[Psidev-pi-dev] Ambiguous residues - CV

[David C. <dc...@ma...>]

Hi all,

We need CV for the <AmbiguousResidue> element in the analysisXML 
MassTable. This is when, for example, a search engine sees an 'X' in the 
fasta file and it tries every other defined residue mass. We decided 
that we wanted to use CV here in case a search engine implements complex 
rules for these ambiguous residues.

I propose 2 initial CV items to allow either mass or previously defined 
residue.  An example of each type shown in context below:

<MassTable is="MT1">
  <Residue Code="A" Mass="71.037114"/>
  ...
  <Residue Code="Y" Mass="163.063329"/>

  <AmbiguousResidue Code="B">
    <pf:cvParam accession="PI:xxxx" name="Alternate single letter codes" 
cvRef="PSI-PI" value="DN"/>
  </AmbiguousResidue>
  <AmbiguousResidue Code="Z">
    <pf:cvParam accession="PI:yyyy" name="Alternate mass" cvRef="PSI-PI" 
value="129.042593"/>
    <pf:cvParam accession="PI:yyyy" name="Alternate mass" cvRef="PSI-PI" 
value="128.058578"/>
  </AmbiguousResidue>
  . . .
</MassTable>

The "Alternate mass" item would be: unitAccession="UO:0000221" 
unitName="dalton".

Does this sound reasonable?

Cheers,

David

-- 
David Creasy
Matrix Science
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