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The mass spectrum of a molecule is a bar-graph plot of the relative abundance of its component fragments against their mass-to-charge ratio.

For example, consider the mass spectrum of methane. The electron beam incident on the methane molecule knocks off an electron to generate a methane radical cation. The mass signal at a mass-to-charge ratio of sixteen is the molecular ion peak.

The molecular ion undergoes fragmentation and generates radicals, cations, and radical cations. Losing the four hydrogens one at a time leads to mass signals at progressively lower mass-to-charge ratios.

Alternatively, losing a proton from the molecular ion results in a methyl radical, which is neutral and not detected in the mass spectrum without further ionization.

The base peak possesses the maximum abundance, set to one hundred percent. The abundances of the other peaks are scaled relative to the base peak.

In methane, the base peak and the molecular ion peak are the same. But, in other molecules, these peaks can be different. In some molecules, the molecular ion peak is not detected due to the instability of the molecular ion.