A proteomics and bioinformatics study of peptides in the human immunopeptidome

The presentation of protein degraded peptides by human leukocyte antigen class I (HLA-I) molecules forms the basis of the CD8+ T cell mediated immune response. However, current knowledge on how factors can determine peptide’s immunogenicity remains to be explored. This thesis has focused on two significant factors post-translational modification (PTM) as well as binding between peptide and HLA-I. The outcome has revealed that a predominant of HLA-I bound peptides bearing asparagine deamidation, one type of PTM, is associated with N-glycosylated precursors and potentially being utilized by the immune system for monitoring aberrant glycosylation. Additionally, tools for the prediction ofHLA-I peptide binding has been extensively reviewed and evaluated for guiding researchers to select most suitable predictors. Finally, a new tool with the model customisation function has been developed to solve the current limitation and to facilitate the development of immunotherapy.