Mass spectrometers are used in both quantitative and qualitative analysis, including high-resolution accurate mass measurements for the determination of elemental compositions. Mass spectrometry (MS) is an analytical spectroscopic tool primarily concerned with the separation of molecular (and atomic) species according to their mass. MS can be used in the analysis of many types of samples, from elemental to large proteins and polymers.

Important performance parameters to consider when specifying mass spectrometers include mass range, resolution, mass accuracy and mass spectrum.  Mass range is a measure of the atomic mass range detected by the spectrometer in Atomic Mass Units. May also be measured in Daltons.  The resolution is the ratio of the mass divided by the change in mass over the area of two peaks. (m/dm).  The mass spectrum is a spectrum obtained when ions (usually in a beam) are separated according to the mass-to-charge (m/z) ratios of the ionic species present. This plot is a graphical representation of m/z values versus measured ion abundance information.

Mass spectrometers have one of five common mass analyzer designs.  The mass analyzer is the part of the spectrometer that analyzes the process by which a mixture of ionic species is separated according to the mass-to-charge ratio (m/z). The analysis may be qualitative and/or quantitative.  Time of Flight (TOF) instruments utilize the times taken by ions to pass (fly) along an evacuated tube as a means of measuring m/z values and therefore of obtaining a mass spectrum.  Quadrupole mass spectrometers consist of an ion source, ion optics to accelerate and focus the ions through an aperture into the quadrupole filter, the quadrupole filter itself with control voltage supplies, an exit aperture, an ion detector, detection electronics, and a high-vacuum system.  The ion-trap mass spectrometer uses three electrodes to trap ions in a small volume. The advantages of the ion-trap mass spectrometer include compact size and the ability to trap and accumulate ions to increase the signal-to-noise ratio of a measurement.  Fourier-transform mass spectrometry takes advantage of ion-cyclotron resonance to select and detect ions.  Single focusing analyzers use a circular beam path of 180, 90, or 60 degrees. The various forces influencing the particle separate ions with different mass-to-charge ratios. Double focusing analyzers have an electrostatic analyzer added to separate particles with difference in kinetic energies.

Mass spectrometers use one of four ionization methods to ionize the sample for analysis.  The electrospray ionization (ESI) source consists of a very fine needle and a series of skimmers. A sample solution is sprayed into the source chamber to form droplets. The droplets carry charge when they exit the capillary and, as the solvent evaporates, the droplets disappear leaving highly charged analyte molecules. ESI is particularly useful for large biological molecules that are difficult to vaporize or ionize.  In fast atom bombardment (FAB) a high-energy beam of neutral atoms, typically Xe or Ar, strikes a solid or low-vapor-pressure liquid sample causing desorption and ionization. It is used for large biological molecules that are difficult to get into the gas phase. The sample is usually dispersed in a matrix such as glycerol. FAB causes little fragmentation and usually gives a large molecular ion peak, making it useful for molecular weight determination.  Electron impact ionization (EI) source uses an electron beam, usually generated from a tungsten filament, to ionize gas-phase atoms or molecules. An electron from the beam knocks an electron off of analyte atoms or molecules to create ions.  Matrix-assisted laser deposition/ionization (MALDI) is a LIMS method of vaporizing and ionizing large biological molecules such as proteins or DNA fragments. The biological molecules are dispersed in a solid matrix such as nicotinic acid or dihydroxybenzoic acid. A UV laser pulse ablates the matrix that carries some of the large molecules into the gas phase in an ionized form so they can be extracted into a mass spectrometer.