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.

功能基因组学策略现已成为注释基因功能与调控网络的核心支撑手段。本研究将功能基因组学与蛋白质组学相结合，采用数据非依赖采集质谱（data-independent acquisition mass spectrometry）技术，对酿酒酵母（Saccharomyces cerevisiae）的全基因组规模基因敲除文库中的蛋白质丰度开展定量分析。由此构建了一套大规模、系统性的定量蛋白质组学数据集：在4699株酵母基因敲除菌株中，平均可定量到2520种蛋白质。该蛋白质组图谱涵盖超1亿条肽段定量数据与900万条蛋白质定量数据。这些数据可将敲除基因与蛋白质建立关联，并为酿酒酵母79%的编码基因组提供了全基因组规模的分子表型资源。