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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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publishing date
type
Contribution to journal
publication status
published
keywords
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
in
Nature Biotechnology
volume
25
issue
5
pages
8 pages
publisher
Nature Publishing Group
external identifiers
  • scopus:34249717879
  • pmid:17450130
ISSN
1087-0156
DOI
10.1038/nbt1300
language
English
LU publication?
no
id
7be523af-161c-474e-9fbe-2478570c9990
date added to LUP
2016-11-16 20:40:35
date last changed
2024-06-15 20:34:18
@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}},
  keywords     = {{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}},
  doi          = {{10.1038/nbt1300}},
  volume       = {{25}},
  year         = {{2007}},
}