TY - JOUR
T1 - A high-quality catalog of the Drosophila melanogaster proteome
AU - Brunner, Erich
AU - Ahrens, Christian H.
AU - Mohanty, Sonali
AU - Baetschmann, Hansruedi
AU - Loevenich, Sandra
AU - Potthast, Frank
AU - Deutsch, Eric W.
AU - Panse, Christian
AU - De Lichtenberg, Ulrik
AU - Rinner, Oliver
AU - Lee, Hookeun
AU - Pedrioli, Patrick G.A.
AU - Malmstrom, Johan
AU - Koehler, Katja
AU - Schrimpf, Sabine
AU - Krijgsveld, Jeroen
AU - Kregenow, Floyd
AU - Heck, Albert J.R.
AU - Hafen, Ernst
AU - Schlapbach, Ralph
AU - Aebersold, Ruedi
N1 - Funding Information:
We thank Bernd Roschitzki, Bertran Gerrits, Eva Niederer, Marko Jovanovic, Cristian Köpfli and Michael Walser for technical help, Hans Jespersen and Soeren Schandorff from Proxeon Bioinformatics for discussions regarding the proteotypic peptide data analysis and Hubert K. Rehrauer for help with statistical analysis. The project was funded by the University Research Priority Program Systems Biology/Functional Genomics of the University of Zurich. E.B., S.M., S.S. and S.L. are members of the Center for Model Organism Proteomes (C-MOP) which is funded by the University of Zurich (http:// www.mop.unizh.ch). S.L. was supported by a Career Development Award of the University of Zurich. This work was also supported in part by a UBS grant to E.B. and K. Basler, and with federal funds from the US National Heart, Lung, and Blood Institute, National Institutes of Health under contract No. N01-HV-28179.
PY - 2007/5/1
Y1 - 2007/5/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=34249717879&partnerID=8YFLogxK
U2 - 10.1038/nbt1300
DO - 10.1038/nbt1300
M3 - Article
C2 - 17450130
AN - SCOPUS:34249717879
SN - 1087-0156
VL - 25
SP - 576
EP - 583
JO - Nature Biotechnology
JF - Nature Biotechnology
IS - 5
ER -