For research use only. Not for use in diagnostic procedures.
When using a QTRAP® LC/MS/MS system instrument, the isolation of fragment ions in the back end of a linear ion trap is controlled by a DC voltage offset between the rods and is quite broad (3-4 m/z). To generate MS3 fragments, the ions are first isolated, and then the radio frequency excitation field is applied to all fragments remaining in the trap, but at a much narrower m/z range is in resonance with the excitation field. Ions in resonance pick up amplitude (kinetic energy) and collide with gas molecules--leading to their fragmentation. The other ions have different resonant frequencies and pick up much less kinetic energy and do not fragment.
If AF2 (a parameter describing the amplitude of the resonant excitation field) is very large, then off-resonant excitation will begin to increase the kinetic energy of neighboring m/z ions. But for most molecules, the QTRAP system instruments are entirely capable of completely eliminating one peak in a (singly-charged) isotope cluster without attenuating neighboring m/z. The MS3 resonant calibration can be tested. For example, for an ion of mass 1000.5 u, select m/z 1001.5, and then see what happens when AF2 is increased. You shouldn’t see any changes at first (you should still see the whole isotope cluster). But as you increase the AF2 amplitude, the m/z 1001.5 peak should attenuate while the m/z 1000.5 and 1002.5 remain unchanged.