A high-quality catalog of the Drosophila melanogaster proteome

Erich Brunner, Christian H Ahrens, Sonali Mohanty, Hansruedi Baetschmann, Sandra Loevenich, Frank Potthast, Eric W Deutsch, Christian Panse, Ulrik de Lichtenberg, Oliver Rinner, Hookeun Lee, Patrick G A Pedrioli, Johan Malmstrom, Katja Koehler, Sabine Schrimpf, Jeroen Krijgsveld, Floyd Kregenow, Albert J R Heck, Ernst Hafen, Ralph SchlapbachRuedi Aebersold

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)576-83
Number of pages8
JournalNature Biotechnology
Issue number5
Publication statusPublished - 2007 May
Externally publishedYes

Free 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


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