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

Moritz Heusel1,2, Isabell Bludau1,3, George Rosenberger1

  • 1Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.

Molecular Systems Biology
|January 16, 2019
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Summary
This summary is machine-generated.

Researchers developed a new method to quantify hundreds of protein complexes using size exclusion chromatography and mass spectrometry. This technique maps protein complex organization and subunit distribution in the HEK293 proteome.

Keywords:
SWATH‐MSprotein complexesproteome organizationproteomicssize exclusion chromatography

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Area of Science:

  • Proteomics
  • Systems Biology
  • Biochemistry

Background:

  • Proteins function through interactions, forming macromolecular complexes.
  • Understanding protein complex organization and subunit distribution is crucial for biological and clinical insights.

Purpose of the Study:

  • To present an integrated experimental and computational technique for quantifying numerous protein complexes simultaneously.
  • To analyze the HEK293 cell line proteome to identify and quantify protein complexes and their subunit composition.

Main Methods:

  • Size exclusion chromatography (SEC) for native protein complex fractionation.
  • SWATH/DIA mass spectrometry for precise protein quantification in SEC fractions.
  • CCprofiler computational framework for error-controlled, complex-centric analysis using protein interaction maps.

Main Results:

  • Delineation of 462 protein complexes comprising 2,127 subunits in the HEK293 proteome.
  • Identification of novel sub-complexes and assembly intermediates within central regulatory complexes.
  • Assessment of quantitative subunit distribution across identified protein complexes.

Conclusions:

  • The developed technique enables comprehensive quantification of protein complex organization.
  • CCprofiler and SECexplorer provide accessible tools for proteome modularity exploration.
  • This approach advances the study of cellular organization and regulatory mechanisms.