The immune system monitors the proteome of cells in order to detect intracellular pathogens. For this surveillance, cells present degradation products of proteins on their cell surface bound to MHC class I. Recognition of MHC class I-peptide complexes by CD8+ T cells leads to T cell activation and, eventually, to cell death of the antigen presenting cell. Furthermore, professional antigen presenting cells present peptides in complex with MHC class II to CD4+ T cells. Immunopeptidomics allows studying peptides presented via MHC class I and/or MHC class II. To achieve this, MHC-peptide complexes are first immunoprecipitated from non-denatured cell lysates. Peptides are then eluted from the complexes, purified, and identified and quantified by mass spectrometry. Our growing data analysis pipeline covers calculation of Gibbs clusters and corresponding peptide motifs, assigning the HLA source allele with a binding score to each peptide, Venn diagrams, visualizing peptide sources by Voronoi diagrams, and comparing immunopeptidome abundances to abundances of the corresponding proteome.