Interactions of organisms with their environment are complex and environmental regulation at different levels of biological organization is often nonlinear. Therefore, the genotype to phenotype continuum requires study at multiple levels of organization. While studies of transcriptome regulation are now common for many species, quantitative studies of environmental effects on proteomes are needed. Here we report the generation of a data-independent acquisition (DIA) assay library that enables simultaneous targeted proteomics of thousands of Oreochromis niloticus kidney proteins using a label- and gel-free workflow that is well suited for ecologically relevant field samples. We demonstrate the usefulness of this DIA assay library by discerning environmental effects on the kidney proteome of O. niloticus. Moreover, we demonstrate that the DIA assay library approach generates data that are complimentary rather than redundant to transcriptomic data. Transcript and protein abundance differences in kidneys of tilapia acclimated to freshwater and brackish water (25 g/kg) were correlated for 2114 unique genes. A high degree of non-linearity in salinity-dependent regulation of transcriptomes and proteomes was revealed suggesting that the regulation of O. niloticus renal function by environmental salinity relies heavily on post-transcriptional mechanisms. The application of functional enrichment analyses using STRING and KEGG to DIA assay data sets is demonstrated by identifying myo-inositol metabolism, antioxidant and xenobiotic functions, and signalling mechanisms as key elements controlled by salinity in tilapia kidneys. The DIA assay library resource presented here can be adopted for other tissues and other organisms to study proteome dynamics during changing ecological contexts.

中文翻译：

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用于定量环境对尼罗罗非鱼肾脏蛋白质组影响的数据独立采集 (DIA) 分析库

生物与其环境的相互作用是复杂的，生物组织不同层次的环境调节通常是非线性的。因此，基因型到表型连续体需要在多个组织层次上进行研究。虽然转录组调控的研究现在对许多物种来说很常见，但需要对环境对蛋白质组的影响进行定量研究。在这里，我们报告了数据独立采集 (DIA) 分析库的生成，该库使用非常适合生态相关现场样品的无标记和无凝胶工作流程，实现了对数千种尼罗罗非鱼肾脏蛋白质的同步靶向蛋白质组学。我们通过辨别环境对肾脏蛋白质组的影响来证明该 DIA 检测库的有用性尼罗罗非鱼。此外，我们证明 DIA 检测库方法生成的数据与转录组数据互补而不是冗余。适应淡水和微咸水 (25 g/kg) 的罗非鱼肾脏的转录本和蛋白质丰度差异与 2114 个独特基因相关。揭示了转录组和蛋白质组的盐度依赖性调节的高度非线性，表明O的调节。环境盐度引起的尼罗罗非鱼肾功能在很大程度上依赖于转录后机制。通过识别myo证明了使用 STRING 和 KEGG 的功能富集分析在 DIA 测定数据集上的应用-肌醇代谢、抗氧化和异生物质功能，以及作为受罗非鱼肾脏盐度控制的关键因素的信号机制。此处介绍的 DIA 检测库资源可用于其他组织和其他生物体，以研究不断变化的生态环境中的蛋白质组动力学。