We conducted a study coupling metabolomics and mass isotopomer analysis of liver gluconeogenesis and citric acid cycle. Rat livers were perfused with lactate or pyruvate ؎ aminooxyacetate or mercaptopicolinate in the presence of 40% enriched NaH 13 CO 3 . Other livers were perfused with dimethyl [1,4-13 C 2 ]succinate ؎ mercaptopicolinate. In this first of two companion articles, we show that a substantial fraction of gluconeogenic carbon leaves the liver as citric acid cycle intermediates, mostly ␣-ketoglutarate. The efflux of gluconeogenic carbon ranges from 10 to 200% of the rate of liver gluconeogenesis. This cataplerotic efflux of gluconeogenic carbon may contribute to renal gluconeogenesis in vivo. Multiple crossover analyses of concentrations of gluconeogenic intermediates and redox measurements expand previous reports on the regulation of gluconeogenesis and the effects of inhibitors. We also demonstrate the formation of adducts from the condensation, in the liver, of (i) aminooxyacetate with pyruvate, ␣-ketoglutarate, and oxaloacetate and (ii) mercaptopicolinate and pyruvate. These adducts may exert metabolic effects unrelated to their effect on gluconeogenesis.Although hypothesis-based research is the gold standard of biological investigation, it is necessary from time to time to expand its scope by a period of data-based discovery research. The current omic revolution is fulfilling this need. By widening the knowledge base, omics and in particular metabolomics (1-5) identify unknown correlations, allowing the formulation and testing of new hypotheses. We hypothesized that the scope of metabolomics could be enhanced by associating it with mass isotopomer analysis, a powerful technique developed over the past 16 years (reviewed in Refs. 6, 7). This association would allow the identification of unexpected labeling patterns of metabolites, pointing to unknown reactions and/or regulatory mechanisms (8). We used this association of techniques to expand our previous studies on the influence of metabolic zonation of the liver on the labeling patterns of metabolites and on metabolic rates calculated from these labeling patterns.Over the past 12 years, questions were raised on the potential influence of the metabolic zonation of the liver (9) on the 13 Clabeling pattern of glucose released by gluconeogenesis (GNG), 2 glycogenolysis, or both. The zonated structure of the liver results in translobular gradients of enzyme activities and of blood substrate concentrations (glycerol, acetate, and NH 4 ϩ ) (10 -12). Also, the computation of the mass isotopomer distribution (MID) of (i) glucose labeled from [ (10,13,14). This results in underestimations of fractional rates of glucose, fatty acid, and sterol synthesis calculated from the MID of these compounds synthesized from a 13 C-labeled substrate. In this study, we hypothesized that the metabolic zonation of the liver might result in incompatible labeling of intermediates extracted from the whole liver. Such incompatibilities were suggested in 1970 by Veneziale et...