Beer is one of humankind’s oldest biotechnologies, and remains a key industry in Australia and internationally. The process of beer production involves agricultural ingredients with substantial varietal and environmental variability, and a series of bioprocessing steps. We have used mass spectrometry proteomics to investigate the complexity of the proteome throughout the course of beer production. This has uncovered a highly dynamic proteome with a wealth of post-translational modifications including proteolysis, glycosylation, and glycation that together with the bioprocess parameters control the final beer proteome. A key step in beer production is fermentation, where yeast convert sugars to ethanol and carbon dioxide. We have studied the diversity in the cell wall and global proteomes of standard brewing yeasts and wild Australian yeasts to better understand their performance in commercial brewing settings. We see great potential for the use of MS proteomics and related systems biology approaches in understanding and improving the ancient art of beer making.