[Psidev-pi-dev] [HUPO-PSI/mzIdentML] Encoding of cross-linker as part of SearchModifications (#30)

[Lutz F. <not...@gi...>]

Currently SearchModifications do not encode for separate sites of e.g. a cross-linker.
To circumvent this we could use the same method as we encode the peptide modifications. I.e. encode the cross-linker as one modification that holds the mass and the specificities for  one site and have a second 0 mass modification that encodes for the specificities second site of the cross-linker.

E.g. for BS3 alone:
```
      <SearchModification fixedMod="false" massDelta="138.06808" residues="S T Y K">
        <cvParam cvRef="XLMOD" accession="XL:00001" name="Xlink:BS3"></cvParam>
        <cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="0"></cvParam>
      </SearchModification>
      <SearchModification fixedMod="false" massDelta="138.06808" residues=".">
        <SpecificityRules>
          <cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
        </SpecificityRules>
        <cvParam cvRef="XLMOD" accession="XL:00001" name="Xlink:BS3"></cvParam>
        <cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="0"></cvParam>
      </SearchModification>
      <SearchModification fixedMod="false" massDelta="0.0" residues="S T Y K">
        <cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="0"></cvParam>
      </SearchModification>
      <SearchModification fixedMod="false" massDelta="0.0" residues=".">
        <SpecificityRules>
          <cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
        </SpecificityRules>
        <cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="0"></cvParam>
      </SearchModification>

```

both sides of the cross-linker are linked (the same as in peptide modifications) vi cvterms:
```
<cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="X">
<cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="X">
```


For a case with two cross-linker (e.g BS3-d0/BS3-d4) thsi would look like this:
```
      <SearchModification fixedMod="false" massDelta="138.06808" residues="S T Y K">
        <cvParam cvRef="XLMOD" accession="XL:00001" name="Xlink:BS3"></cvParam>
        <cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="0"></cvParam>
      </SearchModification>
      <SearchModification fixedMod="false" massDelta="138.06808" residues=".">
        <SpecificityRules>
          <cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
        </SpecificityRules>
        <cvParam cvRef="XLMOD" accession="XL:00001" name="Xlink:BS3"></cvParam>
        <cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="0"></cvParam>
      </SearchModification>
      <SearchModification fixedMod="false" massDelta="0.0" residues="S T Y K">
        <cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="0"></cvParam>
      </SearchModification>
      <SearchModification fixedMod="false" massDelta="0.0" residues=".">
        <SpecificityRules>
          <cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
        </SpecificityRules>
        <cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="0"></cvParam>
      </SearchModification>
      <SearchModification fixedMod="false" massDelta="142.09317" residues="S T Y K">
        <cvParam cvRef="XLMOD" accession="XL:00005" name="Xlink:BS3:d4"></cvParam>
        <cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="1"></cvParam>
      </SearchModification>
      <SearchModification fixedMod="false" massDelta="142.09317" residues=".">
        <SpecificityRules>
          <cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
        </SpecificityRules>
        <cvParam cvRef="XLMOD" accession="XL:00005" name="Xlink:BS3:d4"></cvParam>
        <cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="1"></cvParam>
      </SearchModification>
      <SearchModification fixedMod="false" massDelta="0.0" residues="S T Y K">
        <cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="1"></cvParam>
      </SearchModification>
      <SearchModification fixedMod="false" massDelta="0.0" residues=".">
        <SpecificityRules>
          <cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
        </SpecificityRules>
        <cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="1"></cvParam>
      </SearchModification>
```


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