The ionization process imparts significant internal energy to the molecules. As a result many of them quickly dissociate to give fragment ions and fragment neutrals. Fragmentation often occurs by predictable mechanisms and the mass of the fragment ions can provide additional structural information about the compound. The actual mass spectrum consists of signals (peaks) for the molecular ion and all of its fragment ions and is displayed as a plot of relative intensity on the y-axis versus mass to charge ratio on the x-axis. The relative intensity is given as a percent of the most intense peak often called the base peak, which is assigned intensity 100%. The base peak often represents a fragment ion. The neutral fragments are not detected. Examples of fragmentation mechanisms will be presented later.
Figure 2. An electron impact mass spectrum (EI/MS) of 1-pentene showing the molecular ion, an isotope molecular ion, and fragment ions.
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