At different times, the MS can apply an ion isolation waveform voltage, a resonance excitation RF voltage, or a resonance ejection RF voltage to the X-rods to promote the ions to gain kinetic energy in the X direction. When the AC frequency applied to the rods equals the frequency of the motion of the trapped ion (which depends on its mass), the ion gains kinetic energy. If the magnitude of the applied voltage is large enough or if the ion is given sufficient time, the ion is ejected out of the slots in the X-rods.

The ion isolation waveform voltage is a multifrequency resonance ejection waveform. The ion isolation waveform voltage ejects all ions except those within narrow ranges of m/z values or those of a selected m/z value.

The MS can apply a resonance excitation AC voltage to the X-rods to fragment precursor ions into product ions. Ion motion is enhanced and the ion gains kinetic energy. After many energetic collisions with the helium damping gas, which is present in the mass analyzer, the ion gains enough internal energy to cause it to dissociate into product ions. The mass analyzer then analyzes the product ions.

During ion scan-out, the resonance ejection AC voltage allows for the ejection of ions from the mass analyzer, which improves mass resolution and sensitivity. The MS applies the resonance ejection AC voltage during the ramp of the main RF voltage. Ions consecutively move into resonance with the resonance ejection RF voltage. When an ion approaches resonance, the amplitude of its motion increases and it is subsequently ejected.