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 May 2010 build contains 56304 distinct non-singleton peptides above P≥0.9 from 234 samples.

Available Builds:
Human May 2010 Build
Human Jun 2009 Build
Human Mar 2009 Build
Human Jul 2004 Build (published in Desiere et al. 2004)
[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) is included here, in addition to many other major contributors. The current May 2010 build contains 16987 distinct peptides above P≥0.9 from 91 samples. The false discovery rate for peptides in this list is estimated at .

Available Builds:
Human plasma May 2010 Build
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 June 2010 build contains 3953 total distinct peptides above P≥0.9 from 6 samples.

Available Builds:
Human urine June 2010 Build
Human Urine Jan 2009 Build
[DOWNLOAD]

Mouse (Mus musculus)

The Mouse PeptideAtlas contains data from mass spec analysis of different mouse tissue samples. This June 2010 build contains 38574 distinct peptides from 84 samples.

Available Builds:
Mouse June 2010 Build
Mouse Aug 2009 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 June 2010 build contains 5946 distinct non-singleton peptides above P≥0.9 from 19 samples. The false discovery rate for peptides in this list is estimated at .

Available Builds:
Mouse Plasma June 2010 Build
Mouse Plasma Dec 2009 Build
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 June 2010 build contains 49438 distinct non-singleton peptides above P≥0.9 from 25 samples. The false discovery rate for peptides in this list is estimated at .

Available Builds:
C Elegans June 2010 Build
Caenorhabditis elegans May 2008 Build
[DOWNLOAD]

C Elegans Phospho (Caenorhabditis elegans)

Caenorhabditis elegans Phospho June 2010 build contains 4918 distinct non-singleton peptides above PSM FDR = 0.015 from 2 samples.

Available Builds:
C Elegans phoso June 2010 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 June 2010 build contains 32234 distinct peptides above spectrum FDR threshold of 0.0008 from 53 samples.

Available Builds:
Drosophila June 2010 Build
Drosophila July 2009 Build
[DOWNLOAD]