title: Differential label-free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach.
abstract: We describe the application of LC-MS without the use of stable isotope labeling for differential quantitative proteomic analysis of whole cell lysates of Shewanella oneidensis MR-1 cultured under aerobic and suboxic conditions. LC-MS/MS was used to initially identify peptide sequences, and LC-FTICR was used to confirm these identifications as well as measure relative peptide abundances. 2343 peptides covering 668 proteins were identified with high confidence and quantified. Among these proteins, a subset of 56 changed significantly using statistical approaches such as statistical analysis of microarrays, whereas another subset of 56 that were annotated as performing housekeeping functions remained essentially unchanged in relative abundance. Numerous proteins involved in anaerobic energy metabolism exhibited up to a 10-fold increase in relative abundance when S. oneidensis was transitioned from aerobic to suboxic conditions.
authors.affiliation: Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland Washington 99352, USA.
authors.forename: Ruihua
authors.initials: R
authors.lastname: Fang
authors.forename: Dwayne A
authors.initials: DA
authors.lastname: Elias
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Monroe
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Shen
authors.forename: Martin
authors.initials: M
authors.lastname: McIntosh
authors.forename: Pei
authors.initials: P
authors.lastname: Wang
authors.forename: Carrie D
authors.initials: CD
authors.lastname: Goddard
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Callister
authors.forename: Ronald J
authors.initials: RJ
authors.lastname: Moore
authors.forename: Yuri A
authors.initials: YA
authors.lastname: Gorby
authors.forename: Joshua N
authors.initials: JN
authors.lastname: Adkins
authors.forename: Jim K
authors.initials: JK
authors.lastname: Fredrickson
authors.forename: Mary S
authors.initials: MS
authors.lastname: Lipton
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000378:metabolism*; D002853:Chromatography, Liquid; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D010100:Oxygen / Q000378:metabolism*; D040901:Proteomics; D020592:Shewanella / Q000254:growth & development / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D010100:Oxygen