Reliable identification of protein-protein interactions by crosslinking mass spectrometry

Swantje Lenz, Ludwig R. Sinn, Francis J. O’Reilly, Lutz Fischer, Fritz Wegner and Juri Rappsilber ()
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Swantje Lenz: Technische Universität Berlin
Ludwig R. Sinn: Technische Universität Berlin
Francis J. O’Reilly: Technische Universität Berlin
Lutz Fischer: Technische Universität Berlin
Fritz Wegner: Technische Universität Berlin
Juri Rappsilber: Technische Universität Berlin

Nature Communications, 2021, vol. 12, issue 1, 1-11

Abstract: Abstract Protein-protein interactions govern most cellular pathways and processes, and multiple technologies have emerged to systematically map them. Assessing the error of interaction networks has been a challenge. Crosslinking mass spectrometry is currently widening its scope from structural analyses of purified multi-protein complexes towards systems-wide analyses of protein-protein interactions (PPIs). Using a carefully controlled large-scale analysis of Escherichia coli cell lysate, we demonstrate that false-discovery rates (FDR) for PPIs identified by crosslinking mass spectrometry can be reliably estimated. We present an interaction network comprising 590 PPIs at 1% decoy-based PPI-FDR. The structural information included in this network localises the binding site of the hitherto uncharacterised protein YacL to near the DNA exit tunnel on the RNA polymerase.

Date: 2021
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DOI: 10.1038/s41467-021-23666-z

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