Hello David,
I'm having a related issue. I'm searching with Comet, X!tandem, and MSGF+,
and results from MSGF+ or tandem that have been filtered with peptide
prophet using xinteract. When I run the following on files from MSGF+
searches or X!tandem searches:
*EXECUTING: cd c:/Inetpub/wwwroot/ISB/data/allDIAv3&
c:\Inetpub\tpp-bin\PTMProphetParser K,42.010565,M,15.994915,NQ,0.984016
MZTOL=0.055
c:/Inetpub/wwwroot/ISB/data/allDIAv3/interact-160611_0001_fulldia_1_q1_msgf.pep.xml
msgf.test1.interact.ptm.pep.xml *
I get many errors in the form of (also see attached text logs):
WARNING: Illegal peptide found in pepXML with non-matching mass:
QRHKQ[129]N[115]LYGDYAFDAN[115]R
Neutral Mass (from pepXML) = 2080.92
Neutral Computed Mass for Evaluation = 2097.95
PPM difference = 8182.22WARNING: Illegal peptide found in pepXML with
non-matching mass: M[147]TISFLLR
Neutral Mass (from pepXML) = 1037.56
Neutral Computed Mass for Evaluation = 995.547
PPM difference = 40489.9
However, these PTM prophet runs finish with error code = 0 and produce pep.xml
files that I can view and that have localization scores. Is this OK?
More importantly, when I run the same command on the comet output, I get
nothing:
*EXECUTING: cd
c:/Inetpub/wwwroot/ISB/data/allDIAv3&
c:\Inetpub\tpp-bin\PTMProphetParser K,42.010565,M,15.994915,NQ,0.984016
MZTOL=0.055
c:/Inetpub/wwwroot/ISB/data/allDIAv3/interact-160611_0001_fulldia_1_q1_c.pep.xml
comet.test1.interact.ptm.pep.xml
*
INFO: Writing file comet.test1.interact.ptm.pep.xml ...
INFO: Reading file
c:/Inetpub/wwwroot/ISB/data/allDIAv3/interact-160611_0001_fulldia_1_q1_c.pep.xml
...
*Command FAILED*
RETURN CODE:65280
I could omit the comet search results if you say that the PTMprophet results
for MSGF+ and X!tandem searches are OK despite the errors.
Here is a link to all the relevant files on google drive:
https://drive.google.com/folderview?id=0B4N83JlasjgsVVBBVDM0NGlCcTQ&usp=sharing
Your help is appreciated.
Best regards,
Jesse Meyer
On Thursday, May 14, 2015 at 1:47:03 PM UTC-7, David Shteynberg wrote:
>
> Hello Delphine,
>
> I have discovered the bug in Mascot2XML that was getting the masses wrong
> in the pepXML. You will need to reconvert from the dat file and rerun the
> PeptideProphet Mascot analysis followed by iProphet analysis followed by
> PTMProphet.
>
> The corrected Mascol2XML binary for windows can be downloaded here for now:
>
> https://dl.dropboxusercontent.com/u/21286225/Mascot2XML.exe
>
> The updated version of PTMProphetParser for windows can be found here for
> now:
>
> https://dl.dropboxusercontent.com/u/21286225/PTMProphetParser.exe
>
>
> Backup and replace the copies you have in C:\Inetpub\tpp-bin with these
> copies if you want to test it out.
>
> Thanks,
> -David
>
>
> On Fri, May 1, 2015 at 11:27 AM, David Shteynberg <
> [email protected] <javascript:>> wrote:
>
>> Hello Delphine,
>>
>> I ran the new version, which gives more information. The problem here is
>> that MASCOT generated and reported massed in the pepXML file are not close
>> enough to the PTMProphet computed masses. The error is small <0.01 for K
>> methylation and is likely related to the masses used internally in MASCOT
>> being different from those used internally by the other search engines you
>> applied.
>>
>> If you can send me the dat file I can dig deeper into the MASCOT issue.
>>
>> Thanks,
>> -David
>>
>> Here are the new warnings:
>>
>> *EXECUTING: cd c:/Inetpub/wwwroot/ISB/data/Delphine&&
>> c:\Inetpub\tpp-bin\PTMProphetParser
>> CQ,-17.0265,M,15.995,K,14.0156,E,-18.0106,n,42.0106 MZTOL=0.2
>> c:/Inetpub/wwwroot/ISB/data/Delphine/327_05_01_020_150417_01_MTCS_0_D_interact.iproph.pep.xml
>>
>> interact.ptm.pep.xml *
>>
>> INFO: Writing file interact.ptm.pep.xml ...
