System for determining the cleanliness of mass spectrometer ion optics

A mass spectrometer is disclosed comprising: an ion detector; ion optics for guiding ions to the ion detector; one or more voltage supply for supplying voltages to said ion optics; control circuitry for controlling the one or more voltage supply so as to switch the ion optics between operating in a first mode in which the ion optics are unable to transmit ions having a first mass to charge ratio or first polarity to the ion detector and a second mode in which the ion optics are able to transmit ions having said first mass to charge ratio or first polarity to the ion detector for a time period; and to repeatedly switch between the first and second modes a plurality of times; and a processor and circuitry configured to: (i) determine the intensity of an ion signal detected by the detector at a first time in each of the time periods that the ion optics are in the second mode; and (ii) determine the intensity of the ion signal detected by the detector at a second, later time in each of the time periods that the ion optics are in the second mode.