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Significance The surface presentation of peptides by human leukocyte antigen (HLA) class I molecules is essential for adaptive immune responses against pathogens and tumors. To date, the repertoire of HLA class I peptides remains largely unexplored, although their identity could lead to new targets for vaccine development or cancer immunotherapy. Here, we demonstrate that recent developments in mass spectrometry (MS)-based sequencing technology can expand the detectable peptide repertoire to an unprecedented depth, revealing unique features in the antigen presentation machinery. Our data include a variety of posttranslational modifications for which evidence is accumulating that they play important roles in human diseases. Hence, next-generation MS-based sequencing can make the important step into the discovery of disease-related HLA class I antigens.

Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD)