≡   PeptideAtlas Links Seattle Proteome Center

PeptideAtlas: Home Overview Contacts Publications Software Database Schema Feedback Funding FAQ
Atlas Data: Data Repository HPPP Data Central PeptideAtlas Builds PeptideAtlas Exports THISP Search Database
Contribute Data

Related: SRMAtlas PASSEL SWATHAtlas
Spectral Libs: Libraries + Info SpectraST Search

Glossary/Terms: Atlas nomenclature Protein ID terms

LOG IN
MENU
Log In

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: 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

Explore

SEARCH
form...


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 1,773 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
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 2024-01 PSM FDR = 0.0001Latest Build
  • Biosequence Set in FASTA format [740MB]
  • Database tables exported as TSV dump file [4GB]
  • Database tables exported as mysql dump file [3GB]
  • Peptide CDS and chromosomal coordinates [10GB]
  • Peptide CDS coordinates [6GB]
  • Peptide sequences in FASTA format [117MB]
Human 2023-01 PSM FDR = 0.0001
  • 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]
View Older Downloads ▲
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

Non-canonical ORFs

PeptideAtlas has been searching for translation evidence for non-canonical ORFs (ncORFs) using sequences of 7264 ncORFs detected by Ribo-seq datasets as published by Mudge et al. (2021).

Other Resources

Acknowledgements

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