In a three-dimensional Paul RF ion trap at least one of the ring electrode and end cap electrodes is structured to produce a high capture efficiency for analyte ions introduced into the trap. The electrode structuring may be produced by an electrode surface profile having edges or protrusions, resulting in a scattering reflection of the introduced ions. Alternatively, at least one electrode may be formed by physically separate electrode components. In one embodiment, the trap can be switched between operating as a linear ion trap with good capture efficiency and operating as a three-dimensional ion trap with good ion reaction conditions.