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A metabolomics approach combining ¹H NMR and gas chromatography−electrospray ionization time-of-flight mass spectrometry (GC−EI-TOFMS) profiling was employed to characterize melon (Cucumis melo L.) fruit. In a first step, quantitative ¹H NMR of polar extracts and principal component analyses (PCA) of the corresponding data highlighted the major metabolites in fruit flesh, including sugars, organic acids, and amino acids. In a second step, the spatial localization of metabolites was investigated using both analytical techniques. Direct ¹H NMR profiling of juice or GC−EI-TOFMS profiling of tissue extracts collected from different locations in the fruit flesh provided information on advantages and drawbacks of each technique for the analysis of a sugar-rich matrix such as fruit. ¹H NMR and GC−EI-TOFMS data sets were compared using independently performed PCA and multiblock hierarchical PCA (HPCA …