KB001696: What are the Steps to Integrate Poorly Shaped Peaks? - MS ChemStation 

Use manual integration mode. Position the mouse cursor over the chromatogram. If the cursor shape is a vertical line ( | ), this indicates that you are in mean spectrum mode. From the [ Tools ] menu, click [ Options ] to open the [ Select Data Analysis Options ] dialog box. select the manual integration check box and then click [ OK ]. The cursor changes to a plus sign ( + ) to indicate manual integration mode. Next, in the chromatogram screen, hold down the right mouse button and drag from the integration start point to the integration end point to specify the region to use as the integration base line. Perpendicular lines are dropped from the start and end points to the chromatogram and integration is performed.