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Large-scale mapping of human protein-protein interactions by mass spectrometry

Large-scale mapping of human protein-protein interactions by mass spectrometry
Large-scale mapping of human protein-protein interactions by mass spectrometry
Mapping protein-protein interactions is an invaluable tool for understanding protein function. Here, we report the first large-scale study of protein-protein interactions in human cells using a mass spectrometry-based approach. The study maps protein interactions for 338 bait proteins that were selected based on known or suspected disease and functional associations. Large-scale immunoprecipitation of Flag-tagged versions of these proteins followed by LC-ESI-MS/MS analysis resulted in the identification of 24,540 potential protein interactions. False positives and redundant hits were filtered out using empirical criteria and a calculated interaction confidence score, producing a data set of 6463 interactions between 2235 distinct proteins. This data set was further cross-validated using previously published and predicted human protein interactions. In-depth mining of the data set shows that it represents a valuable source of novel protein-protein interactions with relevance to human diseases. In addition, via our preliminary analysis, we report many novel protein interactions and pathway associations.
1744-4292
89
Ewing, Rob M.
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Chu, Peter
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Elisma, Fred
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Li, Hongyan
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Taylor, Paul
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Climie, Shane
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McBroom-Cerajewski, Linda
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Robinson, Mark D.
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O'Connor, Liam
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Li, Michael
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Taylor, Rod
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Dharsee, Moyez
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Ho, Yuen
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Heilbut, Adrian
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Moore, Lynda
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Zhang, Shudong
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Ornatsky, Olga
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Bukhman, Yury V
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Ethier, Martin
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Sheng, Yinglun
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Vasilescu, Julian
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Abu-Farha, Mohamed
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Lambert, Jean-Philippe
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Duewel, Henry S.
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Stewart, Ian I.
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Kuehl, Bonnie
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Hogue, Kelly
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Colwill, Karen
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Gladwish, Katharine
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Muskat, Brenda
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Kinach, Robert
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Adams, Sally-Lin
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Moran, Michael F.
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Morin, Gregg B.
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Topaloglou, Thodoros
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Figeys, Daniel
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Ewing, Rob M.
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Chu, Peter
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Elisma, Fred
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Li, Hongyan
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Taylor, Paul
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Climie, Shane
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McBroom-Cerajewski, Linda
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Robinson, Mark D.
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O'Connor, Liam
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Li, Michael
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Taylor, Rod
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Dharsee, Moyez
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Ho, Yuen
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Heilbut, Adrian
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Moore, Lynda
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Zhang, Shudong
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Ornatsky, Olga
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Bukhman, Yury V
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Ethier, Martin
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Sheng, Yinglun
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Vasilescu, Julian
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Abu-Farha, Mohamed
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Lambert, Jean-Philippe
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Duewel, Henry S.
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Stewart, Ian I.
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Kuehl, Bonnie
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Hogue, Kelly
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Colwill, Karen
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Gladwish, Katharine
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Muskat, Brenda
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Kinach, Robert
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Adams, Sally-Lin
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Moran, Michael F.
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Morin, Gregg B.
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Topaloglou, Thodoros
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Figeys, Daniel
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Ewing, Rob M., Chu, Peter, Elisma, Fred, Li, Hongyan, Taylor, Paul, Climie, Shane, McBroom-Cerajewski, Linda, Robinson, Mark D., O'Connor, Liam, Li, Michael, Taylor, Rod, Dharsee, Moyez, Ho, Yuen, Heilbut, Adrian, Moore, Lynda, Zhang, Shudong, Ornatsky, Olga, Bukhman, Yury V, Ethier, Martin, Sheng, Yinglun, Vasilescu, Julian, Abu-Farha, Mohamed, Lambert, Jean-Philippe, Duewel, Henry S., Stewart, Ian I., Kuehl, Bonnie, Hogue, Kelly, Colwill, Karen, Gladwish, Katharine, Muskat, Brenda, Kinach, Robert, Adams, Sally-Lin, Moran, Michael F., Morin, Gregg B., Topaloglou, Thodoros and Figeys, Daniel (2007) Large-scale mapping of human protein-protein interactions by mass spectrometry. Molecular Systems Biology, 3 (89), 89. (doi:10.1038/msb4100134). (PMID:17353931)

Record type: Article

Abstract

Mapping protein-protein interactions is an invaluable tool for understanding protein function. Here, we report the first large-scale study of protein-protein interactions in human cells using a mass spectrometry-based approach. The study maps protein interactions for 338 bait proteins that were selected based on known or suspected disease and functional associations. Large-scale immunoprecipitation of Flag-tagged versions of these proteins followed by LC-ESI-MS/MS analysis resulted in the identification of 24,540 potential protein interactions. False positives and redundant hits were filtered out using empirical criteria and a calculated interaction confidence score, producing a data set of 6463 interactions between 2235 distinct proteins. This data set was further cross-validated using previously published and predicted human protein interactions. In-depth mining of the data set shows that it represents a valuable source of novel protein-protein interactions with relevance to human diseases. In addition, via our preliminary analysis, we report many novel protein interactions and pathway associations.

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More information

Published date: 13 March 2007
Organisations: Molecular and Cellular

Identifiers

Local EPrints ID: 355413
URI: http://eprints.soton.ac.uk/id/eprint/355413
ISSN: 1744-4292
PURE UUID: 30af7ec0-a738-4765-b969-78e04e977038
ORCID for Rob M. Ewing: ORCID iD orcid.org/0000-0001-6510-4001

Catalogue record

Date deposited: 21 Oct 2013 11:17
Last modified: 15 Mar 2024 03:44

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Contributors

Author: Rob M. Ewing ORCID iD
Author: Peter Chu
Author: Fred Elisma
Author: Hongyan Li
Author: Paul Taylor
Author: Shane Climie
Author: Linda McBroom-Cerajewski
Author: Mark D. Robinson
Author: Liam O'Connor
Author: Michael Li
Author: Rod Taylor
Author: Moyez Dharsee
Author: Yuen Ho
Author: Adrian Heilbut
Author: Lynda Moore
Author: Shudong Zhang
Author: Olga Ornatsky
Author: Yury V Bukhman
Author: Martin Ethier
Author: Yinglun Sheng
Author: Julian Vasilescu
Author: Mohamed Abu-Farha
Author: Jean-Philippe Lambert
Author: Henry S. Duewel
Author: Ian I. Stewart
Author: Bonnie Kuehl
Author: Kelly Hogue
Author: Karen Colwill
Author: Katharine Gladwish
Author: Brenda Muskat
Author: Robert Kinach
Author: Sally-Lin Adams
Author: Michael F. Moran
Author: Gregg B. Morin
Author: Thodoros Topaloglou
Author: Daniel Figeys

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