Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome

Abstract

Protein activity is the ultimate arbiter of function in most cellular pathways, and protein concentration is fundamentally connected to protein action. While the proteome of yeast has been subjected to themost comprehensive analysis of any eukaryote, existing datasets are difficult to compare, and thereis no consensus abundance value for each protein.We evaluated 21 quantitative analyses of the S.cerevisiae proteome, normalizing and converting all measurements of protein abundance into the intuitive measurement of absolute molecules per cell. We estimate the cellular abundance of 92% of the proteins in the yeast proteome and assess the variation in each abundance measurement. Using our protein abundance dataset, we find that a global response to diverse environmental stresses is not detected at the level of protein abundance, we find that protein tags have only a modest effect on protein abundance, and we identify proteins that are differentially regulated at the mRNA abundance, mRNA translation, and protein abundance levels.