A high-quality catalog of the Drosophila melanogaster proteome

Research output: Contribution to journalArticle


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.


  • 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
  • Katja Koehler
  • Sabine Schrimpf
  • Jeroen Krijgsveld
  • Floyd Kregenow
  • Albert J R Heck
  • Ernst Hafen
  • Ralph Schlapbach
  • Ruedi Aebersold
External organisations
  • University of Zurich
  • ETH Zürich
Research areas and 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
Original languageEnglish
Pages (from-to)576-83
Number of pages8
JournalNature Biotechnology
Issue number5
Publication statusPublished - 2007 May
Publication categoryResearch
Externally publishedYes