To eliminate the background signal from an active scan, or from the average of spectral scans, a manual background subtraction can be carried out. Mass Frontier allows you to set the location of two representative background scans by pressing the Manual Background Subtraction button and then left-clicking the scan point in the chromatogram pane. The background scans are indicated by a vertical line, which is depicted in a different color (by default green) from the scan line. The resulting spectrum will be displayed in the Scan tab. To cancel a background subtraction, press the Cancel Background Subtraction button. The Selected Ion Chromatogram feature can help you to choose the two most representative background scans. Such background scans can be used in Manual background subtraction option in Automated Components Detection and Spectra Deconvolution procedures.

If you would like to see the effects of the background subtraction on a scan, you can copy both the extracted and original spectra to Database Manager and compare them using the spectra comparison routine in the Compare Spectra tab.

Background subtraction can be used in conjunction with Selected Ion Chromatogram feature. In this case the SIC profiles are extracted from background subtracted scans.