Assessing Major Histocompatibility Complex-Associated Peptide Proteomics assay as a tool to predict immunogenicity potential of protein therapeutics and antigens

Major histocompatibility complex-II (MHC-II)-Associated Peptide Proteomics (MAPPs) is a mass spectrometry-based approach, to identify and relatively quantitate naturally processed and presented MHC-II-associated peptides, that could potentially activate CD4+T cells and elicit a patient immune response against protein therapeutics in the preclinical development phase. Methods to identify these peptide antigens are critical to the development of new vaccines. Conversely, it is critical to bring safer new biological entities (NBEs) as drug candidates into clinical trials, with a reduced risk of triggering an adaptive immune response that could hamper a therapeutic outcome. Here, we describe a robust protocol for the identification of MHCII-bound peptides from Peripheral Blood Mononuclear Cells (PBMCs) of healthy donors, using nano-ultra-performance liquid chromatography coupled to high-resolution mass spectrometry (nUHPLC–MS/MS) and recent improvements in methods for isolation of these peptides.