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The PeptideAtlas project.

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 ( 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.

Pubmed ID: 16381952


  • Desiere F
  • Deutsch EW
  • King NL
  • Nesvizhskii AI
  • Mallick P
  • Eng J
  • Chen S
  • Eddes J
  • Loevenich SN
  • Aebersold R


Nucleic acids research

Publication Data

January 1, 2006

Associated Grants

  • Agency: NHLBI NIH HHS, Id: N01-HV-28179

Mesh Terms

  • Animals
  • Chromosome Mapping
  • Databases, Protein
  • Drosophila Proteins
  • Humans
  • Internet
  • Mass Spectrometry
  • Peptide Fragments
  • Proteome
  • Proteomics
  • Saccharomyces cerevisiae Proteins
  • Sequence Analysis, Protein
  • User-Computer Interface