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 Distinct Peptides |
Target Databases |
C Elegans (June 2010 Build) |
25 |
PSM FDR = 0.0025 |
798263 |
49438 |
Ensembl C elegans Protein Set v57 + wormbase 215 + crap + decoys |
C Elegans phoso (June 2010 Build) |
2 |
PSM FDR = 0.015 |
45887 |
4918 |
Ensembl C elegans Protein Set v57 + wormbase 215 + crap + decoys |
Drosophila (June 2010 Build) |
53 |
PSM FDR = 0.001 |
391447 |
32234 |
fgcz_7227_20050105_Ens52_new |
Halobacterium (July 2006 Build) |
88 |
P>=0.9 |
636,300 |
12,318 |
Halobacterium GFF |
Human (May 2010 Build) |
234 |
PSM FDR = 0.0003 |
5402374 |
56304 |
Ensembl Human Protein Set v57.37+ IPI v3.71 + Swiss-Prot 2010_04 + cRAP + decoys |
Human plasma (May 2010 Build) |
91 |
no single PSM FDR cutoff or probability threshold for this build |
3169067 |
16987 |
Ensembl Human Protein Set v57.37+ IPI v3.71 + Swiss-Prot 2010_04 + cRAP + decoys |
Human urine (June 2010 Build) |
6 |
PSM FDR = 0.003 |
34559 |
3953 |
Ensembl Human Protein Set v57.37+ IPI v3.71 + Swiss-Prot 2010_04 + cRAP + decoys |
Leptospira interrogans (Jan 2008 Build) |
6 |
P>=0.9 |
141933 |
14533 |
LInterrogans_200802_build |
Mouse (June 2010 Build) |
84 |
PSM FDR = 0.001% |
1815096 |
38574 |
Ensembl Mouse Protein Set v37.57 + IPI v3.72 + Swiss-Prot 2010_04 + cRAP + decoys |
Mouse Plasma (June 2010 Build) |
19 |
PSM FDR = 0.0001 |
757887 |
5946 |
Ensembl Mouse Protein Set v37.57 + IPI v3.72 + Swiss-Prot 2010_04 + cRAP + decoys |
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 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]
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