Abundance ratio-dependent proteomic analysis by mass spectrometry

Timothy J. Griffin, Chris M. Lock, Xiao jun Li, Alpesh Patel, Iryna Chervetsova, Hookeun Lee, Michael E. Wright, Jeffrey A. Ranish, Sharon S. Chen, Ruedi Aebersold

Research output: Contribution to journalArticlepeer-review

58 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)867-874
Number of pages8
JournalAnalytical Chemistry
Issue number4
StatePublished - Feb 15 2003


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