207	datasets
989	experiments
16,876	MS runs
505,019,878	spectra searched
58,822,980	PSMs
1,420,208	distinct peptides
14,645	canonical proteins

About

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

This PeptideAtlas build was created from the subset of all human proteomics datasets that are derived from samples enriched in MHC class I- and class II-bound peptides.

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All canonical Human HLA proteins

Chromosome Summary

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

A manuscript describing this build is in progress. For now, if you use these results, please cite:

Latest publication: Deutsch EW, Kok LW, Mudge JM, Valls CF, Jungreis I, Ruiz-Orera J, Sun Z, Kusebauch U, Fierro-Monti I, Abelin JG, Alba MM, Aspden JL, Bandyopadhyay S, Banerjee K, Baranov PV, Bazzini AA, Bourassa F, Bruford EA, Calviello L, Carr SA, Carvunis AR, Chothani S, Clauwaert J, Dean K, Faridi P, Frankish A, Goodale A, Green T, Hubner N, Ingolia NT, Kellis M, Magrane M, Martin MJ, Martinez TF, Menschaert G, Ohler U, Orchard S, Potter A, Rackham OJL, Rees MG, Root DE, Roth JA, Roucou X, Sialana FJ, Slavoff SA, Świrski MI, Tierney JAS, Trifiro FA, Valen E, Vasylieva V, Wacholder A, Wang S, Wang L, Weissman JS, Wu W, Xie Z, Choudhary JS, Bassani-Sternberg M, Vizcaíno JA, Ternette N, Brunet MA, Moritz RL, Prensner JR, van Heesch S; Expanding the human proteome with microproteins and peptideins; Nature. 2026 Jun;654(8119):813-825. doi: 10.1038/s41586-026-10459-x. Epub 2026 May 6. PMID: 42092140
Omenn GS, Lane L, Overall CM, Pineau C, Packer NH, Cristea IM, Lindskog C, Weintraub ST, Orchard S, Roehrl MHA, Nice E, Liu S, Bandeira N, Chen YJ, Guo T, Aebersold R, Moritz RL, Deutsch EW. The 2022 Report on the Human Proteome from the HUPO Human Proteome Project; J Proteome Res. 2022 Nov 1. doi: 10.1021/acs.jproteome.2c00498. PMID: 36318223,
Initial publication: Desiere et al., "Integration of Peptide Sequences Obtained by High-Throughput Mass Spectrometry with the Human Genome", Genome Biology 2004, 6:R9 - [PDF]

Download

Below are individual Human HLA 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=0.0005" denotes a PSM FDR threshold of 0.0005 (0.05%) is applied to every sample in the build.

Human HLA 2025-08 PSM FDR = 0.0005Latest Build

Biosequence Set in FASTA format [679MB]
Database tables exported as TSV dump file [1GB]
Database tables exported as mysql dump file [1GB]
Peptide CDS and chromosomal coordinates [6GB]
Peptide CDS coordinates [4GB]
Peptide sequences in FASTA format [39MB]
Spectral library (HR-EThcD) [95MB]
Spectral library (HR-HCD) [3GB]
Spectral library (HR-IT-CID) [319MB]
Spectral library (HR-IT-ETD) [19MB]
Spectral library (HR-QTOF) [912MB]
Spectral library (LR-HCD) [1MB]
Spectral library (LR-IT-CID) [23MB]
Spectral library (TMT_HR-HCD) [58MB]

Human HLA 2023-11 PSM FDR = 0.0005

Biosequence Set in FASTA format [665MB]
Database tables exported as mysql dump file [786MB]
Peptide CDS and chromosomal coordinates [3GB]
Peptide CDS coordinates [2GB]
Peptide sequences in FASTA format [23MB]
Spectral library (HR-EThcD) [86MB]
Spectral library (HR-HCD) [1GB]
Spectral library (HR-HCD_DECOY) [2GB]
Spectral library (HR-IT-CID) [333MB]
Spectral library (HR-IT-ETD) [10MB]
Spectral library (HR-QTOF) [41MB]
Spectral library (LR-IT-CID) [4MB]

Help

Complete description of each of the available download formats