title: Abundance ratio-dependent proteomic analysis by mass spectrometry.
abstract: 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.
authors.affiliation: Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Griffin
authors.forename: Chris M
authors.initials: CM
authors.lastname: Lock
authors.forename: Xiao-jun
authors.initials: XJ
authors.lastname: Li
authors.forename: Alpesh
authors.initials: A
authors.lastname: Patel
authors.forename: Iryna
authors.initials: I
authors.lastname: Chervetsova
authors.forename: Hookeun
authors.initials: H
authors.lastname: Lee
authors.forename: Michael E
authors.initials: ME
authors.lastname: Wright
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Ranish
authors.forename: Sharon S
authors.initials: SS
authors.lastname: Chen
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: 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
chemical_list: D020543:Proteome