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In mass spectrometry, fragmentation is the dissociation of energetically unstable molecular ions formed from passing the molecules in the ionization chamber of a mass spectrometer. The fragments of a molecule cause a pattern in the mass spectrum used to determine structural information of the molecule.

Mass Spectrometry Techniques
Fragmentation of a molecule can take place by a process of heterolysis or homolysis.

It can occur in the ion source (in-source fragmentation) where it is generally not a desired effect. Ion source conformation is an important criterium in the level of fragmentation observed.

Desired fragmentation is made in the collision zone (post-source fragmentation) of a tandem mass spectrometer. It is a part of gas phase ion chemistry and there are different types of mass fragmentation:
 * collision-induced dissociation (CID),
 * electron-capture dissociation (ECD),
 * electron-transfer dissociation (ETD),
 * negative electron-transfer dissociation (NETD),
 * electron-detachment dissociation (EDD),
 * photodissociation, particularly infrared multiphoton dissociation (IRMPD) and blackbody infrared radiative dissociation (BIRD),
 * surface-induced dissociation (SID),
 * Higher-energy C-trap dissociation (HCD),
 * charge remote fragmentation.

Fragmentation Reactions
Fragmentation of a molecule can take place by a process of heterolysis or homolysis. The certain structures favour fragmentation the α-cleavage and the McLafferty rearrangement are two examples for the often observed fragmentations.

Other schemes includes Heterocyclic ring fission (HRF), benzofuran forming fission (BFF), quinone methide (QM) fission or Retro Diels-Alder (RDA).

Sigma Bond Cleavage
Sigma bond cleavage is most commonly observed in alkanes. This occurs when an alpha electron is removed. The C-C bond elongates and weakens causing fragmentation. Fragmentation at this site produces a charged and a neutral fragment.

Functional Groups
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