Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry*

Abstract

The myriad of peptides presented at the cell surface by class I and class II major histocompatibility complex (MHC) molecules are referred to as the immunopeptidome and are of great importance for basic and translational science. For basic science, the immunopeptidome is a critical component for understanding the immune system; for translational science, exact knowledge of the immunopeptidome can directly fuel and guide the development of next-generation vaccines and immunotherapies against autoimmunity, infectious diseases, and cancers. In this mini-review, we summarize established isolation techniques as well as emerging mass spectrometry-based platforms (i.e. SWATH-MS) to identify and quantify MHC-associated peptides. We also highlight selected biological applications and discuss important current technical limitations that need to be solved to accelerate the development of this field. Molecular & Cellular

A Targeted LC‐MS Strategy for Low‐Abundant HLA Class‐I‐Presented Peptide Detection Identifies Novel Human Papillomavirus T‐Cell Epitopes

“…Moreover, the optimization of the collision energy of individual transitions performed on the synthetic counterparts of the peptides to be analyzed has shown an about twofold sensitivity gain compared with the signals obtained from more generic collision energies computed from the mass of the targeted precursor, which makes this optimization process particularly suited for the detection of low‐abundant HLA‐presented peptides (reviewed in ref. 48), such as the HPV peptides investigated in this study. Furthermore, MS 3 scanning approaches are less prone to interference of co‐eluting species than MS 1 or MS 2 methods 49, 50.…”

MHC class I–associated peptides derive from selective regions of the human genome

“…The various strategies used for high-throughput MS analyses of the immunopeptidome present strengths and limitations (61). In the present study, MAPs were isolated from 18 B-LCLs by mild acid elution and analyzed by data-dependent MS. To gauge the robustness of the model, we tested it on MAPs identified by 2 other groups in JY B-LCLs.…”

Unsupervised HLA Peptidome Deconvolution Improves Ligand Prediction Accuracy and Predicts Cooperative Effects in Peptide–HLA Interactions

“…Using either HLA class I-or class II-specific Abs, HLA-peptide complexes are first isolated from either transfected cell lines expressing a given HLA molecule of interest (15,16), also as a soluble form, or cell lines or tissues expressing the endogenous HLA molecules. The peptides are then eluted and analyzed by liquid chromatography coupled to mass spectrometry (MS) (17). Recent studies using high-sensitivity MS have shown that, in addition to tens of thousands of self-peptides, several mutated peptides can be directly identified from tumor samples (13,18).…”