In a linear ion trap ions of both positive and negative polarities are stored simultaneously for fragmentation reactions caused by electron transfer dissociation (ETD). The ion trap comprises a plurality of parallel pole rods or stacked rings and the ions are stored by applying two phases of a first RF voltage to the pole rods or stacked rings in alternation, thereby radially confining both positive and negative ions. A second, single-phase RF voltage is applied to all the pole rods or stacked rings in common and creates a pseudopotential barrier at the ends of the linear ion trap that acts axially on ions of both polarities in order to maintain the ions in the trap.