Abstract The interaction between HLA class II peptide complexes on antigen‐presenting cells and CD4 + T cells is of fundamental importance for anticancer and antipathogen immunity as well as for the maintenance of immunological tolerance. To study CD4 + T cell reactivities, detailed knowledge of the presented peptides is necessary. In recent years, dramatic advances in the characterization of membranal and soluble HLA class I peptidomes could be observed. However, the same is not true for HLA class II peptidomes, where only few studies identify more than hundred peptides. Here we describe a MS‐based workflow for the characterization of membranal and soluble HLA class II DR and DQ peptidomes. Using this workflow, we identify a total of 8595 and 3727 HLA class II peptides from Maver‐1 and DOHH2 cells, respectively. Based on this data, a motif‐based binding predictor is developed and compared to NetMHCIIpan 3.1. We then apply the workflow to human plasma, resulting in the identification of between 34 and 152 HLA‐DR and between 100 and 180 HLA‐DQ peptides, respectively. Finally, we implement a data‐independent acquisition workflow to increase reproducibility and sensitivity of HLA class II peptidome characterizations.