found in pepXML with non-matching mass:
M[147]QILTPPLQSSVELVADPETR
Neutral Mass (from pepXML) = 2339.21
Neutral Computed Mass for Evaluation = 2339.2WARNING: Illegal peptide
found in pepXML with non-matching mass:
LTPTEIVLILPM[147]PEQRNSLTAK[142]
Neutral Mass (from pepXML) = 2493.4
Neutral Computed Mass for Evaluation = 2493.39WARNING: Illegal
peptide found in pepXML with non-matching mass:
QKLC[160]YVSQGNASFTYGYEYLGC[160]TSR
Neutral Mass (from pepXML) = 2951.33
Neutral Computed Mass for Evaluation = 2951.32WARNING: Illegal
peptide found in pepXML with non-matching mass:
DNEIQMDMTLGPIEEAYAILNRFEVEVTK[142]
Neutral Mass (from pepXML) = 3381.66
Neutral Computed Mass for Evaluation = 3381.65WARNING: Illegal
peptide found in pepXML with non-matching mass:
QM[147]GQEIGNELDEQNEIIDDLANLVENTDEK[142]
Neutral Mass (from pepXML) = 3445.58
Neutral Computed Mass for Evaluation = 3445.57WARNING: Illegal
peptide found in pepXML with non-matching mass:
HLVC[160]SFRLYPFTVHTVSPGNSHLALYQVFK[142]
Neutral Mass (from pepXML) = 3530.84
Neutral Computed Mass for Evaluation = 3530.83WARNING: Illegal
peptide found in pepXML with non-matching mass:
EVK[142]VYLLTTSSAPYC[160]NAFQLLTVAPNHGISLK[142]
Neutral Mass (from pepXML) = 3561.9
Neutral Computed Mass for Evaluation = 3561.89WARNING: Illegal
peptide found in pepXML with non-matching mass:
K[142]GNFQLQGTM[147]LSDGQGFTQDDVQAAEVTYGAMAR
Neutral Mass (from pepXML) = 3663.7
Neutral Computed Mass for Evaluation = 3663.69WARNING: Illegal
peptide found in pepXML with non-matching mass:
K[142]GNFQLQGTMLSDGQGFTQDDVQAAEVTYGAM[147]AR
Neutral Mass (from pepXML) = 3663.7
Neutral Computed Mass for Evaluation = 3663.69WARNING: Illegal
peptide found in pepXML with non-matching mass:
EESLHSILAGSDM[147]TVSQILLTQHGIPVM[147]NLSDGK[142]
Neutral Mass (from pepXML) = 3665.84
Neutral Computed Mass for Evaluation = 3665.83WARNING: Illegal
peptide found in pepXML with non-matching mass:
DPPAQC[160]SAGPVGDDM[147]FHWQATIM[147]GPISNYMLDN
Neutral Mass (from pepXML) = 3666.56
Neutral Computed Mass for Evaluation = 3666.55WARNING: Illegal
peptide found in pepXML with non-matching mass:
DPPAQC[160]SAGPVGDDM[147]FHWQATIMGPISNYM[147]LDN
Neutral Mass (from pepXML) = 3666.56
Neutral Computed Mass for Evaluation = 3666.55WARNING: Illegal
peptide found in pepXML with non-matching mass:
DPPAQC[160]SAGPVGDDMFHWQATIM[147]GPISNYM[147]LDN
Neutral Mass (from pepXML) = 3666.56
Neutral Computed Mass for Evaluation = 3666.55WARNING: Illegal
peptide found in pepXML with non-matching mass:
LYC[160]NGDGEWM[147]VPIGRC[160]TC[160]K[142]PGYEPENSVAC[160]K
Neutral Mass (from pepXML) = 3676.6
Neutral Computed Mass for Evaluation = 3676.59WARNING: Illegal
peptide found in pepXML with non-matching mass:
LYC[160]NGDGEWM[147]VPIGRC[160]TC[160]KPGYEPENSVAC[160]K[142]
Neutral Mass (from pepXML) = 3676.6
Neutral Computed Mass for Evaluation = 3676.59WARNING: Illegal
peptide found in pepXML with non-matching mass:
