Proteomics in non-model organisms: A new analytical frontier

Authors: Heck, Michelle; NEELY, BENJAMIN - National Institute Of Standards & Technology (NIST)

Submitted to: Journal of Proteome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/10/2020
Publication Date: 8/10/2020
Citation: Heck, M.L., Neely, B. 2020. Proteomics in non-model organisms: A new analytical frontier. Journal of Proteome Research. 19:3595-3606. https://doi.org/10.1021/acs.jproteome.0c00448?ref=pdf.
DOI: https://doi.org/10.1021/acs.jproteome.0c00448?ref=pdf

Interpretive Summary: Proteomics is the high-throughput study of proteins that are produced by an organism, tissue, or cell type over time and space, including the post-translational modification of these proteins and protein-protein interactions. Model organisms are a key tool to advance basic research and fundamental studies in molecular biology, but are limited in their ability to understand complex traits in agriculture and human and veterinary diseases. A major challenge to expanding proteomics beyond model organisms is informatics, including the challenge of studying unsequenced genome, including thousands of mammalian and arthropod species. Understanding of complex traits, such as the ability to hibernate for mammals or to cooperate with bacterial symbionts for insects is likely to come from studies of cellular and tissue physiology rather than through genome sequences. In this perspective, scientists discuss the rationales and challenges for studying nonmodel organisms, and provide a blueprint for how to broaden the impact of proteomics.

Technical Abstract: For the last century we have relied on model organisms to help understand fundamental biological processes. Now, with advancements in genome sequencing, assembly, and annotation, non-model organisms may be studied with the same advanced bioanalytical toolkit as model organisms. Proteomics is one such technique, which classically relies on predicted protein sequences to catalog and measure complex proteomes across tissues and biofluids. Applying proteomics to non-model organisms can advance and accelerate biomimicry studies, biomedical advancements, veterinary medicine, agricultural research, behavioral ecology, and food safety. In this postmodel organism era, we can study almost any species, meaning that many non-model organisms are, in fact, important emerging model organisms. Herein we specifically focus on eukaryotic organisms and discuss the steps to generate sequence databases, analyze proteomic data with or without a database, and interpret results as well as future research opportunities. Proteomics is more accessible than ever before and will continue to rapidly advance in the coming years, enabling critical research and discoveries in non-model organisms that were hitherto impossible.