I haven't solve the problem but tried something else: searching each
modification separatly. It worked fined for the methylation of K (14.01565)
and the dimethylation of K (28.0313) but it still fails for the
trimethylation of K (42.04695)...
INFO: Writing file 327_05_01_011_150417_01_MTCS_0_D_interact.ptm.pep.xml ...
INFO: Reading file
/opt/tpp/data/327_05_01_1704_trimethylation/327_05_01_011_150417_01_MTCS_0_D_interact.iproph.pep.xml
...WARNING: Illegal peptide with unknown mod: GC[160]GQARR
WARNING: Unrecognized mod on peptide: AVTHQVK[170]WARNING: Cannot
initialize for sequence: AVTHQVK[170], unknown mods may exist in spectrum
327_05_01_011_150417_01.02270.02270.2
WARNING: Unrecognized mod on peptide: AVTHQVK[170]WARNING: Cannot
initialize for sequence: AVTHQVK[170], unknown mods may exist in spectrum
327_05_01_011_150417_01.02094.02094.2WARNING: Illegal peptide with unknown mod:
GGM[147]KDDR
Segmentation fault
Would you have any idea of the reason why it fails for this modification?
Thanks for your kind help.
If you need any information or file, I will gladly send it
Delphine
Le vendredi 22 mai 2015 14:54:25 UTC+2, Delphine a écrit :
>
> Hello,
>
> I recently asked a question about mods error for the methylation
> identifications with PTMprophet (
> https://mail.google.com/mail/u/0/#14d15557e5baa348_group_thread_1). You
> helped me to partially solve the problem. Now I have to identify
> methylation, di-methylations and tri-methylations on the same data. I
> modified the interrogation parameter files:
> -comet:
> variable_mod01 = 15.9949 M 0 3 -1 0
> variable_mod02 = 14.015650 K 0 3 -1 0
> variable_mod03 = 28.031300 K 0 3 -1 0
> variable_mod04 = 42.046950 K 0 3 -1 0
> -xtandem:
> <note type="input" label="residue, modification mass">57.021464@C</note>
> <note type="input" label="residue, potential modification
> mass">15.994915@M,14.015650@K,28.03130@K,42.046950@K</note>
>
>
> I combine the identification 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_1704_multimethylations;
> /opt/tpp/bin/PTMProphetParser K,14.0156,K,28.03130,K,42.046950,M,15.9949
> MZTOL=0.2
> /opt/tpp/data/327_05_01_1704_multimethylations/327_05_01_014_150417_01_MTCS_0_D_interact.iproph.pep.xml
>
> 327_05_01_014_150417_01_MTCS_0_D_interact.ptm.pep.xml *
> Here is the error:
>
>
> INFO: Writing file 327_05_01_014_150417_01_MTCS_0_D_interact.ptm.pep.xml ...
> INFO: Reading file
> /opt/tpp/data/327_05_01_1704_multimethylations/327_05_01_014_150417_01_MTCS_0_D_interact.iproph.pep.xml
> ...WARNING: Illegal peptide with unknown mod: DGDPLEK[156]WARNING: Illegal
> peptide with unknown mod: NLM[147]TGMKWARNING: Illegal peptide with unknown
> mod: NLMTGM[147]KWARNING: Illegal peptide with unknown mod:
> K[156]AGESHRWARNING: Illegal peptide with unknown mod: IITNLSK[156]WARNING:
> Illegal peptide with unknown mod: AM[147]NVNPK[156]WARNING: Illegal peptide
> with unknown mod: C[160]PGELPRWARNING: Illegal peptide with unknown mod:
> LTPSM[147]LRWARNING: Illegal peptide with unknown mod: VTAAMGK[156]KWARNING:
> Illegal peptide with unknown mod: VTAAMGKK[156]WARNING: Illegal peptide with
> unknown mod: M[147]ANEVIK[142]WARNING: Illegal peptide with unknown mod:
> M[147]ALTQVRWARNING: Illegal peptide with unknown mod:
> M[147]ADAK[156]QKWARNING: Illegal peptide with unknown mod:
> M[147]ADAKQK[156]WARNING: Illegal peptide with unknown mod:
> AM[147]EAELK[156]WARNING: Illegal peptide with unknown mod:
> K[142]ANSMVKWARNING: Illegal peptide with unknown mod:
> K[142]ANSM[147]VK[156]WARNING: Illegal peptide with unknown mod:
> K[156]ANSM[147]VK[142]WARNING: Illegal peptide with unknown mod:
> KANSMVK[142]WARNING: Illegal peptide with unknown mod: K[142]VPSAPPKWARNING:
> Illegal peptide with unknown mod: KVPSAPPK[142]WARNING: Illegal peptide with
> unknown mod: AEHSELK[156]WARNING: Illegal peptide with unknown mod:
> AEHSELK[156]WARNING: Illegal peptide with unknown mod: VASPK[156]ANKWARNING:
> Illegal peptide with unknown mod: VASPKANK[156]WARNING: Illegal peptide with
> unknown mod: AVDQRNK[142]WARNING: Illegal peptide with unknown mod:
> LATWK[156]PLWARNING: Illegal peptide with unknown mod: AMAEWVK[156]WARNING:
> Illegal peptide with unknown mod: DSFDIIK[156]WARNING: Illegal peptide with
> unknown mod: VPPHM[147]LRWARNING: Illegal peptide with unknown mod:
> LPKAEDRWARNING: Illegal peptide with unknown mod: LKDSLPRWARNING: Illegal
> peptide with unknown mod: KEVPLSRWARNING: Illegal peptide with unknown mod:
> AM[147]LAM[147]FK[156]WARNING: Illegal peptide with unknown mod:
> QAVGPEDK[156]WARNING: Illegal peptide with unknown mod: AM[147]LEVHK[156]
> WARNING: Unrecognized mod on peptide: DILTQLK[170]WARNING: Cannot
> initialize for sequence: DILTQLK[170], unknown mods may exist in spectrum
> 327_05_01_014_150417_01.15465.15465.2WARNING: Illegal peptide with unknown
> mod: SSVC[160]IC[160]K[156]
> Segmentation fault
>
> *Command FAILED*
>
> RETURN CODE:35584
>
>
>
> Do you have any idea to solve this problem? What I am doing wrong?
>
> Thanks for your help
>
> Delphine
>
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