A theory of mass isotopomer analysis based on the well‐known principle of isotope dilution mass spectrometry is reviewed. An algorithm for the determination of isotope incorporation into a metabolic substrate from a labeled precursor using mass isotopomer analysis is presented. The steps include the determination of the contribution of the derivatization reagent to the observed spectrum of the derivatized substrate and the correction of contribution from ¹³C natural abundance using multiple linear regression analysis. Examples of the application of this theory to determine the spectrum of the trimethylsilyl derivative of the ‘pure unlabeled’ or mononuclidic cholesterol, and the calculation of mass isotopomer distribution in cholesterol due to tracer incorporation using this ‘pure unlabeled’ spectrum, are also provided.