DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes.

Autor: Frommelt F; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. fabian.frommelt@hotmail.com., Fossati A; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.; J. David Gladstone Institutes, San Francisco, CA, USA., Uliana F; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.; Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland., Wendt F; Department of Health Sciences and Technology (D-HEST), Institute of Translational Medicine (ITM), ETH Zurich, Zurich, Switzerland., Xue P; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.; Guangzhou National Laboratory, Guang Zhou, China., Heusel M; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland., Wollscheid B; Department of Health Sciences and Technology (D-HEST), Institute of Translational Medicine (ITM), ETH Zurich, Zurich, Switzerland., Aebersold R; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland., Ciuffa R; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland., Gstaiger M; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. matthias.gstaiger@imsb.biol.ethz.ch.
Jazyk: angličtina
Zdroj: Nature methods [Nat Methods] 2024 Apr; Vol. 21 (4), pp. 635-647. Date of Electronic Publication: 2024 Mar 26.
DOI: 10.1038/s41592-024-02211-y
Abstrakt: Most proteins are organized in macromolecular assemblies, which represent key functional units regulating and catalyzing most cellular processes. Affinity purification of the protein of interest combined with liquid chromatography coupled to tandem mass spectrometry (AP-MS) represents the method of choice to identify interacting proteins. The composition of complex isoforms concurrently present in the AP sample can, however, not be resolved from a single AP-MS experiment but requires computational inference from multiple time- and resource-intensive reciprocal AP-MS experiments. Here we introduce deep interactome profiling by mass spectrometry (DIP-MS), which combines AP with blue-native-PAGE separation, data-independent acquisition with mass spectrometry and deep-learning-based signal processing to resolve complex isoforms sharing the same bait protein in a single experiment. We applied DIP-MS to probe the organization of the human prefoldin family of complexes, resolving distinct prefoldin holo- and subcomplex variants, complex-complex interactions and complex isoforms with new subunits that were experimentally validated. Our results demonstrate that DIP-MS can reveal proteome modularity at unprecedented depth and resolution.
(© 2024. The Author(s).)
Databáze: MEDLINE
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