[Psidev-pi-dev] Modifications

[Jones, A. <And...@li...>]

Hi all,

 

I'd like to get the mods part of the schema sorted in time for the call this week if possible. There are quite a few different aspects in issues 3 and 35 so I'll try to summarise it here:

 

In the SpectrumIdentificationProtocol we have:

 

        <SearchModification fixedMod="false" >

          <ModName   accession="MOD:TODO" name="SMA (N-term)" cvRef="PSI-MOD" />

          <MassValue value="127.063324" unitAccession="PSI:xxxx" unitName="Da" />

          <SpecificityRule accession="" cvRef="" name="" unitAccession="" unitName="" />

        </SearchModification>

 

On Peptide we have:

 

      <Modification location="13">

        <pf:cvParam accession="TODO: (requires quite a bit of code)" name="SMA (K)" cvRef="PSI-MOD" />

      </Modification>

 

OR

 

      <SubstitutionModification originalResidue="K" replacementResidue="M" location="2">

        <pf:cvParam cvRef="" accession="" name=""/>

      </SubstitutionModification>

 

(Note the datatypes were set to int for original and replaceResidue so I have fixed this to be the same alphabet as for pre and post).

 

OR

 

      <CustomModification location="2" monoisotopicMassDelta="21.21" count="1" residue = "M">

        <pf:cvParam cvRef="" accession="" name=""/>

      </CustomModification>

 

 

PSI-MOD can specify a modification and the residue that has been modified, although the terms are not always intuitive for our purposes. For example, as far  as I can tell "oxidation to L-methionine sulfoxide" would be the standard term for a methionine oxidation, correct?

 

Comments on current schema:

-          I'm not sure we need CustomModification, I would prefer just to have the Modification element, making location optional and adding the mass delta attributes to Modification. I think the count attribute is just confusing, if two modifications have been identified, just have two entries of the Modification element? There would still be an issue of how to specify which residue has been modified but basically this is the same issue for standard and custom mods i.e. the CV tells you the mod and the residue? 

-          I disagree that we should use the same element for the searched and the found modification. We do not need to report the specificity on the found modifications and in most cases you would not report the mass delta for a found modification (presumably this would only make any sense for MS1 data?)

-          On SearchModification, are we agreed that we want to report the MassValue (i.e. mass of residue +/- mod) rather than say a MassDelta (mass of mod only)?

-          I think we should add documentation that MassValue is optional since the mod mass is part of the CV, but if reported the MassValue "overrides" the mass value from the CV.

-          SubstitutionMod inherits a mandatory association to Param, this needs to be changed since in most cases a CV term would not be required.

 

Thoughts?

Cheers, Andy