Default spectra variable names about compounddb HOT 8 OPEN

No objections

from compounddb.

Unsure what kind of things go here exactly.

• cas
• local_identifier
• mslevel
• manufacturer
• ionmode
• precursormz

from compounddb.

• formula formula
• adduct adduct

from compounddb.

Once we agreed on a format, I would like to refactor this in MsBackendMassbank, so they spectra can be directly used without any reformatting

from compounddb.

I would suggest to always use the default for the core spectra variables (see the list of variables in the General description of the Spectra vignette. Thus I would use:

• msLevel instead of mslevel.
• precursorMz instead of precursormz.
• polarity instead of ionmode (if you mean that @stanstrup )

(note my lack of consistency here - sorry for that :( )

from compounddb.

To summarize so far.
We have the spectra core variables:

• acquisitionNum
• centroided
• collisionEnergy
• dataOrigin
• dataStorage
• intensity
• isolationWindowLowerMz
• isolationWindowTargetMz
• isolationWindowUpperMz
• msLevel
• mz
• polarity
• precScanNum
• precursorCharge
• precursorIntensity
• precursorMz
• rtime
• scanIndex
• smoothed

And our "library" variables (plus a few more suggestion from my side)

• name (required)
• exactmass (required)
• adduct (required)
• formula (required)
• splash (required)
• inchi (optional)
• inchikey (optional)
• smiles (optional)
• cas (optional)
• localidentifier (optional)

In case of lipids we often don' have the exact structure, therefore I would like to have inchi, inchikey, smiles optional.

from compounddb.

OK, this means I should update/change the code in CompoundDb to use these new column names, right?

from compounddb.

I would guess so... If there are no objections from @stanstrup ?

from compounddb.