Automatically Subtracting Background Spectra

ProMass supports automatic background subtraction when run in automated mode from the Xcalibur sample list. To activate background subtraction, you use the Spectrum Enhancement features of the Xcalibur Processing Method. 

To activate background subtraction:

1. Open your processing method and select the Spectrum Enhancement tab within Xcalibur Processing Setup.
2. Click the Enable check box. 
3. Select the Combine option and choose your settings.
4. Save your processing method.  Note that Combine is the only spectrum enhancement method currently supported.
5. When processing your data from the Xcalibur sample list, select the Spectrum Enhancement option under the Qual processing actions as shown below.

Example of a background subtraction setup in an Xcalibur processing method.  In the example below, 4 spectra around the top of the peak will be averaged, and 5 spectra on either side of the peak will be subtracted from the averaged scans.  ProMass will not average scans beyond the scans defined by the detected peak.

The background subracted scans are indicated in the ProMass report with the raw ESI mass spectrum.  For example, the following are indicated for the processing method shown above.

Scans Averaged: 67-71 Minus: 61-65, 75-79

To turn off background subtraction:

1. Uncheck the Enable option in the processing method
2. Save your processing method.