Researchers in Zurich present a method for determining protein fold change in highly complex samples using SWATH® Acquisition for high quality quantitation.
Nature Methods features SWATH®-based research in two articles (11.2013)
Two publications in the November issue of Nature Methods demonstrate the power of SWATH® Acquisition combined with affinity purification. The result is an effective tool to quantify dynamic changes in protein complex interaction networks, which is critical for identifying targeted treatments for cancer mutations, diabetes and numerous diseases.
In the University of Toronto-based study, SWATH® provided a scalable pipeline for system biology studies that involved tracking changes in protein networks associated with melanoma. The Swiss Federal Institute of Technology study in Zurich used SWATH® to quantify approximately 2000 proteins across 15 different samples to better understand the dynamics of insulin pathways.
Dr. Ruedi Aebersold (ETH, Zurich), who contributed to both studies, told ProteoMonitor that the results suggest DIA methods like SWATH® enable tracking in protein complexes across many proteins with better dynamic range and accuracy compared to shotgun methods.
Each study was conducted on an SCIEX 5600 TripleTOF® System. Abstracts from papers are below:-
Quantifying protein interaction dynamics by SWATH® mass spectometry: application to the 14-3-3 system Ben C. Collins, Ludovic C. Gillet, George Rosenberger, Hannes L. Röst, Anton Vichalkovski, Matthias Gstaiger, and Ruedi Aebersold
To better understand inherently dynamic biological processes, methods to reliably quantify temporal changes of protein interaction networks are essential.
Mapping differential interactomes by affinity purification coupled with data independent mass spectrometry acquisition Jean-Philippe Lambert, Gordana Ivosev, Amber L. Couzens, Brett Larsen, Mikko Taipale, Zhen-Yuan Lin,Quan Zhong, Susan Lindquist, Marc Vidal, Ruedi Aebersold, Tony Pawson, Ron Bonner, Stephen Tate and Anne-Claude Gingras
Characterizing changes in protein-protein interactions is critical to understanding how protein complexes are built, localized and regulated; yet monitoring interaction changes requires the development of a robust and sensitive quantitative approach, especially for large-scale studies where cost and time are major considerations. Read more ...
SWATH® Takes Center Stage at HUPO 2013
TOKYO - Dr. Christie Hunter of SCIEX, recipient of the HUPO '13 Science and TechnologyAward, presented The Evolution of Targeted Proteomics, from Art Form to Assay - a 10-year retrospective on the evolution of targeted proteomics. Major advances in mass spectrometry, she explained, have enabled effective synergies between non-targeted analysis approaches like MS and MS/MS, and targeted methods, of which MRM and MS/MS has become the de facto standard.