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About

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

Explore

SEARCH(e.g. P78344)




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
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

Download

Below are individual Human 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 2023-01 PSM FDR = 0.0001Latest Build
  • Biosequence Set in FASTA format [633MB]
  • Database tables exported as TSV dump file [3GB]
  • Database tables exported as mysql dump file [2GB]
  • Peptide CDS and chromosomal coordinates [7GB]
  • Peptide CDS coordinates [4GB]
  • Peptide sequences in FASTA format [103MB]
Human 2022-01 PSM FDR = 0.0001
  • Biosequence Set in FASTA format [598MB]
  • Database tables exported as TSV dump file [3GB]
  • Database tables exported as mysql dump file [2GB]
  • Peptide CDS and chromosomal coordinates [5GB]
  • Peptide CDS coordinates [3GB]
  • Peptide sequences in FASTA format [86MB]
Human 2021-01 PSM FDR = 0.00015
  • Biosequence Set in FASTA format [511MB]
  • Database tables exported as TSV dump file [5GB]
  • Database tables exported as mysql dump file [4GB]
  • Peptide CDS and chromosomal coordinates [4GB]
  • Peptide CDS coordinates [2GB]
  • Peptide sequences in FASTA format [73MB]
Human 2020-01 PSM FDR = 0.0002
  • Biosequence Set in FASTA format [449MB]
  • Database tables exported as TSV dump file [2GB]
  • Database tables exported as mysql dump file [2GB]
  • Peptide CDS and chromosomal coordinates [4GB]
  • Peptide CDS coordinates [2GB]
  • Peptide sequences in FASTA format [71MB]
Human 2019-01 PSM FDR = 0.0002
  • Biosequence Set in FASTA format [2GB]
  • Database tables exported as TSV dump file [63MB]
  • Database tables exported as mysql dump file [62MB]
  • Peptide CDS and chromosomal coordinates [2GB]
  • Peptide CDS coordinates [1GB]
  • Peptide sequences in FASTA format [51MB]
Human 2016-12 PSM FDR = 0.0002
  • Biosequence Set in FASTA format [3GB]
  • Database tables exported as an XML file [2GB]
  • Peptide CDS and chromosomal coordinates [212MB]
  • Peptide CDS coordinates [941MB]
  • Peptide sequences in FASTA format [34MB]
Human 2016-01 PSM FDR = 0.0002
  • Biosequence Set in FASTA format [7GB]
  • Database tables exported as an XML file [2GB]
  • Database tables exported as mysql dump file [1GB]
  • Peptide CDS and chromosomal coordinates [1GB]
  • Peptide CDS coordinates [991MB]
  • Peptide sequences in FASTA format [33MB]

Help

Complete description of each of the available download formats

Other Resources

Acknowledgements

We gratefully acknowledge the support for the Human PeptideAtlas from NIGMS grants R01GM087221 and R24GM127667.