MsData

lgatto edited this page Oct 12, 2012 · 6 revisions

Data to be displayed

Data to be displayed

Information box

Experiment information

  • Retention time range for fill loaded experiment (not filtered)
  • Number of MS1, MS2 (there can be MSn > 2) spectra (not filtered)
  • Precursor M/Z range (only relevant for MS n > 1) (not filtered)

Spectrum information

  • Retention time
  • Index
  • Precursor M/Z (if MSn > 1)
  • Precursor intensity (if MSn > 1)
  • ... see middle-layer

Plots

  • Spectrum in profile mode - plot(intensity ~ mz, type = "h")
  • Spectrum centroided - plot(intensity ~ mz, type = "b")
  • Chromatogram - plot(totalIonCurrent ~ mz, type = "l")

Accessing the raw data

From raw files using mzR

See middle-layer

From MSnExp instances

TODO - but will probably be done through raw data file