If the Subtract Baseline radio button is selected in the Goal group in the Start page of the Peak Analyzer, you can use the Peak Analyzer to create a baseline, and then subtract it from the input data. A typical wizard map corresponding to this mode is as follows:
The Baseline Mode page allows you to choose a baseline mode and create the baseline. Then you can go to the Subtract Baseline page to subtract the baseline from the input data. It also allows you to decide whether to ouput the subtracted data and the basline.
Please see the reference for more details on the related pages: