A method for operating tandem ion traps is provided, involving a) accumulating ions in the first ion trap at a first time; b) transmitting a first plurality of ions out of the first ion trap and into the second ion trap at a second time, the first plurality of ions having masses within a first mass range; c) retaining a second plurality of ions in the first ion trap at the second time, the second plurality of ions having masses within a second mass range different from the first mass range; d) transmitting the first plurality of ions out of the second ion trap at a third time; and, e) transmitting the second plurality of ions out of the first ion trap and into the second ion trap at the third time.