Mass spectrometry (MS) is an analytical technique that can be used to determine the mass, elemental composition or chemical structure of molecules. Mass spectrometry (MS) is an analytical technique that can be used to determine the mass, elemental composition or chemical structure of molecules. In a typical configuration the target analytes are first converted into charged particles (ionisation) before introduction into the mass spectrometer. Once inside, the ions are separated by a mass analyser according to their m/z ratio using electromagnetic fields under vacuum. The separated ions are then recorded by a detector, and the detector signal is converted into a mass spectrum that can be stored and manipulated on a computer. Mass spectrometry is often preceded by some form of chromatography (gas, liquid or thin layer chromatography) to separate analytes of interest before analysis. It is also common for mass spectrometers to have multiple mass analysers for targeted manipulation of the ions within the instrument. A widely used example is triple quadrupole mass spectrometry, in which the first analyser is followed by a collision cell for fragmentation of the ions, and a second analyser. This configuration allows for a number of scan experiments that can be used to elucidate the structure of ions of interest, or increase the sensitivity of the instrument to a specific (set of) ion(s). Craig E. Wheelock et al. Eur Respir J 2013;42:802-825 ©2013 by European Respiratory Society