This is probably a pretty basic question, but what is the difference between "scans" in mzR and "spectra" in MSnbase? Why are there more scans than there are spectra? I can plot a spectrum for every scan with plot(peaks(mz, scan)), why are so many spectra missing from my MSnExp?
> mz Mass Spectrometry file handle. Filename: 25May18_Rizzo_MBP.mzML Number of scans: 22703 > mzEXP MSn experiment data ("MSnExp") Object size in memory: 50.62 Mb - - - Spectra data - - - MS level(s): 2 Number of spectra: 9530 MSn retention times: 0:1 - 99:60 minutes - - - Processing information - - - Data loaded: Wed Jun 6 14:50:56 2018 MSnbase version: 2.6.1 - - - Meta data - - - phenoData rowNames: 25May18_Rizzo_MBP.mzML varLabels: sampleNames varMetadata: labelDescription Loaded from: 25May18_Rizzo_MBP.mzML protocolData: none featureData featureNames: F1.S0001 F1.S0002 ... F1.S9530 (9530 total) fvarLabels: spectrum fvarMetadata: labelDescription experimentData: use 'experimentData(object)'