ASVDSGNEDIIEALISLFYGVM[147]TPMLNPLIYSLR
Neutral Mass (from pepXML) = 3756.91
Neutral Computed Mass for Evaluation = 3756.9WARNING: Illegal peptide
found in pepXML with non-matching mass:
ASVDSGNEDIIEALISLFYGVMTPM[147]LNPLIYSLR
Neutral Mass (from pepXML) = 3756.91
Neutral Computed Mass for Evaluation = 3756.9WARNING: Illegal peptide
found in pepXML with non-matching mass:
M[147]GFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGK
Neutral Mass (from pepXML) = 3780.94
Neutral Computed Mass for Evaluation = 3780.93WARNING: Illegal
peptide found in pepXML with non-matching mass:
MGFNRPSKIQENALPLM[147]LAEPPQNLIAQSQSGTGK
Neutral Mass (from pepXML) = 3780.94
Neutral Computed Mass for Evaluation = 3780.93WARNING: Illegal
peptide found in pepXML with non-matching mass:
GFPSQC[160]YSAQTLPELC[160]SPQDELDFLM[147]EALIISK
Neutral Mass (from pepXML) = 3802.79
Neutral Computed Mass for Evaluation = 3802.78WARNING: Illegal
peptide found in pepXML with non-matching mass:
LYTM[147]DGITVTVADLFFAGTETTSTTLRYGLLILMK[142]
Neutral Mass (from pepXML) = 3885.03
Neutral Computed Mass for Evaluation = 3885.02WARNING: Illegal
peptide found in pepXML with non-matching mass:
LYTMDGITVTVADLFFAGTETTSTTLRYGLLILM[147]K[142]
Neutral Mass (from pepXML) = 3885.03
Neutral Computed Mass for Evaluation = 3885.02WARNING: Illegal
peptide found in pepXML with non-matching mass:
FVHKSFVEVNEEGTEAAAASSC[160]FVVAEC[160]C[160]M[147]ESGPR
Neutral Mass (from pepXML) = 3906.7
Neutral Computed Mass for Evaluation = 3906.7WARNING: Illegal peptide
found in pepXML with non-matching mass:
GPLLAQEM[147]PTVSVLEYALPQRPPQGPEDDRDLSER
Neutral Mass (from pepXML) = 3918.95
Neutral Computed Mass for Evaluation = 3918.94
*Command Successful*
RETURN CODE:0
On Thu, Apr 30, 2015 at 2:18 AM, delphine wood <[email protected]> wrote:
> Hi,
>
> I send you the mzxml file through wetransfer.
> I tried with this command
> * /opt/tpp/bin/PTMProphetParser STY,79.966,K,14.0156,M,15.995 MZTOL=0.2
> /opt/tpp/data/327_05_01/327_05_01_020_150417_01_MTCS_0_D_interact.iproph.pep.xml
> interact.ptm.pep.xml *
>
> I got these warnings:
>
> INFO: Writing file interact.ptm.pep.xml ...
> INFO: Reading file
> /opt/tpp/data/327_05_01/327_05_01_020_150417_01_MTCS_0_D_interact.iproph.pep.xml
> ...WARNING: Illegal peptide with unknown mod: GTAGK[142]VIK[142]WARNING:
> Illegal peptide with unknown mod: ILVAIM[147]K[142]WARNING: Illegal peptide
> with unknown mod: VTNLHVK[142]WARNING: Illegal peptide with unknown mod:
> ALK[142]EPPRWARNING: Illegal peptide with unknown mod: ALK[142]EPPRWARNING:
> Illegal peptide with unknown mod: ALK[142]EPPRWARNING: Illegal peptide with
> unknown mod: K[142]EGVK[142]PRWARNING: Illegal peptide with unknown mod:
> VLEPENK[142]WARNING: Illegal peptide with unknown mod: VLNILEK[142]WARNING:
> Illegal peptide with unknown mod: WLVVPDK[142]WARNING: Illegal peptide with
> unknown mod: LLLTTPAK[142]WARNING: Illegal peptide with unknown mod:
