title: Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags.
abstract: 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.
authors.affiliation: Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, WA 99352, USA.
authors.forename: Mary S
authors.initials: MS
authors.lastname: Lipton
authors.forename: Ljiljana
authors.initials: L
authors.lastname: Pasa-Tolic'
authors.forename: Gordon A
authors.initials: GA
authors.lastname: Anderson
authors.forename: David J
authors.initials: DJ
authors.lastname: Anderson
authors.forename: Deanna L
authors.initials: DL
authors.lastname: Auberry
authors.forename: John R
authors.initials: JR
authors.lastname: Battista
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Daly
authors.forename: Jim
authors.initials: J
authors.lastname: Fredrickson
authors.forename: Kim K
authors.initials: KK
authors.lastname: Hixson
authors.forename: Heather
authors.initials: H
authors.lastname: Kostandarithes
authors.forename: Christophe
authors.initials: C
authors.lastname: Masselon
authors.forename: Lye Meng
authors.initials: LM
authors.lastname: Markillie
authors.forename: Ronald J
authors.initials: RJ
authors.lastname: Moore
authors.forename: Margaret F
authors.initials: MF
authors.lastname: Romine
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Shen
authors.forename: Eric
authors.initials: E
authors.lastname: Stritmatter
authors.forename: Nikola
authors.initials: N
authors.lastname: Tolic'
authors.forename: Harold R
authors.initials: HR
authors.lastname: Udseth
authors.forename: Amudhan
authors.initials: A
authors.lastname: Venkateswaran
authors.forename: Kwong-Kwok
authors.initials: KK
authors.lastname: Wong
authors.forename: Rui
authors.initials: R
authors.lastname: Zhao
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
mesh_terms: 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
chemical_list: D001426:Bacterial Proteins; D020543:Proteome; D011938:Rec A Recombinases; D012321:DNA-Directed RNA Polymerases; D014357:Trypsin