Meeting Abstract
The three-spine stickleback (Gasterosteus aculeatus) is a euryhaline teleost that is represented by ancestrally marine populations and has invaded freshwater (FW) habitats since the Pleistocene glacier retreat. Sticklebacks are a suitable candidate for comparative studies due to their global distribution in marine, brackish and FW habitats throughout the northern hemisphere. A standardized data-independent acquisition (DIA) assay for label-free quantitative proteomics of 1505 proteins has been established for three-spine stickleback gills. Spectral libraries created by data-dependent acquisition (DDA) and annotated using multiple search engines were used for DIA assay construction. Skyline and a sample training set were used for automated and manual assay curation to select and validate reproducible transitions for protein quantitation. The resulting gill DIA assay yielded 1505 proteins represented by at least 4 transitions for at least 2 proteotypic peptides per protein. This gill DIA assay identified and quantified gill proteins with unique population-specific abundances between stickleback populations from Lake Solano, CA, resident marine from Bodega Harbor, CA, cold-adapted anadromous from Westchester Lagoon, AK, and warm adapted from La Bocana del Rosario, MX. Curated DIA assays permit comprehensive quantitative assessment of previously unknown biological adaptations associated with specific ecological contexts. The consistent, standardized, and high-throughput nature of curated DIA assays empowers future network approaches for capturing proteome dynamics in diverse ecological contexts. Funded by NSF Grant IOS-1355098
