PeptideAtlas
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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
Caenorhabditis elegans
(May 2008 Build)
23 767,040 52,594 Ensembl C.Elegans Protein Set 49-180a + Worm 170
Halobacterium
(July 2006 Build)
88 636,300 12,318 Halobacterium GFF
Human
(Mar 2009 Build)
220 6683326 83931 Ensembl protein set 49 plus IPI 3.26
Human Plasma SpectraST
(Jul 2007 Build)
40 2,218,286 14,602 Ensembl 43.36e
Human Plasma
(Apr 2007 Build)
52 1,445,022 16,558 Ensembl 43.36e
Leptospira interrogans
(Jan 2008 Build)
6 141933 14533 LInterrogans_200802_build
Mouse Plasma
(May 2007 Build)
4 800,507 13,779 Ensembl 43.36d
Yeast
(Apr 2009 Build)
60 2512202 60720 Yeast Combined Nonredundant sequences 2007-02-07 forward and decoy
Yeast MRM
(Feb 2008 Build)
1 29720 3310 Yeast Combined Nonredundant sequences 2007-02-07 forward and decoy
Streptococcus
(Feb 2007 Build)
5 48174 5360 Streptococcus pyogenes protein list v?


Human (Homo sapiens)

The Human PeptideAtlas contains samples from many types of human tissues, cell lines, and fluids. The current Mar 2009 build contains 83931 distinct non-singleton peptides above P≥0.9 from 220 samples. The false discovery rate for peptides in this list is estimated at 1.1%.

Available Builds:
Human Mar 2009 Build
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 Jul 2007 build contains 14,602 distinct non-singleton peptides above P≥0.9 from 40 samples. The false discovery rate for peptides in this list is estimated at 1.1%.

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]


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
[DOWNLOAD]


Halobacterium (Halobacterium salinarum NRC-1)

The Halobacterium PeptideAtlas July 2006 build contains 12,318 distinct non-singleton peptides above P≥0.9 from 88 samples. The false discovery rate for peptides in this list is estimated at 1.1%. This represents coverage of some 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1.

Available Builds:
[DOWNLOAD]


C. elegans (Caenorhabditis elegans)

Caenorhabditis elegans May 2008 build contains 52,594 distinct non-singleton peptides above P≥0.9 from 23 samples. The false discovery rate for peptides in this list is estimated at 0.9%.

Available Builds:
Caenorhabditis elegans May 2008 Build
[DOWNLOAD]


Streptococcus (Streptococcus pyogenes)

Streptococcus pyogenes Feb 2007 build contains 5360 distinct non-singleton peptides above P≥0.9 from 5 samples. The false discovery rate for peptides in this list is estimated at 0.9%.

Available Builds:
Streptococcus Feb 2007 Build
[DOWNLOAD]


Yeast (Saccharomyces cerevisiae)

Saccharomyces cerevisiae Apr 2009 build contains 60720 distinct non-singleton peptides above P≥0.9 from 60 samples. The false discovery rate for peptides in this list is estimated at 0.09%.

Available Builds:
Yeast Apr 2009 Build
[DOWNLOAD]


Yeast MRM(Saccharomyces cerevisiae)

Saccharomyces cerevisiae Feb 2008 build contains 3310 distinct non-singleton peptides above P≥0.9 from 1 samples. The false discovery rate for peptides in this list is estimated at 1.3%.

Available Builds:
Yeast MRM Feb 2008 Build
[DOWNLOAD]


Leptospira interrogans (Leptospira interrogans)

Leptospira interrogans Jan 2008 build contains 14533 distinct non-singleton peptides above P≥0.9 from 6 samples. The false discovery rate for peptides in this list is estimated at 0.4%.

Available Builds:
Leptospira interrogans Jan 2008 Build
[DOWNLOAD]

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