Abstract: A method of operation of an ion trap mass spectrometer having a ring electrode and pair of end-cap electrodes in a resonance ejection mode is disclosed. The method includes producing ions from a plurality of biomolecules, applying a trapping RF voltage to the ring electrode, applying an excitation voltage to the end-cap electrodes, scanning the trapping RF voltage in order to sequentially eject the ions, controlling a ration of the amplitude of the trapping RF voltage to the amplitude of the excitation voltage in order that the ratio is generally constant, and determining a ratio of mass to charge of the ejected ions. In one embodiment, a feedback voltage which is proportional to the trapping RF voltage is sensed, and the amplitude of the excitation voltage is controlled as a function of the amplitude of the feedback voltage.

Abstract: A method and apparatus for trapping ions in an ion trap having a ring electrode and a plurality of end-cap electrodes. Ions are introduced into a ion trap cavity of the ion trap from an external source or by desorption of a substance in the ion trap cavity. In a first embodiment, as the ions are introduced in the ion trap cavity, the amplitude of an RF voltage being applied to the ring electrode is gradually increased to trap the ions in the ion trap cavity. In a second embodiment, as the ions are introduced in the ion trap cavity, a retarding voltage is applied to the end-caps to reduce the initial kinetic energy of the ions. In a third embodiment, as the ions are introduced in the ion trap cavity from a probe tip inserted in the cavity, a retarding voltage is applied to the probe tip.