Fragmentation (mass spectrometry)

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Toluene Fragmentation

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.[1]

Mass spectrometry techniques[edit]

Fragmentation can occur in the ion source (in-source fragmentation) where it is generally not a desired effect. Ion source conformation is an important criterion 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[edit]

Fragmentation is a type of chemical dissociation that can take place by a process of heterolysis or homolysis.

An example of sigma bond cleavage

Sigma bond cleavage[edit]

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.[2]

An example of radical site-initiated fragmentation

Radical site-initiated fragmentation[edit]

Sigma bond cleavage also occurs on radical cations remote from the site of ionization. The cation has a radical on a heteratom or an unsaturated functional group. The driving force of fragmentation is the strong tendency of the radical ion for electron pairing. Cleavage occurs when the radical and an odd electron from the bonds adjacent to the radical migrate to form a bond between the alpha carbon and either the heteroatom or the unsaturated functional group. The sigma bond breaks; hence this cleavage is also known as homolytic bond cleavage or α-cleavage.[2]

An example of charge site-initiated fragmentation

Charge site-initiated cleavage[edit]

The driving force of charge site-initiated fragmentation is the inductive effect of the charge site in radical cations. The electrons from the bond adjacent to the charged-bearing atom migrate to that atom, neutralizing the original charge and causing it to move to a different site. This term is also called inductive cleavage and is an example of heterolytic bond cleavage.[2]

An example of McLafferty Rearrangement


Rearrangement reactions are fragmentation reactions that form new bonds producing an intermediate structure before cleavage. One of the most studied rearrangement reaction is the McLafferty rearrangement. This occurs to radical cations with unsaturated functional groups.[2] Other rearrangement reactions include Heterocyclic ring fission (HRF), benzofuran forming fission (BFF), quinone methide (QM) fission or Retro Diels-Alder (RDA).[3]

See also[edit]


  1. ^ Fred W. McLafferty (1 January 1993). Interpretation of Mass Spectra. University Science Books. ISBN 978-0-935702-25-5. 
  2. ^ a b c d Dass, Chhabil (2007). Fundamentals of contemporary mass spectrometry ([Online-Ausg.]. ed.). Hoboken, NJ [u.a.]: Wiley. ISBN 978-0-471-68229-5. 
  3. ^ Tandem Mass Spectrometry for Sequencing Proanthocyanidins. Hui-Jing Li and Max L. Deinzer, Anal. Chem., 2007, volume 79, pages 1739-1748, doi:10.1021/ac061823v

External links[edit]