Comparative analysis of protein abundance studies to quantify the Saccharomyces cerevisiae proteome

Abstract

Global gene expression and proteomics tools have allowed large-scale analyses of the transcriptome and proteome in eukaryotic cells. These tools have enabled studies of protein abundance changes that occur in cells under stress conditions, providing insight into regulatory programs required for cellular adaptation. While the proteome of yeast has been subjected to the most comprehensive analysis of any eukary-ote, each of the existing datasets is separate and reported in different units. A comparison of all the available protein abundance data sets is key towards developing a complete understanding of the yeast proteome. We evaluated 19 quantitative proteomic analyses performed under normal and stress conditions and normalized and converted all measurements of protein abundance into absolute molecules per cell. Our analysis yields an estimate of the cellular abundance of 97% of the proteins in the yeast proteome, as well as an assessment of the variation in each abundance measurement. We evaluate the variance and sensitivity associated with different measurement methods. We find that C-terminal tagging of proteins, and the accompanying alterations to the 3 untranslated regions of the tagged genes, has little effect on protein abundance. Finally, our normalization of diverse datasets facilitates comparisons of protein abundance remodeling of the proteome during cellular stresses.