Large‐scale mapping of human protein–protein interactions by mass spectrometry
Rob M. Ewing,Peter Chu,Fred Elisma,Hongyan Li,Paul J. Taylor,Shane Climie,Linda McBroom-Cerajewski,Mark D. Robinson,Liam O'Connor,Michael Li,Rod Taylor,Moyez Dharsee,Yuen Ho,Adrian Heilbut,Lynda Moore,Shudong Zhang,Olga Ornatsky,Yury V. Bukhman,Martin Ethier,Yinglun Sheng,Julian Vasilescu,Mohamed Abu-Farha,Jean-Philippe Lambert,Henry S. Duewel,Ian I. Stewart,Bonnie Kuehl,Kelly Hogue,Karen Colwill,Katharine Gladwish,Brenda Muskat,Robert Kinach,Sally Lin Adams,Michael Moran,Gregg B. Morin,Thodoros Topaloglou,Daniel Figeys +35 more
TLDR
In‐depth mining of the data set shows that it represents a valuable source of novel protein–protein interactions with relevance to human diseases, and via the preliminary analysis, many novel protein interactions and pathway associations are reported.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.read more
Citations
More filters
Journal ArticleDOI
Network Medicine: A Network-Based Approach to Human Disease
TL;DR: Advances in this direction are essential for identifying new disease genes, for uncovering the biological significance of disease-associated mutations identified by genome-wide association studies and full-genome sequencing, and for identifying drug targets and biomarkers for complex diseases.
Journal ArticleDOI
The ClusPro web server for protein-protein docking.
Dima Kozakov,David R. Hall,Bing Xia,Kathryn A. Porter,Dzmitry Padhorny,Christine Yueh,Dmitri Beglov,Sandor Vajda +7 more
TL;DR: This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results of the ClusPro server.
Journal ArticleDOI
High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
Haiyuan Yu,Pascal Braun,Muhammed A. Yildirim,Irma Lemmens,Kavitha Venkatesan,Julie M. Sahalie,Tomoko Hirozane-Kishikawa,Fana Gebreab,Nan Li,Nicolas Simonis,Tong Hao,Jean François Rual,Amélie Dricot,Alexei Vazquez,Ryan R. Murray,Christophe Simon,Leah Tardivo,Stanley Tam,Nenad Svrzikapa,Changyu Fan,Anne-Sophie De Smet,Adriana Motyl,Michael E. Hudson,Juyong Park,Juyong Park,Xiaofeng Xin,Michael E. Cusick,Troy Moore,Charles Boone,Michael Snyder,Frederick P. Roth,Albert-László Barabási,Albert-László Barabási,Jan Tavernier,David E. Hill,Marc Vidal +35 more
TL;DR: A comparative quality assessment of current yeast interactome data sets is carried out, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information.
Journal ArticleDOI
Defining the Human Deubiquitinating Enzyme Interaction Landscape
TL;DR: A global proteomic analysis of Dubs and their associated protein complexes provided the first glimpse into the Dub interaction landscape, places previously unstudied Dubs within putative biological pathways, and identifies previously unknown interactions and protein complexes involved in this increasingly important arm of the ubiquitin-proteasome pathway.
Journal ArticleDOI
The CRAPome: a contaminant repository for affinity purification–mass spectrometry data
Dattatreya Mellacheruvu,Zachary Wright,Amber L. Couzens,Jean-Philippe Lambert,Nicole St-Denis,Tuo Li,Yana Miteva,Simon Hauri,Mihaela E. Sardiu,Teck Yew Low,Vincentius A. Halim,Vincentius A. Halim,Richard D. Bagshaw,Nina C. Hubner,Abdallah Al-Hakim,Annie Bouchard,Denis Faubert,Damian Fermin,Wade H. Dunham,Marilyn Goudreault,Zhen Yuan Lin,Beatriz Gonzalez Badillo,Tony Pawson,Daniel Durocher,Benoit Coulombe,Ruedi Aebersold,Ruedi Aebersold,Giulio Superti-Furga,Jacques Colinge,Albert J. R. Heck,Hyungwon Choi,Matthias Gstaiger,Shabaz Mohammed,Ileana M. Cristea,Keiryn L. Bennett,Michael P. Washburn,Michael P. Washburn,Brian Raught,Rob M. Ewing,Rob M. Ewing,Anne-Claude Gingras,Alexey I. Nesvizhskii +41 more
TL;DR: The contaminant repository for affinity purification (the CRAPome) is presented and its use for scoring protein-protein interactions is described and aggregating negative controls from multiple AP-MS studies can increase coverage and improve the characterization of background associated with a given experimental protocol.
References
More filters
Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Journal ArticleDOI
A novel genetic system to detect protein-protein interactions.
