PeptideAtlas
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Glossary/Terms:
  Atlas nomenclature
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PeptideAtlas Builds

PeptideAtlas builds are performed for individual organisms and important sample groups (e.g., plasma/serum). The data products of these individual builds may accessed interactively in the database or they may be downloaded in their entirety below.

Builds are performed separately for different PeptideProphet cutoff levels. A link named "P≥0.9" denotes a build in which only peptides that were scored by PeptideProphet with a P≥0.9 are included.


Build Name Number of Samples Number of MS/MS spectra (P≥0.9) Number of non-singleton Peptides (P≥0.9) Target Databases
Human
(Apr 2007 Build)
122 1,991,229 53,044 Ensembl 43.36e
Human Plasma
(Apr 2007 Build)
52 1,445,022 16,558 Ensembl 43.36e
Human Plasma SpectraST
(Jul 2007 Build)
40 2,218,286 14,602 Ensembl 43.36e
Saccharomyces cerevisiae
(Feb 2006 Build)
47 600,960 36,133 SGD Feb 2006
Drosophila Melanogaster
(Jul 2004 Build)
3 19,160 4442 Ensembl 22.3a
Mouse Plasma
(May 2007 Build)
4 800,507 13,779 Ensembl 43.36d

Human (Homo sapiens)

The Human PeptideAtlas contains samples from many types of human tissues, cell lines, and fluids. The current Apr 2007 build contains 53,044 distinct non-singleton peptides above P≥0.9 from 122 samples. The false discovery rate for peptides in this list is estimated at 6.6%.

Available Builds:
Human Apr 2007 Build
Human Jul 2006 Build
Human Apr 2006 Build
Human Jul 2004 Build (published in Desiere et al. 2004)
Human Apr 2004 Build
[DOWNLOAD]

Human Plasma (Homo sapiens)

The Human Plasma PeptideAtlas contains only human plasma and serum samples. Plasma is henceforth used here to refer to both plasma and serum. Most of the data generated as part of the Human Proteome Organization (HUPO) Plasma Proteome Project (PPP), for which aliquots of several standard samples were sent to labs around the world for independent analysis, is included here, in addition to other major contributors. The current Apr 2007 build contains 16,558 distinct non-singleton peptides above P≥0.9 from 52 samples. The false discovery rate for peptides in this list is estimated at 6.6%.

Available Builds:
Human Plasma SpectraST Jul 2007 Build (special publication build)
Human Plasma Apr 2007 Build
Human Plasma Aug 2006 Build
Human Plasma Aug 2005 Build
Human Plasma Mar 2005 Build (published in Deutsch et al. 2005)
[DOWNLOAD]

Fly (Drosophila melanogaster)

The Drosophila PeptideAtlas is currently comprised of only 3 samples from the S2 Schneider cell line. Many additional samples are being run at the ETH Zurich and the Functional Genomics Center Zurich in collaboration with the PeptideAtlas project and they will begin generating new Drosophila PeptideAtlas builds with many more datasets.

Available Builds:
Drosophila Melanogaster Jul 2004 Build (published in Desiere et al. 2004)
Drosophila Melanogaster Feb 2004 Build
[DOWNLOAD]

Yeast (Saccharomyces cerevisiae)

The Yeast PeptideAtlas build contains The current Apr 2007 build contains 16,558 distinct non-singleton peptides above P≥0.9 from 52 samples.

Available Builds:

Saccharomyces cerevisiae Feb 2006 Build
[DOWNLOAD]


Mouse Plasma (Mus musculus)

The Mouse Plasma PeptideAtlas contains data from mass spec analysis of plasma samples from various strains of cancer mouse models. This May 2007 build contains 13,779 distinct non-singleton peptides above P≥0.9 from 4 samples. The false discovery rate for peptides in this list is estimated at 1.2%.

Available Builds:

Mouse Plasma May 2007 Build (Zhang et. al 2008, submitted)
[DOWNLOAD]

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