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When organisms encounter external stimuli such as hypoxia, altered nutritional states, or pharmacological interventions, their metabolic networks often undergo systemic reorganisation, manifesting as significant alterations in the levels of characteristic small-molecule metabolites. Such changes not only reflect the dynamic regulatory processes by which cells respond to environmental challenges but also reveal the synergistic and reprogramming mechanisms between metabolic pathways. Endogenous metabolites occupy a central position in the analysis of metabolic pathways, enzyme kinetic studies, and the exploration of molecular mechanisms underlying physiological homeostasis. Whether elucidating the coupling between glycolysis and mitochondrial function or tracing the regulatory role of amino acid metabolism in signal transduction, these endogenous molecules serve as critical reference markers. They assist researchers in integrating genomic, transcriptomic, and proteomic data within a systems biology framework, thereby constructing a more comprehensive, dynamic, and hierarchically structured biological landscape.
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