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Full 2021-07 Build Summary
69datasets
240experiments
59,263,220PSMs
206,001distinct peptides
4,395canonical 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 Schwenk et al. 2017.

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Chromosome Summary

ChromosomeneXtProt entriesCanonicalUncertainRedundantNot Observed
1 2,067 480 23.2% 173 8.4% 230 11.1% 1,184 57.3%
2 1,295 314 24.2% 97 7.5% 131 10.1% 753 58.1%
3 1,079 254 23.5% 74 6.9% 109 10.1% 642 59.5%
4 769 163 21.2% 62 8.1% 122 15.9% 422 54.9%
5 877 200 22.8% 65 7.4% 112 12.8% 500 57.0%
6 1,029 213 20.7% 66 6.4% 134 13.0% 616 59.9%
7 1,025 193 18.8% 60 5.9% 110 10.7% 662 64.6%
8 702 142 20.2% 46 6.6% 64 9.1% 450 64.1%
9 809 170 21.0% 48 5.9% 94 11.6% 497 61.4%
10 748 167 22.3% 68 9.1% 79 10.6% 434 58.0%
11 1,331 275 20.7% 100 7.5% 146 11.0% 810 60.9%
12 1,036 238 23.0% 72 6.9% 117 11.3% 609 58.8%
13 333 58 17.4% 24 7.2% 49 14.7% 202 60.7%
14 735 188 25.6% 39 5.3% 77 10.5% 431 58.6%
15 606 116 19.1% 39 6.4% 77 12.7% 374 61.7%
16 843 162 19.2% 76 9.0% 99 11.7% 506 60.0%
17 1,169 280 24.0% 102 8.7% 128 10.9% 659 56.4%
18 275 62 22.5% 20 7.3% 42 15.3% 151 54.9%
19 1,436 294 20.5% 93 6.5% 161 11.2% 888 61.8%
20 549 116 21.1% 49 8.9% 57 10.4% 327 59.6%
21 254 41 16.1% 26 10.2% 24 9.4% 163 64.2%
22 505 140 27.7% 30 5.9% 66 13.1% 269 53.3%
X 847 130 15.3% 59 7.0% 88 10.4% 570 67.3%
Y 47 1 2.1% 0 0.0% 8 17.0% 38 80.9%
MT 15 1 6.7% 1 6.7% 2 13.3% 11 73.3%
? 4 0 0.0% 0 0.0% 0 0.0% 4 100.0%

PEneXtProt entriesCanonicalUncertainRedundantNot Observed
1 18,357 4,390 23.9% 1,469 8.0% 2,099 11.4% 10,399 56.6%
2 1,265 3 0.2% 11 0.9% 152 12.0% 1,099 86.9%
3 147 0 0.0% 2 1.4% 17 11.6% 128 87.1%
4 9 0 0.0% 0 0.0% 0 0.0% 9 100.0%
5 601 1 0.2% 6 1.0% 58 9.7% 536 89.2%
1-4 19,778 4,393 22.2% 1,482 7.5% 2,268 11.5% 11,635 58.8%
2021-07 Total 20,379 4,394 21.6% 1,488 7.3% 2,326 11.4% 12,171 59.7%

ChromosomePE1PE2PE3PE4PE5PE1-4
1 1,859 139 21 2 46 2,021
2 1,228 45 3 1 18 1,277
3 1,005 52 5 0 17 1,062
4 701 35 11 0 22 747
5 835 26 2 0 14 863
6 940 54 4 1 30 999
7 863 105 6 1 50 975
8 625 34 5 0 38 664
9 706 58 4 0 41 768
10 681 47 0 1 19 729
11 1,069 169 53 0 40 1,291
12 959 52 2 0 23 1,013
13 311 10 1 0 11 322
14 632 75 12 2 14 721
15 535 40 0 0 31 575
16 773 44 0 1 25 818
17 1,087 55 3 0 24 1,145
18 255 9 0 0 11 264
19 1,318 79 8 0 31 1,405
20 504 31 0 0 14 535
21 204 27 2 0 21 233
22 455 23 5 0 22 483
X 764 51 0 0 32 815
Y 37 3 0 0 7 40
MT 15 0 0 0 0 15
? 2 2 0 0 0 4