The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation
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Date
2009-02
Publication Type
Journal Article
ETH Bibliography
yes
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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 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.
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Publication status
published
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Book title
Journal / series
Volume
10
Pages / Article No.
59
Publisher
BioMed Central
Event
Edition / version
Methods
Software
Geographic location
Date collected
Date created
Subject
Proteomics Experiment; Shotgun Proteomics; Proteotypic Peptide; Peptide Data; Consensus Spectrum
Organisational unit
03663 - Aebersold, Rudolf (emeritus) / Aebersold, Rudolf (emeritus)