The compositional space of a set of 120 diverse beer samples was profiled by rapid flow-injection analysis (FIA) Fourier transform ion cyclotron mass spectrometry (FTICR-MS). By the unrivaled mass resolution, it was possible to uncover and assign compositional information to thousands of yet unknown metabolites in the beer matrix. The application of several statistical models enabled the assignment of different molecular pattern to certain beer attributes such as the beer type, the way of adding hops and the grain used. The dedicated van Krevelen diagrams and mass difference networks displayed the structural connectivity of the annotated sum formulae. Thereby it was possible to provide a base of knowledge of the beer metabolome far above database-dependent annotations. Typical metabolic signatures for beer types, which reflect differences in ingredients and ways of brewing, could be extracted. Besides, the complexity of isomeric compounds, initially profiled as single mass values in fast FIA-FTICR-MS, was resolved by selective UHPLC-ToF-MS2 analysis. Thereby structural hypotheses based on FTICR’s sum formulae could be confirmed. Benzoxazinoid hexosides deriving from the wheat’s secondary metabolism were uncovered as suitable marker substances for the use of whole wheat grains, in contrast to merely wheat starch or barley. Furthermore, it was possible to describe Hydroxymethoxybenzoxazinone(HMBOA)-hexosesulfate as a hitherto unknown phytoanticipin derivative in wheat containing beers. These findings raise the potential of ultrahigh resolution mass spectrometry for rapid quality control and inspection purposes as well as deep metabolic profiling, profound search for distinct hidden metabolites and classification of archeological beer samples.