Targeted comparative proteomics by liquid chromatography-tandem Fourier ion cyclotron resonance mass spectrometry.
In proteomics, effective methods are needed for identifying the relatively limited subset of proteins displaying significant changes in abundance between two samples. One way to accomplish this task is to target for identification by MS/MS only the "interesting" proteins based on the abundance ratio of isotopically labeled pairs of peptides. We have developed the software and hardware tools for online LC-FTICR MS/MS studies in which a set of initially unidentified peptides from a proteome analysis can be selected for identification based on their distinctive changes in abundance following a "perturbation". We report here the validation of this method using a mixture of standard proteins combined in different ratios after isotopic labeling. We also demonstrate the application of this method to the identification of Shewanella oneidensis peptides/proteins exhibiting differential abundance in suboxic versus aerobic cell cultures.
Masselon
Christophe
C
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, MSIN K8-98, Richland, Washington 99352, USA.
Pasa-Tolić
Ljiljana
L
Tolić
Nikola
N
Anderson
Gordon A
GA
Bogdanov
Bogdan
B
Vilkov
Andrey N
AN
Shen
Yufeng
Y
Zhao
Rui
R
Qian
Wei-Jun
WJ
Lipton
Mary S
MS
Camp
David G
DG
Smith
Richard D
RD
D001426:Bacterial Proteins / Q000032:analysis*; D002853:Chromatography, Liquid / Q000379:methods*; D009587:Nitrogen Isotopes; D040901:Proteomics / Q000379:methods*; D020592:Shewanella / Q000737:chemistry*; D053719:Tandem Mass Spectrometry / Q000379:methods*
D001426:Bacterial Proteins; D009587:Nitrogen Isotopes