Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

Nevan J. Krogan; Gerard Cagney; Haiyuan Yu; Gouqing Zhong; Xinghua Guo; Alexandr Ignatchenko; Joyce Li; Shuye Pu; Nira Datta; Aaron P. 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 P. Richards; Veronica Canadien; Atanas Lalev; Frank Mena; Peter 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 O'Shea; Jonathan S. Weissman; C. James Ingles; Timothy R. Hughes; John Parkinson; Mark Gerstein; Shoshana J. Wodak; Andrew Emili; Jack F. Greenblatt

doi:10.1038/nature04670

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

Nevan J. Krogan, Gerard Cagney, Haiyuan Yu, Gouqing Zhong, Xinghua Guo, Alexandr Ignatchenko, Joyce Li, Shuye Pu, Nira Datta, Aaron P. Tikuisis, Thanuja Punna, José M. Peregrín-Alvarez, Michael Shales, Xin Zhang, Michael Davey, Mark D. Robinson, Alberto Paccanaro, James E. Bray, Anthony Sheung, Bryan BeattieDawn P. Richards, Veronica Canadien, Atanas Lalev, Frank Mena, Peter 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 O'Shea, Jonathan S. Weissman, C. James Ingles, Timothy R. Hughes, John Parkinson, Mark Gerstein, Shoshana J. Wodak, Andrew Emili^*, Jack F. Greenblatt

^*Corresponding author for this work

Biochemistry and Molecular Genetics

Research output: Contribution to journal › Article › peer-review

2436 Scopus citations

Abstract

Identification of protein-protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ ionization-time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein-protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein-protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.

Original language	English (US)
Pages (from-to)	637-643
Number of pages	7
Journal	Nature
Volume	440
Issue number	7084
DOIs	https://doi.org/10.1038/nature04670
State	Published - Mar 30 2006

Funding

Acknowledgements We thank M. Chow, N. Mohammad, C. Chung and V. Fong for their assistance with the creation of the web resources. We are grateful to J. van Helden and S. Brohée for sharing information on their comparison of clustering methods before publication. This research was supported by grants from Genome Canada and the Ontario Genomics Institute (to J.F.G. and A.E.), the Canadian Institutes of Health Research (to A.E., N.J.K., J.F.G., S.J.W., S.P. and C.J.I.), the National Cancer Institute of Canada with funds from the Canadian Cancer Society (to J.F.G.), the Howard Hughes Medical Institute (to J.S.W. and E.O.), the McLaughlin Centre for Molecular Medicine (to S.J.W. and S.P.), the Hospital for Sick Children (to J.M.P.-A.), the National Sciences and Engineering Research Council (to N.J.K., T.R.H. and A.E.) and the National Institutes of Health (to A.S., M.G., A.P. and H.Y.).

ASJC Scopus subject areas

General

Access to Document

10.1038/nature04670

Cite this

Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A. P., Punna, T., Peregrín-Alvarez, J. M., Shales, M., Zhang, X., Davey, M., Robinson, M. D., Paccanaro, A., Bray, J. E., Sheung, A., ... Greenblatt, J. F. (2006). Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 440(7084), 637-643. https://doi.org/10.1038/nature04670

@article{89deefcd8a774d5cba29b9cb7be9bd54,

title = "Global landscape of protein complexes in the yeast Saccharomyces cerevisiae",

abstract = "Identification of protein-protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ ionization-time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein-protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein-protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.",

author = "Krogan, {Nevan J.} and Gerard Cagney and Haiyuan Yu and Gouqing Zhong and Xinghua Guo and Alexandr Ignatchenko and Joyce Li and Shuye Pu and Nira Datta and Tikuisis, {Aaron P.} and Thanuja Punna and Peregr{\'i}n-Alvarez, {Jos{\'e} M.} and Michael Shales and Xin Zhang and Michael Davey and Robinson, {Mark D.} and Alberto Paccanaro and Bray, {James E.} and Anthony Sheung and Bryan Beattie and Richards, {Dawn P.} and Veronica Canadien and Atanas Lalev and Frank Mena and Peter Wong and Andrei Starostine and Canete, {Myra M.} and James Vlasblom and Samuel Wu and Chris Orsi and Collins, {Sean R.} and Shamanta Chandran and Robin Haw and Rilstone, {Jennifer J.} and Kiran Gandi and Thompson, {Natalie J.} and Gabe Musso and {St Onge}, Peter and Shaun Ghanny and Lam, {Mandy H Y} and Gareth Butland and Altaf-Ul, {Amin M.} and Shigehiko Kanaya and Ali Shilatifard and Erin O'Shea and Weissman, {Jonathan S.} and Ingles, {C. James} and Hughes, {Timothy R.} and John Parkinson and Mark Gerstein and Wodak, {Shoshana J.} and Andrew Emili and Greenblatt, {Jack F.}",

