Reliable identification of protein-protein interactions by crosslinking mass spectrometry

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

Research output: Contribution to journalArticlepeer-review

Abstract

Protein-protein interactions govern most cellular pathways and processes, and multiplete chnologies 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.
Original languageEnglish
JournalNature Communications
Publication statusAccepted/In press - 28 Apr 2021

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