A method of calibrating a mass spectrometer is disclosed comprising mass analyzing first ions derived from an analyte molecule, wherein the first ions have a first charge state; determining a first mass or mass to charge ratio of the first ions; mass analyzing second ions derived from the analyte molecule, wherein the second ions have a second different charge state and wherein the second ions comprise protonated or adduct variants of the first ions; determining a second mass or mass to charge ratio of the second ions; a determining a calibration correction based upon the first mass or mass to charge ratio and the second mass or mass to charge ratio.