Subtracting background

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In order to enhance the mass spectra of the signals within an acquired chromatogram, there are several options to subtract mass spectral background. It is recommended to switch to the "Subtract Mass Spectra" perspective to have full control and access to the background subtraction options. Note, that you can store/load a background subtraction mass spectrum, in case you want to apply it on several chromatograms.

You may subtract

  • a mass spectrum at a user-selected scan
  • a sum of several user-selected mass spectra
  • a summed-up mass spectrum over a user-selected retention time range


  • the entire chromatogram (menu bar > Chromatogram > Filter > MSD > Chromatogram)
  • a user-selected retention time window (menu bar > Chromatogram > Filter > MSD > Chromatogram)
  • a single user-selected peak (menu bar > Chromatogram > Filter > MSD > Peaks)
  • all peaks (menu bar > Chromatogram > Filter > MSD > Peaks)

For quick access the following icons are available:

  • "Subtract Filter Selected Peak" - Icon-SubtractFilterSelectedPeak.png
  • "Subtract Filter All Peaks" - Icon-SubtractFilterAllPeaks.png
  • "Subtract Filter Chromatogram" - Icon-SubtractFilterChromatogram.png
  • "Store Subtract Mass Spectrum" - Icon-StoreSubtractMassSpectrum.png
  • "Load Subtract Mass Spectrum" - Icon-LoadSubtractMassSpectrum.png
  • "Clear Subtract Mass Spectrum( Session)" - Icon-ClearSubtractMassSpectrum(Session).png
  • "Add Selected Scan" - Icon-AddSelectedScan.png
  • "Add Combined Scans" - Icon-AddCombinedScans.png

Subtract mass spectral background from entire chromatogram or user-selected retention time window

Subtract mass spectral background from single or all detected peaks of active chromatogram