Mass Spectrometry: Fragmentation

When a molecule is bombarded with high-energy electrons in a mass spectrometer, the resulting molecular ion M⁺• often has enough excess energy to break apart. This process is called fragmentation, and it is one of the most useful features of mass spectrometry. The pattern of fragment ions acts like a molecular fingerprint, revealing which functional groups and structural units are present.

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Why Fragmentation Happens

Electron impact ionisation transfers a large amount of energy to the molecule — typically around 70 eV, far more than is needed simply to remove one electron. The excess energy is distributed throughout the molecular ion, and bonds break at the weakest points. The resulting fragments appear as peaks at lower m/z values than the molecular ion.

The fragmentation pattern depends on the bond strengths within the molecule and the stability of the resulting fragment ions. More stable ions (such as carbocations stabilised by alkyl groups, resonance, or charge delocalisation) form preferentially and give more intense peaks.

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Common Fragment Ions

Certain fragments recur frequently in mass spectra because they correspond to common structural units. Memorising these is essential for interpreting spectra quickly: