Functional groups can have a significant effect the fragmentation patterns observed in mass spectrometry. For example, aliphatic amines prefer to undergo cleavage at the C-C bond to produce a relatively stable CH₂NH₂⁺ ion. The resulting fragments distinguish primary, secondary, and tertiary amines.

The mass spectra of three different n-pentaneamine isomers are shown in Figure 18. 1-Pentaneamine has an odd number of nitrogen atoms so the molecular ion (m/z 87) has an odd mass to charge ratio and the cleavage fragment (m/z 30) has an even mass to charge ratio. -Cleavage of 1-pentaneamine produces CH₂NH₂⁺ (m/z 30) and C₄H₉. The C₄H₉ fragment is not observed in the mass spectrum because since this is a neutral fragment. 2-Pentaneamine has two alpha-cleavage sites. Loss of CH₃ produces C₄H₈NH₂⁺ (m/z 72) and loss of C₃H₇ produces C₂H₄NH₂⁺ (m/z 44). Both of these ions are observed but the greater abundance of the m/z 44 signal indicates that loss of C₃H₇ is favored. The additional peak at m/z 58 corresponds to C₃H₆NH₂⁺ which could be formed by alpha-cleavage loss of C₂H₅. 3-Pentaneamine has two alpha-cleavage sites but they are symmetric so cleavage at either site results in loss of C₂H₅. Loss of C₂H₅ produces C₃H₆NH₂⁺ (m/z 58), the base peak in the mass spectrum. Now spend some time with a piece of scratch paper and interpret some other peaks in these spectra.