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Reliable identification of protein-protein interactions by crosslinking mass spectrometry

Lenz, Swantje; Sinn, Ludwig; O'Reilly, Francis; Fischer, Lutz; Wegner, Fritz; Rappsilber, Juri

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.
Published in: Nature communications, 10.1038/s41467-021-23666-z, Springer Nature