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PeptideAtlas is a catalog of peptide (and, secondarily, protein) identifications derived from shotgun proteomics experiments. Data is accepted from any lab in the world, then uniformly processed using the TPP to assign probabilities to peptide identifications. Because of the uniform processing, the peptide identifications from all experiments in PeptideAtlas can be compared to one another. The uses of PeptideAtlas include:

  • Seeing which proteins are found in various organisms, tissues, cell types, bodily fluids, and disease states
  • Approximating protein abundance by counting how many spectra correspond to a particular protein
  • Finding proteotypic peptides for targeted proteomics protocols -- in other words, finding peptides that are detectable using mass spectrometry and that can uniquely identify a protein
  • Examining the spectra that correspond to a peptide identification to further evaluate that identification
  • In cases of ambiguous protein identification, viewing a sequence alignment of all proteins that include a particular peptide
  • Learning more about any identified protein via links to external resources


PeptideAtlas:Chromosomal coverage


Eric W Deutsch, Henry Lam & Ruedi Aebersold: PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows,

EMBO reports 9, 5, 429–434 (2008) PDF

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