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Below are individual Human PeptideAtlas builds available for download in various flat file formats. Note that not all files contain all information from the build. A link named "P>=0.9" denotes a build in which only peptides that were scored by PeptideAtlas with a P>=0.9 are included.

CURRENT BUILD: Human plasma 201005

Peptide sequences in FASTA format:
APD_Hs_all.fasta

Biosequence Set in FASTA format:
Homo_sapiens.fasta

Peptide CDS coordinates:
APD_ensembl_hits.tsv

Database tables exported as an XML file:
atlas_build_234.xml.gz

Database tables exported as mysql dump file:
P >= 0.0

Peptide CDS and chromosomal coordinates:
coordinate_mapping.txt

OLDER BUILDS
November 2009 Build

This Build includes results of SpectraST spectral library searching on 69 non-glycocapture experiments, and of X!Tandem searching on 22 glycocapture experiments, and includes all plasma data we have collected at ISB to date, except Q-TOF data. This build is a merging of the Human Plasma Non-Glyco (PSM FDR 0.0002) and Human Plasma Glyco builds (PSM FDR 3.0e-05). Thus, there is no single PSM FDR cutoff or probability threshold for this build. It includes at least thirteen PPP-II experiments to 2007-04 Human Plasma build.

Peptide sequences in FASTA format:
APD_Hs_all.fasta

Biosequence Set in FASTA format:
Homo_sapiens.fasta

Peptide CDS coordinates:
APD_ensembl_hits.tsv

Database tables exported as an XML file:
atlas_build_204.xml.gz

Database tables exported as mysql dump file:
atlas_build_204.mysql.gz

Peptide CDS and chromosomal coordinates:
coordinate_mapping.txt

April 2007 BUILD

Although earlier builds are discussed in greater detail in Deutsch et al. 2005, the latest build is not yet described in a publication. Please cite the latest PeptideAtlas publication in any publications that make use of these data, and be sure to reference the YYYY-MM of the build used for your analysis.

Peptide sequences in FASTA format: P ≥0.9

Peptide CDS coordinates: P ≥0.9

Peptide CDS and chromosomal coordinates: P ≥0.9

Database tables exported as an XML file: P ≥0.9

Database tables exported as mysql dump file: P ≥0.9

SPECIAL BUILD: July 2007 SpectraST Build (limited to published datasets)

Special Build of 40 public human plasma samples described in Lam et al. (submitted)

Peptide sequences in FASTA format: P ≥0.9

Peptide CDS coordinates: P ≥0.9

Peptide CDS and chromosomal coordinates: P ≥0.9

Database tables exported as an XML file: P ≥0.9

Database tables exported as mysql dump file: P ≥0.9

November 2006 Build
Peptide sequences in FASTA format: P ≥0.9

Peptide CDS coordinates: P ≥0.9

Peptide CDS and chromosomal coordinates: P ≥0.9

August 2006 Build

The August 2006 build contains 13,322 distinct peptides observed at least twice with a minimum assigned P≥0.9 from 45 samples. The false discovery rate for peptides in this list is estimated at 6.8%.

Peptide sequences in FASTA format: P ≥0.9

Peptide CDS coordinates: P ≥0.9

Peptide CDS and chromosomal coordinates: P ≥0.9

Database tables exported as an XML file: P ≥0.9

Database tables exported as mysql dump file: P ≥0.9

February 2006 Build

The February 2006 build contains 18,529 distinct peptides observed at least twice with a minimum assigned P≥0.9 from 40 samples. The false discovery rate for peptides in this list is estimated at 2.7%.

Peptide sequences in FASTA format: P ≥0.9

Peptide CDS coordinates: P ≥0.9

Peptide CDS and chromosomal coordinates: P ≥0.9

This build is contaminated with a non-plasma sample and should no longer be used.
August 2005 ALL build

The August 2005 ALL build contains 10,091 distinct peptides observed one or more times with a minimum assigned P≥0.9 from 35 samples.

Peptide sequences in FASTA format: P ≥0.9

Peptide CDS coordinates: P ≥0.9

Peptide CDS and chromosomal coordinates: P ≥0.9

March 2005 ALL build

The March 2005 ALL build contains 6,929 distinct peptides observed one or more times with a minimum assigned P≥0.9 from 28 samples.

These data are discussed in detail in Deutsch et al. 2005. Please cite this paper in any publications that make use of these data.

Peptide sequences in FASTA format: P ≥0.7 - P ≥0.9 - P ≥0.99 -

Peptide CDS coordinates: P ≥0.7 - P ≥0.9 - P ≥0.99 -

Peptide CDS and chromosomal coordinates: P ≥0.7 - P ≥0.9 - P ≥0.99 -

HUPO-ONLY BUILD: March 2005 HUPO build

The current March 2005 HUPO-only build contains 4,761 distinct peptides observed one or more times with a minimum assigned P≥0.9 from 20 HUPO Plasma Proteome Project samples.

Peptide sequences in FASTA format: P ≥0.7 - P ≥0.9 - P ≥0.99 -

Peptide CDS coordinates: P ≥0.7 - P ≥0.9 - P ≥0.99 -

Peptide CDS and chromosomal coordinates: P ≥0.7 - P ≥0.9 - P ≥0.99 -