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A high-quality catalog of the Drosophila melanogaster proteome

Brunner, Erich; Ahrens, Christian H; Mohanty, Sonali; Baetschmann, Hansruedi; Loevenich, Sandra; Potthast, Frank LU ; Deutsch, Eric W; Panse, Christian; de Lichtenberg, Ulrik and Rinner, Oliver, et al. (2007) In Nature Biotechnology 25(5). p.83-576
Abstract

Understanding how proteins and their complex interaction networks convert the genomic information into a dynamic living organism is a fundamental challenge in biological sciences. As an important step towards understanding the systems biology of a complex eukaryote, we cataloged 63% of the predicted Drosophila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. This unprecedented high proteome coverage for a complex eukaryote was achieved by combining sample diversity, multidimensional biochemical fractionation and analysis-driven experimentation feedback loops, whereby data collection is guided by statistical analysis of prior data. We show that high-quality proteomics... (More)

Understanding how proteins and their complex interaction networks convert the genomic information into a dynamic living organism is a fundamental challenge in biological sciences. As an important step towards understanding the systems biology of a complex eukaryote, we cataloged 63% of the predicted Drosophila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. This unprecedented high proteome coverage for a complex eukaryote was achieved by combining sample diversity, multidimensional biochemical fractionation and analysis-driven experimentation feedback loops, whereby data collection is guided by statistical analysis of prior data. We show that high-quality proteomics data provide crucial information to amend genome annotation and to confirm many predicted gene models. We also present experimentally identified proteotypic peptides matching approximately 50% of D. melanogaster gene models. This library of proteotypic peptides should enable fast, targeted and quantitative proteomic studies to elucidate the systems biology of this model organism.

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@article{7be523af-161c-474e-9fbe-2478570c9990,
  abstract     = {<p>Understanding how proteins and their complex interaction networks convert the genomic information into a dynamic living organism is a fundamental challenge in biological sciences. As an important step towards understanding the systems biology of a complex eukaryote, we cataloged 63% of the predicted Drosophila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. This unprecedented high proteome coverage for a complex eukaryote was achieved by combining sample diversity, multidimensional biochemical fractionation and analysis-driven experimentation feedback loops, whereby data collection is guided by statistical analysis of prior data. We show that high-quality proteomics data provide crucial information to amend genome annotation and to confirm many predicted gene models. We also present experimentally identified proteotypic peptides matching approximately 50% of D. melanogaster gene models. This library of proteotypic peptides should enable fast, targeted and quantitative proteomic studies to elucidate the systems biology of this model organism.</p>},
  author       = {Brunner, Erich and Ahrens, Christian H and Mohanty, Sonali and Baetschmann, Hansruedi and Loevenich, Sandra and Potthast, Frank and Deutsch, Eric W and Panse, Christian and de Lichtenberg, Ulrik and Rinner, Oliver and Lee, Hookeun and Pedrioli, Patrick G A and Malmstrom, Johan and Koehler, Katja and Schrimpf, Sabine and Krijgsveld, Jeroen and Kregenow, Floyd and Heck, Albert J R and Hafen, Ernst and Schlapbach, Ralph and Aebersold, Ruedi},
  issn         = {1087-0156},
  keyword      = {Amino Acid Sequence,Animals,Databases, Protein,Drosophila Proteins,Drosophila melanogaster,Molecular Sequence Data,Proteome,Journal Article,Research Support, N.I.H., Extramural,Research Support, Non-U.S. Gov't},
  language     = {eng},
  number       = {5},
  pages        = {83--576},
  publisher    = {Nature Publishing Group},
  series       = {Nature Biotechnology},
  title        = {A high-quality catalog of the Drosophila melanogaster proteome},
  url          = {http://dx.doi.org/10.1038/nbt1300},
  volume       = {25},
  year         = {2007},
}