The Proteomic Landscape of Genome-Wide Genetic Perturbations

Published: 17 April 2023| Version 1 | DOI: 10.17632/w8jtmnszd9.1
Christoph Messner, Georg Kustatscher, Markus Ralser


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.


Steps to reproduce

Raw mass spectrometry data have been deposited to the ProteomeXchange Consortium ( via the massIVE repository with the dataset identifier ProteomeXchange: PXD036062. For a detailed description of the methods please refer to Messner et al., Cell, 2023.


Universitat Zurich, Charite Universitatsmedizin Berlin, The University of Edinburgh, Francis Crick Institute


Systems Biology, Proteomics