MS5 and "merged MSn" spectra

[meowcat]

Hi,

I am working with a contributor who collected a ton of MSn spectra. Two things:

• they have MS5 spectra, which are not currently in RecordParserDefinition.java. Can we add MS5 to the definition?
• they also have "merged MSn" spectra, where all MSn spectra have been pooled to a single spectrum. I would suggest to simply add "MSn" as a definition for those. Would you agree? Or do we want to avoid these?

[schymane]

I can't help with point (1) but agree that it should be added. Regarding point (2), I think these spectra should be included (not avoided), either as "MSn" or "merged MSn"?

[sneumann]

+1 for having the spectra. MS5 can be added right away.

Merged MSn is interesting, and we definitely want those..
It is similar to the idea of ramped spectra, which also are a "merge" of multiple collision energies.
We could add 'em as AC$MASS_SPECTROMETRY: MS_TYPE MSn, and the merging would be mentioned in the MS$DATA_PROCESSING: merged MSn
What about the focused ion, maybe only the MS2 ? What if they also have in-source fragments in another MS2 scan ? Can there be multiple collision energies between levels ? Maybe the title mentions "Merged MSn" ?
Yours,
Steffen

[meowcat]

For the FOCUSED_ION we could either
PRECURSOR_M/Z 581.18649/merged
or just like you suggest
PRECURSOR_M/Z 581.18649

The slashes exist anyway in MSn records so the field is already not numeric. (Same, actually, for the collision energies, both for MSn and for all the stepped/merged MS2.) From that point of view, "merged" would not cause much more damage... One could argue that it's not extra information if the record says "MSn merged" anyway. I guess your suggestion is better.

The suggestion for DATA_PROCESSING would currently be
MS$DATA_PROCESSING: SPECTYPE ALL_MSN_TO_PSEUDO_MS2

[meier-rene]

This is included in release 2.2.6.