Article abstract
Nature Biotechnology 25, 576 - 583 (2007)
Published online: 22 April 2007 | doi:10.1038/nbt1300
A high-quality catalog of the Drosophila melanogaster proteome
Erich Brunner1,10, Christian H Ahrens1,2,10, Sonali Mohanty1,3,10, Hansruedi Baetschmann2, Sandra Loevenich1,3, Frank Potthast2, Eric W Deutsch4, Christian Panse2, Ulrik de Lichtenberg5,6, Oliver Rinner3, Hookeun Lee3, Patrick G A Pedrioli3, Johan Malmstrom3, Katja Koehler3, Sabine Schrimpf1,7, Jeroen Krijgsveld8, Floyd Kregenow4, Albert J R Heck8, Ernst Hafen3, Ralph Schlapbach2 & Ruedi Aebersold3,9
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 data provide crucial information to amend genome annotation and to confirm many predicted gene models. We also present experimentally identified proteotypic peptides matching 
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.
- Center for Model Organism Proteomes, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
- Functional Genomics Center, ETH and University of Zurich, Winterthurerstrasse 190, Y55L70, 8057 Zurich, Switzerland.
- Institute for Molecular Systems Biology, Swiss Federal Institute of Technology, ETH Honggerberg, Wolfgang-Pauli-Str. 16, HPT, CH-8093 Zurich, Switzerland.
- Institute for Systems Biology, 1441 N. 34th Street, Seattle, Washington 98103, USA.
- Center for Biological Sequence Analysis, BioCentrum-DTU, Technical, University of Denmark, Kemitorvet, Building 208, DK-2800 Lyngby, Denmark.
- LEO Pharma, Industriparken 55, DK2750 Ballerup, Denmark.
- Institute for Molecular Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, the Netherlands.
- Faculty of Science, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
- These authors contributed equally to this work.
Correspondence to: Ruedi Aebersold3,9 e-mail: aebersold@imsb.biol.ethz.ch
Correspondence to: Erich Brunner1,10 e-mail: erich.brunner@molbio.uzh.ch
Correspondence to: Christian H Ahrens1,2,10 e-mail: christian.ahrens@fgcz.ethz.ch
