Nowadays, proteomics is recognized as one of the fastest growing tools in many areas of research. This is especially true for the study of Saccharomyces cerevisiae, as it is considered to be a model organism for eukaryotic cells. Proteomic analysis provides an insight into global protein expressions from identification to quantitation, from localization to function, and from individual to network systems. Moreover, many methods for identification and quantitation of proteins based on tandem mass spectrometry workflows have recently been developed and widely applied in S. cerevisiae. The current methods and issues in the proteomic analysis of S. cerevisiae are reviewed here.