A mass spectrum is the graphical representation of the relative abundance of the charged fragments in an analyte plotted against their mass-to-charge ratio (m/z). The plot's x axis represents the ratio of the mass of the charged fragment to the elementary charge it carries. The y axis of the plot represents the relative abundance of each charged species. The relative abundance is calculated from the signal intensity of each charged species recorded at the detector. The most intense signal (the tallest peak in the spectrum) is considered the base peak and is set to an abundance of 100%. The different signal intensities of the other peaks are scaled relative to the base peak. The signal from the molecular ion peak is called the parent peak and appears on the right side of the plot.

In the mass spectrum of methane depicted in Figure 1, the molecular ion peak appears at m/z = 16. The molecular ion is the methane radical cation, which is one electron less than the net electron count in the methane molecule. The methane radical cation fragments into a methyl cation and a hydrogen atom or radical. The methyl cation gives a signal at m/z = 15. The subsequent fragmentation of the methyl cation yields charged species of smaller molecular masses (m/z = 14, 13, and 12). Here, the molecular ion peak is the most intense, and hence it is the spectrum's base peak.

Figure 1. Mass spectrum of methane.

When the relative stability of a molecular ion is higher than that of the fragments formed from it, the base peak and parent peak are the same. In some molecules, the base peak is a fragment ion that is more stable than the corresponding molecular ion. This is illustrated with the mass spectrum of propane provided in Figure 2, where the molecular ion peak appears at m/z = 44 and is shorter than the highest peak at m/z = 29.

Figure 2. Mass spectrum of propane.

If the molecular ion is highly unstable, the molecular ion peak is absent in the mass spectrum.