Large-scale proteome profile of the zebrafish (Danio rerio) gill for physiological and biomarker discovery studies

Zebrafish are an important model in vertebrate genetics, developmental biology, physiology, and toxicology. In this study, we established the first large-scale proteome profile of a teleost fish tissue using a shotgun method based on two-dimensional liquid chromatography-electrospray ionization tandem mass spectrometry. Proteome coverage was significantly improved with the application of a sequential protein solubilization method for protein fractionation and a precursor ion exclusion method for improving peptide and protein identification efficiency. Five thousand seven hundred sixteen proteins were identified with an estimated false-positive matching rate of 1.34%, and the proteome exhibited excellent coverage of important biochemical pathways relevant to the function of the gill in respiration, ion and acid-base homeostasis, and energy metabolism. Numerous established and potential biomarkers of stress, disease, and environmental contamination were also expressed in the gill. Annotation information was completely lacking for >30% of the detected proteins, highlighting the need for advancements in bioinformatics analysis techniques to complement this research. Nevertheless, the results provide important insights into the physiological function of the gill as well as its role as an environmental interface. We discuss the significance of these findings in the context of exploratory physiological and toxicological studies.