ZenoTOF EAD spectra in Spectra objects

[YasinEl]

Hello and thank you for maintaining this!

I am working with ZenoTOF data containing CID and EAD spectra. MS2 scans in such files can contain two different fragmentation energies, which are stored in the mzML files for EAD and CID, respectively. It would be great to be able to access those energies and fragmentation types in Spectra objects. An example file can be downloaded from here. Thank you!

[jorainer]

and these values are not yet reported as spectra variables? if not, we might need to add support for that rather in mzR - which then also depends on proteowizard. do you know by chance if proteowizard can read/handle this mzML file and what the MS OBO for these variables is?

[YasinEl]

Thank you! The mzML file I am referencing has been generated through Proteowizards mzConvert (enabled through ProteoWizard/pwiz#3087).

For EAD you have to set a collision energy and electron beam energy. In the file it looks like this:

EAD name:
MS:1003294: electron activated dissociation
EAD energy:
MS:1003410: electron beam energy
CID energy:
MS:1000045: collision energy

Example:

              <activation>
                <cvParam cvRef="MS" accession="MS:1003294" name="electron activated dissociation" value=""/>
                <cvParam cvRef="MS" accession="MS:1003410" name="electron beam energy" value="24.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
                <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="12.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
              </activation>

For normal CID in TOFs you should have:

CID name:
MS:1000422: beam-type collision-induced dissociation
CID energy:
MS:1000045: collision energy

Example:

              <activation>
                <cvParam cvRef="MS" accession="MS:1000422" name="beam-type collision-induced dissociation" value=""/>
                <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="40.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
              </activation>

[jorainer]

Thanks! but that looks like we need to add support for these terms in mzR. I'll look into that - and once mzR can extract this info it's automatically reported in Spectra

[jorainer]

I made a PR in mzR that extracts also the MS_electron_beam_energy from mzML files: sneumann/mzR#303 - with this you get also a spectra variable (if you read the data into a Spectra object) "electronBeamEnergy" that is non-NA for EAD spectra.

Until it gets included into official mzR you could install my fork with

BiocManager::install("jorainer/mzR", ref = "devel")

[YasinEl]

Thank you, that solves it!

[jorainer]

Note: the PR was merged into mzR (the current developmental version).

Closing the issue - feel free to re-open if needed.