>> INFO: Reading file
>> c:/Inetpub/wwwroot/ISB/data/Delphine/327_05_01_020_150417_01_MTCS_0_D_interact.iproph.pep.xml
>> ...WARNING: Illegal peptide found in pepXML with non-matching mass:
>> GTAGK[142]VIK[142]
>> Neutral Mass (from pepXML) = 800.52
>> Neutral Computed Mass for Evaluation = 800.512WARNING: Illegal peptide
>> found in pepXML with non-matching mass: ILVAIM[147]K[142]
>> Neutral Mass (from pepXML) = 816.522
>> Neutral Computed Mass for Evaluation = 816.514WARNING: Illegal peptide
>> found in pepXML with non-matching mass: VTNLHVK[142]
>> Neutral Mass (from pepXML) = 823.499
>> Neutral Computed Mass for Evaluation = 823.492WARNING: Illegal peptide
>> found in pepXML with non-matching mass: ALK[142]EPPR
>> Neutral Mass (from pepXML) = 823.499
>> Neutral Computed Mass for Evaluation = 823.492WARNING: Illegal peptide
>> found in pepXML with non-matching mass: ALK[142]EPPR
>> Neutral Mass (from pepXML) = 823.499
>> Neutral Computed Mass for Evaluation = 823.492WARNING: Illegal peptide
>> found in pepXML with non-matching mass: ALK[142]EPPR
>> Neutral Mass (from pepXML) = 823.499
>> Neutral Computed Mass for Evaluation = 823.492WARNING: Illegal peptide
>> found in pepXML with non-matching mass: K[142]EGVK[142]PR
>> Neutral Mass (from pepXML) = 840.526
>> Neutral Computed Mass for Evaluation = 840.518WARNING: Illegal peptide
>> found in pepXML with non-matching mass: VLEPENK[142]
>> Neutral Mass (from pepXML) = 841.462
>> Neutral Computed Mass for Evaluation = 841.455WARNING: Illegal peptide
>> found in pepXML with non-matching mass: VLNILEK[142]
>> Neutral Mass (from pepXML) = 841.535
>> Neutral Computed Mass for Evaluation = 841.527WARNING: Illegal peptide
>> found in pepXML with non-matching mass: WLVVPDK[142]
>> Neutral Mass (from pepXML) = 869.509
>> Neutral Computed Mass for Evaluation = 869.501WARNING: Illegal peptide
>> found in pepXML with non-matching mass: LLLTTPAK[142]
>> Neutral Mass (from pepXML) = 869.566
>> Neutral Computed Mass for Evaluation = 869.559WARNING: Illegal peptide
>> found in pepXML with non-matching mass: K[142]PHPPKR
>> Neutral Mass (from pepXML) = 872.542
>> Neutral Computed Mass for Evaluation = 872.534WARNING: Illegal peptide
>> found in pepXML with non-matching mass: KPHPPK[142]R
>> Neutral Mass (from pepXML) = 872.542
>> Neutral Computed Mass for Evaluation = 872.534WARNING: Illegal peptide
>> found in pepXML with non-matching mass: DADFNGTK[142]
>> Neutral Mass (from pepXML) = 880.4
>> Neutral Computed Mass for Evaluation = 880.393WARNING: Illegal peptide
>> found in pepXML with non-matching mass: LYSC[160]TPR
>> Neutral Mass (from pepXML) = 895.43
>> Neutral Computed Mass for Evaluation = 895.422WARNING: Illegal peptide
>> found in pepXML with non-matching mass: KAVVVC[160]PK
>> Neutral Mass (from pepXML) = 899.534
>> Neutral Computed Mass for Evaluation = 899.526WARNING: Illegal peptide
>> found in pepXML with non-matching mass: KTPM[147]C[160]EK
>> Neutral Mass (from pepXML) = 908.417
>> Neutral Computed Mass for Evaluation = 908.41WARNING: Illegal peptide
>> found in pepXML with non-matching mass: LAALAEALK[142]
>> Neutral Mass (from pepXML) = 912.572
>> Neutral Computed Mass for Evaluation = 912.564WARNING: Illegal peptide
>> found in pepXML with non-matching mass: VK[142]THLFR
>> Neutral Mass (from pepXML) = 913.558
>> Neutral Computed Mass for Evaluation = 913.55WARNING: Illegal peptide
>> found in pepXML with non-matching mass: M[147]EFLKQK
>> Neutral Mass (from pepXML) = 938.497
