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 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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Figure 1: Description of the directed shotgun proteomics workflow.
Figure 2: Count of distinct protein identifications as a function of overall high-quality peptide identifications and results of several Monte Carlo simulations.
Figure 3: Benefits of the ADE strategy visualized by combined protein parameter histograms and difference histograms.
Figure 4: Additional biases among the experimentally identified proteins.
Figure 5: Identification of new genes/exons using proteomics data.
Figure 6: Outline of a typical PTP experiment.


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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.

Author information




E.B. and S.M. conducted most of the experimental work; E.B. performed most of the LTQ measurements, coordinated the interdisciplinary project and carried out the proteomics-based genome annotation work. S.M. performed the GO analyses; C.H.A. coordinated and carried out the bioinformatic analyses of the data set (Pfam analysis with C.P.), and conceived the ADE strategy; H.B. established the necessary statistical infrastructure for the project, carried out statistical analyses together with C.H.A. and performed the simulations; S.L. implemented the SBEAMS database, generated the Drosophila Peptide Atlas (supported by E.W.D.) and supported E.B with the proteomics-based genome annotation work; F.P. and C.P. (supported by E.W.D.) implemented and maintained the computational infrastructure at the Functional Genomics Center Zurich (FGCZ); U.L. provided the protein parameter computations; O.R. performed the gel-filtration experiments; H.L. helped with the setup of the LTQ instrument and LTQ MS analyses; P.G.A.P. generated the software for FCF calculations; J.M. set up the Free Flow Electrophoresis system and helped with experiments; K.K. and S.S. helped with selected experiments; F.K. helped with LCQ, and the initial experimental strategy; J.K. shared large data sets and performed the LTQ and LTQ-FT-ICR measurements in the lab of A.J.R.H.; R.S. supported the project with FGCZ resources; E.H. and R.A initiated the project and provided intellectual and financial support; R.A carried senior authorship responsibility.

Corresponding authors

Correspondence to Erich Brunner or Christian H Ahrens or Ruedi Aebersold.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Schematic drawing that depicts the various steps and procedures used to prepare samples for mass spectrometric analysis. (PDF 381 kb)

Supplementary Fig. 2

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)

Supplementary Table 1

The Drosophila melanogaster proteome based on Berkeley Drosophila Genome Project (BDGP) release 3.2. (DOC 27 kb)

Supplementary Table 2

Overview of all experiments grouped by developmental stage or cell line. (DOC 121 kb)

Supplementary Table 3

PFAM and GO slim analysis. (DOC 324 kb)

Supplementary Table 4

List of unvalidated peptides identified by cross-comparative database searches. (XLS 60 kb)

Supplementary Table 5

List of experimentally observed proteotypic peptides (PTPs). (XLS 2743 kb)

Supplementary Results (DOC 115 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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