Measuring proteome dynamics in vivo: as easy as adding water?

Proteomics investigations typically yield information regarding static gene expression profiles. The central issues that limit the study of proteome dynamics include how to (i) administer a labeled amino acid in vivo, (ii) measure the isotopic labeling of a protein(s) (which may be low), and (iii) reliably interpret the precursor/product labeling relationships. In this study, we demonstrate the potential of quantifying proteome dynamics by coupling the administration of stable isotopes with mass spectrometric assays. Although the direct administration of a labeled amino acid(s) is typically used to measure protein synthesis, we explain the application of labeled water, comparing (2)H(2)O versus H(2)(18)O for measuring albumin biosynthesis in vivo. This application emphasizes two distinct advantages of using labeled water over a labeled amino acid(s). First, in long term studies (e.g. days or weeks), it is not practical to continuously administer a labeled amino acid(s); however, in the presence of labeled water, organisms will generate labeled amino acids. Second, to calculate rates of protein synthesis in short term studies (e.g. hours), one must utilize a precursor/product labeling ratio; when using labeled water it is possible to reliably identify and easily measure the precursor labeling (i.e. water). We demonstrate that labeled water permits studies of protein synthesis (e.g. albumin synthesis in mice) during metabolic "steady-state" or "non-steady-state" conditions, i.e. integrating transitions between the fed and fasted state or during an acute perturbation (e.g. following a meal), respectively. We expect that the use of labeled water is applicable to wide scale investigations of proteome dynamics and can therein be used to obtain a functional image of gene expression in vivo.