>> Neutral Computed Mass for Evaluation = 938.49WARNING: Illegal peptide
>> found in pepXML with non-matching mass: M[147]DK[142]TFER
>> Neutral Mass (from pepXML) = 955.451
>> Neutral Computed Mass for Evaluation = 955.443WARNING: Illegal peptide
>> found in pepXML with non-matching mass: GAGM[147]SFSRK
>> Neutral Mass (from pepXML) = 955.462
>> Neutral Computed Mass for Evaluation = 955.455WARNING: Illegal peptide
>> found in pepXML with non-matching mass: ALLVYC[160]VK
>> Neutral Mass (from pepXML) = 964.549
>> Neutral Computed Mass for Evaluation = 964.542WARNING: Illegal peptide
>> found in pepXML with non-matching mass: ALLVYC[160]VK
>> Neutral Mass (from pepXML) = 964.549
>> Neutral Computed Mass for Evaluation = 964.542WARNING: Illegal peptide
>> found in pepXML with non-matching mass: VFISC[160]K[142]VQ
>> Neutral Mass (from pepXML) = 993.54
>> Neutral Computed Mass for Evaluation = 993.532WARNING: Illegal peptide
>> found in pepXML with non-matching mass: VM[147]LYPSRI
>> Neutral Mass (from pepXML) = 993.539
>> Neutral Computed Mass for Evaluation = 993.532WARNING: Illegal peptide
>> found in pepXML with non-matching mass: M[147]C[160]GDC[160]VEK
>> Neutral Mass (from pepXML) = 1013.37
>> Neutral Computed Mass for Evaluation = 1013.36WARNING: Illegal peptide
>> found in pepXML with non-matching mass: LSLHLSPIK[142]
>> Neutral Mass (from pepXML) = 1020.64
>> Neutral Computed Mass for Evaluation = 1020.63WARNING: Illegal peptide
>> found in pepXML with non-matching mass: M[147]SVNISTAGK
>> Neutral Mass (from pepXML) = 1022.51
>> Neutral Computed Mass for Evaluation = 1022.51WARNING: Illegal peptide
>> found in pepXML with non-matching mass: NLMANRPAK[142]
>> Neutral Mass (from pepXML) = 1027.57
>> Neutral Computed Mass for Evaluation = 1027.56WARNING: Illegal peptide
>> found in pepXML with non-matching mass: TAM[147]LLALQR
>> Neutral Mass (from pepXML) = 1031.59
>> Neutral Computed Mass for Evaluation = 1031.58WARNING: Illegal peptide
>> found in pepXML with non-matching mass: LSSC[160]KPPKK
>> Neutral Mass (from pepXML) = 1043.59
>> Neutral Computed Mass for Evaluation = 1043.58WARNING: Illegal peptide
>> found in pepXML with non-matching mass: K[142]QLYPFFK
>> Neutral Mass (from pepXML) = 1083.62
>> Neutral Computed Mass for Evaluation = 1083.61WARNING: Illegal peptide
>> found in pepXML with non-matching mass: KQLYPFFK[142]
>> Neutral Mass (from pepXML) = 1083.62
>> Neutral Computed Mass for Evaluation = 1083.61WARNING: Illegal peptide
>> found in pepXML with non-matching mass: TK[142]LNYNPPK
>> Neutral Mass (from pepXML) = 1087.61
>> Neutral Computed Mass for Evaluation = 1087.6WARNING: Illegal peptide
>> found in pepXML with non-matching mass: TKLNYNPPK[142]
>> Neutral Mass (from pepXML) = 1087.61
>> Neutral Computed Mass for Evaluation = 1087.6WARNING: Illegal peptide
>> found in pepXML with non-matching mass: IIK[142]ALDLPAK
>> Neutral Mass (from pepXML) = 1094.71
>> Neutral Computed Mass for Evaluation = 1094.71WARNING: Illegal peptide
>> found in pepXML with non-matching mass: IIKALDLPAK[142]
>> Neutral Mass (from pepXML) = 1094.71
>> Neutral Computed Mass for Evaluation = 1094.71WARNING: Illegal peptide
>> found in pepXML with non-matching mass: VK[142]PNVAVLSR
>> Neutral Mass (from pepXML) = 1095.68
>> Neutral Computed Mass for Evaluation = 1095.68WARNING: Illegal peptide
>> found in pepXML with non-matching mass: ASSLPSSAPAVK[142]
>> Neutral Mass (from pepXML) = 1127.63
>> Neutral Computed Mass for Evaluation = 1127.62WARNING: Illegal peptide
