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Mol Syst Biol. 2019 Jan 14;15(1):e8438. doi: 10.15252/msb.20188438.

Complex-centric proteome profiling by SEC-SWATH-MS.

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Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
PhD Program in Molecular and Translational Biomedicine of the Competence Center Personalized Medicine UZH/ETH, Zurich, Switzerland.
PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland.
Department of Computer Science, ETH Zurich, Zurich, Switzerland.
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
Faculty of Science, University of Zurich, Zurich, Switzerland.


Proteins are major effectors and regulators of biological processes that can elicit multiple functions depending on their interaction with other proteins. The organization of proteins into macromolecular complexes and their quantitative distribution across these complexes is, therefore, of great biological and clinical significance. In this paper, we describe an integrated experimental and computational technique to quantify hundreds of protein complexes in a single operation. The method consists of size exclusion chromatography (SEC) to fractionate native protein complexes, SWATH/DIA mass spectrometry to precisely quantify the proteins in each SEC fraction, and the computational framework CCprofiler to detect and quantify protein complexes by error-controlled, complex-centric analysis using prior information from generic protein interaction maps. Our analysis of the HEK293 cell line proteome delineates 462 complexes composed of 2,127 protein subunits. The technique identifies novel sub-complexes and assembly intermediates of central regulatory complexes while assessing the quantitative subunit distribution across them. We make the toolset CCprofiler freely accessible and provide a web platform, SECexplorer, for custom exploration of the HEK293 proteome modularity.


SWATH‐MS; protein complexes; proteome organization; proteomics; size exclusion chromatography

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