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Title: Plasma Protein Turnover Rates in Rats Using Stable Isotope Labeling, Global Proteomics, and Activity-Based Protein Profiling

Abstract

Protein turnover is important for general health on cellular and organism scales providing a strategy to replace old, damaged, or dysfunctional proteins. Protein turnover also informs of biomarker kinetics, as a better understanding of synthesis and degradation of proteins increases the clinical utility of biomarkers. Here, turnover rates of plasma proteins in rats were measured in vivo using a pulse-chase stable isotope labeling experiment. During the pulse, rats (n=5) were fed 13C6-labeled lysine (“heavy”) feed for 23 days to label proteins. During the chase, feed was changed to an unlabeled equivalent feed (“light”), and blood was repeatedly sampled from rats over 10 time points for 28 days. Plasma samples were digested with trypsin, and analyzed with liquid chromatography-tandem mass spectrometry (LC-MS/MS). MaxQuant was used to identify peptides and proteins, and quantify heavy:light lysine ratios. A system of ordinary differential equations was used to calculate protein turnover rates. Using this approach, 273 proteins were identified, and turnover rates were quantified for 157 plasma proteins with half-lives ranging 0.3-103 days. For the ~70 most abundant proteins, variability in turnover rates among rats was low (median coefficient of variation: 0.09). Activity-based protein profiling was applied to pooled plasma samples to enrich serine hydrolasesmore » using a fluorophosphonate (FP2) activity-based probe. This enrichment resulted in turnover rates for an additional 17 proteins. This study is the first to measure global plasma protein turnover rates in rats in vivo, measure variability of protein turnover rates in any animal model, and utilize activity-based protein profiling for enhancing measurements of targeted, low-abundant proteins, such as those commonly used as biomarkers. Measured protein turnover rates will be important for understanding of the role of protein turnover in cellular and organism health as well as increasing the utility of protein biomarkers through better understanding of processes governing biomarker kinetics.« less

Authors:
ORCiD logo [1];  [1];  [1]; ORCiD logo [1];  [1];  [1];  [1];  [1];  [1]; ORCiD logo [1];  [1]
  1. Pacific Northwest National Laboratory, Richland, Washington 99354, United States
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1415090
Report Number(s):
PNNL-SA-129561
Journal ID: ISSN 0003-2700
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Analytical Chemistry; Journal Volume: 89; Journal Issue: 24
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES

Citation Formats

Smith, Jordan Ned, Tyrrell, Kimberly J., Hansen, Joshua R., Thomas, Dennis G., Murphree, Taylor A., Shukla, Anil, Luders, Teresa, Madden, James M., Li, Yunying, Wright, Aaron T., and Piehowski, Paul D. Plasma Protein Turnover Rates in Rats Using Stable Isotope Labeling, Global Proteomics, and Activity-Based Protein Profiling. United States: N. p., 2017. Web. doi:10.1021/acs.analchem.7b03984.
Smith, Jordan Ned, Tyrrell, Kimberly J., Hansen, Joshua R., Thomas, Dennis G., Murphree, Taylor A., Shukla, Anil, Luders, Teresa, Madden, James M., Li, Yunying, Wright, Aaron T., & Piehowski, Paul D. Plasma Protein Turnover Rates in Rats Using Stable Isotope Labeling, Global Proteomics, and Activity-Based Protein Profiling. United States. doi:10.1021/acs.analchem.7b03984.
Smith, Jordan Ned, Tyrrell, Kimberly J., Hansen, Joshua R., Thomas, Dennis G., Murphree, Taylor A., Shukla, Anil, Luders, Teresa, Madden, James M., Li, Yunying, Wright, Aaron T., and Piehowski, Paul D. Wed . "Plasma Protein Turnover Rates in Rats Using Stable Isotope Labeling, Global Proteomics, and Activity-Based Protein Profiling". United States. doi:10.1021/acs.analchem.7b03984.
@article{osti_1415090,
title = {Plasma Protein Turnover Rates in Rats Using Stable Isotope Labeling, Global Proteomics, and Activity-Based Protein Profiling},
author = {Smith, Jordan Ned and Tyrrell, Kimberly J. and Hansen, Joshua R. and Thomas, Dennis G. and Murphree, Taylor A. and Shukla, Anil and Luders, Teresa and Madden, James M. and Li, Yunying and Wright, Aaron T. and Piehowski, Paul D.},
abstractNote = {Protein turnover is important for general health on cellular and organism scales providing a strategy to replace old, damaged, or dysfunctional proteins. Protein turnover also informs of biomarker kinetics, as a better understanding of synthesis and degradation of proteins increases the clinical utility of biomarkers. Here, turnover rates of plasma proteins in rats were measured in vivo using a pulse-chase stable isotope labeling experiment. During the pulse, rats (n=5) were fed 13C6-labeled lysine (“heavy”) feed for 23 days to label proteins. During the chase, feed was changed to an unlabeled equivalent feed (“light”), and blood was repeatedly sampled from rats over 10 time points for 28 days. Plasma samples were digested with trypsin, and analyzed with liquid chromatography-tandem mass spectrometry (LC-MS/MS). MaxQuant was used to identify peptides and proteins, and quantify heavy:light lysine ratios. A system of ordinary differential equations was used to calculate protein turnover rates. Using this approach, 273 proteins were identified, and turnover rates were quantified for 157 plasma proteins with half-lives ranging 0.3-103 days. For the ~70 most abundant proteins, variability in turnover rates among rats was low (median coefficient of variation: 0.09). Activity-based protein profiling was applied to pooled plasma samples to enrich serine hydrolases using a fluorophosphonate (FP2) activity-based probe. This enrichment resulted in turnover rates for an additional 17 proteins. This study is the first to measure global plasma protein turnover rates in rats in vivo, measure variability of protein turnover rates in any animal model, and utilize activity-based protein profiling for enhancing measurements of targeted, low-abundant proteins, such as those commonly used as biomarkers. Measured protein turnover rates will be important for understanding of the role of protein turnover in cellular and organism health as well as increasing the utility of protein biomarkers through better understanding of processes governing biomarker kinetics.},
doi = {10.1021/acs.analchem.7b03984},
journal = {Analytical Chemistry},
number = 24,
volume = 89,
place = {United States},
year = {Wed Dec 06 00:00:00 EST 2017},
month = {Wed Dec 06 00:00:00 EST 2017}
}