Abstract 7247: Leveraging advanced mass spectrometry for enhanced immunopeptidomics in human and murine cells

Abstract Immunopeptidomics is the study of peptides presented by Class I and Class II Major Histocompatibility Complexes (MHC). Presented peptides originate from a complex intracellular processing pipeline, culminating in the presentation of proteolytically derived fragments on the cell surface bound to MHC molecules. Advances in our understanding of the immune system have spurred significant interest in identifying these peptides and characterizing the immunopeptidome. Recent advances in mass spectrometry have significantly increased sensitivity, enabling unprecedented depth of immunopeptidome coverage and facilitating assays with reduced starting material requirements. To build on recent advancements, we utilized the Orbitrap Astral mass spectrometer, a cutting-edge technology offering superior sensitivity and resolution, to profile immunopeptidomes from human and murine cell lines. Comparative analyses with traditional immunopeptidomics workflows highlighted the Orbitrap Astral's remarkable ability to enhance peptide identification, particularly for low-abundance peptides that were previously challenging to detect. This advancement enabled a deeper and more comprehensive characterization of the immunopeptidome, unveiling valuable insights into antigen presentation. The integration of the Orbitrap Astral represents a major advancement in the field of immunopeptidomics, facilitating unprecedented sensitivity in the profiling of antigen presentation. These findings have important implications for cancer research, particularly in the development of targeted immunotherapies and the broader understanding of immune responses in oncology. Citation Format: Richard C. Jones, Michael J. Ford, Daneil A. Bochar, Michael R. Pisano. Leveraging advanced mass spectrometry for enhanced immunopeptidomics in human and murine cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7247.