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lgatto / MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics
http://lgatto.github.io/MSnbase/
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Support Spectrum objects without MS level #452

Closed jorainer closed 5 years ago

jorainer commented 5 years ago

Thinking out loud here: @stanstrup has a use case with UV data (spectrum like) but that has no MS level. Also Michele Stravs has some use cases for spectrum data neither MS1 nor MS2.

Should we either add a new Spectrum0 object extending Spectrum? Or support MS level 0? Any thoughts @lgatto @sgibb ?

lgatto commented 5 years ago

If there's no MS level, it should probably be set to NA, but I suspect that one can't instantiate a Spectrum1 object and setting the MS level to NA.

But what about the simplest solution to just use a Spectrum1 object and ignore the MS level? Is everything else except the MS level relevant? Are there not other packages for Nuclear magnetic resonance or Raman spectroscopy that would be a better fit? (See https://cran.r-project.org/web/views/ChemPhys.html)

My point here is that I don't think we should support other types of spectro-technology that measure spectra in MSnbase. We could start a new package that uses MSnbase's infrastucture for non MS spectra, if that would be relevant.

lgatto commented 5 years ago

@stanstrup - I'm closing this issue for now, but please feel free to re-open it if needed and/or to document your solution here too.

lgatto commented 3 years ago

I think that with Spectra, we are bypassing this issue altogether. @stanstrup - did you ever get a chance to try it?

stanstrup commented 3 years ago

No, I have not dealt with UV/PDA data since before Spectra.