Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes

Nature Protocols
Isabell BludauRuedi Aebersold

Abstract

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 ...Continue Reading

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Citations

Feb 24, 2021·Emerging Topics in Life Sciences·Amanda L Smythers, Leslie M Hicks
Mar 31, 2021·The Plant Journal : for Cell and Molecular Biology·Devang MehtaR Glen Uhrig
May 1, 2021·International Journal of Molecular Sciences·Isabell Bludau
May 4, 2021·Biochimica Et Biophysica Acta. Bioenergetics·Hendrik Nolte, Thomas Langer
May 29, 2021·Cellular and Molecular Life Sciences : CMLS·Teck Yew LowChris Soon Heng Tan
Jun 18, 2021·Cell Systems·Leah V Schaffer, Trey Ideker
Jun 23, 2021·Nature Communications·Isabell BludauRuedi Aebersold
Jul 3, 2021·Cell·Michael A SkinniderLeonard J Foster
Nov 5, 2020·Analytical Chemistry·Jiangnan ZhengRuijun Tian
Sep 10, 2021·Expert Review of Proteomics·Lindsay Pino, Birgit Schilling

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Methods Mentioned

BETA
affinity-purification
size exclusion chromatography
affinity purification
electron microscopy
electrophoresis
ion-exchange chromatography
protein assay

Software Mentioned

OpenSWATH docker
MS
PrInCe
script
wget
SWATH
EPIC
R
ComplexCentricAnalysis
package

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