Stanley Fields,Ok-kyu Song +1 more
TL;DR: A novel genetic system to study protein-protein interactions between two proteins by taking advantage of the properties of the GAL4 protein of the yeast Saccharomyces cerevisiae, which may be applicable as a general method to identify proteins that interact with a known protein by the use of a simple galactose selection.
Journal ArticleDOI
Functional organization of the yeast proteome by systematic analysis of protein complexes
Anne-Claude Gavin,Markus Bösche,Roland Krause,Paola Grandi,Martina Marzioch,Andreas Bauer,Jörg Schultz,Jens Rick,Anne-Marie Michon,Cristina-Maria Cruciat,Marita Remor,Christian Höfert,Malgorzata Schelder,Miro Brajenovic,Heinz Ruffner,Alejandro Merino,Karin Klein,Manuela Hudak,David Dickson,Tatjana Rudi,Volker Gnau,Angela Bauch,Sonja Bastuck,Bettina Huhse,Christina Leutwein,Marie-Anne Heurtier,Richard R. Copley,Angela Edelmann,Erich Querfurth,Vladimir Rybin,Gerard Drewes,Manfred Raida,Tewis Bouwmeester,Peer Bork,Bertrand Séraphin,Bernhard Kuster,Gitte Neubauer,Giulio Superti-Furga +37 more
TL;DR: The analysis provides an outline of the eukaryotic proteome as a network of protein complexes at a level of organization beyond binary interactions, which contains fundamental biological information and offers the context for a more reasoned and informed approach to drug discovery.
Journal ArticleDOI
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
Yuen Ho,Albrecht Gruhler,Adrian Heilbut,Gary D. Bader,Gary D. Bader,Lynda Moore,Sally-Lin Adams,Anna Millar,Paul J. Taylor,Keiryn L. Bennett,Kelly Boutilier,Lingyun Yang,Cheryl Wolting,Ian Donaldson,Søren Schandorff,Juanita Shewnarane,Mai Vo,Joanne Taggart,Marilyn Goudreault,Brenda Muskat,Cris Alfarano,Danielle Dewar,Zhen Lin,Katerina Michalickova,Katerina Michalickova,Andrew Willems,Andrew Willems,Holly Sassi,Peter A Nielsen,Karina Juhl Rasmussen,Jens R. Andersen,Lene E. Johansen,Lykke Haastrup Hansen,Hans Jespersen,Alexandre V. Podtelejnikov,Eva Nielsen,Janne S. Crawford,Vibeke Poulsen,Birgitte D Sørensen,Jesper Matthiesen,Ronald C. Hendrickson,Frank Gleeson,Tony Pawson,Tony Pawson,Michael Moran,Daniel Durocher,Daniel Durocher,Matthias Mann,Christopher W. V. Hogue,Christopher W. V. Hogue,Daniel Figeys,Mike Tyers,Mike Tyers +52 more
TL;DR: Comparison of the HMS-PCI data set with interactions reported in the literature revealed an average threefold higher success rate in detection of known complexes compared with large-scale two-hybrid studies.
Journal ArticleDOI
Towards a proteome-scale map of the human protein–protein interaction network
Jean François Rual,Kavitha Venkatesan,Tong Hao,Tomoko Hirozane-Kishikawa,Amélie Dricot,Ning Li,Gabriel F. Berriz,Francis D. Gibbons,Matija Dreze,Nono Ayivi-Guedehoussou,Niels Klitgord,Christophe Simon,Mike Boxem,Stuart Milstein,Jennifer Rosenberg,Debra S. Goldberg,Lan V. Zhang,Sharyl L. Wong,Giovanni Franklin,Siming Li,Joanna S. Albala,Joanna S. Albala,Janghoo Lim,Carlene Fraughton,Estelle Llamosas,Sebiha Cevik,Camille Bex,Philippe Lamesch,Robert S. Sikorski,Jean Vandenhaute,Huda Y. Zoghbi,Alex Smolyar,Stephanie Bosak,Reynaldo Sequerra,Lynn Doucette-Stamm,Michael E. Cusick,David E. Hill,Frederick P. Roth,Marc Vidal +38 more
TL;DR: An initial version of a proteome-scale map of human binary protein–protein interactions is described, which increases by ∼70% the set of available binary interactions within the tested space and reveals more than 300 new connections to over 100 disease-associated proteins.
