title: Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system.
abstract: Protein complexes and protein interaction networks are essential mediators of most biological functions. Complexes supporting transient functions such as signal transduction processes are frequently subject to dynamic remodeling. Currently, the majority of studies on the composition of protein complexes are carried out by affinity purification and mass spectrometry (AP-MS) and present a static view of the system. For a better understanding of inherently dynamic biological processes, methods to reliably quantify temporal changes of protein interaction networks are essential. Here we used affinity purification combined with sequential window acquisition of all theoretical spectra (AP-SWATH) mass spectrometry to study the dynamics of the 14-3-3β scaffold protein interactome after stimulation of the insulin-PI3K-AKT pathway. The consistent and reproducible quantification of 1,967 proteins across all stimulation time points provided insights into the 14-3-3β interactome and its dynamic changes following IGF1 stimulation. We therefore establish AP-SWATH as a tool to quantify dynamic changes in protein-complex interaction networks.
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors.forename: Ben C
authors.initials: BC
authors.lastname: Collins
authors.forename: Ludovic C
authors.initials: LC
authors.lastname: Gillet
authors.forename: George
authors.initials: G
authors.lastname: Rosenberger
authors.forename: Hannes L
authors.identifier: 0000000309907488
authors.initials: HL
authors.lastname: Röst
authors.forename: Anton
authors.initials: A
authors.lastname: Vichalkovski
authors.forename: Matthias
authors.initials: M
authors.lastname: Gstaiger
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D048948:14-3-3 Proteins / Q000737:chemistry*; D002846:Chromatography, Affinity / Q000379:methods; D019295:Computational Biology / Q000379:methods; D015723:Gene Library; D057809:HEK293 Cells; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D000076222:Mechanistic Target of Rapamycin Complex 1; D000076225:Mechanistic Target of Rapamycin Complex 2; D046912:Multiprotein Complexes / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D019869:Phosphatidylinositol 3-Kinases / Q000737:chemistry; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry; D040901:Proteomics / Q000379:methods; D015398:Signal Transduction; D058570:TOR Serine-Threonine Kinases / Q000737:chemistry; D013997:Time Factors
chemical_list: D048948:14-3-3 Proteins; D000076222:Mechanistic Target of Rapamycin Complex 1; D000076225:Mechanistic Target of Rapamycin Complex 2; D046912:Multiprotein Complexes; D010455:Peptides; D019869:Phosphatidylinositol 3-Kinases; D011506:Proteins; D058570:TOR Serine-Threonine Kinases