>> found in pepXML with non-matching mass: SLASSAQPGLGK[142]
>> Neutral Mass (from pepXML) = 1128.62
>> Neutral Computed Mass for Evaluation = 1128.61WARNING: Illegal peptide
>> found in pepXML with non-matching mass: AEM[147]EELM[147]EK
>> Neutral Mass (from pepXML) = 1140.48
>> Neutral Computed Mass for Evaluation = 1140.47WARNING: Illegal peptide
>> found in pepXML with non-matching mass: NDC[160]TTQSNVK
>> Neutral Mass (from pepXML) = 1165.51
>> Neutral Computed Mass for Evaluation = 1165.5WARNING: Illegal peptide
>> found in pepXML with non-matching mass: LNK[142]TPIPQTK[142]
>> Neutral Mass (from pepXML) = 1166.71
>> Neutral Computed Mass for Evaluation = 1166.7WARNING: Illegal peptide
>> found in pepXML with non-matching mass: SSLLGTGITSPK[142]
>> Neutral Mass (from pepXML) = 1173.67
>> Neutral Computed Mass for Evaluation = 1173.66WARNING: Illegal peptide
>> found in pepXML with non-matching mass: LIDLC[160]QPTQK[142]
>> Neutral Mass (from pepXML) = 1228.66
>> Neutral Computed Mass for Evaluation = 1228.65WARNING: Illegal peptide
>> found in pepXML with non-matching mass: RNQDRPSLLK[142]
>> Neutral Mass (from pepXML) = 1239.71
>> Neutral Computed Mass for Evaluation = 1239.7WARNING: Illegal peptide
>> found in pepXML with non-matching mass: K[142]RPDEMLLPK
>> Neutral Mass (from pepXML) = 1239.71
>> Neutral Computed Mass for Evaluation = 1239.7WARNING: Illegal peptide
>> found in pepXML with non-matching mass: KRPDEMLLPK[142]
>> Neutral Mass (from pepXML) = 1239.71
>> Neutral Computed Mass for Evaluation = 1239.7WARNING: Illegal peptide
>> found in pepXML with non-matching mass: LAERPNIKM[147]R
>> Neutral Mass (from pepXML) = 1242.69
>> Neutral Computed Mass for Evaluation = 1242.69WARNING: Illegal peptide
>> found in pepXML with non-matching mass: K[142]ITGEIMHALK
>> Neutral Mass (from pepXML) = 1253.72
>> Neutral Computed Mass for Evaluation = 1253.72WARNING: Illegal peptide
>> found in pepXML with non-matching mass: KITGEIMHALK[142]
>> Neutral Mass (from pepXML) = 1253.72
>> Neutral Computed Mass for Evaluation = 1253.72WARNING: Illegal peptide
>> found in pepXML with non-matching mass: NVQTPQC[160]K[142]LR
>> Neutral Mass (from pepXML) = 1256.67
>> Neutral Computed Mass for Evaluation = 1256.67WARNING: Illegal peptide
>> found in pepXML with non-matching mass: VGAWGISGEPRK[142]
>> Neutral Mass (from pepXML) = 1269.69
>> Neutral Computed Mass for Evaluation = 1269.68WARNING: Illegal peptide
>> found in pepXML with non-matching mass: DLLHPSPEEEK[142]
>> Neutral Mass (from pepXML) = 1306.65
>> Neutral Computed Mass for Evaluation = 1306.64WARNING: Illegal peptide
>> found in pepXML with non-matching mass: GALGPGGPLGHPGEK[142]
>> Neutral Mass (from pepXML) = 1356.72
>> Neutral Computed Mass for Evaluation = 1356.71WARNING: Illegal peptide
>> found in pepXML with non-matching mass: KAGTVM[147]FEYGMR
>> Neutral Mass (from pepXML) = 1404.66
>> Neutral Computed Mass for Evaluation = 1404.65WARNING: Illegal peptide
>> found in pepXML with non-matching mass: KAGTVMFEYGM[147]R
>> Neutral Mass (from pepXML) = 1404.66
>> Neutral Computed Mass for Evaluation = 1404.65WARNING: Illegal peptide
>> found in pepXML with non-matching mass: REENQNEVNM[147]K
>> Neutral Mass (from pepXML) = 1405.63
>> Neutral Computed Mass for Evaluation = 1405.63WARNING: Illegal peptide
>> found in pepXML with non-matching mass: K[142]NSGC[160]TEVC[160]HTR
>> Neutral Mass (from pepXML) = 1461.65
>> Neutral Computed Mass for Evaluation = 1461.65WARNING: Illegal peptide
