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" -
- "Subtract Filter All Peaks" -
- "Subtract Filter Chromatogram" -
- "Store Subtract Mass Spectrum" -
- "Load Subtract Mass Spectrum" -
- "Clear Subtract Mass Spectrum( Session)" -
- "Add Selected Scan" -
- "Add Combined Scans" -
Subtract mass spectral background from entire chromatogram or user-selected retention time window
1. Open the perspective switcher (A) and select the perspective "Subtract Mass Spectra" (B). Alternatively, if you prefer to keep your current perspective, you could add the views "Combined Mass Spectrum" and "Subtract Mass Spectrum (Session)" to your current perspective. The various background subtraction steps can be accessed via the menu bar (as mentioned here or via the icons (C)).
2. In the displayed example a retention time window between 65 and 77 minutes is selected and no peak has been detected (no arrow showing at any apex). In this case background subtraction will affect the entire retention time window selected by the user. The mass spectrum of the peak at 71.1 minutes (D) is displayed in the view "Scan (Nominal)" (E) after left double-click. The summed up mass spectrum of the current retention time (RT) window is automatically displayed in the view "Combined Mass Spectrum (Chromatogram Selection)" (F) and updated when a different RT window is selected. The view "Subtract Mass Spectrum (Session)" displays the default "background" mass spectrum (G), which will be used for any subtraction action if it is not replaced. To remove this default mass spectrum use the icon .
3. In order to remove background signal from the entire RT window currently displayed a suitable scan may be selected (here e.g. at 71.309 min (H)). To use the scan for subtraction press the icon "Add Selected Scan" , so it will be displayed in the view "Subtract Mass Spectrum (Session)" (I). Note, that any mass spectrum which has been previously added for subtraction and is displayed in the view "Subtract Mass Spectrum (Session)" is not replaced, but rather added together with the currently added mass spectrum. So if desired, further user-selected mass spectra may be added this way. For replacement of the previous subtraction mass spectrum use the icon "Clear Subtract Mass Spectrum (Session)" prior to adding a mass spectrum.
4. Now the subtraction action may be done via the menu bar (menu bar > Chromatogram > Filter > MSD > Chromatogram) or via the icon "Subtract Filter Chromatogram" . If now the scan at 71.1 minutes is selected again a background subtracted mass spectrum will be displayed (J). Note, that also the summed-up mass spectrum displayed in the view "Combined Mass Spectrum (Chromatogram Selection)" has fundamentally changed.
6. It is also possible to select a summed-up mass spectrum over a user-selected retention time range for a subsequent background subtraction. The view "Combined Mass Spectrum (Chromatogram Selection)" shows the summed-up mass spectrum of the currently displayed RT window in the Chromatogram Editor. This can be added via the icon "Add Combined Scans" to the mass spectrum to be used for subtraction (displayed in the the view "Subtract Mass Spectrum (Session)"). The subtraction action is equivalent to the subtraction of single scans.
7. If you want to apply background subtraction on the entire chromatogram with the previously selected mass spectrum, you simply unzoom (reset 1:1) and press the icon (or access the action via the menu bar as explained above).