Algorithm

Deconvolution

Biology

Computer science

Acoustics

Computational biology

Immunology

Physics

Antigen

Motif (music)

Chemistry

Human leukocyte antigen

Epitope

Nature Biotechnology

Predictions of epitopes presented by class II human leukocyte antigen molecules (HLA-II) have limited accuracy, restricting vaccine and therapy design. Here we combined unbiased mass spectrometry with a motif deconvolution algorithm to profile and analyze a total of 99,265 unique peptides eluted from HLA-II molecules. We then trained an epitope prediction algorithm with these data and improved prediction of pathogen and tumor-associated class II neoepitopes.

Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes