ETciD and EThcD annotation

[rolivella]

Could you please take a look at this? OpenMS/OpenMS#7499

Thanks

[timosachsenberg]

Quick question: do you know by chance if there is no distinction between CID ETciD and EThcD in proteowizard and TRFP anymore? (e.g., just based on the energy)

[caetera]

Hi @timosachsenberg ,

I am afraid I don't understand your question completely. ETciD is a "combination" of ETD and CID, while ETD and HCD.

In TRFP it is represented as a different supplemental activation - see the last CV term

ETciD

<activation>
  <cvParam cvRef="MS" accession="MS:1000045" value="100.179542541504" name="collision energy" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
  <cvParam cvRef="MS" accession="MS:1000598" value="" name="electron transfer dissociation" />
  <cvParam cvRef="MS" accession="MS:1002680" value="35" name="supplemental collision energy" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
  <cvParam cvRef="MS" accession="MS:1002679" value="" name="supplemental collision-induced dissociation" />
</activation>

EThcD

<activation>
  <cvParam cvRef="MS" accession="MS:1000045" value="100.179542541504" name="collision energy" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
  <cvParam cvRef="MS" accession="MS:1000598" value="" name="electron transfer dissociation" />
  <cvParam cvRef="MS" accession="MS:1002680" value="15" name="supplemental collision energy" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
  <cvParam cvRef="MS" accession="MS:1002678" value="" name="supplemental beam-type collision-induced dissociation" />
</activation>

MSconvert (I downloaded the latest version) adds a "plain" CID and plain HCD term on top of that. I'm not sure why - it does not make much sense to me.

ETciD

<activation>
  <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
  <cvParam cvRef="MS" accession="MS:1000598" name="electron transfer dissociation" value=""/>
  <cvParam cvRef="MS" accession="MS:1002679" name="supplemental collision-induced dissociation" value=""/>
  <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="100.179542541504" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
   <cvParam cvRef="MS" accession="MS:1002680" name="supplemental collision energy" value="35.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
</activation>

EThcD

<activation>
  <cvParam cvRef="MS" accession="MS:1000598" name="electron transfer dissociation" value=""/>
  <cvParam cvRef="MS" accession="MS:1000422" name="beam-type collision-induced dissociation" value=""/>
  <cvParam cvRef="MS" accession="MS:1002678" name="supplemental beam-type collision-induced dissociation" value=""/>
  <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="100.179542541504" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
  <cvParam cvRef="MS" accession="MS:1002680" name="supplemental collision energy" value="15.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
</activation>

I am happy to find a consensus way to represent ETciD and EThcD and implement it in TRFP, but, I believe, we need to have ProteoWizard people on board as well.

[timosachsenberg]

Ah, thanks for the clarification and for taking the time to look into that.
I think my confusion also came from the different ways of encoding it. I don't have a strong feeling what is better, but I guess consistency between both converters would be a win.