>> found in pepXML with non-matching mass: QILLLLPVM[147]INM[147]LK[142]
>> Neutral Mass (from pepXML) = 1684.01
>> Neutral Computed Mass for Evaluation = 1684WARNING: Illegal peptide
>> found in pepXML with non-matching mass: QILLLLPVM[147]INM[147]LK[142]
>> Neutral Mass (from pepXML) = 1684.01
>> Neutral Computed Mass for Evaluation = 1684WARNING: Illegal peptide
>> found in pepXML with non-matching mass: LQGEGLSVAGIVC[160]HVGK
>> Neutral Mass (from pepXML) = 1722.92
>> Neutral Computed Mass for Evaluation = 1722.91WARNING: Illegal peptide
>> found in pepXML with non-matching mass: SWAEAYK[142]DLENSDEFK[142]
>> Neutral Mass (from pepXML) = 1958.9
>> Neutral Computed Mass for Evaluation = 1958.89WARNING: Illegal peptide
>> found in pepXML with non-matching mass: DLVSGGSNEGNGK[142]EDWAMK[142]
>> Neutral Mass (from pepXML) = 2020.92
>> Neutral Computed Mass for Evaluation = 2020.92WARNING: Illegal peptide
>> found in pepXML with non-matching mass: AVATGKM[147]DENQFVAVTSTNAAK
>> Neutral Mass (from pepXML) = 2268.11
>> Neutral Computed Mass for Evaluation = 2268.11WARNING: Illegal peptide
>> found in pepXML with non-matching mass: LPMASSMEHGK[142]DLPSVQLLMK[142]
>> Neutral Mass (from pepXML) = 2339.21
>> Neutral Computed Mass for Evaluation = 2339.21WARNING: Illegal peptide
>> found in pepXML with non-matching mass: M[147]QILTPPLQSSVELVADPETR
>> Neutral Mass (from pepXML) = 2339.21
>> Neutral Computed Mass for Evaluation = 2339.2WARNING: Illegal peptide
>> found in pepXML with non-matching mass: LTPTEIVLILPM[147]PEQRNSLTAK[142]
>> Neutral Mass (from pepXML) = 2493.4
>> Neutral Computed Mass for Evaluation = 2493.39WARNING: Illegal peptide
>> found in pepXML with non-matching mass: QKLC[160]YVSQGNASFTYGYEYLGC[160]TSR
>> Neutral Mass (from pepXML) = 2951.33
>> Neutral Computed Mass for Evaluation = 2951.32WARNING: Illegal peptide
>> found in pepXML with non-matching mass: DNEIQMDMTLGPIEEAYAILNRFEVEVTK[142]
>> Neutral Mass (from pepXML) = 3381.66
>> Neutral Computed Mass for Evaluation = 3381.65WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> QM[147]GQEIGNELDEQNEIIDDLANLVENTDEK[142]
>> Neutral Mass (from pepXML) = 3445.58
>> Neutral Computed Mass for Evaluation = 3445.57WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> HLVC[160]SFRLYPFTVHTVSPGNSHLALYQVFK[142]
>> Neutral Mass (from pepXML) = 3530.84
>> Neutral Computed Mass for Evaluation = 3530.83WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> EVK[142]VYLLTTSSAPYC[160]NAFQLLTVAPNHGISLK[142]
>> Neutral Mass (from pepXML) = 3561.9
>> Neutral Computed Mass for Evaluation = 3561.89WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> K[142]GNFQLQGTM[147]LSDGQGFTQDDVQAAEVTYGAMAR
>> Neutral Mass (from pepXML) = 3663.7
>> Neutral Computed Mass for Evaluation = 3663.69WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> K[142]GNFQLQGTMLSDGQGFTQDDVQAAEVTYGAM[147]AR
>> Neutral Mass (from pepXML) = 3663.7
>> Neutral Computed Mass for Evaluation = 3663.69WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> EESLHSILAGSDM[147]TVSQILLTQHGIPVM[147]NLSDGK[142]
>> Neutral Mass (from pepXML) = 3665.84
>> Neutral Computed Mass for Evaluation = 3665.83WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> DPPAQC[160]SAGPVGDDM[147]FHWQATIM[147]GPISNYMLDN
>> Neutral Mass (from pepXML) = 3666.56
>> Neutral Computed Mass for Evaluation = 3666.55WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> DPPAQC[160]SAGPVGDDM[147]FHWQATIMGPISNYM[147]LDN
