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.

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]