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Complex-centric pro...
Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes
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- Bludau, Isabell (author)
- Max Planck Institute of Biochemistry,ETH Zürich
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- Heusel, Moritz (author)
- Lund University,Lunds universitet,Infection Medicine Proteomics,Forskargrupper vid Lunds universitet,Lund University Research Groups,ETH Zürich
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- Frank, Max (author)
- ETH Zürich,European Molecular Biology Laboratory Heidelberg
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- Rosenberger, George (author)
- ETH Zürich,Columbia University
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- Hafen, Robin (author)
- ETH Zürich
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- Banaei-Esfahani, Amir (author)
- ETH Zürich
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- van Drogen, Audrey (author)
- ETH Zürich
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- Collins, Ben C. (author)
- Queen's University Belfast,ETH Zürich
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- Gstaiger, Matthias (author)
- ETH Zürich
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- Aebersold, Ruedi (author)
- ETH Zürich,University of Zurich
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(creator_code:org_t)
- 2020-07-20
- 2020
- English 46 s.
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In: Nature Protocols. - : Springer Science and Business Media LLC. - 1754-2189 .- 1750-2799. ; 15:8, s. 2341-2386
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Abstract
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- Most catalytic, structural and regulatory functions of the cell are carried out by functional modules, typically complexes containing or consisting of proteins. The composition and abundance of these complexes and the quantitative distribution of specific proteins across different modules are therefore of major significance in basic and translational biology. However, detection and quantification of protein complexes on a proteome-wide scale is technically challenging. We have recently extended the targeted proteomics rationale to the level of native protein complex analysis (complex-centric proteome profiling). The complex-centric workflow described herein consists of size exclusion chromatography (SEC) to fractionate native protein complexes, data-independent acquisition mass spectrometry to precisely quantify the proteins in each SEC fraction based on a set of proteotypic peptides and targeted, complex-centric analysis where prior information from generic protein interaction maps is used to detect and quantify protein complexes with high selectivity and statistical error control via the computational framework CCprofiler (https://github.com/CCprofiler/CCprofiler). Complex-centric proteome profiling captures most proteins in complex-assembled state and reveals their organization into hundreds of complexes and complex variants observable in a given cellular state. The protocol is applicable to cultured cells and can potentially also be adapted to primary tissue and does not require any genetic engineering of the respective sample sources. At present, it requires ~8 d of wet-laboratory work, 15 d of mass spectrometry measurement time and 7 d of computational analysis.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Cell- och molekylärbiologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Cell and Molecular Biology (hsv//eng)
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- By the author/editor
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Bludau, Isabell
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Heusel, Moritz
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Frank, Max
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Rosenberger, Geo ...
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Hafen, Robin
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Banaei-Esfahani, ...
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show more...
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van Drogen, Audr ...
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Collins, Ben C.
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Gstaiger, Matthi ...
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Aebersold, Ruedi
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show less...
- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Cell and Molecul ...
- Articles in the publication
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Nature Protocols
- By the university
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Lund University