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Isotopomers are isomers having the same number of each isotopic atom but differing in their positions. The term is a contraction of 'isotopic isomer'. Isotopomers can be either constitutional isomers (e.g. CH2DCH=O and CH3CD=O) or isotopic stereoisomers [e.g. (R)- and (S)-CH3CHDOH or (Z)- and (E)-CH3CH=CHD].


Isotopomers are useful agents for various mass spectroscopy techniques in which isotopically-labeled tags are attached to other molecules of interest. The iTRAQ method is one example, in which either 4 or 8 chemically equivalent chemical tags are added to different protein samples. Although the overall mass of the tags are identical, the cleavage products of the tags into smaller units create either 4 or 8 different masses so that peptides from each sample can be directly compared to the others to determine relative concentrations.