Using Heavy Mass Isotopomers for Protein Turnover in Heavy Water Metabolic Labeling

Metabolic labeling followed by LC-MS-based proteomics is a powerful tool to study proteome dynamics in high-throughput experiments both in vivo and in vitro. High mass resolution and accuracy allow differentiation in isotope profiles and the quantification of partially labeled peptide species. Metabolic labeling duration introduces a time domain in which the gradual incorporation of labeled isotopes is recorded. Different stable isotopes are used for labeling. Labeling with heavy water has advantages because it is cost-effective and easy to use. The protein degradation rate constant has been modeled using exponential decay models for the relative abundances of mass isotopomers. The recently developed closed-form equations were applied to study the analytic behavior of the heavy mass isotopomers in the time domain of metabolic labeling. The predictions from the closed-form equations are compared with the practices that have been used to extract degradation rate constants from the time-course profiles of heavy mass isotopomers. It is shown that all mass isotopomers, except for the monoisotope, require data transformations to obtain the exponential depletion, which serves as a basis for the rate constant model. Heavy mass isotopomers may be preferable choices for modeling high-mass peptides or peptides with a high number of labeling sites. The results are also applicable to stable isotope labeling with other atom-based labeling agents.