Dynamic Proteomics: In Vivo Proteome-Wide Measurement of Protein Kinetics Using Metabolic Labeling

Area of Science:

• Biochemistry
• Proteomics
• Systems Biology

Background:

• Control of protein synthesis and degradation is crucial for cellular function, adaptation, and disease.
• Advances in stable isotope labeling and mass spectrometry allow in vivo measurement of protein dynamics.

Purpose of the Study:

• To describe principles and protocols for measuring protein dynamics using (2)H2O labeling and mass spectrometry.
• To detail Mass Isotopomer Distribution Analysis (MIDA) for kinetic analysis of proteins.

Main Methods:

• Metabolic labeling with deuterium-labeled water ((2)H2O).
• Tandem mass spectrometry to analyze mass isotopomer abundances in peptides.
• Mass Isotopomer Distribution Analysis (MIDA) for quantitation and kinetic calculations.

Main Results:

• Accurate measurement of protein synthesis and turnover rates across the proteome.
• Demonstration of optimal labeling protocols, sample preparation, and data analysis.
• Application in noninvasive 'virtual biopsy' and lipidomics.

Conclusions:

• The combination of (2)H2O labeling and mass spectrometry is a powerful tool for characterizing protein dynamics.
• This approach has broad applications in biological research and clinical medicine.
• Future applications in understanding complex biological systems and diseases are envisioned.