Fig. 8. The three-compartment model used by ApplE Turnover.

The three compartments (circles) each contain a time-dependent ratio of unlabeled (blue) to labeled (red) lysine. Unlabeled lysine enters the free amino acids compartment from metabolized food. Protein degradation from the all proteins compartment contributes labeled, as well as some unlabeled, lysine to the free amino acids compartment—amino acid recycling from any individual protein of interest is considered negligible. The pool of free amino acids is available for synthesis of all proteins, as well as the protein of interest. Finally, lysine is removed from the system as waste to accommodate nutrient influx and maintain a consistent pool of free amino acids. Note that while this schematic depicts the introduction of unlabeled lysine to a system containing labeled lysine (consistent with the experiments used to generate this resource), the three-compartment model and ApplE Turnover are equally applicable to experiments in which labeled lysine is introduced to a system containing unlabeled lysine.