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Mol Cell Proteomics. 2012 Feb;11(2):M111.012682. doi: 10.1074/mcp.M111.012682. Epub 2011 Oct 13.

Direct iterative protein profiling (DIPP) - an innovative method for large-scale protein detection applied to budding yeast mitosis.

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  • 1Inserm U1085, IRSET, Proteomics Core Facility Biogenouest, Universit√© de Rennes 1, F-35042 Rennes, France.


The budding yeast Saccharomyces cerevisiae is a major model organism for important biological processes such as mitotic growth and meiotic development, it can be a human pathogen, and it is widely used in the food-, and biotechnology industries. Consequently, the genomes of numerous strains have been sequenced and a very large amount of RNA profiling data is available. Moreover, it has recently become possible to quantitatively analyze the entire yeast proteome; however, efficient and cost-effective high-throughput protein profiling remains a challenge. We report here a new approach to direct and label-free large-scale yeast protein identification using a tandem buffer system for protein extraction, two-step protein prefractionation and enzymatic digestion, and detection of peptides by iterative mass spectrometry. Our profiling study of diploid cells undergoing rapid mitotic growth identified 86% of the known proteins and its output was found to be widely concordant with genome-wide mRNA concentrations and DNA variations between yeast strains. This paves the way for comprehensive and straightforward yeast proteome profiling across a wide variety of experimental conditions.

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