A method of operating a tandem mass spectrometer system is disclosed including accumulating ions in an ion trap, transmitting a plurality of ions out of the ion trap into a timed-ion selector, applying a pulsed DC voltage to the timed-ion selector, the pulsed DC voltage being modulated to match an ejection time for selecting a first portion of ions from the plurality of ions, corresponding to a specific m/z window, transmitting the first portion of selected ions out of the timed-ion selector into a reaction cell, transmitting dissociation product ions and the remaining ions of the first portion of selected ions out of the reaction cell into a mass analyzer, and mass-selectively transmitting at least some of the fragment ions and the remaining ions of the first portion of selected ions out of the mass analyzer into a detector.