Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents

Mark R. Flory, Hookeun Lee, Richard Bonneau, Parag Mallick, Kyle Serikawa, David R. Morris, Ruedi Aebersold

Research output: Contribution to journalArticle

Abstract

Quantitative profiling of proteins, the direct effectors of nearly all biological functions, will undoubtedly complement technologies for the measurement of mRNA, Systematic proteomic measurement of the cell cycle is now possible by using stable isotopic labeling with isotope-coded affinity tag reagents and software tools for high-throughput analysis of LC-MS/MS data. We provide here the first such study achieving quantitative, global proteomic measurement of a time-course gene expression experiment in a model eukaryote, the budding yeast Saccharomyces cerevisiae, during the cell cycle. We sampled 48% of all predicted ORFs, and provide the data, including identifications, quantitations, and statistical measures of certainty, to the community in a sortable matrix. We do not detect significant concordance in the dynamics of the system over the time-course tested between our proteomic measurements and microarray measures collected from similarly treated yeast cultures. Our proteomic dataset therefore provides a necessary and complementary measure of eukaryotic gene expression, establishes a rich database for the functional analysis of S. cerevisiae proteins, and will enable further development of technologies for global proteomic analysis of higher eukaryotes.

Original languageEnglish (US)
Pages (from-to)6146-6157
Number of pages12
JournalProteomics
Volume6
Issue number23
DOIs
StatePublished - Dec 2006

Fingerprint

Saccharomycetales
Isotopes
Proteomics
Yeast
Cell Cycle
Cells
Acids
Eukaryota
Gene expression
Isotope Labeling
Saccharomyces cerevisiae Proteins
Technology
Gene Expression
Functional analysis
Microarrays
Labeling
Open Reading Frames
Saccharomyces cerevisiae
Software
Yeasts

Keywords

  • Cell cycle
  • Electrospray ionization-tandem mass spectrometry
  • Isotope-coded affinity tags
  • Proteome profiling
  • Saccharomyces cerevisiae

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents. / Flory, Mark R.; Lee, Hookeun; Bonneau, Richard; Mallick, Parag; Serikawa, Kyle; Morris, David R.; Aebersold, Ruedi.

In: Proteomics, Vol. 6, No. 23, 12.2006, p. 6146-6157.

Research output: Contribution to journalArticle

Flory, Mark R. ; Lee, Hookeun ; Bonneau, Richard ; Mallick, Parag ; Serikawa, Kyle ; Morris, David R. ; Aebersold, Ruedi. / Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents. In: Proteomics. 2006 ; Vol. 6, No. 23. pp. 6146-6157.
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