A method for automatically checking and adjusting a calibration of a mass spectrometer having a first quadrupole (Q1), a fragmentation cell and a mass analyzer comprises: introducing a sample having at least one known chemical entity; decreasing a kinetic energy so as to prevent fragmentation of ions in the fragmentation cell; optionally applying a drag field to the fragmentation cell; ionizing the at least one known chemical entity sample to generate a set of ions; performing a mass scan of the set of ions using Q1; transmitting the scanned ions through Q1 to and through the fragmentation cell; detecting the scanned and transmitted ions by a detector of the mass analyzer; and comparing the results with expected results. Embodiments may include automatic recalibration or notification of possible errors, need for further data processing or an analysis of system performance.