Direct injection Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), and ultra-high performance liquid chromatography coupled to mass spectrometry (UPLC-MS) were combined for the non-targeted analysis of wine metabolites. The unrivalled resolution on mass measurement allowed by the former and the separation ability of isomeric and isobaric substances by the latter, clearly increases the scope of detectable unknown metabolites in wines. Such methodology is illustrated through the comparison of chemical spaces of a young and an older Pinot noir wine. RP and HILIC chromatography could reveal up to five isomers for a given mass, throughout the explored mass range. CHO, CHOS and CHONS chemical spaces exhibited higher diversities in the older wine, illustrating a molecular oeno-diagenesis process during wine ageing, whereas nitrogen-containing compounds (CHON chemical space) appeared to be fewer in the older wine, likely due to precipitation. This methodological combination is a promising contribution to the wine metabolomics toolkit.