Measurement of human plasma proteome dynamics with ²H₂O and liquid chromatography tandem mass spectrometry

• Published in: Analytical biochemistry Vol. 420; no. 1; pp. 73 - 83
• Main Authors: Price, John C, Holmes, William E, Li, Kelvin W, Floreani, Nicholas A, Neese, Richard A, Turner, Scott M, Hellerstein, Marc K
• Format: Journal Article
• Language: English
• Published: Elsevier Inc 2012
• Subjects: amino acids; deuterium; deuterium oxide; half life; homeostasis; human diseases; humans; liquid chromatography; peptides; protein metabolism; proteins; proteome; stable isotopes; tandem mass spectrometry
• ISSN: 0003-2697; 1096-0309
• DOI: 10.1016/j.ab.2011.09.007

Dysfunction of protein turnover is a feature of many human diseases, and proteins are substrates in important biological processes. Currently, no method exists for the measurement of global protein turnover (i.e., proteome dynamics) that can be applied in humans. Here we describe the use of metabolic labeling with deuterium (²H) from ²H₂O and liquid chromatography tandem mass spectrometry (LC–MS/MS) analysis of mass isotopomer patterns to measure protein turnover. We show that the positions available for ²H label incorporation in vivo can be calculated using peptide sequence. The isotopic incorporation values calculated by combinatorial analysis of mass isotopomer patterns in peptides correlate very closely with values established for individual amino acids. Inpatient and outpatient heavy water labeling protocols resulted in ²H label incorporation sufficient for reproducible quantitation in humans. Replacement rates were similar for peptides deriving from the same protein. Using a kinetic model to account for the time course of each individual’s ²H₂O enrichment curves, dynamics of approximately 100 proteins with half-lives ranging from 0.4 to 40days were measured using 8μl of plasma. The measured rates were consistent with literature values. This method can be used to measure in vivo proteome homeostasis in humans in disease and during therapeutic interventions.