In one aspect, a method of modulating transmission of ions in a mass spectrometer is disclosed, which comprises generating an ion beam comprising a plurality of ions, directing the ion beam to an ion optic positioned in the path of the ion beam, wherein the ion optic includes at least one opening through which the ions can pass, and applying one or more voltage pulses at a selected duty cycle to said ion optic so as to obtain a desired attenuation of brightness of the ion beam passing through the ion optic, where a pulse width of said voltage pulses at said selected duty cycle is determined by identifying a pulse width on a calibration normalized ion intensity versus pulse width relation for said ions that corresponds to said desired attenuation on an ideal normalized ion intensity versus pulse width relation for said ions.