> K[142]PHPPKRWARNING: Illegal peptide with unknown mod: KPHPPK[142]RWARNING:
> Illegal peptide with unknown mod: DADFNGTK[142]WARNING: Illegal peptide with
> unknown mod: LYSC[160]TPRWARNING: Illegal peptide with unknown mod:
> KAVVVC[160]PKWARNING: Illegal peptide with unknown mod:
> KTPM[147]C[160]EKWARNING: Illegal peptide with unknown mod:
> LAALAEALK[142]WARNING: Illegal peptide with unknown mod: VK[142]THLFRWARNING:
> Illegal peptide with unknown mod: M[147]EFLKQKWARNING: Illegal peptide with
> unknown mod: M[147]DK[142]TFERWARNING: Illegal peptide with unknown mod:
> GAGM[147]SFSRKWARNING: Illegal peptide with unknown mod:
> ALLVYC[160]VKWARNING: Illegal peptide with unknown mod: ALLVYC[160]VKWARNING:
> Illegal peptide with unknown mod: VFISC[160]K[142]VQWARNING: Illegal peptide
> with unknown mod: VM[147]LYPSRIWARNING: Illegal peptide with unknown mod:
> M[147]C[160]GDC[160]VEKWARNING: Illegal peptide with unknown mod:
> LSLHLSPIK[142]WARNING: Illegal peptide with unknown mod:
> M[147]SVNISTAGKWARNING: Illegal peptide with unknown mod:
> NLMANRPAK[142]WARNING: Illegal peptide with unknown mod:
> TAM[147]LLALQRWARNING: Illegal peptide with unknown mod:
> LSSC[160]KPPKKWARNING: Illegal peptide with unknown mod:
> K[142]QLYPFFKWARNING: Illegal peptide with unknown mod: KQLYPFFK[142]WARNING:
> Illegal peptide with unknown mod: TK[142]LNYNPPKWARNING: Illegal peptide with
> unknown mod: TKLNYNPPK[142]WARNING: Illegal peptide with unknown mod:
> IIK[142]ALDLPAKWARNING: Illegal peptide with unknown mod:
> IIKALDLPAK[142]WARNING: Illegal peptide with unknown mod:
> VK[142]PNVAVLSRWARNING: Illegal peptide with unknown mod:
> ASSLPSSAPAVK[142]WARNING: Illegal peptide with unknown mod:
> SLASSAQPGLGK[142]WARNING: Illegal peptide with unknown mod:
> AEM[147]EELM[147]EKWARNING: Illegal peptide with unknown mod:
> NDC[160]TTQSNVKWARNING: Illegal peptide with unknown mod:
> LNK[142]TPIPQTK[142]WARNING: Illegal peptide with unknown mod:
> SSLLGTGITSPK[142]WARNING: Illegal peptide with unknown mod:
> LIDLC[160]QPTQK[142]WARNING: Illegal peptide with unknown mod:
> RNQDRPSLLK[142]WARNING: Illegal peptide with unknown mod:
> K[142]RPDEMLLPKWARNING: Illegal peptide with unknown mod:
> KRPDEMLLPK[142]WARNING: Illegal peptide with unknown mod:
> LAERPNIKM[147]RWARNING: Illegal peptide with unknown mod:
> K[142]ITGEIMHALKWARNING: Illegal peptide with unknown mod:
> KITGEIMHALK[142]WARNING: Illegal peptide with unknown mod:
> NVQTPQC[160]K[142]LRWARNING: Illegal peptide with unknown mod:
> VGAWGISGEPRK[142]WARNING: Illegal peptide with unknown mod:
> DLLHPSPEEEK[142]WARNING: Illegal peptide with unknown mod:
> GALGPGGPLGHPGEK[142]WARNING: Illegal peptide with unknown mod:
> KAGTVM[147]FEYGMRWARNING: Illegal peptide with unknown mod:
> KAGTVMFEYGM[147]RWARNING: Illegal peptide with unknown mod:
> REENQNEVNM[147]KWARNING: Illegal peptide with unknown mod:
