Calculation of the protein turnover rate using the number of incorporated 2H atoms and proteomics analysis of a single labeled sample

Serguei Ilchenko, Andrew Haddad, Prabodh Sadana, Fabio A. Recchia, Rovshan Sadygov, Takhar Kasumov

Research output: Contribution to journalArticle

Abstract

Rate constant estimation with heavy water requires a long-term experiment with data collection at multiple time points (3-4 weeks for mitochondrial proteome dynamics in mice and much longer in other species). When tissue proteins are analyzed, this approach requires euthanizing animals at each time point or multiple tissue biopsies in humans. Although short-term protocols are available, they require knowledge of the maximum number of isotope labels (N) and accurate quantification of observed 2H-enrichment in the peptide. The high-resolution accurate mass spectrometers used for proteome dynamics studies are characterized by a systematic spectral error that compromises these measurements. To circumvent these issues, we developed a simple algorithm for the rate constant calculation based on a single labeled sample and comparable unlabeled (time 0) sample. The algorithm determines N for all proteogenic amino acids from a long-term experiment to calculate the predicted plateau 2H-labeling of peptides for a short-term protocol and estimates the rate constant based on the measured baseline and the predicted plateau 2H-labeling of peptides. The method was validated based on the rate constant estimation in a long-term experiment in mice and dogs. The improved 2 time-point method enables the rate constant calculation with less than 10% relative error compared to the bench-marked multi-point method in mice and dogs and allows us to detect diet-induced subtle changes in ApoAI turnover in mice. In conclusion, we have developed and validated a new algorithm for protein rate constant calculation based on 2-time point measurements that could also be applied to other biomolecules. ©

Original languageEnglish (US)
JournalAnalytical Chemistry
DOIs
StateAccepted/In press - Jan 1 2019

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Rate constants
Atoms
Proteins
Proteome
Labeling
Peptides
Tissue
Deuterium Oxide
Biopsy
Experiments
Biomolecules
Mass spectrometers
Nutrition
Isotopes
Proteomics
Labels
Animals
Amino Acids

ASJC Scopus subject areas

  • Analytical Chemistry

Cite this

Calculation of the protein turnover rate using the number of incorporated 2H atoms and proteomics analysis of a single labeled sample. / Ilchenko, Serguei; Haddad, Andrew; Sadana, Prabodh; Recchia, Fabio A.; Sadygov, Rovshan; Kasumov, Takhar.

In: Analytical Chemistry, 01.01.2019.

Research output: Contribution to journalArticle

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