Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition
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 pur...
| Main Authors: | , , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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Nature Publishing Group
2015
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| Online Access: | http://hdl.handle.net/1721.1/96689 https://orcid.org/0000-0003-1307-882X |
| _version_ | 1811096103732379648 |
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| author | Lambert, Jean-Philippe Ivosev, Gordana Couzens, Amber L Larsen, Brett Taipale, Mikko Lin, Zhen-Yuan Zhong, Quan Lindquist, Susan Vidal, Marc Aebersold, Ruedi Pawson, Tony Bonner, Ron Tate, Stephen Gingras, Anne-Claude |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Lambert, Jean-Philippe Ivosev, Gordana Couzens, Amber L Larsen, Brett Taipale, Mikko Lin, Zhen-Yuan Zhong, Quan Lindquist, Susan Vidal, Marc Aebersold, Ruedi Pawson, Tony Bonner, Ron Tate, Stephen Gingras, Anne-Claude |
| author_sort | Lambert, Jean-Philippe |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T16:38:18Z |
| format | Article |
| id | mit-1721.1/96689 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T16:38:18Z |
| publishDate | 2015 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/966892022-09-29T20:28:59Z Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition Lambert, Jean-Philippe Ivosev, Gordana Couzens, Amber L Larsen, Brett Taipale, Mikko Lin, Zhen-Yuan Zhong, Quan Lindquist, Susan Vidal, Marc Aebersold, Ruedi Pawson, Tony Bonner, Ron Tate, Stephen Gingras, Anne-Claude Massachusetts Institute of Technology. Department of Biology Lindquist, Susan 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. 2015-04-21T18:50:58Z 2015-04-21T18:50:58Z 2013-10 2013-02 Article http://purl.org/eprint/type/JournalArticle 1548-7091 1548-7105 http://hdl.handle.net/1721.1/96689 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. https://orcid.org/0000-0003-1307-882X en_US http://dx.doi.org/10.1038/nmeth.2702 Nature Methods 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. application/pdf Nature Publishing Group PMC |
| spellingShingle | Lambert, Jean-Philippe Ivosev, Gordana Couzens, Amber L Larsen, Brett Taipale, Mikko Lin, Zhen-Yuan Zhong, Quan Lindquist, Susan Vidal, Marc Aebersold, Ruedi Pawson, Tony Bonner, Ron Tate, Stephen Gingras, Anne-Claude Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition |
| title | Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition |
| title_full | Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition |
| title_fullStr | Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition |
| title_full_unstemmed | Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition |
| title_short | Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition |
| title_sort | mapping differential interactomes by affinity purification coupled with data independent mass spectrometry acquisition |
| url | http://hdl.handle.net/1721.1/96689 https://orcid.org/0000-0003-1307-882X |
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