A data-independent acquisition (DIA) assay library for targeted quantitation of thousands of Oreochromis niloticus gill proteins using a label- and gel-free workflow was generated and used to compare protein and mRNA abundances. This approach generated complimentary rather than redundant data for 1899 unique genes in gills of tilapia acclimated to freshwater and brackish water. Functional enrichment analyses identified mitochondrial energy metabolism, serine protease and immunity-related functions, and cytoskeleton/ extracellular matrix organization as major processes controlled by salinity in O. niloticus gills. Non-linearity in salinity-dependent transcriptome versus proteome regulation was revealed for specific functional groups of genes. The relationship was more linear for other molecular functions/ cellular processes, suggesting that the salinity-dependent regulation of O. niloticus gill function relies on post-transcriptional mechanisms for some functions/ processes more than others. This integrative systems biology approach can be adopted for other tissues and organisms to study cellular dynamics for many changing ecological contexts.

生成了一个数据独立采集 (DIA) 分析库，用于使用无标记和无凝胶工作流程对数千种尼罗罗非鱼鳃蛋白进行靶向定量，并用于比较蛋白质和 mRNA 丰度。这种方法为适应淡水和微咸水的罗非鱼鳃中的 1899 个独特基因生成了互补而非冗余的数据。功能富集分析确定线粒体能量代谢、丝氨酸蛋白酶和免疫相关功能以及细胞骨架/细胞外基质组织是尼罗罗非鱼中受盐度控制的主要过程鳃。对于特定的基因功能组，揭示了盐度依赖性转录组与蛋白质组调节的非线性关系。对于其他分子功能/细胞过程，这种关系更为线性，这表明尼罗罗非鱼鳃功能的盐度依赖性调节比其他功能/过程更依赖于某些功能/过程的转录后机制。这种综合系统生物学方法可用于其他组织和生物体，以研究许多不断变化的生态环境的细胞动力学。