Numbers of Exchangeable Hydrogens from LC-MS Data of Heavy Water Metabolically Labeled Samples
Henock M Deberneh1, Michael E Taylor2, Agnieszka K Borowik2
1Department of Biochemistry and Molecular Biology The University of Texas Medical Branch 301 University of Blvd, Galveston, Texas 77555, United States.
Journal of the American Society for Mass Spectrometry
|July 26, 2024
Summary
This study introduces new methods to accurately calculate deuterium incorporation (D2O) for measuring protein synthesis rates. The best method improves the accuracy of determining labeling sites for each amino acid in specific experimental conditions.
Area of Science:
- Biochemistry
- Proteomics
- Analytical Chemistry
Background:
- Deuterium oxide (D2O) labeling is crucial for in vivo protein synthesis rate measurement.
- Accurate modeling of mass shifts in peptides relies on the theoretical maximum enrichment (NEH) of labeling sites.
- Existing NEH values may not reflect species- or tissue-specific variations.
Purpose of the Study:
- To develop and validate methods for experimentally determining NEH values for each amino acid.
- To enhance the precision of protein synthesis rate calculations under specific experimental conditions.
- To address limitations of using universal NEH values in D2O labeling studies.
Main Methods:
- Four computational methods were employed to calculate NEH values.
- A de novo approach computed NEH and enrichment from mass isotopomer abundances.
- Three methods utilized complete isotope profiles and deuterium enrichment, including residual sum of squares minimization.
Main Results:
- The residual sum of squares minimization method demonstrated superior performance in test samples.
- The study successfully computed experiment-specific NEH values for individual amino acids.
- Validation was performed using two publicly available datasets.
Conclusions:
- Experiment-specific NEH determination is essential for accurate protein synthesis rate measurements using D2O.
- The developed methods and implemented tool provide a more precise approach to D2O labeling analysis.
- This work offers a significant improvement for quantitative proteomics research.