> K[142]NSGC[160]TEVC[160]HTRWARNING: Illegal peptide with unknown mod:
> QILLLLPVM[147]INM[147]LK[142]WARNING: Illegal peptide with unknown mod:
> QILLLLPVM[147]INM[147]LK[142]WARNING: Illegal peptide with unknown mod:
> LQGEGLSVAGIVC[160]HVGKWARNING: Illegal peptide with unknown mod:
> SWAEAYK[142]DLENSDEFK[142]WARNING: Illegal peptide with unknown mod:
> DLVSGGSNEGNGK[142]EDWAMK[142]WARNING: Illegal peptide with unknown mod:
> AVATGKM[147]DENQFVAVTSTNAAKWARNING: Illegal peptide with unknown mod:
> LPMASSMEHGK[142]DLPSVQLLMK[142]WARNING: Illegal peptide with unknown mod:
> M[147]QILTPPLQSSVELVADPETRWARNING: Illegal peptide with unknown mod:
> LTPTEIVLILPM[147]PEQRNSLTAK[142]WARNING: Illegal peptide with unknown mod:
> QKLC[160]YVSQGNASFTYGYEYLGC[160]TSRWARNING: Illegal peptide with unknown mod:
> DNEIQMDMTLGPIEEAYAILNRFEVEVTK[142]WARNING: Illegal peptide with unknown mod:
> QM[147]GQEIGNELDEQNEIIDDLANLVENTDEK[142]WARNING: Illegal peptide with unknown
> mod: HLVC[160]SFRLYPFTVHTVSPGNSHLALYQVFK[142]WARNING: Illegal peptide with
> unknown mod: EVK[142]VYLLTTSSAPYC[160]NAFQLLTVAPNHGISLK[142]WARNING: Illegal
> peptide with unknown mod:
> K[142]GNFQLQGTM[147]LSDGQGFTQDDVQAAEVTYGAMARWARNING: Illegal peptide with
> unknown mod: K[142]GNFQLQGTMLSDGQGFTQDDVQAAEVTYGAM[147]ARWARNING: Illegal
> peptide with unknown mod:
> EESLHSILAGSDM[147]TVSQILLTQHGIPVM[147]NLSDGK[142]WARNING: Illegal peptide
> with unknown mod: DPPAQC[160]SAGPVGDDM[147]FHWQATIM[147]GPISNYMLDNWARNING:
> Illegal peptide with unknown mod:
> DPPAQC[160]SAGPVGDDM[147]FHWQATIMGPISNYM[147]LDNWARNING: Illegal peptide with
> unknown mod: DPPAQC[160]SAGPVGDDMFHWQATIM[147]GPISNYM[147]LDNWARNING: Illegal
> peptide with unknown mod:
> LYC[160]NGDGEWM[147]VPIGRC[160]TC[160]K[142]PGYEPENSVAC[160]KWARNING: Illegal
> peptide with unknown mod:
> LYC[160]NGDGEWM[147]VPIGRC[160]TC[160]KPGYEPENSVAC[160]K[142]WARNING: Illegal
> peptide with unknown mod: ASVDSGNEDIIEALISLFYGVM[147]TPMLNPLIYSLRWARNING:
> Illegal peptide with unknown mod:
> ASVDSGNEDIIEALISLFYGVMTPM[147]LNPLIYSLRWARNING: Illegal peptide with unknown
> mod: M[147]GFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKWARNING: Illegal peptide with
> unknown mod: MGFNRPSKIQENALPLM[147]LAEPPQNLIAQSQSGTGKWARNING: Illegal peptide
> with unknown mod: GFPSQC[160]YSAQTLPELC[160]SPQDELDFLM[147]EALIISKWARNING:
> Illegal peptide with unknown mod:
> LYTM[147]DGITVTVADLFFAGTETTSTTLRYGLLILMK[142]WARNING: Illegal peptide with
> unknown mod: LYTMDGITVTVADLFFAGTETTSTTLRYGLLILM[147]K[142]WARNING: Illegal
> peptide with unknown mod:
> FVHKSFVEVNEEGTEAAAASSC[160]FVVAEC[160]C[160]M[147]ESGPRWARNING: Illegal
> peptide with unknown mod: GPLLAQEM[147]PTVSVLEYALPQRPPQGPEDDRDLSER
> Failed to open input file
> '/opt/tpp/data/327_05_01/spectrast/327_05_01_020_150417_01.mzXML'.ERROR:
> cannot read scan in data file
> /opt/tpp/data/327_05_01/spectrast/327_05_01_020_150417_01.mzXML exiting ...
