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Protein microarrays are the arrays of protein, or in the case of yeast, nearly the entire proteome, which will expedite the study of the proteome by providing a platform to elucidate a protein's function and the way it relates to other proteins on a global scale. This chapter discusses many challenges and options that exist in designing a yeast protein array and the many questions that have been addressed using this technology, predominantly in the form of functional protein microarrays. All technologies involving proteins are challenged by the large scale of the proteome and the difficulty in working with proteins, given that their chemistry and solubility are much more variable. The goals of proteomics and a sample of the common technologies applied to each are listed in tabulated form in the chapter. Many techniques have been used to address different aspects of these goals. Mass spectrometry has …