Reference
Reference TypeLiterature
TitleMembranal and Blood-Soluble HLA Class II Peptidome Analyses Using Data-Dependent and Independent Acquisition.
AuthorsDanilo Ritz; Emiliano Sani; Hanna Debiec; Pierre Ronco; Dario Neri; Tim Fugmann
AffiliationsPhilochem AG, Libernstrasse 3, Otelfingen, Switzerland; Philogen SpA, Monteriggioni, Italy; Inserm UMRS 1155, Hôpital Tenon, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, Paris, France; Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland.
JournalProteomics
Year2018
AbstractThe interaction between HLA class II peptide complexes on antigen-presenting cells and CD4<sup>+</sup> T cells is of fundamental importance for anticancer and antipathogen immunity as well as for the maintenance of immunological tolerance. To study CD4<sup>+</sup> 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.
Curation Last Updated2023-08-19 00:08:04
Related Information
Epitopes
Bcell Assays0
Tcell Assays0
MHC Ligand Assays