Related Papers (5)
Towards a proteome-scale map of the human protein–protein interaction network
Jean François Rual,Kavitha Venkatesan,Tong Hao,Tomoko Hirozane-Kishikawa,Amélie Dricot,Ning Li,Gabriel F. Berriz,Francis D. Gibbons,Matija Dreze,Nono Ayivi-Guedehoussou,Niels Klitgord,Christophe Simon,Mike Boxem,Stuart Milstein,Jennifer Rosenberg,Debra S. Goldberg,Lan V. Zhang,Sharyl L. Wong,Giovanni Franklin,Siming Li,Joanna S. Albala,Joanna S. Albala,Janghoo Lim,Carlene Fraughton,Estelle Llamosas,Sebiha Cevik,Camille Bex,Philippe Lamesch,Robert S. Sikorski,Jean Vandenhaute,Huda Y. Zoghbi,Alex Smolyar,Stephanie Bosak,Reynaldo Sequerra,Lynn Doucette-Stamm,Michael E. Cusick,David E. Hill,Frederick P. Roth,Marc Vidal +38 more
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
Nevan J. Krogan,Gerard Cagney,Gerard Cagney,Haiyuan Yu,Gouqing Zhong,Xinghua Guo,Alexandr Ignatchenko,Joyce Li,Shuye Pu,Nira Datta,Aaron Tikuisis,Thanuja Punna,José M. Peregrín-Alvarez,Michael Shales,Xin Zhang,Michael Davey,Mark D. Robinson,Alberto Paccanaro,James E. Bray,Anthony Sheung,Bryan Beattie,Dawn Richards,Veronica Canadien,Atanas Iliev Lalev,Frank Mena,Peter D Wong,Andrei Starostine,Myra M. Canete,James Vlasblom,Samuel Wu,Chris Orsi,Sean R. Collins,Shamanta Chandran,Robin Haw,Jennifer J. Rilstone,Kiran Gandi,Natalie J. Thompson,Gabe Musso,Peter St Onge,Shaun Ghanny,Mandy H. Y. Lam,Gareth Butland,Amin M. Altaf-Ul,Shigehiko Kanaya,Ali Shilatifard,Erin K. O'Shea,Jonathan S. Weissman,C. James Ingles,Timothy P. Hughes,John Parkinson,Mark Gerstein,Shoshana J. Wodak,Andrew Emili,Jack Greenblatt +53 more
Functional organization of the yeast proteome by systematic analysis of protein complexes
Anne-Claude Gavin,Markus Bösche,Roland Krause,Paola Grandi,Martina Marzioch,Andreas Bauer,Jörg Schultz,Jens Rick,Anne-Marie Michon,Cristina-Maria Cruciat,Marita Remor,Christian Höfert,Malgorzata Schelder,Miro Brajenovic,Heinz Ruffner,Alejandro Merino,Karin Klein,Manuela Hudak,David Dickson,Tatjana Rudi,Volker Gnau,Angela Bauch,Sonja Bastuck,Bettina Huhse,Christina Leutwein,Marie-Anne Heurtier,Richard R. Copley,Angela Edelmann,Erich Querfurth,Vladimir Rybin,Gerard Drewes,Manfred Raida,Tewis Bouwmeester,Peer Bork,Bertrand Séraphin,Bernhard Kuster,Gitte Neubauer,Giulio Superti-Furga +37 more
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
Yuen Ho,Albrecht Gruhler,Adrian Heilbut,Gary D. Bader,Gary D. Bader,Lynda Moore,Sally-Lin Adams,Anna Millar,Paul J. Taylor,Keiryn L. Bennett,Kelly Boutilier,Lingyun Yang,Cheryl Wolting,Ian Donaldson,Søren Schandorff,Juanita Shewnarane,Mai Vo,Joanne Taggart,Marilyn Goudreault,Brenda Muskat,Cris Alfarano,Danielle Dewar,Zhen Lin,Katerina Michalickova,Katerina Michalickova,Andrew Willems,Andrew Willems,Holly Sassi,Peter A Nielsen,Karina Juhl Rasmussen,Jens R. Andersen,Lene E. Johansen,Lykke Haastrup Hansen,Hans Jespersen,Alexandre V. Podtelejnikov,Eva Nielsen,Janne S. Crawford,Vibeke Poulsen,Birgitte D Sørensen,Jesper Matthiesen,Ronald C. Hendrickson,Frank Gleeson,Tony Pawson,Tony Pawson,Michael Moran,Daniel Durocher,Daniel Durocher,Matthias Mann,Christopher W. V. Hogue,Christopher W. V. Hogue,Daniel Figeys,Mike Tyers,Mike Tyers +52 more
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Peter Uetz,Loic Giot,Gerard Cagney,Traci A. Mansfield,Richard S. Judson,James R. Knight,Daniel Lockshon,Vaibhav A. Narayan,Maithreyan Srinivasan,Pascale Pochart,Alia Qureshi-Emili,Ying Li,Brian C. Godwin,Diana Conover,Theodore S. Kalbfleisch,Govindan Vijayadamodar,Meijia Yang,Mark Johnston,Stanley Fields,Jonathan M. Rothberg +19 more