Duplexing metabolic deuterated water-labeled samples using dimethyl labeling to estimate protein turnover rates
Year: 2025
Type: article
Abstract: Metabolic labeling with deuterated water (D2O), combined with liquid chromatography coupled to mass spectrometry (LC-MS), is used to study turnover rates of individual proteins in vivo. Often, protein turnover rates from two (treatment and control) conditions are compared. The turnover rates are obtained from time course LC-MS experiments for each condition. Here, we explore dimethyl duplexing to directly compare label enrichment from two D2O-labeled samples in a single LC-MS experiment. Light and heavy dimethyl channels carry two metabolically labeled samples. Protein turnover is modeled as a time course of the ratio of the monoisotopic relative abundance of a peptide in the heavy dimethyl channel to that in the light dimethyl channel. The turnover rates computed using the duplexed samples were close to those of non-duplexed samples. We illustrate the advantages of this method through the analysis of liver proteome dynamics in rapamycin-treated mice compared to control mice. Dimethyl duplexing of metabolically deuterated water-labeled samples addresses challenges in dynamic proteome studies by enabling direct comparison of label enrichment. Here, the authors demonstrate that this approach allows accurate protein turnover modeling and efficient analysis of liver proteome dynamics in rapamycin-treated versus control mice.
Source: Communications Chemistry
Authors: Henock M. Deberneh, Michael E. Taylor, Kamil A. Kobak, Michael T. Kinter, Benjamin F. Miller, Rovshan G. Sadygov
Language: English
Subfield: Spectroscopy
Field: Chemistry
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $3,690
Awards: G1026900435, Novel computational methods for in vivo proteome dynamics estimation using heavy water metabolic labeling and LC-MS, G4446352502, G485138746, G5068849984, Chondrocyte Metabolic Stress in the Development of Osteoarthritis, G6638384071, G9000235769, Protein turnover estimation from fragment ions and precursor enrichment in heavy water labeled LC-MS experiments
OpenAlex ID: W4416718953