High-Resolution Mass Spectrometry for In Vivo Proteome Dynamics using Heavy Water Metabolic Labeling

Sadygov, Rovshan G.

doi:10.3390/ijms21217821

Cited by 5 publications

(3 citation statements)

References 39 publications

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“…With knowledge of the initial predicted precursor labelling (based on body water levels), and the peptide amino acid composition i.e. knowledge of the number of each theoretically labelled AA, rates of turnover of individual peptides and hence the parent proteins, can be calculated [77,79]. This has been extensively validated in animal and cell culture models [80e82] and more recently in humans too [71,78,83].…”

Section: Referencementioning

confidence: 99%

Principles of stable isotope research – with special reference to protein metabolism

Wilkinson

Brook

Smith

2021

Clinical Nutrition Open Science

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The key to understanding the mechanisms regulating disease stems from the ability to accurately quantify the dynamic nature of the metabolism underlying the physiological and pathological changes occurring as a result of the disease. Stable isotope tracer technologies have been at the forefront of this for almost 80 years now, and through a combination of both intense theoretical and technological development over these decades, it is now possible to utilise stable isotope tracers to investigate the complexities of in vivo human metabolism from a whole body perspective, down to the regulation of sub-nanometer cellular components (i.e organelles, nucleotides and individual proteins). This review therefore aims to highlight; 1) the advances made in these stable isotope tracer approaches e with special reference given to their role in understanding the nutritional regulation of protein metabolism, 2) some considerations required for the appropriate application of these stable isotope techniques to study protein metabolism, 3) and finally how new stable isotopes approaches

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Section: Referencementioning

confidence: 99%

Principles of stable isotope research – with special reference to protein metabolism

Wilkinson

Brook

Smith

2021

Clinical Nutrition Open Science

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“…We therefore employed a high-resolution tribrid mass spectrometer using HCD and ETD fragmentation methods to investigate changes in the proteome of the left ventricle of the heart, including the identification of 4-HNE–modified proteins, of control and exercised mice. According to the study published several months ago, it is possible that lowering the value for the mass resolution of the mass spectrometer would lead to better protein identification ( Sadygov, 2020 ). In addition, proteins with modifications that were not specified in the database search may result in the lack of protein identification.…”

Section: Discussionmentioning

confidence: 99%

Proteomic Analysis of Cardiac Adaptation to Exercise by High Resolution Mass Spectrometry

Al-Menhali

Anderson

Gourine

et al. 2021

Front. Mol. Biosci.

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Regular exercise has many health benefits, among which is a significant reduction of cardiovascular risk. Although many beneficial effects of exercise are well described, the exact mechanisms by which exercise confers cardiovascular benefits are yet to be fully understood. In the current study, we have used high resolution mass spectrometry to determine the proteomic responses of the heart to exercise training in mice. The impact of exercise-induced oxidative stress on modifications of cardiomyocyte proteins with lipid peroxidation biomarker 4-hydroxynonenal (4-HNE) was examined as well. Fourteen male mice were randomized into the control (sedentary) group and the exercise group that was subjected to a swim exercise training program for 5 days a week for 5 months. Proteins were isolated from the left ventricular tissue, fractionated and digested for shotgun proteomics. Peptides were separated by nanoliquid chromatography and analyzed on an Orbitrap Fusion mass spectrometer using high-energy collision–induced dissociation and electron transfer dissociation fragmentation. We identified distinct ventricular protein signatures established in response to exercise training. Comparative proteomics identified 23 proteins that were upregulated and 37 proteins that were downregulated with exercise, in addition to 65 proteins that were identified only in ventricular tissue samples of exercised mice. Most of the proteins specific to exercised mice are involved in respiratory electron transport and/or implicated in glutathione conjugation. Additionally, 10 proteins were found to be modified with 4-HNE. This study provides new data on the effects of exercise on the cardiac proteome and contributes to our understanding of the molecular mechanisms underlying the beneficial effects of exercise on the heart.

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“…For the Orbitrap instrument, it is not preferable to use too high a mass resolution. It was observed that 60,000 is the best choice for the balance between resolving interference peaks and spectral accuracy (Naylor et al, 2017; Sadygov, 2020a). Zoom scan or target‐SIM mode (e.g.…”

Section: Protein Turnover Rate Calculation For Metabolic Study With 2...mentioning

confidence: 99%

Measurement of protein in vivo turnover rate with metabolic labeling using LC–MS

Shi

Weng

Jian

2023

Biomedical Chromatography

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Understanding the protein dynamics of a drug target is important for pharmaceutical research because it provides insight into drug design, target engagement, pharmacodynamics and drug efficacy. Nonradioactive isotope labeling has been the method of choice for protein turnover measurement thanks to the advancement of high‐resolution mass spectrometry. While the changes in proteome in cell cultures can be monitored precisely, as the culture media can be completely replaced with 2H‐, 15N‐ or 13C‐labeled essential amino acids, quantifying rates of protein synthesis in vivo is more challenging. The amount of isotope tracer that can be administered into the body is relatively small compared with the existing protein, thus requiring more sensitive detection, and the precursor‐product labeling relationship is more complicated to interpret. The purpose of this review is to provide an overview of the principles of in vivo protein turnover studies using deuterium water (2H2O) with an emphasis on targeted protein analysis by hybrid LC–MS assay platforms. The pursuit of these opportunities will facilitate drug discovery and research in preclinical and clinical stages.

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High-Resolution Mass Spectrometry for In Vivo Proteome Dynamics using Heavy Water Metabolic Labeling

Cited by 5 publications

References 39 publications

Principles of stable isotope research – with special reference to protein metabolism

Principles of stable isotope research – with special reference to protein metabolism

Proteomic Analysis of Cardiac Adaptation to Exercise by High Resolution Mass Spectrometry

Measurement of protein in vivo turnover rate with metabolic labeling using LC–MS

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