Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags.
Understanding biological systems and the roles of their constituents is facilitated by the ability to make quantitative, sensitive, and comprehensive measurements of how their proteome changes, e.g., in response to environmental perturbations. To this end, we have developed a high-throughput methodology to characterize an organism's dynamic proteome based on the combination of global enzymatic digestion, high-resolution liquid chromatographic separations, and analysis by Fourier transform ion cyclotron resonance mass spectrometry. The peptides produced serve as accurate mass tags for the proteins and have been used to identify with high confidence >61% of the predicted proteome for the ionizing radiation-resistant bacterium Deinococcus radiodurans. This fraction represents the broadest proteome coverage for any organism to date and includes 715 proteins previously annotated as either hypothetical or conserved hypothetical.
Lipton
Mary S
MS
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, WA 99352, USA.
Pasa-Tolic'
Ljiljana
L
Anderson
Gordon A
GA
Anderson
David J
DJ
Auberry
Deanna L
DL
Battista
John R
JR
Daly
Michael J
MJ
Fredrickson
Jim
J
Hixson
Kim K
KK
Kostandarithes
Heather
H
Masselon
Christophe
C
Markillie
Lye Meng
LM
Moore
Ronald J
RJ
Romine
Margaret F
MF
Shen
Yufeng
Y
Stritmatter
Eric
E
Tolic'
Nikola
N
Udseth
Harold R
HR
Venkateswaran
Amudhan
A
Wong
Kwong-Kwok
KK
Zhao
Rui
R
Smith
Richard D
RD
D001419:Bacteria / Q000201:enzymology / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D002197:Capillary Action; D002874:Chromosome Mapping; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D007700:Kinetics; D020543:Proteome; D011938:Rec A Recombinases / Q000235:genetics; D014357:Trypsin
D001426:Bacterial Proteins; D020543:Proteome; D011938:Rec A Recombinases; D012321:DNA-Directed RNA Polymerases; D014357:Trypsin