>
>
> There is an error at the end. I don't understand why it is looking for the
> mzxml file in the spectrast folder... Thus I copied the mzxml file to the
> spectrast folder and it seems to work.
> Could you please check if the latest PTMprophet version gives the same
> warnings?
>
> Thanks for your help :-)
>
> Delphine
>
> 2015-04-29 19:30 GMT+02:00 David Shteynberg <
> [email protected]>:
>
>> Hi,
>>
>> There may be several things going on here, which will require a new copy
>> of PTMProphet for you to process the results. I think that you are using
>> an older version of PTMProphet which has seen recent improvements to cover
>> more PTM user cases. PTMProphet compares the internally calculated mass to
>> the search engine reported mass, these may not agree and cause this problem
>> for the K[142] peptides. The other peptides are M containing with oxidized
>> Methionine so you PTMProphet settings should include M,15.9949 to make
>> those go away. If you also send the mzXML file, I can try the latest code
>> on you data.
>>
>>
>> Thanks,
>> -David
>>
>> On Wed, Apr 29, 2015 at 8:16 AM, Delphine <[email protected]> wrote:
>>
>>> Hello,
>>>
>>> I'm trying to use ptmprophet to identify methylation on lysines. First I
>>> identify the peptides with comet, xtandem, spectraST and mascot. Here are
>>> the lines where the modification is discribed in the xtandem and comet
>>> parameter files I used:
>>> comet: variable_mod02 = 14.015650 K 0 3 -1 0
>>> xtandem: <note type="input" label="residue, potential modification
>>> mass">15.994915@M,14.015650@K</note>
>>>
>>> I combine the 4 results with iprophet (file joined) and tried to use
>>> PTMprophet on this file.
>>>
>>> Here is the command line:
>>> * cd /opt/tpp/data/327_05_01; /opt/tpp/bin/PTMProphetParser K,14.0156
>>> MZTOL=0.2
>>> /opt/tpp/data/327_05_01/327_05_01_020_150417_01_MTCS_0_D_interact.iproph.pep.xml
>>> interact.ptm.pep.xml *
>>>
>>> And here is the error message:
>>>
>>> INFO: Writing file interact.ptm.pep.xml ...
>>> INFO: Reading file
>>> /opt/tpp/data/327_05_01/327_05_01_020_150417_01_MTCS_0_D_interact.iproph.pep.xml
>>> ...WARNING: Illegal peptide with unknown mod: GTAGK[142]VIK[142]WARNING:
>>> Illegal peptide with unknown mod: ILVAIMK[142]WARNING: Illegal peptide with
>>> unknown mod: VTNLHVK[142]WARNING: Illegal peptide with unknown mod:
>>> ALK[142]EPPRWARNING: Illegal peptide with unknown mod: ALK[142]EPPRWARNING:
>>> Illegal peptide with unknown mod: ALK[142]EPPRWARNING: Illegal peptide with
>>> unknown mod: K[142]EGVK[142]PRWARNING: Illegal peptide with unknown mod:
>>> VLEPENK[142]WARNING: Illegal peptide with unknown mod: VLNILEK[142]WARNING:
>>> Illegal peptide with unknown mod: WLVVPDK[142]WARNING: Illegal peptide with
>>> unknown mod: LLLTTPAK[142]WARNING: Illegal peptide with unknown mod:
>>> K[142]PHPPKRWARNING: Illegal peptide with unknown mod: KPHPPK[142]RWARNING:
>>> Illegal peptide with unknown mod: DADFNGTK[142]WARNING: Illegal peptide
>>> with unknown mod: LYSC[160]TPRWARNING: Illegal peptide with unknown mod:
>>> KAVVVC[160]PKWARNING: Illegal peptide with unknown mod:
>>> KTPMC[160]EKWARNING: Illegal peptide with unknown mod:
>>> LAALAEALK[142]WARNING: Illegal peptide with unknown mod:
>>> VK[142]THLFRWARNING: Illegal peptide with unknown mod: MEFLKQKWARNING:
