Patent ID: 8766170

Claim:
A method of operating a tandem mass spectrometer system having a first ion trap and a second ion trap, the method comprising: a) accumulating ions in the first ion trap; b) mass-selectively ejecting ions out of the first ion trap and into the second ion trap to accumulate ions in the second ion trap; and c) mass-selectively ejecting ions out of the second ion trap while ions are being mass-selectively ejected from the first ion trap into the second ion trap; and d) controlling a scan rate of ions being mass-selectively ejected into the second ion trap from the first ion trap using a first RF voltage and a first auxiliary AC excitation waveform provided to the first ion trap, and controlling a scan rate of ions being mass-selectively ejected out of the second ion trap using a second RF voltage and a second auxiliary AC excitation waveform provided to the second ion trap, such that during an operating time interval during step (c) a ratio of the first RF voltage to the second RF voltage remains substantially constant.