PT  - JOURNAL ARTICLE
AU  - Heusel, Moritz
AU  - Bludau, Isabell
AU  - Rosenberger, George
AU  - Hafen, Robin
AU  - Frank, Max
AU  - Banaei-Esfahani, Amir
AU  - Collins, Ben C.
AU  - Gstaiger, Matthias
AU  - Aebersold, Ruedi
TI  - Complex-centric proteome profiling by SEC-SWATH-MS
AID  - 10.1101/323683
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 323683
4099  - http://biorxiv.org/content/early/2018/06/15/323683.short
4100  - http://biorxiv.org/content/early/2018/06/15/323683.full
AB  - 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 2127 protein subunits. The technique identifies novel subcomplexes 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.Introduction of the concept of complex-centric proteome profilingDevelopment of CCprofiler, a software framework for complex-centric data analysisDetection and quantification of subunit distribution of 462 distinct protein complexes containing 2127 proteins from a SEC-SWATH-MS dataset of HEK293 cells, and identification of novel complex variants such as assembly intermediatesStatistical target-decoy model to estimate accurate false discovery rates for complexes quantified by complex-centric analysisSECexplorer, an online platform to support custom complex-centric exploration of SEC-SWATH-MS datasets.