期刊
PROTEOMICS
卷 18, 期 12, 页码 -出版社
WILEY
DOI: 10.1002/pmic.201700246
关键词
biomarker; DIA; HLA class II; HLA peptidomics; immunopeptidomics
资金
- ETH Zurich
- Swiss National Science Foundation
- European Union's Seventh Framework Programme (FP7) [305309, 305608]
- European Research Council (ERC)
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.
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