Protein turnover estimation from fragment ions and precursor enrichment in heavy water labeled LC-MS experiments

Metabolic labeling with heavy water followed by LC-MS quantifies the turnover of thousands of proteins in vivo. As a cost-effective and easy-to-use stable isotope labeling tracer, heavy water has been used to study the turnover of proteins in the heart, liver, kidney, blood, and brain of various model animals such as mice, rats, dogs, and fish. Since the deuterium in heavy water is incorporated into all non-essential amino acids, virtually all peptides are labeled. However, despite the ubiquitous nature of heavy water labeling, only 30-40% of all quantified peptides are useful for protein turnover rate estimation. Most of the mass spectral data is filtered out due to the low goodness-of-fit characteristics (such as the coefficient of determination, R2). Our long-term goal is to develop a unified dynamics of biomolecules (proteins, lipids, and metabolites) using heavy water labeling and LC-MS-MS/MS to study changes in diseases. The objective of this project is to develop techniques to increase the throughput, statistical power, and accuracy of protein turnover estimation.