use a standardised format to store the raw spectra and the processed spectra

[cpauvert]

Currently, the spectra and peaks are stored as RDS files containing MassSpectrum or MassPeaks R objects. These objects are metadata-rich which is fundamental.

There is indeed a couple of standard file format (e.g., mzML) to which these objects can be exported using MALDIquantForeign, but the metadata are loss in the process..

[cpauvert]

The https://www.rformassspectrometry.org/ initiative could be useful there.