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Full 2023-11 Build Summary
10,095MS runs
240,296,325spectra searched
1,342,941distinct peptides
13,799canonical proteins


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.


SEARCH(e.g. P00747)


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


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=0.002" denotes a PSM FDR threshold of 0.002 (0.2%) is applied to every sample in the build.

Human HLA 2023-11 PSM FDR = 0.0005Latest Build
  • 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]


Complete description of each of the available download formats

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