An ion trap (104) for a mass spectrometer includes an RF trapping voltage source (112) for applying an RF trapping voltage to at least one of a plurality of electrodes (102, 106, 110) of the ion trap (104) to trap at least a portion of ions in the ion trap (104); a resonance excitation voltage source (114) for applying a resonance excitation voltage pulse to the electrodes(102, 106, 110) to cause at least a portion of a selected set of ions to undergo collisions and break into ion fragments; and a computer (116) for controlling the RF trapping voltage source (112) to reduce the RF trapping voltage after a predetermined delay period following termination of the resonance excitation voltage pulse to a second amplitude for retaining a low mass ion fragments in the ion trap (104) for later analysis.