Natural products are a reliable source of bioactive molecules and represent an industrial and pharmaceu-tical stake. Indeed, the model yeast species Saccharomyces cerevisiae is a well-known eukaryotic organismlargely used as a biotechnological tool, but still a topical subject of study. In this work, the exploration ofSaccharomyces cerevisiae is taken further through an untargeted metabolomics workflow. The aim is toenrich databases and bring new information about the standard S. cerevisiae strain in a given medium.Analytical methods and bioinformatics tools were combined in a high-throughput methodology useableto dereplicate many types of biological extracts and cartography secondary metabolites. Ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analyses were carriedout and spectral data were pre-processed to build molecular networks. Annotations were attributedto compounds through comparison with databases and manual investigation of networks. Ultra-high-resolution Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) brought additionalinformation thanks to a higher dynamic range and enhanced UHPLC-MS/MS results by unveiling ambi-guities and bringing accurate molecular formulae. Therefore, accurate and reliable annotated featuresresulted from the UHPLC-MS/MS data while FTICR-MS provided an overall cartography of metabolitesthanks to van Krevelen diagrams. Various small molecules such as amino acids derivatives and indolealkaloids have been determined for the first time in this yeast. The complementarity of FTICR-MS and UHPLC-MS/MS for secondary metabolite annotation brought this new mapping of S. cerevisiae.