Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

• Published in: Nature methods Vol. 10; no. 12; pp. 1246 - 1253
• Main Authors: Collins, Ben C, Gillet, Ludovic C, Rosenberger, George, Röst, Hannes L, Vichalkovski, Anton, Gstaiger, Matthias, Aebersold, Ruedi
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.12.2013; Nature Publishing Group
• Subjects: 14-3-3 Proteins - chemistry; 631/1647/2067; 631/1647/527/296; 631/45/475/2290; 631/553; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical Engineering/Biotechnology; Chromatography, Affinity - methods; Computational Biology - methods; Gene Library; HEK293 Cells; Humans; Insulin; Interactomes; Life Sciences; Mass spectrometry; Mass Spectrometry - methods; Mechanistic Target of Rapamycin Complex 1; Mechanistic Target of Rapamycin Complex 2; Methods; Multiprotein Complexes - chemistry; Peptides - chemistry; Phosphatidylinositol 3-Kinases - chemistry; Physiological aspects; Protein Binding; Protein Interaction Mapping - methods; Protein research; Proteins; Proteins - chemistry; Proteomics; Proteomics - methods; Signal Transduction; Time Factors; TOR Serine-Threonine Kinases - chemistry; Switzerland
• ISSN: 1548-7091; 1548-7105
• DOI: 10.1038/nmeth.2703

Dynamic changes to the 14-3-3 protein interactome are robustly followed over time using affinity-purification data-independent analysis–based mass spectrometry. Also in this issue, Lambert et al . describe a similar method. 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.