Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

Yuen Ho; Albrecht Gruhler; Adrian Heilbut; Gary D Bader; Lynda Moore; Sally-Lin Adams; Anna Millar; Paul Taylor; Keiryn 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; Andrew R Willems; Holly Sassi; Peter A Nielsen; Karina J Rasmussen; Jens R Andersen; Lene E Johansen; Lykke H Hansen; Hans Jespersen; Alexandre Podtelejnikov; Eva Nielsen; Janne Crawford; Vibeke Poulsen; Birgitte D Sørensen; Jesper Matthiesen; Ronald C Hendrickson; Frank Gleeson; Tony Pawson; Michael F Moran; Daniel Durocher; Matthias Mann; Christopher W V Hogue; Daniel Figeys; Mike Tyers

doi:10.1038/415180a

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

Yuen Ho
, Albrecht Gruhler
, Adrian Heilbut
, Gary D Bader
, Lynda Moore
, Sally-Lin Adams
, Anna Millar
, Paul Taylor
, Keiryn 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, Andrew R Willems, Holly Sassi, Peter A Nielsen, Karina J Rasmussen, Jens R Andersen, Lene E Johansen, Lykke H Hansen, Hans Jespersen, Alexandre Podtelejnikov, Eva Nielsen, Janne Crawford, Vibeke Poulsen, Birgitte D Sørensen, Jesper Matthiesen, Ronald C Hendrickson, Frank Gleeson, Tony Pawson, Michael F Moran, Daniel Durocher, Matthias Mann, Christopher W V Hogue, Daniel Figeys, Mike Tyers

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

Abstract

Udgivelsesdato: 2002-Jan-10

Originalsprog	Engelsk
Tidsskrift	Nature
Vol/bind	415
Udgave nummer	6868
Sider (fra-til)	180-3
Antal sider	3
ISSN	0028-0836
DOI	https://doi.org/10.1038/415180a
Status	Udgivet - 2002

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10.1038/415180a

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Citationsformater

Ho, Y., Gruhler, A., Heilbut, A., Bader, G. D., Moore, L., Adams, S.-L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L., Wolting, C., Donaldson, I., Schandorff, S., Shewnarane, J., Vo, M., Taggart, J., Goudreault, M., Muskat, B., ... Tyers, M. (2002). Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415(6868), 180-3. https://doi.org/10.1038/415180a

@article{d1095f80ba9811dc9626000ea68e967b,

title = "Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry",

abstract = "The recent abundance of genome sequence data has brought an urgent need for systematic proteomics to decipher the encoded protein networks that dictate cellular function. To date, generation of large-scale protein-protein interaction maps has relied on the yeast two-hybrid system, which detects binary interactions through activation of reporter gene expression. With the advent of ultrasensitive mass spectrometric protein identification methods, it is feasible to identify directly protein complexes on a proteome-wide scale. Here we report, using the budding yeast Saccharomyces cerevisiae as a test case, an example of this approach, which we term high-throughput mass spectrometric protein complex identification (HMS-PCI). Beginning with 10\% of predicted yeast proteins as baits, we detected 3,617 associated proteins covering 25\% of the yeast proteome. Numerous protein complexes were identified, including many new interactions in various signalling pathways and in the DNA damage response. 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. Given the high degree of connectivity observed in this study, even partial HMS-PCI coverage of complex proteomes, including that of humans, should allow comprehensive identification of cellular networks.",

keywords = "Amino Acid Sequence, Cell Cycle Proteins, Cloning, Molecular, DNA Damage, DNA Repair, DNA, Fungal, Humans, Macromolecular Substances, Mass Spectrometry, Molecular Sequence Data, Phosphoric Monoester Hydrolases, Protein Binding, Protein Kinases, Proteome, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Sequence Alignment, Signal Transduction",

author = "Yuen Ho and Albrecht Gruhler and Adrian Heilbut and Bader, \{Gary D\} and Lynda Moore and Sally-Lin Adams and Anna Millar and Paul Taylor and Keiryn Bennett and Kelly Boutilier and Lingyun Yang and Cheryl Wolting and Ian Donaldson and S{\o}ren Schandorff and Juanita Shewnarane and Mai Vo and Joanne Taggart and Marilyn Goudreault and Brenda Muskat and Cris Alfarano and Danielle Dewar and Zhen Lin and Katerina Michalickova and Willems, \{Andrew R\} and Holly Sassi and Nielsen, \{Peter A\} and Rasmussen, \{Karina J\} and Andersen, \{Jens R\} and Johansen, \{Lene E\} and Hansen, \{Lykke H\} and Hans Jespersen and Alexandre Podtelejnikov and Eva Nielsen and Janne Crawford and Vibeke Poulsen and S{\o}rensen, \{Birgitte D\} and Jesper Matthiesen and Hendrickson, \{Ronald C\} and Frank Gleeson and Tony Pawson and Moran, \{Michael F\} and Daniel Durocher and Matthias Mann and Hogue, \{Christopher W V\} and Daniel Figeys and Mike Tyers",

