When the molecule is ionised in the ionisation chamber it gains considerable kinetic energy. This results in vigorous bond vibration which causes the molecule to fragment , that is to break up.
Fragmentation gives rise to a neutral free radical component and an ion .
Many molecules are ionised in the mass spectrometer and so various different fragments are possible. As a result the mass spectrum of an organic molecule is generally quite complex, consisting of numerous peaks. The base peak corresponds to the most stable fragmentation ion. Isotope effects Isotopic effects are very useful for identifying compounds containing chlorine and bromine . Naturally occurring bromine consists of two isotopes in approximately equal proportions.