Membranal and Blood-Soluble HLA Class II Peptidome Analyses Using Data-Dependent and Independent Acquisition

Proteomics. 2018 Jun;18(12):e1700246. doi: 10.1002/pmic.201700246. Epub 2018 Mar 14.


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.

Keywords: DIA; HLA class II; HLA peptidomics; biomarker; immunopeptidomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Blood Proteins / metabolism*
  • Cell Membrane / metabolism*
  • Data Mining / methods*
  • Healthy Volunteers
  • Histocompatibility Antigens Class II / analysis*
  • Humans
  • Lymphoma, Mantle-Cell / metabolism
  • Lymphoma, Mantle-Cell / pathology
  • Mass Spectrometry / methods*
  • Peptide Fragments / analysis*
  • Tumor Cells, Cultured


  • Blood Proteins
  • Histocompatibility Antigens Class II
  • Peptide Fragments