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.
| Build Name |
Number of Samples |
Peptide Inclusion Cutoff |
Number of Peptide-Spectrum Matches (PSMs) |
Number of multiply observed Distinct Peptides |
Target Databases |
Caenorhabditis elegans (May 2008 Build) |
23 |
P>=0.9 |
767,040 |
52,594 |
Ensembl C.Elegans Protein Set 49-180a + Worm 170 |
Drosophila (July 2009 Build) |
51 |
PSM FDR =0.0008 |
367788 |
31184 |
fgcz_7227_20050105_Ens52 |
Halobacterium (July 2006 Build) |
88 |
P>=0.9 |
636,300 |
12,318 |
Halobacterium GFF |
Human (Jun 2009 Build) |
220 |
PSM FDR = 0.0001 |
2754771 |
38732 |
Ensembl + Swiss-Prot (incl. splice variants) + IPI |
Human Plasma (Nov 2009 Build) |
91 |
protein FDR 1.0% |
3,176,380 |
20,709 |
Ensembl + Swiss-Prot (incl. splice variants) + IPI |
Human Urine (Jan 2009 Build) |
6 |
P>=0.9 |
37,762 |
4012 |
Ensembl + IPI |
Leptospira interrogans (Jan 2008 Build) |
6 |
P>=0.9 |
141933 |
14533 |
LInterrogans_200802_build |
Mouse Plasma (Dec 2009 Build) |
4 |
PSM FDR = 0.001% |
263,986 |
2310 |
Ensembl + Swiss-Prot (incl. splice variants) + IPI |
Yeast (May 2009 Build) |
62 |
PSM FDR=0.01% |
2,697,580 |
47,923 |
Yeast Combined Nonredundant sequences 2007-02-07 forward and decoy |
Yeast MRM (Feb 2008 Build) |
1 |
P>=0.9 |
29720 |
3310 |
Yeast Combined Nonredundant sequences 2007-02-07 forward and decoy |
Streptococcus (Feb 2007 Build) |
5 |
P>=0.9 |
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 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]
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