Database

The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation

Sandra N Loevenich^1,2,3 , Erich Brunner² , Nichole L King^4,5 , Eric W Deutsch⁴ , Stephen E Stein⁶ , The FlyBase Consortium , Ruedi Aebersold^1,4,7,8 and Ernst Hafen¹

¹Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland

²Center for Model Organism Proteomes, University of Zurich, 8057 Zurich, Switzerland

³Ph.D. Program in Molecular Life Sciences, University of Zurich, 8093 Zurich, Switzerland

⁴Institute for Systems Biology, Seattle, WA 98103-8904, USA

⁵Incorporated Research Institutions for Seismology, Data Management Center, Seattle, WA 98105, USA

⁶National Institute of Standards & Technology, Gaithersburg, MD 20899-8380, USA

⁷Faculty of Science, University of Zurich, 8057 Zurich, Switzerland

⁸Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland

author email corresponding author email

BMC Bioinformatics 2009, 10:59doi:10.1186/1471-2105-10-59

Published:	11 February 2009

Abstract

Background

Crucial foundations of any quantitative systems biology experiment are correct genome and proteome annotations. Protein databases compiled from high quality empirical protein identifications that are in turn based on correct gene models increase the correctness, sensitivity, and quantitative accuracy of systems biology genome-scale experiments.

Results

In this manuscript, we present the Drosophila melanogaster PeptideAtlas, a fly proteomics and genomics resource of unsurpassed depth. Based on peptide mass spectrometry data collected in our laboratory the portal http://www.drosophila-peptideatlas.org webcite allows querying fly protein data observed with respect to gene model confirmation and splice site verification as well as for the identification of proteotypic peptides suited for targeted proteomics studies. Additionally, the database provides consensus mass spectra for observed peptides along with qualitative and quantitative information about the number of observations of a particular peptide and the sample(s) in which it was observed.

Conclusion

PeptideAtlas is an open access database for the Drosophila community that has several features and applications that support (1) reduction of the complexity inherently associated with performing targeted proteomic studies, (2) designing and accelerating shotgun proteomics experiments, (3) confirming or questioning gene models, and (4) adjusting gene models such that they are in line with observed Drosophila peptides. While the database consists of proteomic data it is not required that the user is a proteomics expert.