A mass spectrometer comprising: an ion source configured to produce an ion beam from a sample, an ion guide; a first gate; a first mass filter configured to selectively transmit ions within a mass-to-charge range and reject ions outside of the mass-to-charge range; a fragmentation cell; a second mass filter configured to selectively transmit ions within a mass-to-charge range and reject ions outside of the mass-to-charge range; a detector configured to measure the intensity of the transmitted ion beam; and a controller configured to: close the first ion gate to prevent ions from entering the first mass filter; switch a first quadrupole voltage of the first mass filter to a voltage of a first transition; and open the first ion gate to allow ions to enter the first mass filter, the opening offset from the switching by a settling time of the first mass filter, the settling time including the time required to adjust the voltage of the first mass filter; characterised in that the controller is further configured to: switch a fragmentation cell collision energy to a collision energy for the first transition, wherein switching the collision energy is offset in time from switching the first quadrupole voltage by an amount of time not greater than a time it takes for ions entering the first mass filter to exit the first mass filter. an ion source configured to produce an ion beam from a sample, an ion guide; a first gate; a first mass filter configured to selectively transmit ions within a mass-to-charge range and reject ions outside of the mass-to-charge range; a fragmentation cell; a second mass filter configured to selectively transmit ions within a mass-to-charge range and reject ions outside of the mass-to-charge range; a detector configured to measure the intensity of the transmitted ion beam; and a controller configured to: close the first ion gate to prevent ions from entering the first mass filter; switch a first quadrupole voltage of the first mass filter to a voltage of a first transition; and open the first ion gate to allow ions to enter the first mass filter, the opening offset from the switching by a settling time of the first mass filter, the settling time including the time required to adjust the voltage of the first mass filter; characterised in that the controller is further configured to: switch a fragmentation cell collision energy to a collision energy for the first transition, wherein switching the collision energy is offset in time from switching the first quadrupole voltage by an amount of time not greater than a time it takes for ions entering the first mass filter to exit the first mass filter. close the first ion gate to prevent ions from entering the first mass filter; switch a first quadrupole voltage of the first mass filter to a voltage of a first transition; and open the first ion gate to allow ions to enter the first mass filter, the opening offset from the switching by a settling time of the first mass filter, the settling time including the time required to adjust the voltage of the first mass filter; characterised in that the controller is further configured to: switch a fragmentation cell collision energy to a collision energy for the first transition, wherein switching the collision energy is offset in time from switching the first quadrupole voltage by an amount of time not greater than a time it takes for ions entering the first mass filter to exit the first mass filter.