Abstract: The methods of the invention exploit the mass-to-charge ratio dependent motion of ions in an electrodynamic ion traps in synergy with a charge quenching process. In an electrodynamic ion trap, each mass-to-charge ratio is characterized by a unique set of frequencies of motion. Accordingly, by tailoring the time-varying electrical potential of the ion trap the invention controls which ions are allowed or retained in the ion trap and which ions are subjected to charge quenching reactions. Control of ion retention and charge quenching is used to improve sample throughput, dynamic mass range and signal discrimination in the mass spectrometry of multiply charged ions.