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.
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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.
The authors declare no competing financial interests.
Schematic drawing that depicts the various steps and procedures used to prepare samples for mass spectrometric analysis. (PDF 381 kb)
Visualization of the statistical analysis of protein parameter distributions of all Drosophila proteins (population) and a subset of experimentally identified proteins (sample) using graphs of cumulative distributions and combined histograms. (PDF 524 kb)
The Drosophila melanogaster proteome based on Berkeley Drosophila Genome Project (BDGP) release 3.2. (DOC 27 kb)
Overview of all experiments grouped by developmental stage or cell line. (DOC 121 kb)
PFAM and GO slim analysis. (DOC 324 kb)
List of unvalidated peptides identified by cross-comparative database searches. (XLS 60 kb)
List of experimentally observed proteotypic peptides (PTPs). (XLS 2743 kb)
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Brunner, E., Ahrens, C., Mohanty, S. et al. A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol 25, 576–583 (2007). https://doi.org/10.1038/nbt1300
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