Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.
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.
Ho
Yuen
Y
MDS Proteomics, 251 Attwell Drive, Toronto, Canada M9W 7H4, and Staermosegaardsvej 6, DK-5230 Odense M, Denmark.
Gruhler
Albrecht
A
Heilbut
Adrian
A
Bader
Gary D
GD
Moore
Lynda
L
Adams
Sally-Lin
SL
Millar
Anna
A
Taylor
Paul
P
Bennett
Keiryn
K
Boutilier
Kelly
K
Yang
Lingyun
L
Wolting
Cheryl
C
Donaldson
Ian
I
Schandorff
Søren
S
Shewnarane
Juanita
J
Vo
Mai
M
Taggart
Joanne
J
Goudreault
Marilyn
M
Muskat
Brenda
B
Alfarano
Cris
C
Dewar
Danielle
D
Lin
Zhen
Z
Michalickova
Katerina
K
Willems
Andrew R
AR
Sassi
Holly
H
Nielsen
Peter A
PA
Rasmussen
Karina J
KJ
Andersen
Jens R
JR
Johansen
Lene E
LE
Hansen
Lykke H
LH
Jespersen
Hans
H
Podtelejnikov
Alexandre
A
Nielsen
Eva
E
Crawford
Janne
J
Poulsen
Vibeke
V
Sørensen
Birgitte D
BD
Matthiesen
Jesper
J
Hendrickson
Ronald C
RC
Gleeson
Frank
F
Pawson
Tony
T
Moran
Michael F
MF
Durocher
Daniel
D
Mann
Matthias
M
Hogue
Christopher W V
CW
Figeys
Daniel
D
Tyers
Mike
M
D000595:Amino Acid Sequence; D018797:Cell Cycle Proteins; D003001:Cloning, Molecular; D004249:DNA Damage; D004260:DNA Repair; D004271:DNA, Fungal; D006801:Humans; D046911:Macromolecular Substances; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D010744:Phosphoric Monoester Hydrolases / Q000378:metabolism; D011485:Protein Binding; D011494:Protein Kinases / Q000737:chemistry / Q000378:metabolism; D017346:Protein Serine-Threonine Kinases; D020543:Proteome; D012441:Saccharomyces cerevisiae / Q000737:chemistry*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000302:isolation & purification*; D016415:Sequence Alignment; D015398:Signal Transduction
D018797:Cell Cycle Proteins; D004271:DNA, Fungal; D046911:Macromolecular Substances; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D011494:Protein Kinases; C104169:DUN1 protein, S cerevisiae; D017346:Protein Serine-Threonine Kinases; D010744:Phosphoric Monoester Hydrolases