The peak area is integrated through a data processing method. There is no manual integration in ChromaTOF like there is in some other software. (You can manually add a peak - but automated peak find is much preferred.) Create a data processing method and include the width of the narrower peaks of interset - at baseline, as seen along the linear trace, In the second dimension give the width of the peaks as they would appear in a "normal" chromatogram - but in multiples of the modulation period. If your modulation period is 4 seconds, then give the first dimension peak with (the second peak width asked for in the method) as 4, 8, 16, etc. seconds - as appropriate.
Try processing the sample and see what you get. You may have to adjust the time late and early allowed for the peak apex from one chromatograpic slice to the next to get the automatic combinng of peaks to match peak slices up properly.
Ideally, you want to modulate several times through a chromatographic peak. so, if your peak width in one dimension is 10 seconds wide at base, you would like to use a 2 or three second modulation period. This is not always practical. This becomes less critical if the peaks of interest are wel resolved from other chromatographic peaks.
There are training materials for the ChromaTOF software - and even a class. See if you can get to a class, as the first option, or if not, see if you can get a copy of the training materials.
