[Psidev-ms-dev] amino acid modifications in TraML

[Andreas B. <be...@in...>]

Dear mzTargetML community ;),

during the implementation of the current draft version, some questions  
and comments came up.

Cheers,
A.

1. Currently, peptide modifications in traML are specified using the  
mass only. This can lead to ambiguous meanings.

  <peptide id="ADTHFLLNIYDQLR-M1" proteinRef="Q12149">
       <cvParam cvRef="MS" accession="MS:1000888" name="unmodified  
peptide sequence" value="ADTHFLLNIYDQLR"/>
       <cvParam cvRef="MS" accession="MS:1000889" name="modified  
peptide sequence" value="ADTHFLLNIYDQLR[162.10111]"/>

The same problem has been solved by the PI group in mzIdentML using  
the modification definitions of UniMod (snippet from the  
Macot_MSMS_example.mzid):
.....
  <Peptide id="peptide_3_9">
       <peptideSequence>MSKPAGSTSRILDIPCK</peptideSequence>
       <Modification location="0" monoisotopicMassDelta="127.063324">
         <cvParam accession="UNIMOD:29" name="SMA" cvRef="UNIMOD" />
       </Modification>
       <Modification location="1" residues="M"  
monoisotopicMassDelta="15.994919">
         <cvParam accession="UNIMOD:35" name="Oxidation"  
cvRef="UNIMOD" />
         .....
       </Modification>
     </Peptide>
.....

If the modification itself is not known, the following term can be  
used (and is allowed in mzIdentML)

[Term]
id: MS:1001460
name: unknown modification

2.  Modeling the peptide sequence using a CV term seems odd to me. I  
think this can be an attribute, or like in mzIdentML modeled as a  
subtag of peptide. The sequence must be given, I suppose, otherwise it  
can be modeled as a (unkown) compound.

3 . Additionally, the proteinRef is not necessarily restricted to one  
single protein. There might be several proteins that contain that  
peptide and it should be possible to represent that. Make that a CV  
term?



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