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.

Each build has a peptide inclusion cutoff criterion. A build with a cutoff of "P≥0.9" is a build in which only peptides with a PeptideProphet probability of at least 0.9 are included. A cutoff of "FDR 1%" denotes a build (generally including peptides with much higher probabilities than 0.9) with a protein false discovery rate of 1%.

For builds with P≥0.9 cutoffs, PSMs and peptides are counted only for multiply observed peptides; singletons are omitted because these identifications are quite unreliable at this generous cutoff.

Human (Homo sapiens)

The Human PeptideAtlas contains samples from many types of human tissues, cell lines, and fluids. The current Jun 2009 build contains 38732 distinct non-singleton peptides above P≥0.9 from 220 samples.

Available Builds:
Human Jun 2009 Build
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]

Sorry, download not yet available for June 2009 build.

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) is included here, in addition to many other major contributors. The current Nov 2009 build contains 20,709 distinct peptides above P≥0.9 from 91 samples. The false discovery rate for peptides in this list is estimated at 0.02%.

Available Builds:
Human Plasma Nov 2009 Build
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]

Human Urine (Homo sapiens)

The current Jan 2009 build contains 4012 total distinct peptides above P≥0.9 from 6 samples.

Available Builds:
Human Urine Jan 2009 Build

Sorry, download not yet available.

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 Dec 2009 build contains 2310 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 Dec 2009 Build
Mouse Plasma May 2007 Build
[DOWNLOAD]

Sorry, download not yet available for 2009 build.

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 May 2009 build contains 47,923 distinct non-singleton peptides above P≥0.9 from 62 samples. The false discovery rate for peptides in this list is estimated at .

Available Builds:
Yeast May 2009 Build
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]

Drosophila (Drosophila melanogaster)

Drosophila melanogaster July 2009 build contains 31184 distinct peptides above spectrum FDR threshold of 0.0008 from 51 samples.

Available Builds:
Drosophila July 2009 Build
[DOWNLOAD]