A mass spectrometer is a device designed to separate ions and record their intensities. A typical mass spectrometer comprises three parts: an ion source, a mass analyzer, and a detector. Mass spectroscopy allows detection of compounds by unique ion fragment fingerprints.
The most common form of mass spectroscopy is gas chromatography-mass spectroscopy (GC/MS). In this technique a gas chromatograph is used to separate compounds. This stream is fed into the ion source, a metallic filament to which voltage is applied. This filament discharges electrons which fracture the test compounds into predictable ions. The stream then passes into the detector.
For large molecules typical of biological applications, special techniques are used. The ion source subjects a sample of material to an electrical charge that causes the material to emit ionized particles. These particles are then moved as a gas to the separator or mass analyzer. Types of ion sources include electrospray ionization and matrix-assisted laser desorption ionization.
Another ionization mode is Atmospheric Pressure chemical Ionization (APcI). APcI allows for high flow rates typical of HPLC to be used directly, often without diverting the larger fraction of volume to waste. Typically these mobile phase / analyte sytems are heated to temperatures in excess of 400 degrees Celsius, sprayed with high flow rates of nitrogen and the entire aerosol cloud is subjected to a corona discharge that creates ions. The term "chemical" ionization comes from the fact that the initial ions produced are typically those of the mobile phase and its modifiers. The analyte is ionized by charge transfer during collisions in the high (atmospheric) pressure region of the outer source.
The mass analyzer is the most flexible part of the mass spectrometer. Since an electric or magnetic field can deflect charged particles, and since the kinetic energy imparted by motion through an electric field gives the particles an inertia dependent on the particle's mass, the mass analyzer uses these facts to steer certain masses to the detector based on their mass-to-charge ratios (m/z) by varying the electrical or magnetic field. It can be used to select a narrow range of m/z or to scan through a range of m/z to catalog the ions present. Besides the original magnetic-sector types, several types are currently in more common use, including time-of-flight, ion trap, and quadrupole mass analyzers.
The detector simply records the charge induced when an ion passes by or hits a surface. If a scan is conducted in the mass analyzer, the charge induced in the detector during the course of the scan will produce a mass spectrum, a record of the m/z's at which ions are present.
A tandem mass spectrometer is one that is capable of multiple rounds of mass spectrometry. For example, one mass analyzer can isolate one peptide from many entering a mass spectrometer. A second mass analyzer then stabilizes the peptide ions while gas collides with them, causing them to fragment. A third mass analyzer then catalogs the fragments produced from the peptides. This process, called collision induced dissociation, is the basis of many experiments in proteomics.