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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: 869 million PSMs
Full 2024-01 Build Summary
772datasets
3,160experiments
170,701MS runs
4,770,407,917spectra searched
868,849,459PSMs
3,945,444distinct peptides
17,416canonical neXtProt proteins

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PeptideAtlas and the Chromosome-Centric Human Proteome Project

Chromosome Explorer
Human non-HLA
PeptideAtlas
Human HLA
PeptideAtlas
BROWSE

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

Chromosome Summary

ChromosomeneXtProt entriesCanonicalUncertainRedundantNot Observed
1 2,065 1,773 85.9% 91 4.4% 134 6.5% 67 3.2%
2 1,295 1,173 90.6% 48 3.7% 43 3.3% 31 2.4%
3 1,076 967 89.9% 35 3.3% 40 3.7% 34 3.2%
4 766 681 88.9% 26 3.4% 39 5.1% 20 2.6%
5 887 805 90.8% 24 2.7% 37 4.2% 21 2.4%
6 1,029 880 85.5% 41 4.0% 54 5.2% 54 5.2%
7 1,029 800 77.7% 72 7.0% 102 9.9% 55 5.3%
8 706 600 85.0% 25 3.5% 40 5.7% 41 5.8%
9 806 668 82.9% 41 5.1% 54 6.7% 43 5.3%
10 748 652 87.2% 37 4.9% 31 4.1% 28 3.7%
11 1,333 1,006 75.5% 60 4.5% 163 12.2% 104 7.8%
12 1,035 922 89.1% 43 4.2% 38 3.7% 32 3.1%
13 333 291 87.4% 12 3.6% 12 3.6% 18 5.4%
14 736 618 84.1% 33 4.5% 48 6.5% 36 4.9%
15 609 519 85.2% 31 5.1% 34 5.6% 25 4.1%
16 843 746 88.5% 29 3.4% 35 4.2% 33 3.9%
17 1,170 1,021 87.3% 46 3.9% 54 4.6% 49 4.2%
18 270 242 89.6% 10 3.7% 6 2.2% 12 4.4%
19 1,437 1,262 87.8% 45 3.1% 90 6.3% 40 2.8%
20 550 484 88.0% 24 4.4% 17 3.1% 25 4.5%
21 247 170 68.8% 21 8.5% 13 5.3% 43 17.4%
22 506 425 84.0% 32 6.3% 34 6.7% 15 3.0%
X 850 687 80.8% 67 7.9% 63 7.4% 33 3.9%
Y 48 14 29.2% 11 22.9% 14 29.2% 9 18.8%
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 17,283 93.9% 516 2.8% 424 2.3% 174 0.9%
2 1,188 47 4.0% 282 23.7% 507 42.7% 352 29.6%
3 180 0 0.6% 14 7.8% 115 63.9% 50 27.8%
4 13 0 0.0% 2 15.4% 2 15.4% 9 69.2%
5 611 86 14.1% 90 14.7% 149 24.4% 286 46.8%
1-4 19,778 17,330 87.6% 814 4.1% 1,048 5.3% 585 3.0%
2024-01 Total 20,389 17,416 85.4% 904 4.4% 1,197 5.9% 871 4.3%

ChromosomeAll (PE 1-5)PE1PE2PE3PE4PE5PE1-4
1 2,065 1,864 124 28 2 47 2,018
2 1,295 1,229 47 1 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 53 3 1 34 995
7 1,029 878 93 5 2 51 978
8 706 627 34 9 0 36 670
9 806 703 57 2 2 42 764
10 748 690 39 0 1 18 730
11 1,333 1,072 159 61 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 59 14 2 13 723
15 609 534 41 3 0 31 578
16 843 775 42 0 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 79 10 1 29 1,408
20 550 509 24 1 0 16 534
21 247 198 22 4 0 23 224
22 506 454 25 3 1 23 483
X 850 758 57 2 0 33 817
Y 48 33 8 0 0 7 41
MT 15 15 0 0 0 0 15
? 6 2 4 0 0 0 6