The Proteomic Landscape of Genome-Wide Genetic Perturbations

Functional genomic strategies have become fundamental for annotating gene function and regulatory networks. Here, we combined functional genomics with proteomics by quantifying protein abundances in a genome-scale knock-out library in Saccharomyces cerevisiae, using data-independent acquisition mass spectrometry. We thus created a large, systematic, and quantitative proteomic dataset, with an average of 2,520 proteins quantified across 4,699 yeast gene knock-out strains. The proteome profiles comprise over 100 million peptide quantitations and 9 million protein quantitations. These link deleted genes to proteins and provide a genome-scale resource of molecular phenotypes for 79% of the coding yeast genome.