Method for operating a mass spectrometer includes supplying a quantity of ions to an ion detector. The ion detector can include a conversion dynode operating in a first polarity and an electron multiplier. The method further includes adjusting the gain of the electron multiplier to determine a first set of calibration parameters, and calculating a second set of calibration parameters for the electron multiplier from the first set of calibration parameters. The second set of calibration parameters are for a second polarity of the conversion dynode. The method can further include configuring the ion detector to operate at the second polarity based on the second set of calibration parameters, and supplying ions of the second polarity to the mass spectrometer, and detecting an ion at a particular mass to charge ratio using the ion detector.