Measurement of human plasma proteome dynamics with 2H2O and liquid chromatography tandem mass spectrometry

Price, John C.; Holmes, William E.; Li, Kelvin W.; Floreani, Nicholas A.; Neese, Richard A.; Turner, Scott; Hellerstein, Marc K.

doi:10.1016/j.ab.2011.09.007

Cited by 96 publications

(187 citation statements)

References 49 publications

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“…Translation of this BM approach in these models may therefore be possible by measuring plasma protein RRs, a technique already established in humans (Price et al ., 2012a). …”

Section: Discussionmentioning

confidence: 99%

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Reduced in vivo hepatic proteome replacement rates but not cell proliferation rates predict maximum lifespan extension in mice

et al. 2015

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SummaryCombating the social and economic consequences of a growing elderly population will require the identification of interventions that slow the development of age‐related diseases. Preserved cellular homeostasis and delayed aging have been previously linked to reduced cell proliferation and protein synthesis rates. To determine whether changes in these processes may contribute to or predict delayed aging in mammals, we measured cell proliferation rates and the synthesis and replacement rates (RRs) of over a hundred hepatic proteins in vivo in three different mouse models of extended maximum lifespan (maxLS): Snell Dwarf, calorie‐restricted (CR), and rapamycin (Rapa)‐treated mice. Cell proliferation rates were not consistently reduced across the models. In contrast, reduced hepatic protein RRs (longer half‐lives) were observed in all three models compared to controls. Intriguingly, the degree of mean hepatic protein RR reduction was significantly correlated with the degree of maxLS extension across the models and across different Rapa doses. Absolute rates of hepatic protein synthesis were reduced in Snell Dwarf and CR, but not Rapa‐treated mice. Hepatic chaperone levels were unchanged or reduced and glutathione S‐transferase synthesis was preserved or increased in all three models, suggesting a reduced demand for protein renewal, possibly due to reduced levels of unfolded or damaged proteins. These data demonstrate that maxLS extension in mammals is associated with improved hepatic proteome homeostasis, as reflected by a reduced demand for protein renewal, and that reduced hepatic protein RRs hold promise as an early biomarker and potential target for interventions that delay aging in mammals.

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“…Translation of this BM approach in these models may therefore be possible by measuring plasma protein RRs, a technique already established in humans (Price et al ., 2012a). …”

Section: Discussionmentioning

confidence: 99%

“…Details of f calculations were described previously (Price et al ., 2012a), and calculation of k , RPS, and WPASR values for individual proteins is presented in Supporting Information. Individual protein‐level k , RPS, and WPASR data and individual peptide‐level f and RPS data are presented in Spreadsheet S1.…”

Section: Methodsmentioning

confidence: 99%

Reduced in vivo hepatic proteome replacement rates but not cell proliferation rates predict maximum lifespan extension in mice

et al. 2015

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“…Data Analysis-A recent investigation by Price and coworkers (18) further elevated the utilities of the 2 H 2 O labeling method in evaluating protein turnovers. In their elegantly designed study, A(ϱ) was determined from the precursor enrichment and the theoretical number of 2 H incorporation into a peptide, derived from its sequence and established labeling sites for each amino acid.…”

Section: Rates Of Protein Turnover In Cardiac and Hepatic Mitochondrimentioning

confidence: 99%

“…Isotope tracers are particularly useful for tracking such continual renewal of the proteome in living systems, because they allow differentiation between preexisting and newly synthesized proteins (5 (11)(12)(13)(14) and peptide analysis in MALDI-TOF MS (15) and LC-MS (16,17). More recently, Price et al described an approach for measuring protein turnover by calculating the theoretical number of 2 H-labeling sites on a peptide sequence (18) and reported the turnover rates of ϳ100 human plasma proteins. Here we describe another novel strategy to determine protein turnover rates on a proteomic scale using 2 H 2 O labeling.…”

