The identification of antigenic epitopes, linear and conformational, that are recognized by the immune system is fundamental to understanding host-pathogen interactions, vaccine development, and immune diagnostics. Recent advances in high-throughput technologies, such as immunopeptidomics, peptide microarrays, cryo-electron microscopy (Cryo-EM), and next-generation sequencing, have significantly expanded our capacity to identify epitopes and assess their immunoprevalence across diverse populations. Combined with powerful bioinformatics tools, these approaches are reshaping how researchers define immunodominant and immunoprevalent targets, with implications for designing broadly protective vaccines and targeted immunotherapies.

The primary goal of this Research Topic is to bring together cutting-edge research and reviews that explore how high-throughput platforms and computational tools are transforming the landscape of epitope discovery and immunoprevalence mapping. A central challenge in immunology is to identify epitopes that are not only immunogenic and specific but also widely recognized across human populations with diverse HLA backgrounds. This collection aims to highlight recent breakthroughs that address this challenge, including large-scale datasets of epitope mapping, improved predictive algorithms, and immunopeptidomics. By spotlighting innovative methodologies and their applications, we aim to encourage a novel approach that connects molecular immunology with translational immunology, such as vaccine design, biomarker identification, diagnostic, and immune monitoring tools.

We welcome original research, reviews, and mini-review articles that align with the theme of epitope discovery and immunoprevalence analysis. Submissions should emphasize integrative approaches and technological innovations in epitope mapping. Specific themes of interest include:

• Experimental platforms for epitope identification

• Computational tools and algorithms for epitope prediction and immunoprevalence modeling

• Integration of immunopeptidomics and mass spectrometry in antigen discovery

• Population studies of HLA diversity and epitope recognition

• Applications in vaccine design, diagnostics, and personalized immunotherapies

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High-throughput epitope discovery and immunoprevalence analysis