Abundance ratio-dependent proteomic analysis by mass spectrometry.
The goal of quantitative proteomics is to determine the identity and relative quantity of each protein present in two or more complex protein samples. Here we describe a novel approach to quantitative proteomics. It is based on a highly accurate algorithm for the automated quantification of chromatographically fractionated, isotope-coded affinity-tagged peptides and MALDI quadrupole time-of-flight tandem mass spectrometry for their identification. The method is capable of detecting and selectively identifying those proteins within a complex mixture that show a difference in relative abundance. We demonstrate the effectiveness and the versatility of this approach in the analysis of a standard protein mixture, protein expression profiling in a human prostate cancer cell line model, and identification of the specific components of the multiprotein transcriptional machinery in S. cerevisiae.
Griffin
Timothy J
TJ
Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA.
Lock
Chris M
CM
Li
Xiao-jun
XJ
Patel
Alpesh
A
Chervetsova
Iryna
I
Lee
Hookeun
H
Wright
Michael E
ME
Ranish
Jeffrey A
JA
Chen
Sharon S
SS
Aebersold
Ruedi
R
D006801:Humans; D008297:Male; D011471:Prostatic Neoplasms / Q000737:chemistry; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000295:instrumentation* / Q000379:methods; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D014407:Tumor Cells, Cultured
D020543:Proteome