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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
|
Human
(Apr 2007 Build) |
122 |
1,991,229 |
53,044 |
Ensembl 43.36e |
Human Plasma
(Apr 2007 Build) |
52 |
1,445,022 |
16,558 |
Ensembl 43.36e |
Human Plasma SpectraST
(Jul 2007 Build) |
40 |
2,218,286 |
14,602 |
Ensembl 43.36e |
Saccharomyces cerevisiae
(Feb 2006 Build) |
47 |
600,960 |
36,133 |
SGD Feb 2006 |
Drosophila Melanogaster
(Jul 2004 Build) |
3 |
19,160 |
4442 |
Ensembl 22.3a |
Mouse Plasma
(May 2007 Build) |
4 |
800,507 |
13,779 |
Ensembl 43.36d |
Human (Homo sapiens)
The Human PeptideAtlas contains samples from many types of human tissues,
cell lines, and fluids. The current Apr 2007 build contains
53,044 distinct non-singleton peptides above P≥0.9 from 122 samples.
The false discovery rate for peptides in this list is estimated at 6.6%.
Available Builds:
 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 Apr 2007 build contains
16,558 distinct non-singleton peptides above P≥0.9 from 52 samples.
The false discovery rate for peptides in this list is estimated at 6.6%.
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]
Fly (Drosophila melanogaster)
The Drosophila PeptideAtlas is currently comprised of only 3 samples
from the S2 Schneider cell line. Many additional samples are being
run at the ETH Zurich and the Functional Genomics Center Zurich in
collaboration with the PeptideAtlas project and they will begin
generating new Drosophila PeptideAtlas builds with many more datasets.
Available Builds:
Drosophila Melanogaster Jul 2004 Build (published in Desiere et al. 2004)
Drosophila Melanogaster Feb 2004 Build
[DOWNLOAD]
Yeast (Saccharomyces cerevisiae)
The Yeast PeptideAtlas build contains
The current Apr 2007 build contains
16,558 distinct non-singleton peptides above P≥0.9 from 52 samples.
Available Builds:
Saccharomyces cerevisiae Feb 2006 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 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 (Zhang et. al 2008, submitted)
[DOWNLOAD]
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