year = "2002",

doi = "10.1038/415180a",

language = "English",

volume = "415",

pages = "180--3",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "6868",

}

Ho, Y, Gruhler, A, Heilbut, A, Bader, GD, Moore, L, Adams, S-L, Millar, A, Taylor, P, Bennett, K, Boutilier, K, Yang, L, Wolting, C, Donaldson, I, Schandorff, S, Shewnarane, J, Vo, M, Taggart, J, Goudreault, M, Muskat, B, Alfarano, C, Dewar, D, Lin, Z, Michalickova, K, Willems, AR, Sassi, H, Nielsen, PA, Rasmussen, KJ, Andersen, JR, Johansen, LE , Hansen, LH, Jespersen, H, Podtelejnikov, A, Nielsen, E, Crawford, J, Poulsen, V, Sørensen, BD, Matthiesen, J, Hendrickson, RC, Gleeson, F, Pawson, T, Moran, MF, Durocher, D, Mann, M, Hogue, CWV, Figeys, D & Tyers, M 2002, 'Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry', Nature, bind 415, nr. 6868, s. 180-3. https://doi.org/10.1038/415180a

TY - JOUR

T1 - Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

AU - Ho, Yuen

AU - Gruhler, Albrecht

AU - Heilbut, Adrian

AU - Bader, Gary D

AU - Moore, Lynda

AU - Adams, Sally-Lin

AU - Millar, Anna

AU - Taylor, Paul

AU - Bennett, Keiryn

AU - Boutilier, Kelly

AU - Yang, Lingyun

AU - Wolting, Cheryl

AU - Donaldson, Ian

AU - Schandorff, Søren

AU - Shewnarane, Juanita

AU - Vo, Mai

AU - Taggart, Joanne

AU - Goudreault, Marilyn

AU - Muskat, Brenda

AU - Alfarano, Cris

AU - Dewar, Danielle

AU - Lin, Zhen

AU - Michalickova, Katerina

AU - Willems, Andrew R

AU - Sassi, Holly

AU - Nielsen, Peter A

AU - Rasmussen, Karina J

AU - Andersen, Jens R

AU - Johansen, Lene E

AU - Hansen, Lykke H

AU - Jespersen, Hans

AU - Podtelejnikov, Alexandre

AU - Nielsen, Eva

AU - Crawford, Janne

AU - Poulsen, Vibeke

AU - Sørensen, Birgitte D

AU - Matthiesen, Jesper

AU - Hendrickson, Ronald C

AU - Gleeson, Frank

AU - Pawson, Tony

AU - Moran, Michael F

AU - Durocher, Daniel

AU - Mann, Matthias

AU - Hogue, Christopher W V

AU - Figeys, Daniel

AU - Tyers, Mike

PY - 2002

Y1 - 2002

N2 - The recent abundance of genome sequence data has brought an urgent need for systematic proteomics to decipher the encoded protein networks that dictate cellular function. To date, generation of large-scale protein-protein interaction maps has relied on the yeast two-hybrid system, which detects binary interactions through activation of reporter gene expression. With the advent of ultrasensitive mass spectrometric protein identification methods, it is feasible to identify directly protein complexes on a proteome-wide scale. Here we report, using the budding yeast Saccharomyces cerevisiae as a test case, an example of this approach, which we term high-throughput mass spectrometric protein complex identification (HMS-PCI). Beginning with 10% of predicted yeast proteins as baits, we detected 3,617 associated proteins covering 25% of the yeast proteome. Numerous protein complexes were identified, including many new interactions in various signalling pathways and in the DNA damage response. 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. Given the high degree of connectivity observed in this study, even partial HMS-PCI coverage of complex proteomes, including that of humans, should allow comprehensive identification of cellular networks.

AB - The recent abundance of genome sequence data has brought an urgent need for systematic proteomics to decipher the encoded protein networks that dictate cellular function. To date, generation of large-scale protein-protein interaction maps has relied on the yeast two-hybrid system, which detects binary interactions through activation of reporter gene expression. With the advent of ultrasensitive mass spectrometric protein identification methods, it is feasible to identify directly protein complexes on a proteome-wide scale. Here we report, using the budding yeast Saccharomyces cerevisiae as a test case, an example of this approach, which we term high-throughput mass spectrometric protein complex identification (HMS-PCI). Beginning with 10% of predicted yeast proteins as baits, we detected 3,617 associated proteins covering 25% of the yeast proteome. Numerous protein complexes were identified, including many new interactions in various signalling pathways and in the DNA damage response. 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. Given the high degree of connectivity observed in this study, even partial HMS-PCI coverage of complex proteomes, including that of humans, should allow comprehensive identification of cellular networks.

KW - Amino Acid Sequence

KW - Cell Cycle Proteins

KW - Cloning, Molecular

KW - DNA Damage

KW - DNA Repair

KW - DNA, Fungal

KW - Humans

KW - Macromolecular Substances

KW - Mass Spectrometry

KW - Molecular Sequence Data

KW - Phosphoric Monoester Hydrolases

KW - Protein Binding

KW - Protein Kinases

KW - Proteome

KW - Saccharomyces cerevisiae

KW - Saccharomyces cerevisiae Proteins

KW - Sequence Alignment

KW - Signal Transduction

U2 - 10.1038/415180a

DO - 10.1038/415180a

M3 - Journal article

C2 - 11805837

SN - 0028-0836

VL - 415

SP - 180

EP - 183

JO - Nature

JF - Nature

IS - 6868

ER -

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

Abstract

Dokumenter og links

SDU link

Fingeraftryk

Citationsformater