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confidence: 99%

Metabolic Labeling Reveals Proteome Dynamics of Mouse Mitochondria

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et al. 2012

Molecular & Cellular Proteomics

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Mitochondrial dysfunction is associated with many human diseases. Mitochondrial damage is exacerbated by inadequate protein quality control and often further contributes to pathogenesis. The maintenance of mitochondrial functions requires a delicate balance of continuous protein synthesis and degradation, i.e. protein turnover. To understand mitochondrial protein dynamics in vivo, we designed a metabolic heavy water ( 2 H 2 O) labeling strategy customized to examine individual protein turnover in the mitochondria in a systematic fashion. Mice were fed with 2 H 2 O at a minimal level (<5% body water) without physiological impacts. Mitochondrial proteins were analyzed from 9 mice at each of the 13 time points between 0 and 90 days (d) of labeling. A novel multiparameter fitting approach computationally determined the normalized peak areas of peptide mass isotopomers at initial and steady-state time points and permitted the protein halflife to be determined without plateau-level 2 H incorporation. We characterized the turnover rates of 458 proteins in mouse cardiac and hepatic mitochondria and found median turnover rates of 0.0402 d ؊1 and 0.163 d ؊1 , respectively, corresponding to median half-lives of 17.2 d and 4.26 d. Mitochondria in the heart and those in the liver exhibited distinct turnover kinetics, with limited synchronization within functional clusters. We observed considerable interprotein differences in turnover rates in both organs, with half-lives spanning from hours to months (ϳ60 d). Our proteomics platform demonstrates the first large-scale analysis of mitochondrial protein turnover rates in vivo, with potential applications in translational research. Molecular & Cellular

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“…Measuring protein turnover in vivo entails additional technical challenges including label delivery and tolerance, determination of precursor enrichment, and data interpretation (3,12,16). Stable isotope labeling using deuterium oxide ( 2 H 2 O) tracers has shown great potential for tracing protein turnover in mammals (17)(18)(19)(20)(21). However, widespread adjudged to capture the turnover of most cardiac proteins (16).…”

Section: Introductionmentioning

confidence: 99%

Protein kinetic signatures of the remodeling heart following isoproterenol stimulation

et al. 2014

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Protein temporal dynamics play a critical role in time-dimensional pathophysiological processes, including the gradual cardiac remodeling that occurs in early-stage heart failure. Methods for quantitative assessments of protein kinetics are lacking, and despite knowledge gained from single-protein studies, integrative views of the coordinated behavior of multiple proteins in cardiac remodeling are scarce. Here, we developed a workflow that integrates deuterium oxide ( 2 H 2 O) labeling, high-resolution mass spectrometry (MS), and custom computational methods to systematically interrogate in vivo protein turnover. Using this workflow, we characterized the in vivo turnover kinetics of 2,964 proteins in a mouse model of β-adrenergic-induced cardiac remodeling. The data provided a quantitative and longitudinal view of cardiac remodeling at the molecular level, revealing widespread kinetic regulations in calcium signaling, metabolism, proteostasis, and mitochondrial dynamics. We translated the workflow to human studies, creating a reference dataset of 496 plasma protein turnover rates from 4 healthy adults. The approach is applicable to short, minimal label enrichment and can be performed on as little as a single biopsy, thereby overcoming critical obstacles to clinical investigations. The protein turnover quantitation experiments and computational workflow described here should be widely applicable to largescale biomolecular investigations of human disease mechanisms with a temporal perspective.

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Measurement of human plasma proteome dynamics with 2H2O and liquid chromatography tandem mass spectrometry

Cited by 96 publications

References 49 publications

Reduced in vivo hepatic proteome replacement rates but not cell proliferation rates predict maximum lifespan extension in mice

Reduced in vivo hepatic proteome replacement rates but not cell proliferation rates predict maximum lifespan extension in mice

Metabolic Labeling Reveals Proteome Dynamics of Mouse Mitochondria

Protein kinetic signatures of the remodeling heart following isoproterenol stimulation

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