Proteomics Approaches to Ecoimmunology: New Insights into Wildlife Immunity and Disease

Understanding wildlife immune responses is crucial for assessing disease risks, environmental stress effects, and conservation challenges. Traditional ecoimmunology approaches rely on targeted assays, which, while informative, often provide a fragmented and species-limited view of immune function. Proteomics offers a powerful alternative by enabling the high-throughput, system-wide quantification of immune-related proteins, providing a functional perspective on immunity that overcomes many limitations of conventional methods. However, proteomics remains underutilized in ecoimmunology despite its potential to enhance biomarker discovery, host-pathogen interaction studies, and environmental health assessments. This perspective highlights proteomics as a transformative tool for ecoimmunology, disease ecology, and conservation biology. We discuss its unique advantages over other -omics approaches, including its ability to capture realized immune function rather than inferred gene expression, its applicability to diverse wildlife taxa, and its potential for longitudinal immune monitoring of individuals using minimally invasive sampling. We also address key challenges, including limited genomic reference resources, sample constraints, reproducibility issues, and the need for standardized protocols. To overcome these barriers, we propose practical solutions, such as leveraging proteomes of closely related species for annotation and using their annotated genomes as search spaces for peptide mapping. Additionally, we highlight the importance of alternative quality control strategies and improved data-sharing practices to enhance the utility of proteomics in wildlife research. To fully integrate proteomics into ecoimmunology, we recommend expanding public reference databases for non-model species, refining field-adapted workflows, and fostering interdisciplinary collaboration between ecologists, immunologists, and bioinformaticians. By embracing these advancements, the field can leverage proteomics to bridge the gap between molecular mechanisms and ecological processes, ultimately improving our ability to monitor wildlife health, predict disease risks, and inform conservation strategies in the face of environmental change.