Abstract: A method of using a quadrupole ion trap mass spectrometer for high resolution mass spectroscopy is disclosed. High resolution of a mass spectrum of a desired species is achieved by first using a slow scanning rate and by first ridding the trap of unwanted ions. Accurate mass calibration is achieved by using a reference compound of known mass and using a second supplemental AC dipole voltage to eject the reference ions at nearly the same time as the sample ions of interest are ejected from the trap. This eliminates the need to scan the trap between the masses of the sample and reference ions. Space charge in the trap is held constant, thereby eliminating a major source of mass axis instability, by using the results of one scan to control the ionization time during the next scan. Preferably, during ionization a broadband supplemental dipole voltage is applied to the ion trap to rid it of unwanted ions.

Abstract: A variable cooling time is imposed on ions in a quadrupole ion trap prior to excitation through border effect operation. Continuous variation of the cooling time brings about continuous variation of the selected ion internal energy when subjected to the boundary effect such that the boundary effect competes more favorably with ion loss in the trap, and fragmentation reaction channels having successively greater energies of activation can be accessed preferentially.