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There is a growing demand for functional foodstuffs naturally rich in nutrients and bioactive compounds associated with putative health benefits. This study followed a strategy integrating metabolomic with chemometric to identify quality markers that can be used to distinguish function related bioactivity of fruits, using hawthorn (Crataegus cuneata) fruit as an example. The integrated strategy was reduced to characterization of metabolic processes and discovered potential bioactive ingredients that were further investigated for function