Immunoproteomics: The Evolution from Classical Methods to Emerging Techniques

The dynamic landscape of the adaptive immune response is shaped by peptides presented on the surface of immune cells, originating from viral or microbial pathogens or cancerous cells. The study of immune biomarkers and antigens has a long history, with classical techniques such as agglutination, enzyme-linked immunosorbent assays (ELISA), and western blotting being widely used to investigate immune responses to vaccination and disease. However, these traditional methods often face limitations in protein and peptide identification, creating bottlenecks in antigen discovery. Recent advancements in genomics and proteomics have significantly accelerated the development of novel analytical approaches. Immunoproteomics has emerged as a rapidly evolving field that integrates a diverse set of methodologies aimed at identifying and quantifying antigenic peptides and proteins. These approaches include gel-based and array-based techniques, mass spectrometry, DNA-based methods, and in silico modeling. By leveraging these tools, immunoproteomics is providing deeper insights into disease mechanisms, immune system dynamics, biomarker discovery, and vaccine development. This review offers an introductory overview of immunoproteomics and related technologies that help define the complete repertoire of protein antigens recognized by the immune system during disease, advancing both diagnostic and therapeutic applications.