A method for calibrating an ion trap mass spectrometer is disclosed. The method includes steps of identifying a phase (defined by the RF trapping and resonant ejection voltages) that optimizes peak characteristics, and then determining, for each of a plurality of calibrant ions, an optimal resonant ejection voltage amplitude when the ion trap is operated at the identified phase. The resonant ejection voltage applied to the electrodes of the ion trap may then be controlled during analytical scans in accordance with the established relationship between m/z and resonant ejection voltage amplitude.