PTM mod and methylations

[Delphine]

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]TGMK
WARNING: Illegal peptide with unknown mod: NLMTGM[147]K
WARNING: Illegal peptide with unknown mod: K[156]AGESHR
WARNING: 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]PGELPR
WARNING: Illegal peptide with unknown mod: LTPSM[147]LR
WARNING: Illegal peptide with unknown mod: VTAAMGK[156]K
WARNING: 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]ALTQVR
WARNING: Illegal peptide with unknown mod: M[147]ADAK[156]QK
WARNING: 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]ANSMVK
WARNING: 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]VPSAPPK
WARNING: 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]ANK
WARNING: Illegal peptide with unknown mod: VASPKANK[156]
WARNING: Illegal peptide with unknown mod: AVDQRNK[142]
WARNING: Illegal peptide with unknown mod: LATWK[156]PL
WARNING: Illegal peptide with unknown mod: AMAEWVK[156]
WARNING: Illegal peptide with unknown mod: DSFDIIK[156]
WARNING: Illegal peptide with unknown mod: VPPHM[147]LR
WARNING: Illegal peptide with unknown mod: LPKAEDR
WARNING: Illegal peptide with unknown mod: LKDSLPR
WARNING: Illegal peptide with unknown mod: KEVPLSR
WARNING: 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_01.15465.15465.2
WARNING: 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

[Delphine]

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_01.02094.02094.2
WARNING: 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

[David Shteynberg]

Hi Delphine,

Unfortunately, with the version of PTMProphet you have this will not be for you to process this type of data.  For linux processing, you will need to compile and use the latest PTMProphet code from the SVN repository, as it is not available as a release yet.  Alternatively, you can install the windows version of the code on another machine, migrate your results and run the binary I sent a link for that includes the latest PTMProphet code.  Our build manager has recently switched jobs so the building of the software and the releases have been lagging behind the development at the moment.

Thanks for you patience,

-David

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[delphine wood]

Hi David,

We will try to compile the PTMProphet code from the svn repository: could you tell me how to access this repository please?

Thanks.

Delphine

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[David Shteynberg]

Hello Delphine,

Sorry about the delay.  I have compiled a linux version of PTMProphetParser and placed it in my Dropbox for your testing purposes,  please see: https://dl.dropboxusercontent.com/u/21286225/PTMProphetParser

If you haven't compiled your own version from the latest source, this may be an alternative, although it may fail due to system dependencies. Let me know how it goes.

Thank you,

-David