Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. A common use of tandem MS is the analysis of biomolecules, such as proteins and peptides. The molecules of a given sample are ionized and the first spectrometer (designated MS1) separates these ions by their mass-to-charge ratio (often given as m/z or m/Q). Ions of a particular m/z-ratio coming from MS1 are selected and then made to split into smaller fragment ions, e.g. by collision-induced dissociation, ion-molecule reaction, or photodissociation. These fragments are then introduced into the second mass spectrometer (MS2), which in turn separates the fragments by their m/z-ratio and detects them. The fragmentation step makes it possible to identify and separate ions that have very similar m/z-ratios in regular mass spectrometers. Structure Typical tandem mass spectrometry instrumentation setups include triple quadrupole mass spectrometers (QqQ), multi-sector mass spectrometer, quadrupole–time of flight (Q-TOF), Fourier transform ion cyclotron resonance mass spectrometers, and hybrid mass spectrometers. Triple quadrupole mass spectrometer Triple quadrupole mass spectrometers use the first and third quadrupoles as mass filters. When analytes pass the second quadrupole, the fragmentation proceeds through collision with gas. Quadrupole–time of flight (Q-TOF) Q-TOF mass spectrometer combines TOF and quadrupole instruments, which cause high mass accuracy for product ions, accurate quantitation capability, and fragmentation experiment applicability. This is a method of mass spectrometry that ion fragmentation (m/z) ratio determined through a time of flight measurement. Hybrid mass spectrometer Hybrid mass spectrometer consists of more than two mass analyzers. Instrumentation Multiple stages of mass analysis separation can be accomplished with individual mass spectrometer elements separated in space or using a single mass spectrometer with the MS steps separated in time. For tandem mass spectrometry in space, the different elements are often noted in a shorthand, giving the type of mass selector used. Tandem in space In tandem mass spectrometry in space, the separation elements are physically separated and distinct, although there is a physical connection between the elements to maintain high vacuum. These elements can be sectors, transmission quadrupole, or time-of-flight. When using multiple quadrupoles, they can act as both mass analyzers and collision chambers. Common notation for mass analyzers is Q – quadrupole mass analyzer; q – radio frequency collision quadrupole; TOF – time-of-flight mass analyzer; B –