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

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

PSM stands for Peptide Spectrum Match. It refers to the matching of a spectrum generated from a mass spectrometry experiment to a peptide sequence from a protein database. More ▲

In a typical proteomics experiment, proteins are first digested into peptides using enzymes such as trypsin. These peptides are then separated and ionized before being introduced into a mass spectrometer for analysis. The mass spectrometer generates a spectrum of the ionized peptides, which is then searched against a database of protein sequences to identify the proteins present in the sample.

Each identified peptide sequence generates a PSM, which represents the match between the experimental spectrum and the theoretical spectrum generated from the peptide sequence. PSMs are commonly used to filter and validate peptide identifications, as they provide a measure of the quality of the match between the experimental data and the database search results.

PSMs PER BUILD TYPE Total: 750 million PSMs
Full 2023-01 Build Summary
559datasets
2,416experiments
189,827MS runs
3,683,878,875spectra searched
750,664,324PSMs
3,480,387distinct peptides
17,245canonical neXtProt proteins

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PeptideAtlas and the Chromosome-Centric Human Proteome Project

Chromosome Explorer
Human non-HLA
PeptideAtlas
Human HLA
PeptideAtlas

Human Plasma
PeptideAtlas
Human Plasma
Extracellular Vesicle
Human Urine
PeptideAtlas
Human Phospho
PeptideAtlas

Chromosome Summary

ChromosomeneXtProt entriesCanonicalUncertainRedundantNot Observed
1 2,065 1,764 85.4% 90 4.4% 131 6.3% 80 3.9%
2 1,295 1,160 89.6% 49 3.8% 51 3.9% 35 2.7%
3 1,076 952 88.5% 43 4.0% 42 3.9% 39 3.6%
4 766 673 87.9% 22 2.9% 44 5.7% 27 3.5%
5 887 795 89.6% 28 3.2% 34 3.8% 30 3.4%
6 1,029 869 84.5% 48 4.7% 49 4.8% 63 6.1%
7 1,029 791 76.9% 71 6.9% 102 9.9% 65 6.3%
8 706 594 84.1% 23 3.3% 37 5.2% 52 7.4%
9 806 662 82.1% 41 5.1% 52 6.5% 51 6.3%
10 748 648 86.6% 31 4.1% 38 5.1% 31 4.1%
11 1,333 998 74.9% 59 4.4% 151 11.3% 125 9.4%
12 1,035 919 88.8% 39 3.8% 36 3.5% 41 4.0%
13 333 289 86.8% 13 3.9% 13 3.9% 18 5.4%
14 736 611 83.0% 34 4.6% 42 5.7% 49 6.7%
15 609 513 84.2% 27 4.4% 42 6.9% 27 4.4%
16 843 737 87.4% 33 3.9% 40 4.7% 33 3.9%
17 1,170 1,013 86.6% 49 4.2% 54 4.6% 54 4.6%
18 270 242 89.6% 10 3.7% 8 3.0% 10 3.7%
19 1,437 1,250 87.0% 54 3.8% 84 5.8% 49 3.4%
20 550 479 87.1% 26 4.7% 16 2.9% 29 5.3%
21 247 167 67.6% 22 8.9% 13 5.3% 45 18.2%
22 506 415 82.0% 35 6.9% 38 7.5% 18 3.6%
X 850 681 80.1% 61 7.2% 69 8.1% 39 4.6%
Y 48 13 27.1% 9 18.8% 16 33.3% 10 20.8%
MT 15 13 86.7% 0 0.0% 0 0.0% 2 13.3%
? 6 2 33.3% 0 0.0% 2 33.3% 2 33.3%

PEneXtProt entriesCanonicalUncertainRedundantNot Observed
1 18,397 17,168 93.3% 560 3.0% 451 2.5% 218 1.2%
2 1,151 7 0.6% 262 22.8% 481 41.8% 401 34.8%
3 215 0 0.0% 16 7.4% 121 56.3% 78 36.3%
4 15 0 0.0% 1 6.7% 2 13.3% 12 80.0%
5 611 70 11.5% 78 12.8% 149 24.4% 314 51.4%
1-4 19,778 17,175 86.8% 839 4.2% 1,055 5.3% 709 3.6%
2023-01 Total 20,389 17,245 84.6% 917 4.5% 1,204 5.9% 1,023 5.0%

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