Not to be confused with mass spectroscopy—the term’s use is discouraged due to the possibility of confusion with light spectroscopy—MS measures the distribution of ions by mass, or mass-to-charge ratio (m/z), of molecules (and/or its fragments) and atoms by ionizing the atoms and molecules with a high-energy electron beam and then deflecting the ions through a magnetic field based on their mass-to-charge ratios (m/z). These measurements can often be used to calculate the molecular weight of the sample.

A mass spectrometer—the device that utilizes MS—consists of an ion source, a mass analyzer, and a detector. Typically, as a sample is introduced into the spectrometer, it is bombarded with electrons and ionized, allowing the compounds to become charged and fragmented.

Using the mass analyzer, the ions are separated by an electromagnetic field according to their mass-to-charge ratio (m/z). The detector system then ascertains the relative abundance of each of the resolved ionic species.

The spectrometer will then create a graphical representation of the ion’s specific ion abundance vs. m/z that were separated during analysis. This plotting is referred to as the mass spectrum. It can represent many different types of information based on the type of mass spectrometer and the specific experiment applied. These spectra are used to determine the elemental or isotopic signature of a sample, the masses of both particles and molecules, and to elucidate the chemical structure or identity of molecules and chemical compounds.

MS is used in a diverse range of fields that includes proteomics, metabolomics, forensic toxicology, as well as general clinical research. It has become a particularly powerful tool used in proteomics as well. Using the technique enables researchers to perform proteome-wide analysis and characterization of proteins from a wide range of cell types and organisms.