A method of calibrating a mass spectrometer is disclosed. The mass spectrometer includes a first quadrupole, a second mass analyzer and a detection means. The method includes calibrating the second mass analyzer at a first time, calibrating the first quadrupole at a second time later than the first including a) determining for each of several selected masses a corresponding value of the amplitude of the RF voltage and DC voltage applied to the electrodes of the first quadrupole, b) fitting a function of the selected mass to the values of the amplitude of the RF voltage and DC voltage corresponding to the several selected masses, c) detecting the selected mass in a filter window width over a mass range, d) evaluating a shift of the peak position and/or a deviation of the filter window width, and e) repeating the calibration steps under certain conditions.