Differential label-free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach.
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.
Fang
Ruihua
R
Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland Washington 99352, USA.
Elias
Dwayne A
DA
Monroe
Matthew E
ME
Shen
Yufeng
Y
McIntosh
Martin
M
Wang
Pei
P
Goddard
Carrie D
CD
Callister
Stephen J
SJ
Moore
Ronald J
RJ
Gorby
Yuri A
YA
Adkins
Joshua N
JN
Fredrickson
Jim K
JK
Lipton
Mary S
MS
Smith
Richard D
RD
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*
D001426:Bacterial Proteins; D010100:Oxygen