Once ions leave the ion source, they pass into a mass analyzer. The function of the analyzer is to separate the ions and to measure their masses. (In fact, what is really measured is the mass-to-charge ratio (m/z) for each ion. However, because in most cases the charge is 1, the m/z value can be taken as being equivalent to the ion mass.)

In each short time interval, ions of a particular mass are allowed to pass through the analyzer whereupon they are counted by the detector. In the next short time interval, ions of a different mass are allowed to pass through the analyzer and again the detector counts how many ions are present. In this way, the analyzer scans through a large range of masses.

In MS, scanning speed is important, because components that have been separated on the column may all elute in a short time interval.

In addition, the instruments can be used to monitor selected ion masses. Selected Ion Monitoring (SIM) is typically used to look for ions that are characteristic of a target compound or family of compounds. It is this ability of a quadrupole to spend up to 100% of it's duty cycle monitoring for a specific ion of interest that makes it the best detector for demanding quantitative applications requiring high sensitivity, the lowest Limit of Quantitation possible and the best RSD's.