Re: [Psidev-pi-dev] Cross-linker Search-modification

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Thanks Lutz – would you mind opening this as an issue on GitHub so we remember to discuss it, but your encoding looks sensible.
Best wishes
Andy

From: Lutz Fischer [mailto:lfi...@st...]
Sent: 27 May 2016 13:24
To: Jones, Andy <jo...@li...>; 'psi...@li...' <psi...@li...>
Subject: Cross-linker Search-modification

Hi Andy,

I am implementing the ProteinDetection (just have another 9000 or so error messages from the validator to go through ...)

But I realised so far I never did write out cross-linker as SearchModification so I got some questions there:
How to encode can link K,S,T,Y and N-terminals?
How to encode the two site of the cross-linker?

I currently address that by (example is BS3) first writing one SearchModification for K,S,T and Y and one for the N-terminal.
For the second site I did write out A acceptor modification of zero-mass - actually again two. one for K,S,T,Y and one for N-terminal.

so for BS3 I have currently following SearchModifications:

      <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>

The modification that denote the same cross-linker are here marked also with the same value for

cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="0">

So for two cross-linker (e.g. BS3 and BS3-d0) it 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>

In this example the acceptor looks exactly the same for both but e.g. if EDC and BS3 where mixed then the acceptor would differ as well.

Not sure if that would be needed/wanted - but I think that keeps things in line on how it is used for peptide modifications

Currently there seems to be no specification for this in the spec-document and probably would need to be added.

I send this also to the psi-pi mailing list. I assume other people might encounter the same questions.

Best wishes,
Lutz

On 26/05/16 17:21, Jones, Andy wrote:
Hi Lutz,

No these will have to go onto the PDH level. A simple protein ID process is fine, the software doesn’t need to do grouping info. Each Protein group can contain a single protein, with whatever score you want to give it.

DBSequence simply means a database protein, so we don’t put inferred values from the experiment on here.

Best wishes
Andy

From: Lutz Fischer [mailto:lfi...@st...]
Sent: 26 May 2016 17:10
To: Jones, Andy
Subject: mzIdentML +Protein Pair Information

Hi Andy,

Just realized that with the current way to store residue-pair information we force people to do protein grouping - even if all they want to store are a score or FDR for residue pairs.

Would it be sensible to move these to DBSequence? If we take your suggested way and just move it to DBSeqeunce it would still work for residue pairs. Admittedly when it comes to protein pairs it only really makes sense with protein groups.

I have an example without residue and protein pair information - but some trouble with the validator came up - so didn't upload the example yet.

As I am currently struggling a bit with writing out protein-groups, the example is not quite ready and would then also need to pass the validator.

Lutz

--

Lutz Fischer

lfi...@st...<mailto:lfi...@st...>

+44 131 6517057

--

Lutz Fischer

lfi...@st...<mailto:lfi...@st...>

+44 131 6517057