Defining Explicit Background Subtraction Regions

Automatic background subtraction of spectra prior to deconvolution can be configured using two different methods when performing automated deconvolution from the Xcalibur sample list.

1. Automatic background subtraction can be configured as part of the Xcalibur processing method, as described in the Automatically Subtracting Background Spectra topic.  Use this method if you want the background subtraction to occur very near where each peak is eluting.  Since background subtraction is driven by the peak picking method, explicit time regions of background subtraction cannot be defined with this method.  If you want to define explicit time regions for background subtraction, use method 2 below.
2. Explicit regions of background subtraction can be defined in the ZNova parameter file.  The subtract regions are set in the Auto Processing Options area of the Reporting tab of the Build ZNova Params utility.  For example, you might want to define regions at the beginning and end of a chromatogram as background subtraction regions.  ProMass allows you to enter up to 2 different regions for backgound subtraction.  You enter the regions as retention times.  For example, if you enter values of 2 and 2.5 in the Region 1 boxes and 20 and 20.5 in the Region 2 boxes, ProMass will use these 2 retention time regions when producing a background subtracted ESI spectrum as input for deconvolution.  Subtraction regions entered in the ZNova parameter file will override any settings from the Xcalibur Processing method.  Be sure the region settings are all set to 0 to use Xcalibur processing method subtraction regions, or to turn off explicit background subtraction regions.  The screen capture below demonstrates explicit background subtraction regions of 2-2.5 minutes and 20-20.5 minutes retention time.