ChromaTOF limits the number of peaks found two ways - first by the number of peaks you tell it is the maximum to select. The second is by the signal to noise threshold you select. ChromaTOF will limit the number of peaks by the first condition met.
One thing that confuses people is that ChromaTOF may report peaks showing a signal to noise ratio lower than the selected threshold for the ion it selects as the best quant ion for the peak. This is a case where one ion for the peak has a signal that passes above the selected threshold but it shows a less than ideal characteristic for quantitation, like partial coelution with a neighboring peak. So the software found a "cleaner" ion trace and used it. This is particulalry apparent in GC/MS, but shows up in LC/MS when there is some fragmentation or an isotope cluster present.
If you want to look at the masses that show an apex at the peak, you can elect to show apexing masses in ChromaTOF -- and even select a different mass for quantiation.
