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