title: A high-quality catalog of the Drosophila melanogaster proteome.
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 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.
authors: Center for Model Organism Proteomes, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. erich.brunner@molbio.uzh.ch
authors: Erich
authors: E
authors: Brunner
authors: Christian H
authors: CH
authors: Ahrens
authors: Sonali
authors: S
authors: Mohanty
authors: Hansruedi
authors: H
authors: Baetschmann
authors: Sandra
authors: S
authors: Loevenich
authors: Frank
authors: F
authors: Potthast
authors: Eric W
authors: EW
authors: Deutsch
authors: Christian
authors: C
authors: Panse
authors: Ulrik
authors: U
authors: de Lichtenberg
authors: Oliver
authors: O
authors: Rinner
authors: Hookeun
authors: H
authors: Lee
authors: Patrick G A
authors: PG
authors: Pedrioli
authors: Johan
authors: J
authors: Malmstrom
authors: Katja
authors: K
authors: Koehler
authors: Sabine
authors: S
authors: Schrimpf
authors: Jeroen
authors: J
authors: Krijgsveld
authors: Floyd
authors: F
authors: Kregenow
authors: Albert J R
authors: AJ
authors: Heck
authors: Ernst
authors: E
authors: Hafen
authors: Ralph
authors: R
authors: Schlapbach
authors: Ruedi
authors: R
authors: Aebersold
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D030562:Databases, Protein; D029721:Drosophila Proteins / Q000737:chemistry* / Q000235:genetics*; D004331:Drosophila melanogaster / Q000737:chemistry* / Q000235:genetics*; D008969:Molecular Sequence Data; D020543:Proteome / Q000737:chemistry* / Q000235:genetics*
chemical_list: D029721:Drosophila Proteins; D020543:Proteome