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Full 2025-08 Build Summary
158datasets
356experiments
30,695MS runs
183,728,465PSMs
282,399distinct peptides
4,583canonical proteins

About

The Human Plasma PeptideAtlas provides a compendium of results from uniformly reprocessed mass spectrometry proteomics datasets.

Available Human Plasma datasets were reprocessed from the raw files using the Trans-Proteomic Pipeline suite of tools.

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The Human Proteome Organization (HUPO) in 2003 launched an effort to combine results from the many labs around the world who were working on the human plasma proteome. This effort, the Human Plasma Proteome Project (HPPP), continues today and the PeptideAtlas is an integral part of that effort.

Phase I of the effort, completed in 2005, involved the collection of plasma proteomics results from 18 laboratories and resulted in a list of 3020 identified proteins identified with two or more peptides regardless of laboratory or specimen. (Omenn et al., Proteomics, 2005). Later that year, States et al. applied rigorous statistical approach to the same data, yielding a reduced set of 889 proteins with at least 95% confidence in protein identification. Also in that same year, the first Human Plasma PeptideAtlas was constructed from 28 datasets, 20 of them from PPP I. The last PeptideAtlas build contained over 3000 distinct proteins.

The latest publication summarizing the state of the Human Plasma Proteome Project can be found at Advances and Utility of the Human Plasma Proteome, Deutsch EW, Omenn GS, Sun Z, Maes M, Pernemalm M, Palaniappan KK, Letunica N, Vandenbrouck Y, Brun V, Tao SC, Yu X, Geyer PE, Ignjatovic V, Moritz RL, Schwenk JM, J Proteome Res. 2021 Dec 3;20(12):5241-5263

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Chromosome Summary

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Column descriptions ▲
Entries: Number of entries in each chromosome
Canonical: Proteins seen with 2 distinct, uniquely mapping peptides
Uncertain: Proteins with some evidence that is not sufficient for canonical status
Redundant: Proteins that have peptides that map to them, but not uniquely and thus not needed to explain the observed peptides
Not Observed: No detections at all in PeptideAtlas above our very stringent threshold

Publications

If you use the Human Plasma PeptideAtlas builds for your work, please cite:

  • Deutsch EW, Omenn GS, Sun Z, Maes M, Pernemalm M, Palaniappan KK, Letunica N, Vandenbrouck Y, Brun V, Tao SC, Yu X, Geyer PE, Ignjatovic V, Moritz RL, Schwenk JM, Advances and Utility of the Human Plasma Proteome, J Proteome Res. 2021 Dec 3;20(12):5241-5263

    • Older Publications

    Original HPPP Papers

    Download

    Below are individual Human Plasma PeptideAtlas builds available for download in various flat file formats. Note that not all files contain all information from the build. A build subtitled "PSM FDR=0.002" denotes a PSM FDR threshold of 0.002 (0.2%) is applied to every sample in the build.

    Human Plasma 2025-08 PSM FDR = 0.00005Latest Build
    • Biosequence Set in FASTA format [548MB]
    • Database tables exported as TSV dump file [265MB]
    • Database tables exported as mysql dump file [286MB]
    • Peptide CDS and chromosomal coordinates [481MB]
    • Peptide CDS coordinates [279MB]
    • Peptide sequences in FASTA format [8MB]
    Human Plasma 2023-04 PSM FDR = 0.00008
    • Biosequence Set in FASTA format [700MB]
    • Peptide CDS and chromosomal coordinates [484MB]
    • Peptide CDS coordinates [282MB]
    • Peptide sequences in FASTA format [8MB]
    View Older Downloads ▲
    Human Plasma 2021-07 PSM FDR = 0.0002
    • Biosequence Set in FASTA format [511MB]
    • Database tables exported as mysql dump file [158MB]
    • Peptide CDS and chromosomal coordinates [305MB]
    • Peptide CDS coordinates [173MB]
    • Peptide sequences in FASTA format [6MB]
    Human Plasma 2017-04 PSM FDR = 0.00025
    • Biosequence Set in FASTA format [2GB]
    • Peptide CDS and chromosomal coordinates [177MB]
    • Peptide CDS coordinates [97MB]
    • Peptide sequences in FASTA format [3MB]
    Human Plasma 2015-09 PSM FDR = 0.0003
    • Biosequence Set in FASTA format [4GB]
    • Peptide CDS and chromosomal coordinates [132MB]
    • Peptide CDS coordinates [72MB]
    • Peptide sequences in FASTA format [2MB]
    Human Plasma 2013-08 PSM FDR = 0.0003
    • Biosequence Set in FASTA format [278MB]
    • Database tables exported as an XML file [56MB]
    • Database tables exported as mysql dump file [30MB]
    • Peptide CDS and chromosomal coordinates [49MB]
    • Peptide CDS coordinates [23MB]
    • Peptide sequences in FASTA format [1MB]
    Human Plasma 2012-08 PSM FDR = 0.00005
    • Biosequence Set in FASTA format [229MB]
    • Database tables exported as an XML file [286MB]
    • Database tables exported as mysql dump file [167MB]
    • Peptide CDS and chromosomal coordinates [43MB]
    • Peptide CDS coordinates [20MB]
    • Peptide sequences in FASTA format [1MB]
    Human Plasma 2010-05 PSM FDR = 0.00004
    • Biosequence Set in FASTA format [157MB]
    • Database tables exported as an XML file [109MB]
    • Database tables exported as mysql dump file [65MB]
    • Peptide CDS and chromosomal coordinates [17MB]
    • Peptide CDS coordinates [8MB]
    • Peptide sequences in FASTA format [616KB]
    Human Plasma 2009-11 Protein FDR = 0.01
    • Biosequence Set in FASTA format [131MB]
    • Database tables exported as an XML file [176MB]
    • Database tables exported as mysql dump file [76KB]
    • Peptide CDS and chromosomal coordinates [13MB]
    • Peptide CDS coordinates [6MB]
    • Peptide sequences in FASTA format [619KB]

    Help

    Complete description of each of the available download formats

    Other Resources

    Acknowledgements

    We gratefully acknowledge the support for the Human Plasma PeptideAtlas from NSF grant 2324882 “Globally harmonized re-analysis of Data Independent Acquisition (DIA) proteomics datasets enables the creation of new resources (DIA-eXchange)”.

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