Meeting Abstract
Understanding the complex biochemical mechanisms behind the evolution of salinity tolerance in euryhaline fish is best achieved using systems biology approaches. The proteome provides a wealth of information regarding the molecular phenotype of an organism. The abundance and state of certain proteins indicates life history and environmental exposures. Recent advances in mass spectrometry have allowed for the development of data-independent acquisition (DIA) assays to simultaneously monitor thousands of proteins in virtually any context. Since protein abundance information for only select proteins in response to salinity or temperature challenges provides a limited scope for determining the overall molecular phenotype of an animal, we are continuing to develop comprehensive DIA assay libraries for organisms of interest. These assay libraries permit highly accurate and consistent quantitation of exactly the same sets of proteins in all samples. The consistent proteome coverage enables systematic network and topological data analysis (TDA) approaches that yield detailed mechanistic insight into environmental and developmental effects on organisms. These approaches will be illustrated by discussing salinity and temperature effects on the three-spine stickleback (Gasterosteus aculeatus) gill proteome. Our results indicate that differences in habitat salinity and temperature are accurately reflected in the dynamic changes of the gill proteome. Therefore, DIA quantitative proteomics assays and corresponding bioinformatics analyses enable deduction of molecular mechanisms associated with environmental changes in aquatic organisms. This work was supported by NSF grant 1656371.
