6.1.1 Assignment of the Molecular Ion

The molecular ion may be, but often is not, the largest mass ion observed in the spectrum. Reasons that the largest mass ion detected may not be the undecomposed molecular ion include:

• Background signals, such as column bleed or pump oil contamination, may include ions of very high mass.
• In some experiments, such as chemical ionization, the ionized molecule may form addition products with background or reagent gases. These addition products result in ions of larger mass than that of the molecular ion. In methane CI, one usually observes the [M+1]$^{\textrm{+}}$ ion rather than [M] $^{\textrm{+.}}$.
• Facile, rapid decomposition of the molecular ion (MI) may mean the molecular ion signal is not observed. Some functional classes do not typically exhibit molecular ion signals in the mass spectrum, so the absence of the MI can be taken to be a positive indicator in these cases.
• Isotope peaks, representing one or more isotopic substitutions in the molecule (due to the natural abundances of heavier than 'normal' isotopes), may lie at higher masses than the MI comprised of only the most abundant isotopes.