note = "Funding Information: Acknowledgements We thank M. Chow, N. Mohammad, C. Chung and V. Fong for their assistance with the creation of the web resources. We are grateful to J. van Helden and S. Broh{\'e}e for sharing information on their comparison of clustering methods before publication. This research was supported by grants from Genome Canada and the Ontario Genomics Institute (to J.F.G. and A.E.), the Canadian Institutes of Health Research (to A.E., N.J.K., J.F.G., S.J.W., S.P. and C.J.I.), the National Cancer Institute of Canada with funds from the Canadian Cancer Society (to J.F.G.), the Howard Hughes Medical Institute (to J.S.W. and E.O.), the McLaughlin Centre for Molecular Medicine (to S.J.W. and S.P.), the Hospital for Sick Children (to J.M.P.-A.), the National Sciences and Engineering Research Council (to N.J.K., T.R.H. and A.E.) and the National Institutes of Health (to A.S., M.G., A.P. and H.Y.).",

year = "2006",

month = mar,

day = "30",

doi = "10.1038/nature04670",

language = "English (US)",

volume = "440",

pages = "637--643",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7084",

}

Krogan, NJ, Cagney, G, Yu, H, Zhong, G, Guo, X, Ignatchenko, A, Li, J, Pu, S, Datta, N, Tikuisis, AP, Punna, T, Peregrín-Alvarez, JM, Shales, M, Zhang, X, Davey, M, Robinson, MD, Paccanaro, A, Bray, JE, Sheung, A, Beattie, B, Richards, DP, Canadien, V, Lalev, A, Mena, F, Wong, P, Starostine, A, Canete, MM, Vlasblom, J, Wu, S, Orsi, C, Collins, SR, Chandran, S, Haw, R, Rilstone, JJ, Gandi, K, Thompson, NJ, Musso, G, St Onge, P, Ghanny, S, Lam, MHY, Butland, G, Altaf-Ul, AM, Kanaya, S, Shilatifard, A, O'Shea, E, Weissman, JS, Ingles, CJ, Hughes, TR, Parkinson, J, Gerstein, M, Wodak, SJ, Emili, A & Greenblatt, JF 2006, 'Global landscape of protein complexes in the yeast Saccharomyces cerevisiae', Nature, vol. 440, no. 7084, pp. 637-643. https://doi.org/10.1038/nature04670

TY - JOUR

T1 - Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

AU - Krogan, Nevan J.

AU - Cagney, Gerard

AU - Yu, Haiyuan

AU - Zhong, Gouqing

AU - Guo, Xinghua

AU - Ignatchenko, Alexandr

AU - Li, Joyce

AU - Pu, Shuye

AU - Datta, Nira

AU - Tikuisis, Aaron P.

AU - Punna, Thanuja

AU - Peregrín-Alvarez, José M.

AU - Shales, Michael

AU - Zhang, Xin

AU - Davey, Michael

AU - Robinson, Mark D.

AU - Paccanaro, Alberto

AU - Bray, James E.

AU - Sheung, Anthony

AU - Beattie, Bryan

AU - Richards, Dawn P.

AU - Canadien, Veronica

AU - Lalev, Atanas

AU - Mena, Frank

AU - Wong, Peter

AU - Starostine, Andrei

AU - Canete, Myra M.

AU - Vlasblom, James

AU - Wu, Samuel

AU - Orsi, Chris

AU - Collins, Sean R.

AU - Chandran, Shamanta

AU - Haw, Robin

AU - Rilstone, Jennifer J.

AU - Gandi, Kiran

AU - Thompson, Natalie J.

AU - Musso, Gabe

AU - St Onge, Peter

AU - Ghanny, Shaun

AU - Lam, Mandy H Y

AU - Butland, Gareth

AU - Altaf-Ul, Amin M.

AU - Kanaya, Shigehiko

AU - Shilatifard, Ali

AU - O'Shea, Erin

AU - Weissman, Jonathan S.

AU - Ingles, C. James

AU - Hughes, Timothy R.

AU - Parkinson, John

AU - Gerstein, Mark

AU - Wodak, Shoshana J.

AU - Emili, Andrew

AU - Greenblatt, Jack F.

N1 - Funding Information: Acknowledgements We thank M. Chow, N. Mohammad, C. Chung and V. Fong for their assistance with the creation of the web resources. We are grateful to J. van Helden and S. Brohée for sharing information on their comparison of clustering methods before publication. This research was supported by grants from Genome Canada and the Ontario Genomics Institute (to J.F.G. and A.E.), the Canadian Institutes of Health Research (to A.E., N.J.K., J.F.G., S.J.W., S.P. and C.J.I.), the National Cancer Institute of Canada with funds from the Canadian Cancer Society (to J.F.G.), the Howard Hughes Medical Institute (to J.S.W. and E.O.), the McLaughlin Centre for Molecular Medicine (to S.J.W. and S.P.), the Hospital for Sick Children (to J.M.P.-A.), the National Sciences and Engineering Research Council (to N.J.K., T.R.H. and A.E.) and the National Institutes of Health (to A.S., M.G., A.P. and H.Y.).

PY - 2006/3/30

Y1 - 2006/3/30

N2 - Identification of protein-protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ ionization-time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein-protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein-protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.

AB - Identification of protein-protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ ionization-time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein-protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein-protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.

UR - http://www.scopus.com/inward/record.url?scp=33645453254&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33645453254&partnerID=8YFLogxK

U2 - 10.1038/nature04670

DO - 10.1038/nature04670

M3 - Article

C2 - 16554755

AN - SCOPUS:33645453254

SN - 0028-0836

VL - 440

SP - 637

EP - 643

JO - Nature

JF - Nature

IS - 7084

ER -

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

Abstract

Funding

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this