Method of calibrating a mass spectrometer

A mass spectrometer comprising:

• an ion source configured to generate calibration ions;
• an ion optics device configured to receive calibration ions from the ion source;
• a mass analyser configured to receive calibration ions from the ion optics device;
• and
• a controller, wherein the controller is configured to calibrate the mass spectrometer by:
• causing the ion source to generate calibration ions;
• causing the mass spectrometer to transport the calibration ions from the ion source to the mass analyser of the mass spectrometer via the ion optics device, wherein a characteristic voltage is applied to the ion optics device to control transit of ions into the ion optics device and/or out of the ion optics device, wherein the characteristic voltage applied results in an amount of unintentional dissociation of the calibration ions;
• causing the mass analyser to perform an MS1 analysis of the calibration ions to obtain an MS1 spectrum of the calibration ions;
• determining the amount of unintentional dissociation of the calibration ions present in the MS1 spectrum;
• and
• calibrating the characteristic voltage of the ion optics device based on the amount of unintentional dissociation of the calibration ions present in the MS1 spectrum to provide a target amount of unintentional dissociation of calibration ions during an MS1 analysis.