Scans vs Spectra
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Ed Siefker ▴ 230
@ed-siefker-5136
Last seen 15 months ago
United States

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)'

 

mass spectrometry mzr/ msnbase • 285 views
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