Metabolic deuterium oxide (D2O) labeling in quantitative omics studies: A tutorial review

Kim, Jong-Hyun; Seo, Seungwoo; Kim, Tae-Young

doi:10.1016/j.aca.2022.340722

Cited by 7 publications

(5 citation statements)

References 111 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Tracing in vivo labeled stable isotopes with mass spectrometry has become a powerful tool in metabolic flux analysis and the study of metabolic pathways (Freund and Hegeman, 2017;De Feyter and de Graaf, 2021). Deuterium is a versatile tracer that can be incorporated into most biomolecules by simply replacing H 2 O with D 2 O in the growing medium (Kim et al, 2023). Nicotinamide adenine dinucleotide phosphate (NADPH) is the primary cellular reductant in most biosynthesis and half of NADPH's redox active hydrogen is the result of enzyme-catalyzed hydrogen transfer from water (Zhang et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

Rapid detection of antimicrobial resistance in methicillin-resistant Staphylococcus aureus using MALDI-TOF mass spectrometry

Rensner,

Lueth,

Bellaire

et al. 2023

Front. Cell. Infect. Microbiol.

View full text Add to dashboard Cite

Antimicrobial resistance is a growing problem in modern healthcare. Most antimicrobial susceptibility tests (AST) require long culture times which delay diagnosis and effective treatment. Our group has previously reported a proof-of-concept demonstration of a rapid AST in Escherichia coli using deuterium labeling and MALDI mass spectrometry. Culturing bacteria in D2O containing media incorporates deuterium in newly synthesized lipids, resulting in a mass shift that can be easily detected by mass spectrometry. The extent of new growth is measured by the average mass of synthesized lipids that can be correlated with resistance in the presence of antimicrobials. In this work, we adapt this procedure to methicillin-resistant Staphylococcus aureus using the Bruker MALDI-TOF Biotyper, a low-cost instrument commonly available in diagnostic laboratories. The susceptible strain showed a significant decrease in average mass in on-target microdroplet cultures after 3 hours of incubation with 10 µg/mL methicillin, while the resistant strain showed consistent labeling regardless of methicillin concentration. This assay allows us to confidently detect methicillin resistance in S. aureus after only 3 hours of culture time and minimal sample processing, reducing the turn-around-time significantly over conventional assays. The success of this work suggests its potential as a rapid AST widely applicable in many clinical microbiology labs with minimal additional costs.

show abstract

Section: Discussionmentioning

confidence: 99%

Rapid detection of antimicrobial resistance in methicillin-resistant Staphylococcus aureus using MALDI-TOF mass spectrometry

Rensner,

Lueth,

Bellaire

et al. 2023

Front. Cell. Infect. Microbiol.

View full text Add to dashboard Cite

show abstract

“…This pool, in turn, rapidly labels proteogenic amino acids and generates 2 H-labeled proteins 1 . All non-essential amino acids equilibrate to the enrichment of deuterium enrichment in the body water according to their numbers of non-labile hydrogens 8 . Labeling with heavy water is cost-effective 9 , easy to apply, and requires no dietary adaptation.…”

Section: Background and Summarymentioning

confidence: 99%

A large-scale LC-MS dataset of murine liver proteome from time course of heavy water metabolic labeling

Deberneh,

Abdelrahman,

Verma

et al. 2023

Sci Data

View full text Add to dashboard Cite

Metabolic stable isotope labeling with heavy water followed by liquid chromatography coupled with mass spectrometry (LC-MS) is a powerful tool for in vivo protein turnover studies. Several algorithms and tools have been developed to determine the turnover rates of peptides and proteins from time-course stable isotope labeling experiments. The availability of benchmark mass spectrometry data is crucial to compare and validate the effectiveness of newly developed techniques and algorithms. In this work, we report a heavy water-labeled LC-MS dataset from the murine liver for protein turnover rate analysis. The dataset contains eighteen mass spectral data with their corresponding database search results from nine different labeling durations and quantification outputs from d2ome+ software. The dataset also contains eight mass spectral data from two-dimensional fractionation experiments on unlabeled samples.

