Timepoint Selection Strategy for in Vivo Proteome Dynamics from Heavy Water Metabolic Labeling and LC-MS

Vugar R. Sadygov, William Zhang, Rovshan G. Sadygov

Research output: Contribution to journalArticle

Abstract

Protein homeostasis, proteostasis, is essential for healthy cell functioning and is dysregulated in many diseases. Metabolic labeling with heavy water followed by liquid chromatography coupled online to mass spectrometry (LC-MS) is a powerful high-throughput technique to study proteome dynamics in vivo. Longer labeling duration and dense timepoint sampling (TPS) of tissues provide accurate proteome dynamics estimations. However, the experiments are expensive, and they require animal housing and care, as well as labeling with stable isotopes. Often, the animals are sacrificed at selected timepoints to collect tissues. Therefore, it is necessary to optimize TPS for a given number of sampling points and labeling duration and target a specific tissue of study. Currently, such techniques are missing in proteomics. Here, we report on a formula-based stochastic simulation strategy for TPS for in vivo studies with heavy water metabolic labeling and LC-MS. We model the rate constant (lognormal), measurement error (Laplace), peptide length (gamma), relative abundance of the monoisotopic peak (beta regression), and the number of exchangeable hydrogens (gamma regression). The parameters of the distributions are determined using the corresponding empirical probability density functions from a large-scale dataset of murine heart proteome. The models are used in the simulations of the rate constant to minimize the root-mean-square error (rmse). The rmse for different TPSs shows structured patterns. They are analyzed to elucidate common features in the patterns.

Original languageEnglish (US)
Pages (from-to)2105-2112
Number of pages8
JournalJournal of Proteome Research
Volume19
Issue number5
DOIs
StatePublished - May 1 2020

Keywords

  • conditional independence of relative abundance and number of exchangeable hydrogens
  • distribution of turnover rates
  • error of relative abundances
  • heavy water metabolic labeling
  • isotope distributions
  • LC-MS
  • model of protein degradation rate constant
  • protein turnover
  • stochastic simulations
  • timepoint selection

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

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