摘要：SummaryCD4+T cell activation in infectious diseases and cancer is governed by the recognition of peptides presented on class II human leukocyte antigen (HLA-II) molecules. Therefore, HLA-II ligands represent promising targets for vaccine design and personalized cancer immunotherapy. Much work has been done to identify and predict unmodified peptides presented on HLA-II molecules. However, little is known about the presentation of phosphorylated HLA-II ligands. Here, we analyzed Mass Spectrometry HLA-II peptidomics data and identified 1,943 unique phosphorylated HLA-II ligands. This enabled us to precisely define phosphorylated binding motifs for more than 30 common HLA-II alleles and to explore various molecular properties of phosphorylated peptides. Our data were further used to develop the first predictor of phosphorylated peptide presentation on HLA-II molecules.Graphical abstractDisplay OmittedHighlights•1,943 unique phosphorylated HLA-II ligands from MS HLA-II peptidomics data•Binding motifs of phosphorylated HLA-II ligands identified for more than 30 alleles•Predictor trained on phosphorylated peptides achieves higher accuracyImmunology; Cell biology; Omics
