When in an MS/MS scan mode, the MS uses the strength of the axial drag field to remove the ions of the previous reaction from the collision cell.
The collision cell surrounds the ICRM and is usually pressurized at 8 × 10–3 Torr with nitrogen collision gas. The collision cell is where HCD takes place.
HCD is a process where an ion collides with a neutral atom or molecule and then dissociates into smaller fragments. The mechanism of dissociation involves converting some of the kinetic energy of the ion into internal energy. This collision places the ion in an excited state. If the internal energy is sufficient, the ion fragments.