It has been shown that through the process of resonant excitation the fragmentation of ions confined in a low-pressure (<0.05 mTorr) linear ion trap (LIT) can be accomplished while maintaining both high fragmentation efficiency and high resolution of excitation. The ion reserpine, 609.23 Da, has been fragmented with efficiencies greater than 90% while a higher mass ion, a homogeneously substituted triazatriphosphorine of mass 2721.89 Da, has been fragmented with 48% efficiency. This was accomplished by extended resonant excitation by low-amplitude auxiliary RF signals. Computer modelling of ion trajectories and analysis of the trapping potentials have demonstrated that a reduction in neutralization of ions on the rods (or losses on the rods) and increased fragmentation is a consequence of higher order terms in the potential introduced by the round-rod geometry of the LIT. © 2003 American Society for Mass Spectrometry.