>>> Illegal peptide with unknown mod: MDK[142]TFERWARNING: Illegal peptide with
>>> unknown mod: GAGMSFSRKWARNING: Illegal peptide with unknown mod:
>>> ALLVYC[160]VKWARNING: Illegal peptide with unknown mod:
>>> ALLVYC[160]VKWARNING: Illegal peptide with unknown mod:
>>> VFISC[160]K[142]VQWARNING: Illegal peptide with unknown mod:
>>> VMLYPSRIWARNING: Illegal peptide with unknown mod:
>>> MC[160]GDC[160]VEKWARNING: Illegal peptide with unknown mod:
>>> LSLHLSPIK[142]WARNING: Illegal peptide with unknown mod: MSVNISTAGKWARNING:
>>> Illegal peptide with unknown mod: NLMANRPAK[142]WARNING: Illegal peptide
>>> with unknown mod: TAMLLALQRWARNING: Illegal peptide with unknown mod:
>>> LSSC[160]KPPKKWARNING: Illegal peptide with unknown mod:
>>> K[142]QLYPFFKWARNING: Illegal peptide with unknown mod:
>>> KQLYPFFK[142]WARNING: Illegal peptide with unknown mod:
>>> TK[142]LNYNPPKWARNING: Illegal peptide with unknown mod:
>>> TKLNYNPPK[142]WARNING: Illegal peptide with unknown mod:
>>> IIK[142]ALDLPAKWARNING: Illegal peptide with unknown mod:
>>> IIKALDLPAK[142]WARNING: Illegal peptide with unknown mod:
>>> VK[142]PNVAVLSRWARNING: Illegal peptide with unknown mod:
>>> ASSLPSSAPAVK[142]WARNING: Illegal peptide with unknown mod:
>>> SLASSAQPGLGK[142]WARNING: Illegal peptide with unknown mod:
>>> AEMEELMEKWARNING: Illegal peptide with unknown mod: NDC[160]TTQSNVKWARNING:
>>> Illegal peptide with unknown mod: LNK[142]TPIPQTK[142]WARNING: Illegal
>>> peptide with unknown mod: SSLLGTGITSPK[142]WARNING: Illegal peptide with
>>> unknown mod: LIDLC[160]QPTQK[142]WARNING: Illegal peptide with unknown mod:
>>> RNQDRPSLLK[142]WARNING: Illegal peptide with unknown mod:
>>> K[142]RPDEMLLPKWARNING: Illegal peptide with unknown mod:
>>> KRPDEMLLPK[142]WARNING: Illegal peptide with unknown mod:
>>> LAERPNIKMRWARNING: Illegal peptide with unknown mod:
>>> K[142]ITGEIMHALKWARNING: Illegal peptide with unknown mod:
>>> KITGEIMHALK[142]WARNING: Illegal peptide with unknown mod:
>>> NVQTPQC[160]K[142]LRWARNING: Illegal peptide with unknown mod:
>>> VGAWGISGEPRK[142]WARNING: Illegal peptide with unknown mod:
>>> DLLHPSPEEEK[142]WARNING: Illegal peptide with unknown mod:
>>> GALGPGGPLGHPGEK[142]WARNING: Illegal peptide with unknown mod:
>>> KAGTVMFEYGMRWARNING: Illegal peptide with unknown mod: REENQNEVNMKWARNING:
>>> Illegal peptide with unknown mod: K[142]NSGC[160]TEVC[160]HTRWARNING:
>>> Illegal peptide with unknown mod: QILLLLPVMINMLK[142]WARNING: Illegal
>>> peptide with unknown mod: QILLLLPVMINMLK[142]WARNING: Illegal peptide with
>>> unknown mod: LQGEGLSVAGIVC[160]HVGKWARNING: Illegal peptide with unknown
>>> mod: SWAEAYK[142]DLENSDEFK[142]WARNING: Illegal peptide with unknown mod:
>>> DLVSGGSNEGNGK[142]EDWAMK[142]WARNING: Illegal peptide with unknown mod:
>>> AVATGKMDENQFVAVTSTNAAKWARNING: Illegal peptide with unknown mod:
>>> LPMASSMEHGK[142]DLPSVQLLMK[142]WARNING: Illegal peptide with unknown mod:
>>> MQILTPPLQSSVELVADPETRWARNING: Illegal peptide with unknown mod:
>>> LTPTEIVLILPMPEQRNSLTAK[142]WARNING: Illegal peptide with unknown mod:
>>> QKLC[160]YVSQGNASFTYGYEYLGC[160]TSRWARNING: Illegal peptide with unknown
>>> mod: DNEIQMDMTLGPIEEAYAILNRFEVEVTK[142]WARNING: Illegal peptide with
>>> unknown mod: QMGQEIGNELDEQNEIIDDLANLVENTDEK[142]WARNING: Illegal peptide
>>> with unknown mod: HLVC[160]SFRLYPFTVHTVSPGNSHLALYQVFK[142]WARNING: Illegal
