The basis of mass spectrometry is the production of ions from neutral compounds and, particularly in chemistry and biochemistry, the examination of the subsequent decomposition of those ions. In mass spectrometry, a substance can be characterized by investigating the chemistry of ions resulting from that substance. Because the technique involves a chemical reaction, the sample being investigated is not recoverable; however, only very small quantities of material are required for the analysis. Most other physical methods of analysis deal with a narrowly defined property of a molecule, but this is not so in mass spectrometry. As with any chemical reaction, the precise outcome, the mass spectrum, is dependent on a considerable number of factors, such as temperature, concentration, effects of the medium and so on. It is this uncertainty which lends mass spectrometry its versatility, intricacy and charm.

Chemical reactions in solids, liquids and gases are usually discussed in terms of isolated molecules whereas their actual behaviour is the result of ‘group’ effects arising from collisional or other activation of molecules. Most mass spectra are measured at low pressures when collisions between ions and molecules are so rare that interpretation of mass spectra in terms of isolated species is more satisfactory. For practical purposes, these low concentrations of ions impose severe restraints on methods of investigating them.