Methods and apparatus are disclosed for reducing ion reflections between multipole segments in a mass spectrometer by matching the effective potential between the two segments. Mass spectrometers having at least two multipole segments separated from each other along a longitudinal axis of the mass spectrometer such that a boundary region exists through which ions are drawn from an upstream segment to a downstream segment, and wherein each multipole segment further includes a set of spaced-apart rod-shaped electrodes disposed around the longitudinal axis and having a field radius defined by an inscribed circle between the innermost portions of each electrode. Effective potential matching can be achieved by either supplying RF signals of different amplitudes to each segment and/or by modifying the field strength of the segments. In one embodiment, the multipole segments are configured such that the upstream multipole segment has a smaller field radius than the downstream segment.