Chlorine isotopes exist as ³⁵Cl and ³⁷Cl in a 3:1 ratio, while bromine isotopes exist as ⁷⁹Br and ⁸¹Br in a 1:1 ratio. The mass spectrum of alkyl halides typically produces two distinct molecular ion peaks, the molecular ion peak, [M], and the molecular ion plus two, [M + 2] peak. The relative heights of these two peaks are proportional to the isotopic abundance ratios of the halide. For example, 2‐chloropropane and 1‐bromopropane display two peaks with relative peak heights in a 3:1 and 1:1 ratio, respectively.

Alkyl halides typically lose a non-bonding electron from the halogen to form molecular ions. The base peak results from the heterolytic cleavage of the carbon–halogen bond, where the bonding electrons go to the most electronegative atom, forming a cation and halogen atom. Interestingly, the ⍺-cleavage is observed only in alkyl chlorides, not alkyl bromides. In alkyl chlorides, the C–Cl and C–C bonds exhibit similar strengths, while in alkyl bromides, the C–Br bond is weaker than the C–C bond. Consequently, the alkyl chlorides form a stable cation, where the positive charge is shared between the two atoms.

While less commonly discussed, fluoroalkanes and iodoalkanes exhibit unique fragmentation behavior. Fluoroalkanes, due to the strength of the C–F bond and the presence of only one isotope (¹⁹F), show limited fragmentation and lack isotopic peaks. Iodoalkanes, with their weak C–I bond and a single isotope (¹²⁷I), predominantly fragment by losing iodine, resulting in simpler spectra with less isotopic splitting.