>>> peptide with unknown mod:
>>> EVK[142]VYLLTTSSAPYC[160]NAFQLLTVAPNHGISLK[142]WARNING: Illegal peptide
>>> with unknown mod: K[142]GNFQLQGTMLSDGQGFTQDDVQAAEVTYGAMARWARNING: Illegal
>>> peptide with unknown mod: EESLHSILAGSDMTVSQILLTQHGIPVMNLSDGK[142]WARNING:
>>> Illegal peptide with unknown mod:
>>> DPPAQC[160]SAGPVGDDMFHWQATIMGPISNYMLDNWARNING: Illegal peptide with unknown
>>> mod: LYC[160]NGDGEWMVPIGRC[160]TC[160]K[142]PGYEPENSVAC[160]KWARNING:
>>> Illegal peptide with unknown mod:
>>> LYC[160]NGDGEWMVPIGRC[160]TC[160]KPGYEPENSVAC[160]K[142]WARNING: Illegal
>>> peptide with unknown mod: ASVDSGNEDIIEALISLFYGVMTPMLNPLIYSLRWARNING:
>>> Illegal peptide with unknown mod:
>>> MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKWARNING: Illegal peptide with unknown
>>> mod: GFPSQC[160]YSAQTLPELC[160]SPQDELDFLMEALIISKWARNING: Illegal peptide
>>> with unknown mod: LYTMDGITVTVADLFFAGTETTSTTLRYGLLILMK[142]WARNING: Illegal
>>> peptide with unknown mod:
>>> FVHKSFVEVNEEGTEAAAASSC[160]FVVAEC[160]C[160]MESGPRWARNING: Illegal peptide
>>> with unknown mod: GPLLAQEMPTVSVLEYALPQRPPQGPEDDRDLSERWARNING: Illegal
>>> peptide with unknown mod: GGEC[160]HGMDAEQEMRWARNING: Illegal peptide with
>>> unknown mod: WAAVMVPSGEEQRWARNING: Illegal peptide with unknown mod:
>>> MTSMMC[160]TVMLK[142]TWARNING: Illegal peptide with unknown mod:
>>> MSFSEMNRWARNING: Illegal peptide with unknown mod: MSFAGTVAWMAPEVIRWARNING:
>>> Illegal peptide with unknown mod: GSQDFSFREIMGSRWARNING: Illegal peptide
>>> with unknown mod: RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with
>>> unknown mod: RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown
>>> mod: EMSEEMDK[142]WARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> MVLLAGTGPEGGGARWARNING: Illegal peptide with unknown mod:
>>> QDFNMMEQRK[142]WARNING: Illegal peptide with unknown mod:
>>> MEAMGEWNPNVKWARNING: Illegal peptide with unknown mod:
>>> AVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> TK[142]EMDVYGITDKWARNING: Illegal peptide with unknown mod:
>>> TKEMDVYGITDK[142]WARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> VMAMAIDYRWARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> AVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> AVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> IKFEMEQNLRWARNING: Illegal peptide with unknown mod: MNGLRNKWARNING:
>>> Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MKWARNING: Illegal
>>> peptide with unknown mod: AVGIWHC[160]GSC[160]MKWARNING: Illegal peptide
>>> with unknown mod: AVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with
>>> unknown mod: AVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown
>>> mod: RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> VMLYPSRWARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> VMLYPSRWARNING: Illegal peptide with unknown mod: KLIMEAMKWARNING: Illegal
>>> peptide with unknown mod: MC[160]GDC[160]VEKWARNING: Illegal peptide with
>>> unknown mod: SESMDYSRWARNING: Illegal peptide with unknown mod:
>>> GMPGGRNLYKWARNING: Illegal peptide with unknown mod:
>>> AVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> MNAFYDAQVEFVKWARNING: Illegal peptide with unknown mod: IITVMSMGMKWARNING:
>>> Illegal peptide with unknown mod: LNIFDMMAVTKWARNING: Illegal peptide with
