Complex‐centric proteome profiling by SEC‐SWATH‐MS
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Abstract
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.
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“…the experimental procedure, most notably upon dilution imposed during lysis and subsequent size exclusion chromatography, reducing protein concentration by ca. five orders of magnitude from the cellular environment ( ca. 300 mg/ml; Milo, 2013) to the conditions on the SEC column ( ca. 0.06 mg/ml).”
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Self-citation
- Authors
- Heusel, M., Bludau, I., Rosenberger, G., Hafen, R., Frank, M., Banaei‐Esfahani, A., van Drogen, A., Collins, B. C., Gstaiger, M., & Aebersold, R.
- Affiliations
- University of Zurich (CH)
- ETH Zurich (CH)
- Corresponding author
- Gstaiger, Matthias
- Aebersold, Ruedi
- ORCID
- Venue
- Molecular Systems Biology
- Published
- 2019-01-01
- Volume
- 15
- Issue
- 1
- Pages
- e8438-e8438
- ISSN
- 1744-4292 (ISSN-L)
- PMC
- PMC6346213
- OpenAlex
- W2951603212
- Cited by
- 141
- References
- 66
- Citations by year
- 2026: 7 · 2025: 12 · 2024: 22 · 2023: 19 · 2022: 17 · 2021: 24 · 2020: 26 · 2019: 13 · 2018: 1
- FWCI
- 7.97
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Molecular Systems Biology (publishedVersion, other-oa)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research Portal (Queen's University Belfast) (publishedVersion, cc-by)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- ETH Zürich Research Collection (cc-by)
- Funders
- H2020 European Research Council (ERC‐20140AdG 670821)
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (PZ00P3_161435, 31003A_166435)
- National Institutes of Health (U19 AI106761)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Keywords
- protein complexes, size exclusion chromatography, SWATH mass spectrometry, data-independent acquisition, protein interaction maps, subcomplexes, assembly intermediates
- MeSH terms
- Algorithms, Chromatography, Gel, Humans, Mass Spectrometry, Computational Biology, Proteome, Proteomics, Multiprotein Complexes, HEK293 Cells, Protein Interaction Maps
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