The Center for Proteomics and Metabolomics (CPM) of the LUMC combines mass spectrometry with advanced separation techniques for supporting research into molecular pathways underlying diseases. Within the presentation, the HLA-peptidomics research line of the CPM will be introduced, focusing on the study of proteolytic peptides presented by HLA molecules triggering T-cell mediated immune responses. Glycosylation changes of human antibodies in rheumatoid arthritis and pregnancy will be described, as well as a urinary prostate-specific antigen (PSA) assay aiming at supporting the diagnosis of prostate cancer. Finally, mass spectrometry imaging will be presented which allows the analysis of the spatial distribution of various analytes including peptides, proteins, glycans and lipids in the context of e.g. tumor development.