>> Neutral Mass (from pepXML) = 3666.56
>> Neutral Computed Mass for Evaluation = 3666.55WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> DPPAQC[160]SAGPVGDDMFHWQATIM[147]GPISNYM[147]LDN
>> Neutral Mass (from pepXML) = 3666.56
>> Neutral Computed Mass for Evaluation = 3666.55WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> LYC[160]NGDGEWM[147]VPIGRC[160]TC[160]K[142]PGYEPENSVAC[160]K
>> Neutral Mass (from pepXML) = 3676.6
>> Neutral Computed Mass for Evaluation = 3676.59WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> LYC[160]NGDGEWM[147]VPIGRC[160]TC[160]KPGYEPENSVAC[160]K[142]
>> Neutral Mass (from pepXML) = 3676.6
>> Neutral Computed Mass for Evaluation = 3676.59WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> ASVDSGNEDIIEALISLFYGVM[147]TPMLNPLIYSLR
>> Neutral Mass (from pepXML) = 3756.91
>> Neutral Computed Mass for Evaluation = 3756.9WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> ASVDSGNEDIIEALISLFYGVMTPM[147]LNPLIYSLR
>> Neutral Mass (from pepXML) = 3756.91
>> Neutral Computed Mass for Evaluation = 3756.9WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> M[147]GFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGK
>> Neutral Mass (from pepXML) = 3780.94
>> Neutral Computed Mass for Evaluation = 3780.93WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> MGFNRPSKIQENALPLM[147]LAEPPQNLIAQSQSGTGK
>> Neutral Mass (from pepXML) = 3780.94
>> Neutral Computed Mass for Evaluation = 3780.93WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> GFPSQC[160]YSAQTLPELC[160]SPQDELDFLM[147]EALIISK
>> Neutral Mass (from pepXML) = 3802.79
>> Neutral Computed Mass for Evaluation = 3802.78WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> LYTM[147]DGITVTVADLFFAGTETTSTTLRYGLLILMK[142]
>> Neutral Mass (from pepXML) = 3885.03
>> Neutral Computed Mass for Evaluation = 3885.02WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> LYTMDGITVTVADLFFAGTETTSTTLRYGLLILM[147]K[142]
>> Neutral Mass (from pepXML) = 3885.03
>> Neutral Computed Mass for Evaluation = 3885.02WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> FVHKSFVEVNEEGTEAAAASSC[160]FVVAEC[160]C[160]M[147]ESGPR
>> Neutral Mass (from pepXML) = 3906.7
>> Neutral Computed Mass for Evaluation = 3906.7WARNING: Illegal peptide
>> found in pepXML with non-matching mass:
>> GPLLAQEM[147]PTVSVLEYALPQRPPQGPEDDRDLSER
>> Neutral Mass (from pepXML) = 3918.95
>> Neutral Computed Mass for Evaluation = 3918.94
>>
>> *Command Successful*
>> RETURN CODE:0
>>
>>
>>
>>
>> On Thu, Apr 30, 2015 at 2:18 AM, delphine wood <[email protected]
>> <javascript:>> 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] <javascript:>>:
>>>
>>>> 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]
>>>> <javascript:>> 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
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>>>>> an email to [email protected] <javascript:>.
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>>>>> <javascript:>.
>>>>> Visit this group at http://groups.google.com/group/spctools-discuss.
>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>
>>>>
>>>> --
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>>>> To unsubscribe from this group and all its topics, send an email to
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>>>> Visit this group at http://groups.google.com/group/spctools-discuss.
>>>> For more options, visit https://groups.google.com/d/optout.
>>>>
>>>
>>>
>>
>
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