>>> unknown mod: RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown
>>> mod: DVDNAYMIKWARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> MNWENESSPKWARNING: Illegal peptide with unknown mod: LNIFDMMAVTKWARNING:
>>> Illegal peptide with unknown mod: YYADGEDAYAMKWARNING: Illegal peptide with
>>> unknown mod: APAMFNIRWARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> APAMFNIRWARNING: Illegal peptide with unknown mod: GFMVQTGDPTGTGRWARNING:
>>> Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MKWARNING: Illegal
>>> peptide with unknown mod: MTLDDFRWARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> QVLDNLTMEKWARNING: Illegal peptide with unknown mod: QVLDNLTMEKWARNING:
>>> Illegal peptide with unknown mod: RAVGIWHC[160]GSC[160]MKWARNING: Illegal
>>> peptide with unknown mod: RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide
>>> with unknown mod: QVLDNLTMEKWARNING: Illegal peptide with unknown mod:
>>> NTPGFMYK[142]WARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> EGMLMMMSPSPRWARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> RAVGIWHC[160]GSC[160]MKWARNING: Illegal peptide with unknown mod:
>>> K[142]ALMPPVKWARNING: Illegal peptide with unknown mod:
>>> KALMPPVK[142]WARNING: Illegal peptide with unknown mod:
>>> K[142]PVMPK[142]KWARNING: Illegal peptide with unknown mod:
>>> K[142]PVMPKK[142]WARNING: Illegal peptide with unknown mod:
>>> KPVMPK[142]K[142]WARNING: Illegal peptide with unknown mod:
>>> K[142]PVMPK[142]KWARNING: Illegal peptide with unknown mod:
>>> K[142]PVMPKK[142]WARNING: Illegal peptide with unknown mod:
>>> KPVMPK[142]K[142]WARNING: Illegal peptide with unknown mod:
>>> VTMQK[142]SDDVLHDLGQKWARNING: Illegal peptide with unknown mod:
>>> VTMQKSDDVLHDLGQK[142]WARNING: Illegal peptide with unknown mod:
>>> VMLYPSRIWARNING: Illegal peptide with unknown mod: VMLYPSRIWARNING: Illegal
>>> peptide with unknown mod: VMLYPSRIWARNING: Illegal peptide with unknown
>>> mod: VMLYPSRIWARNING: Illegal peptide with unknown mod: MAGGLFAVSKKWARNING:
>>> Illegal peptide with unknown mod: IGQQLGMTFISVGHRWARNING: Illegal peptide
>>> with unknown mod: VMLYPSRIWARNING: Illegal peptide with unknown mod:
>>> VMLYPSRIWARNING: Illegal peptide with unknown mod:
>>> K[142]PVMPK[142]KWARNING: Illegal peptide with unknown mod:
>>> K[142]PVMPKK[142]WARNING: Illegal peptide with unknown mod:
>>> KPVMPK[142]K[142]WARNING: Illegal peptide with unknown mod:
>>> VMLYPSRIWARNING: Illegal peptide with unknown mod:
>>> LEVVAIFGSVQMAMSRIINLHHHRWARNING: Illegal peptide with unknown mod:
>>> GLIFYDTKVTVMNRWARNING: Illegal peptide with unknown mod:
>>> LK[142]LSHLVQYEELPDYIMVMVANK[142]WARNING: Illegal peptide with unknown mod:
>>> AVLVDLEPGTMDSVRWARNING: Illegal peptide with unknown mod:
>>> AVLVDLEPGTMDSVRWARNING: Illegal peptide with unknown mod: TMADQQARR
>>> WARNING: Unrecognized mod on peptide: TVVGQITVDM[147]WARNING: Cannot
>>> initialize for sequence: TVVGQITVDM[147], unknown mods may exist in
>>> spectrum 327_05_01_020_150417_01.05584.05584.2
>>> Segmentation fault
>>>
>>>
>>> I am not very familliar with the search of PTM....
>>> Thanks in advance for your help!
>>>
>>> Delphine
>>>
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>>
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>
>
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