≡   PeptideAtlas Links Seattle Proteome Center

PeptideAtlas: Home Overview Contacts Publications Software Database Schema Feedback Funding FAQ
Atlas Data: Data Repository HPPP Data Central PeptideAtlas Builds PeptideAtlas Exports THISP Search Database
Contribute Data

Related: SRMAtlas PASSEL SWATHAtlas
Spectral Libs: Libraries + Info SpectraST Search

Glossary/Terms: Atlas nomenclature Protein ID terms

LOG IN
MENU
Log In
Full 2023-04 Build Summary
113datasets
313experiments
35,801MS runs
108,946,902PSMs
263,150distinct peptides
4,608canonical 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.

Read more ▲

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

Explore

SEARCH(e.g. P00747)

Chromosome Summary

ChromosomeneXtProt entriesCanonicalUncertainRedundantNot Observed
1 2,065 505 24.5% 183 8.9% 217 10.5% 1,160 56.2%
2 1,295 326 25.2% 96 7.4% 137 10.6% 736 56.8%
3 1,076 269 25.0% 85 7.9% 101 9.4% 621 57.7%
4 766 178 23.2% 69 9.0% 96 12.5% 423 55.2%
5 887 205 23.1% 72 8.1% 114 12.9% 496 55.9%
6 1,029 222 21.6% 91 8.8% 136 13.2% 580 56.4%
7 1,029 206 20.0% 83 8.1% 101 9.8% 639 62.1%
8 706 153 21.7% 56 7.9% 70 9.9% 427 60.5%
9 806 179 22.2% 54 6.7% 79 9.8% 494 61.3%
10 748 179 23.9% 69 9.2% 71 9.5% 429 57.4%
11 1,333 293 22.0% 104 7.8% 136 10.2% 800 60.0%
12 1,035 239 23.1% 99 9.6% 99 9.6% 598 57.8%
13 333 61 18.3% 31 9.3% 49 14.7% 192 57.7%
14 736 199 27.0% 44 6.0% 73 9.9% 420 57.1%
15 609 120 19.7% 48 7.9% 66 10.8% 375 61.6%
16 843 172 20.4% 89 10.6% 99 11.7% 483 57.3%
17 1,170 293 25.0% 104 8.9% 123 10.5% 650 55.6%
18 270 61 22.6% 19 7.0% 44 16.3% 146 54.1%
19 1,437 312 21.7% 113 7.9% 146 10.2% 866 60.3%
20 550 119 21.6% 56 10.2% 61 11.1% 314 57.1%
21 247 46 18.6% 23 9.3% 26 10.5% 152 61.5%
22 506 143 28.3% 40 7.9% 60 11.9% 263 52.0%
X 850 132 15.5% 76 8.9% 93 10.9% 549 64.6%
Y 48 0 0.0% 2 4.2% 8 16.7% 38 79.2%
MT 15 1 6.7% 0 0.0% 4 26.7% 10 66.7%
? 6 0 0.0% 0 0.0% 0 0.0% 6 100.0%

PEneXtProt entriesCanonicalUncertainRedundantNot Observed
1 18,397 4,603 25.0% 1,672 9.1% 2,028 11.0% 10,094 54.9%
2 1,151 3 0.3% 23 2.0% 106 9.2% 1,019 88.5%
3 215 0 0.0% 1 0.5% 16 7.4% 198 92.1%
4 15 0 0.0% 0 0.0% 0 0.0% 15 100.0%
5 611 2 0.3% 10 1.6% 59 9.7% 540 88.4%
1-4 19,778 4,606 23.3% 1,696 8.6% 2,150 10.9% 11,326 57.3%
2023-04 Total 20,389 4,608 22.6% 1,706 8.4% 2,209 10.8% 11,866 58.2%

ChromosomeAll (PE 1-5)PE1PE2PE3PE4PE5PE1-4
1 2,065 1,864 117 35 2 47 2,018
2 1,295 1,229 45 3 0 18 1,277
3 1,076 1,006 45 6 0 19 1,057
4 766 707 27 12 0 20 746
5 887 838 34 2 0 13 874
6 1,029 938 52 4 1 34 995
7 1,029 878 90 7 3 51 978
8 706 627 32 10 1 36 670
9 806 703 51 8 2 42 764
10 748 690 38 1 1 18 730
11 1,333 1,072 151 69 0 41 1,292
12 1,035 962 40 8 0 25 1,010
13 333 310 10 2 0 11 322
14 736 648 58 15 2 13 723
15 609 534 41 3 0 31 578
16 843 775 40 2 1 25 818
17 1,170 1,080 60 4 0 26 1,144
18 270 255 5 0 0 10 260
19 1,437 1,318 77 12 1 29 1,408
20 550 509 24 1 0 16 534
21 247 198 22 4 0 23 224
22 506 454 24 4 1 23 483
X 850 758 57 2 0 33 817
Y 48 33 7 1 0 7 41
MT 15 15 0 0 0 0 15
? 6 2 4 0 0 0 6
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 2023-04 PSM FDR = 0.00008Latest Build
    • Biosequence Set in FASTA format [700MB]
    • Peptide CDS and chromosomal coordinates [484MB]
    • Peptide CDS coordinates [282MB]
    • Peptide sequences in FASTA format [8MB]
    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 1933311 “PTMexchange: Globally harmonized re-analysis and sharing of data on post-translational modifications”.