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.

Below are individual Human Plasma PeptideAtlas builds available for download in various flat file formats. Not all of the files contain complete information from the build, nor are all file formats available for every build. A complete description of each of the available download formats is available. Link names encode the PeptideProphet cutoff used when creating that build, for example a link named "P≥0.9" denotes a build in which only peptides where P≥0.9 are included.

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

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

Peptide CDS coordinates: P ≥0.9

Peptide CDS and chromosomal coordinates: P ≥0.9

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

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

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

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 -

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 -