The present invention pertains to a method and apparatus which increases the efficiency with which ions are transported from a first ion trap to a second ion trap, and subsequently trapped in the second ion trap. In one aspect the invention, increased efficiency takes the form or enabling ions of both high and low mass to charge ratios to be trapped in the second ion trap at substantially the same time, or at least within a relatively small window of time. This can be achieved by minimizing the undesirable time-of-flight separation by the high and low mass to charge ratio ions as they are transported from a first ion trap to the second ion trap. This minimization can be realized by adjusting the potential energy applied to ion transfer optics disposed between the two ion traps.