Abstract: Methods for operating a mass spectrometer having a skimmer and a circuit configured to apply an electric potential to the skimmer comprise obtaining an initial mass spectrum of a sample and measuring a value indicating an ion beam intensity of one or more ion species. A varying DC electric potential is applied to the skimmer to identify an operational electric potential, wherein the DC electric potential is varied until the value indicating the ion beam intensity of the one or more ion species changes by a predetermined amount. The mass spectrum with the operational electric potential applied to the skimmer is output. In some examples, a pressure within the mass spectrometer is varied to identify an operational pressure, and the mass spectrum with the pressure within the mass spectrometer at the operational pressure is output.