show abstract

“…Proteins are continuously synthesized and degraded to maintain the proteome (i.e., proteostasis) appropriate for the cellular environment . Mass spectrometry-based proteomics of metabolically stable-isotope labeled samples is a relatively high-throughput approach to studying turnover rates of individual proteins in vivo . − Among the stable-isotope labeling agents, − deuterated water (D 2 O) offers several advantageous properties such as (1) easy administration of D 2 O, as it can be given orally as drinking water, (2) a low dose of D 2 O is safe for consumption, (3) it is relatively inexpensive, and (4) it freely and rapidly equilibrates with total body water in all organs, organelles, and cells within an organism . For in vivo labeling, the initial bolus of deuterated water (also referred to as heavy water) is followed by the provision of deuterium-enriched (typically around 8%) drinking water for a predetermined period.…”

Section: Introductionmentioning

confidence: 99%

“…Models for peptide turnover rate estimations often use the time course of the depletion of the monoisotopic relative isotope abundance (RIA), for which N EH serves as a parameter. In the models, the robustness of turnover rate estimation depends on the accuracy of isotope profiles in liquid chromatography coupled to mass spectrometry (LC–MS) experiments, measurement of body water enrichment (e.g., by gas chromatography coupled to mass spectrometry (GC-MS)), and the accuracy of number of labeling sites of a peptide. ,, …”

Section: Introductionmentioning

confidence: 99%

“…coupled to mass spectrometry (LC−MS) experiments, measurement of body water enrichment (e.g., by gas chromatography coupled to mass spectrometry (GC-MS) 16 ), and the accuracy of number of labeling sites of a peptide. 14,17,18 The number of labeling sites for each proteogenic amino acid was obtained from experiments 19 that labeled mice with tritium, 3 H. These numbers have been used in studies of various biological systems. However, they may be dependent on species, 5 their diet, 20 and other environmental factors.…”

Section: ■ Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Numbers of Exchangeable Hydrogens from LC–MS Data of Heavy Water Metabolically Labeled Samples

Deberneh,

Taylor,

Borowik

et al. 2024

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

Labeling with deuterium oxide (D 2 O) has emerged as one of the preferred approaches for measuring the synthesis of individual proteins in vivo. In these experiments, the synthesis rates of proteins are determined by modeling mass shifts in peptides during the labeling period. This modeling depends on a theoretical maximum enrichment determined by the number of labeling sites (N EH ) of each amino acid in the peptide sequence. Currently, N EH is determined from one set of published values. However, it has been demonstrated that N EH can differ between species and potentially tissues. The goal of this work was to determine the number of N EH for each amino acid within a given experiment to capture the conditions unique to that experiment. We used four methods to compute the N EH values. To test these approaches, we used two publicly available data sets. In a de novo approach, we compute N EH values and the label enrichment from the abundances of three mass isotopomers. The other three methods use the complete isotope profiles and body water enrichment in deuterium as an input parameter. They determine the N EH values by (1) minimizing the residual sum of squares, (2) from the mole percent excess of labeling, and (3) the time course profile of the depletion of the relative isotope abundance of monoisotope. In the test samples, the method using residual sum of squares performed the best. The methods are implemented in a tool for determining the N EH for each amino acid within a given experiment to use in the determination of protein synthesis rates using D 2 O.

show abstract

Metabolic deuterium oxide (D2O) labeling in quantitative omics studies: A tutorial review

Cited by 7 publications

References 111 publications

Rapid detection of antimicrobial resistance in methicillin-resistant Staphylococcus aureus using MALDI-TOF mass spectrometry

Rapid detection of antimicrobial resistance in methicillin-resistant Staphylococcus aureus using MALDI-TOF mass spectrometry

A large-scale LC-MS dataset of murine liver proteome from time course of heavy water metabolic labeling

Numbers of Exchangeable Hydrogens from LC–MS Data of Heavy Water Metabolically Labeled Samples

Contact Info

Product

Resources

About