Background: Crucial foundations of any quantitative systems biology experiment are correct genome and proteome annotations in the reference databases used. Protein databases compiled from high quality empirical protein identifications, which are - in turn - based on correct gene models, increase the sensitivity and quantitative accuracy of proteomics experiments. Results: In this manuscript, we present the Drosophila melanogaster PeptideAtlas, a fly proteomics and genomics resource of unsurpassed depth. The portal www.drosophila-peptideatlas.org
allows querying the observed proteome of the fly with respect to gene model confirmation and splice site verification as well as for the identification of proteotypic peptides suited for targeted mass spectrometric studies. The database also provides consensus mass spectra for observed peptides as well as qualitative and quantitative information about the number of observations of a particular peptide and the sample(s) in which it was observed. Conclusions: PeptideAtlas can be used for the design and improved application of shotgun as well as targeted proteomics experiments. We also show how the data contained in the atlas can be used to confirm or draw in question gene models.