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.
Krogan
Nevan J
NJ
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.
Cagney
Gerard
G
Yu
Haiyuan
H
Zhong
Gouqing
G
Guo
Xinghua
X
Ignatchenko
Alexandr
A
Li
Joyce
J
Pu
Shuye
S
Datta
Nira
N
Tikuisis
Aaron P
AP
Punna
Thanuja
T
Peregrín-Alvarez
José M
JM
Shales
Michael
M
Zhang
Xin
X
Davey
Michael
M
Robinson
Mark D
MD
Paccanaro
Alberto
A
Bray
James E
JE
Sheung
Anthony
A
Beattie
Bryan
B
Richards
Dawn P
DP
Canadien
Veronica
V
Lalev
Atanas
A
Mena
Frank
F
Wong
Peter
P
Starostine
Andrei
A
Canete
Myra M
MM
Vlasblom
James
J
Wu
Samuel
S
Orsi
Chris
C
Collins
Sean R
SR
Chandran
Shamanta
S
Haw
Robin
R
Rilstone
Jennifer J
JJ
Gandi
Kiran
K
Thompson
Natalie J
NJ
Musso
Gabe
G
St Onge
Peter
P
Ghanny
Shaun
S
Lam
Mandy H Y
MH
Butland
Gareth
G
Altaf-Ul
Amin M
AM
Kanaya
Shigehiko
S
Shilatifard
Ali
A
O'Shea
Erin
E
Weissman
Jonathan S
JS
Ingles
C James
CJ
Hughes
Timothy R
TR
Parkinson
John
J
Gerstein
Mark
M
Wodak
Shoshana J
SJ
Emili
Andrew
A
Greenblatt
Jack F
JF
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