Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
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.
Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, Ontario M5S 3E1, Canada.
Nevan J
NJ
Krogan
Gerard
G
Cagney
Haiyuan
H
Yu
Gouqing
G
Zhong
Xinghua
X
Guo
Alexandr
A
Ignatchenko
Joyce
J
Li
Shuye
S
Pu
Nira
N
Datta
Aaron P
AP
Tikuisis
Thanuja
T
Punna
José M
JM
Peregrín-Alvarez
Michael
M
Shales
Xin
X
Zhang
Michael
M
Davey
Mark D
MD
Robinson
Alberto
A
Paccanaro
James E
JE
Bray
Anthony
A
Sheung
Bryan
B
Beattie
Dawn P
DP
Richards
Veronica
V
Canadien
Atanas
A
Lalev
Frank
F
Mena
Peter
P
Wong
Andrei
A
Starostine
Myra M
MM
Canete
James
J
Vlasblom
Samuel
S
Wu
Chris
C
Orsi
Sean R
SR
Collins
Shamanta
S
Chandran
Robin
R
Haw
Jennifer J
JJ
Rilstone
Kiran
K
Gandi
Natalie J
NJ
Thompson
Gabe
G
Musso
Peter
P
St Onge
Shaun
S
Ghanny
Mandy H Y
MH
Lam
Gareth
G
Butland
Amin M
AM
Altaf-Ul
Shigehiko
S
Kanaya
Ali
A
Shilatifard
Erin
E
O'Shea
Jonathan S
JS
Weissman
C James
CJ
Ingles
Timothy R
TR
Hughes
John
J
Parkinson
Mark
M
Gerstein
Shoshana J
SJ
Wodak
Andrew
A
Emili
Jack F
JF
Greenblatt
D005075:Biological Evolution; D017124:Conserved Sequence; D013058:Mass Spectrometry; D046912:Multiprotein Complexes / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D020543:Proteome / Q000737:chemistry / Q000378:metabolism*; D040901:Proteomics; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000378:metabolism*
D046912:Multiprotein Complexes; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins