A control system and method of determining a signal to noise (S/N) ratio of an ion detector system, including an ion detector, electron multiplier or photomultiplier, operates by determining an area of a noise peak, determining an area of a signal peak and determining a ratio of the area of the signal peak to the area of the noise peak. Based thereon, the signal to noise ratio can be optimized. The system has particular applicability for use in mass spectrometry.