Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition
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Lindquist_Mapping differential.pdf
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Author(s)
Lambert, Jean-Philippe
Ivosev, Gordana
Couzens, Amber L
Larsen, Brett
Taipale, Mikko
Lin, Zhen-Yuan
Zhong, Quan
Lindquist, Susan
Vidal, Marc
Aebersold, Ruedi
Date Issued
October 2013
Journal
Nature Methods
Publisher
Nature Publishing Group
Citation
Lambert, Jean-Philippe, Gordana Ivosev, Amber L Couzens, Brett Larsen, Mikko Taipale, Zhen-Yuan Lin, Quan Zhong, et al. “Mapping Differential Interactomes by Affinity Purification Coupled with Data-Independent Mass Spectrometry Acquisition.” Nature Methods 10, no. 12 (October 27, 2013): 1239–1245.
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Author's final manuscript
Abstract
Characterizing changes in protein-protein interactions associated with sequence variants (e.g., disease-associated mutations or splice forms) or following exposure to drugs, growth factors or hormones is critical to understanding how protein complexes are built, localized and regulated. Affinity purification (AP) coupled with mass spectrometry permits the analysis of protein interactions under near-physiological conditions, yet monitoring interaction changes requires the development of a robust and sensitive quantitative approach, especially for large-scale studies in which cost and time are major considerations. We have coupled AP to data-independent mass spectrometric acquisition (sequential window acquisition of all theoretical spectra, SWATH) and implemented an automated data extraction and statistical analysis pipeline to score modulated interactions. We used AP-SWATH to characterize changes in protein-protein interactions imparted by the HSP90 inhibitor NVP-AUY922 or melanoma-associated mutations in the human kinase CDK4. We show that AP-SWATH is a robust label-free approach to characterize such changes and propose a scalable pipeline for systems biology studies.
MIT Department
Massachusetts Institute of Technology. Department of Biology
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Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
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DOI of Published Version
https://doi.org/10.1038/nmeth.2702
