Software Tool for Visualization and Validation of Protein Turnover Rates Using Heavy Water Metabolic Labeling and LC-MS

Henock M. Deberneh, Rovshan G. Sadygov

Research output: Contribution to journalArticlepeer-review

Abstract

Metabolic stable isotope labeling followed by liquid chromatography coupled with mass spectrometry (LC-MS) is a powerful tool for in vivo protein turnover studies of individual proteins on a large scale and with high throughput. Turnover rates of thousands of proteins from dozens of time course experiments are determined by data processing tools, which are essential components of the workflows for automated extraction of turnover rates. The development of sophisticated algorithms for estimating protein turnover has been emphasized. However, the visualization and annotation of the time series data are no less important. The visualization tools help to validate the quality of the model fits, their goodness-of-fit characteristics, mass spectral features of peptides, and consistency of peptide identifications, among others. Here, we describe a graphical user interface (GUI) to visualize the results from the protein turnover analysis tool, d2ome, which determines protein turnover rates from metabolic D2O labeling followed by LC-MS. We emphasize the specific features of the time series data and their visualization in the GUI. The time series data visualized by the GUI can be saved in JPEG format for storage and further dissemination.

Original languageEnglish (US)
Article number14620
JournalInternational journal of molecular sciences
Volume23
Issue number23
DOIs
StatePublished - Dec 2022

Keywords

  • graphical user interface for mass spectral data
  • heavy water metabolic labeling
  • in vivo protein turnover
  • isotope distribution
  • time series of isotope labeling

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry

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