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WIREs Syst Biol Med
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Isotope labeling experiments in metabolomics and fluxomics

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Abstract Metabolomics, the study of all the small molecules in and outside a cell and fluxomics, comprising all conversion rates in a cell, are increasingly used in fundamental and applied sciences to unravel structures and activities of cellular networks and their regulation, to investigate mechanisms of diseases and toxicity, and to improve producing strains among other applications. For both fluxomics and metabolomics the application of isotopes became almost indispensable. Their use in these techniques is discussed, focusing primarily on studies applying stable isotopes and using mass spectrometry. This includes the underlying principles, experimental and computational methods used, and examples of application. WIREs Syst Biol Med 2012 doi: 10.1002/wsbm.1167 This article is categorized under: Analytical and Computational Methods > Analytical Methods Models of Systems Properties and Processes > Cellular Models Laboratory Methods and Technologies > Metabolomics

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The eukaryotic cell including the flow of information from the genome to the metabolome (white arrows) and their interaction in terms of regulation (gray arrows). The hierarchy in the network is displayed by the prefixed numbers.

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Carbon isotopomers and labeling transfer in metabolism. (a) Isotopomers of a molecule with three carbon atoms, e.g., pyruvate or alanine. Eight carbon isotopomers and four mass isotopomers are depicted. (b) Principles of carbon transfer starting with [1 −13C] glucose. Degradation of three molecules of glucose via glycolysis yields three labeled and three unlabeled C3 molecules each. Metabolism via the PPP with the loss of all the labeling information resulting in five unlabeled pyruvate molecules. Using the ratio of unlabeled and labeled pyruvate it is possible to calculate the participation of each pathway to the degradation of glucose.

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Experimental procedure in metabolomics and fluxomics and possible applications for isotopes.

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Connection of metabolome and fluxome measurements exemplified with a simple consecutive reaction with metabolites M1, M2, and M3 and rates r1 and r2. Michaelis–Menten‐type kinetics is assumed. The two horizontal lines, dashed and dotted, indicate two stationary fluxes, r1 = r2. Vertical dashed lines indicate measured metabolite concentrations, CM1. Cases a/b and a′/b′ indicate two different flux states with corresponding rates. Cases a/c and a′/c′ indicate situations with lower concentration of CM2 and higher expression of the enzyme catalyzing reaction 2.

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