This technology improves the dynamic range of a mass spectrometer by first passing a sample of ions through a mass spectrometer having a quadupole ion filter and measuring the intensities of the mass spectrum of the sample. From the first mass spectrum, ions are then identified for subsequent ejection using Rf voltages.

A second spectrum of the remaining ions is then generated. In this way, a higher population of desired ions may be collected for a longer period of time in an ion trap and the clarity of the spectrum for these desired ions is significantly improved. The invention is particularly useful for improving identification and characterization of potentially important low abundance ions that may be masked by the presence of high-abundance ions in an ion trap or Fourier transform ion cyclotron mass spectrometer when conventional analytical methods are used.