Various non-targeted approaches have already shed light on the thousands of compounds that are present at various concentrations in grape and wine. Among them, direct injection Ion Cyclotron Resonance Fourier Transform Mass Spectrometry (FTICR-MS) undoubtedly provides the most comprehensive chemical fingerprints, based on unrivalled resolution on mass measurement, but limited to structural assumptions. Here, we show that the combination of FTICR-MS and Ultra-Performance Liquid Chromatography Mass Spectrometry (UPLC-QTOF-MS), which increases the scope of detectable unknown metabolites and allows the separation between isomers, provides an unprecedented synoptic characterization of the chemical complexity of wines, where results obtained with one platform can directly be validated with data from the other. To that respect, wine ageing appears to be particularly interesting when related to the oeno-diagenesis processes that operate in bottle, and which depend on the actual initial composition of the wine. Applied to Pinot noir red wines from three different appellations in Burgundy, and over three vintages (1979, 1989, 1999), this approach revealed that the ageing chemistry is fundamentally driven by the metabolic baggage at bottling, characterized here by thousands of compounds from various chemical families including carbohydrates, amino acids, or polyphenols, but with a remarkably high distribution of nitrogen and sulfur-containing compounds.