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PeptideAtlas and the Chromosome-Centric Human Proteome Project (C-HPP)

In 2010, the Chromosome-centric Human Proteome Project (C-HPP) was launched as a component of the Human Proteome Project (HPP) with the initial goal of characterizing a single protein form for each currently identified protein-coding gene. The Human PeptideAtlas builds are an essential resource for the project, combining data from over 1000 experiments, covering a wide variety of sample types, all processed through a uniform computational pipeline to yield a final protein list with a stringent, less than 1% FDR (false discovery rate).

PeptideAtlas vs C-HPP Summary Table

PeptideAtlas Builds:
ChromosomeneXtProt entriesCanonicalUncertainRedundantNot Observed
1 2,066 1,765 85.4% 88 4.3% 133 6.4% 80 3.9%
2 1,295 1,160 89.6% 47 3.6% 53 4.1% 35 2.7%
3 1,079 953 88.3% 44 4.1% 43 4.0% 39 3.6%
4 768 672 87.5% 22 2.9% 45 5.9% 29 3.8%
5 875 795 90.9% 25 2.9% 29 3.3% 26 3.0%
6 1,029 871 84.6% 45 4.4% 52 5.1% 61 5.9%
7 1,026 791 77.1% 67 6.5% 106 10.3% 62 6.0%
8 701 594 84.7% 23 3.3% 39 5.6% 45 6.4%
9 807 662 82.0% 40 5.0% 54 6.7% 51 6.3%
10 745 646 86.7% 31 4.2% 37 5.0% 31 4.2%
11 1,331 1,000 75.1% 58 4.4% 151 11.3% 122 9.2%
12 1,034 920 89.0% 35 3.4% 38 3.7% 41 4.0%
13 333 289 86.8% 13 3.9% 13 3.9% 18 5.4%
14 735 611 83.1% 34 4.6% 43 5.9% 47 6.4%
15 606 512 84.5% 27 4.5% 42 6.9% 25 4.1%
16 842 736 87.4% 33 3.9% 40 4.8% 33 3.9%
17 1,168 1,012 86.6% 49 4.2% 54 4.6% 53 4.5%
18 275 241 87.6% 12 4.4% 12 4.4% 10 3.6%
19 1,435 1,250 87.1% 52 3.6% 86 6.0% 47 3.3%
20 549 478 87.1% 25 4.6% 17 3.1% 29 5.3%
21 248 167 67.3% 22 8.9% 13 5.2% 46 18.5%
22 504 414 82.1% 35 6.9% 38 7.5% 17 3.4%
X 847 680 80.3% 61 7.2% 68 8.0% 38 4.5%
Y 47 13 27.7% 9 19.1% 15 31.9% 10 21.3%
MT 15 13 86.7% 0 0.0% 0 0.0% 2 13.3%
? 5 2 40.0% 0 0.0% 2 40.0% 1 20.0%

PEneXtProt entriesCanonicalUncertainRedundantNot Observed
1 18,407 17,124 93.0% 590 3.2% 480 2.6% 213 1.2%
2 1,135 50 4.4% 219 19.3% 472 41.6% 394 34.7%
3 195 0 0.0% 11 5.6% 120 61.5% 64 32.8%
4 13 0 0.0% 1 7.7% 2 15.4% 10 76.9%
5 609 68 11.2% 76 12.5% 149 24.5% 316 51.9%
1-4 19,750 17,174 87.0% 821 4.2% 1,074 5.4% 681 3.4%
2023-01 Total 20,359 17,242 84.7% 897 4.4% 1,223 6.0% 997 4.9%

ChromosomeAll (PE 1-5)PE1PE2PE3PE4PE5PE1-4
1 2,066 1,864 120 33 2 47 2,019
2 1,295 1,231 43 3 0 18 1,277
3 1,079 1,011 44 5 0 19 1,060
4 768 706 29 12 0 21 747
5 875 834 27 2 0 12 863
6 1,029 940 53 4 1 31 998
7 1,026 867 100 5 3 51 975
8 701 626 32 5 0 38 663
9 807 705 50 8 2 42 765
10 745 686 40 0 1 18 727
11 1,331 1,074 149 68 0 40 1,291
12 1,034 962 42 7 0 23 1,011
13 333 311 9 2 0 11 322
14 735 642 60 17 2 14 721
15 606 537 37 0 0 32 574
16 842 773 41 1 1 26 816
17 1,168 1,085 57 3 0 23 1,145
18 275 257 7 0 0 11 264
19 1,435 1,327 67 10 1 30 1,405
20 549 512 21 1 0 15 534
21 248 199 21 4 0 24 224
22 504 452 25 4 0 23 481
X 847 762 51 1 0 33 814
Y 47 32 8 0 0 7 40
MT 15 15 0 0 0 0 15
? 5 3 2 0 0 0 5

Column descriptions:

neXtProt 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