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

Régis Lavigne 1 Emmanuelle Becker 2 Yuchen Liu 2 Bertrand Evrard 2 Aurélie Lardenois 2 Michael Primig 2 Charles Pineau 1, *
* Corresponding author
1 Plateforme Protéomique-Biogenouest (PPB)
Irset - Institut de recherche en santé, environnement et travail, Protim - Proteomics Core Facility
Abstract : 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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Submitted on : Tuesday, March 27, 2012 - 9:43:48 AM
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Régis Lavigne, Emmanuelle Becker, Yuchen Liu, Bertrand Evrard, Aurélie Lardenois, et al.. Direct iterative protein profiling (DIPP) - an innovative method for large-scale protein detection applied to budding yeast mitosis.. Molecular and Cellular Proteomics, American Society for Biochemistry and Molecular Biology, 2012, 11 (2), pp.M111.012682. ⟨10.1074/mcp.M111.012682⟩. ⟨hal-00682837⟩

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