Highly accurate measurements of the amount of substance of organic molecules in a test material can be obtained using exactly matched calibration solutions and internal standards that are labeled with stable isotope atoms by measuring the amount ratio of analyte to internal standard using mass spectrometry. Estimating the uncertainty of quantitative measurements of organic molecules is a means of evaluating accuracy and of establishing traceability to the International System of Units (SI) and requires a measurement function that fully describes the measuring system. This paper presents the derivation of the equation (measurement function) that describes this complete measurement after the internal standard has equilibrated with the test material matrix. It is similar to the equation for inorganic measurements using isotope dilution techniques, but potential biases during chemical processing arising from whole organic molecule analysis compared to inorganic atomic analysis required greater investigation of the yield factors that occur during organic molecule measurements. In the new equation, a series of ratios of proportionality factors are used to relate the amount of substance in a test material to chromatographic peak area ratios corresponding to mass spectrometer ion current ratios. All the proportionality factors are grouped together to define a measuring system factor F(X), the value of which is determined by the fundamental chemical processes affecting the yields of analyte, internal standard, and reference standard of the analyte in the measurement process. Any factors in the measurement process that affect the mole ratio of analyte to internal standard in the calibration solution differently from the test solution will result in a nonunity value for F(X) and a proportional bias to the measurement, and in this way F(X) represents the concept of recovery of the amount ratio of analyte to internal standard. Thus highly accurate measurements require F(X) or its constituent factors to be evaluated. In addition, the uncertainty in the evaluation of F(X) or of its constituent factors must be included in a complete uncertainty estimation of the analytical procedure. The many different permutations of proportionality factor ratios that may result in a unity value of F(X) are discussed resulting in a case for evaluating F(X) rather than the more common practice of evaluating individual factors for each major stage of the measurement procedure. Since the new measurement function describes the complete chemical process that constitutes the measurement, traceability to the SI is assured when all factors in the function are measured traceably and have their associated uncertainty estimated correctly. Ignoring F(X) would invalidate traceability to the SI and would prevent a complete estimation of measurement uncertainty.