The area-under-the curve analysis reports Total area and Total peak area and (sometimes) Net Peak Area. What's the difference?

What counts as a peak?

By default, Prism only considers points above the baseline to be part of peaks, so only reports peaks that stick above the baseline. You can choose to also consider peaks that go below the baseline.

By default, Prism ignores any peaks whose height is less than 10% of the distance from minimum to maximum Y value, but you can change this definition in the area under the curve parameters dialog. You can also tell it to ignore peaks that are very narrow.

Total peak area vs. total area vs. net area

Prism always reports the Total Area, which includes: Positive peaks, negative peaks, peaks that are not high enough to count, and peaks that are too narrow to count. The only choice you make in the analysis dialog that affects the definition of total area is the definition of the baseline. 

Prism also reports the Total Peak Area. Here Prism only includes the peaks you ask it to consider. This value is affected by several choices in the analysis dialog: The definition of baseline, your choice about including or ignoring negative peaks, and your definition of peaks too small to count.  

If you ask Prism to define peaks below the baseline as peaks, then Prism subtracts the area of peaks below the baseline from the area of peaks above the baseline, and reports this difference as the Net Area.