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. 2006 Jan 1;34(Database issue):D655-8.
doi: 10.1093/nar/gkj040.

The PeptideAtlas project

Frank Desiere  1 , Eric W Deutsch, Nichole L King, Alexey I Nesvizhskii, Parag Mallick, Jimmy Eng, Sharon Chen, James Eddes, Sandra N Loevenich, Ruedi Aebersold
Affiliations

The PeptideAtlas project

Frank Desiere et al. Nucleic Acids Res. .

Abstract

The completion of the sequencing of the human genome and the concurrent, rapid development of high-throughput proteomic methods have resulted in an increasing need for automated approaches to archive proteomic data in a repository that enables the exchange of data among researchers and also accurate integration with genomic data. PeptideAtlas (http://www.peptideatlas.org/) addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms. A meaningful comparison of data across different experiments generated by different groups using different types of instruments is enabled by the implementation of a uniform analytic process. This uniform statistical validation ensures a consistent and high-quality set of peptide and protein identifications. The raw data from many diverse proteomic experiments are made available in the associated PeptideAtlas repository in several formats. Here we present a summary of our process and details about the Human, Drosophila and Yeast PeptideAtlas builds.

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Figures

Figure 1
Figure 1
PeptideAtlas analysis pipeline for the annotation of genomes with high-quality peptide sequences derived from high-throughput 2D-LC-MS/MS analysis of biological samples.
Figure 2
Figure 2
Plots: cumulative number of MS/MS spectra versus cumulative number of distinct peptides (all spectra and peptides correspond to peptide identifications with probabilities ≥0.9). The figure will show saturation when new spectra do not yield new peptide identifications. Tables: statistics for atlas builds (number of experiments, number of spectra that yielded a peptide identification with probability P ≥ 0.9, number of distinct peptides identified, number of proteins identified and percentage of all genes to which the proteins map).
Figure 3
Figure 3
Peptide view in the PeptideAtlas web-based database interface. For the specified peptide (by accession number or sequence) a summary is displayed indicating individual attributes of the peptide, protein and genome mapping information, and the samples in which it has been observed. Different information is available in other views. Additionally there are two-way links to the Ensembl genome browser that allow users to see PeptideAtlas peptides as tracks in the genome browser and link out for more information. Additional information is available at our website.
See this image and copyright information in PMC

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