CEA-Marcoule, DRF/Li2D, Laboratory "Innovative technologies for Detection and Diagnostics,", Bagnols-sur-Cèze, France.
Methods Mol Biol. 2025;2859:181-195. doi: 10.1007/978-1-0716-4152-1_10.
Aquatic invertebrates account for many known animal species. Their diversity of form and lifestyle and adaptation to various habitats are outstanding. Several of these animals are considered reliable indicators of watershed health and are thus frequently used as environmental sentinels in ecotoxicology programs. Although aquatic invertebrates cover a large spectrum of the Tree of Life, few representatives have been sufficiently studied at the most intimate molecular level to be considered reference models. Proteogenomics has completely changed the game since the full molecular characterization of a proteome can be obtained straightforwardly for any invertebrate, thus helping to define conserved features or specific characteristics of distinct phylogenetic groups and to propose biomarkers for environmental monitoring. Typically, to obtain the most comprehensive analysis, a database of putative protein sequences is informed by sequencing full transcripts. The extracted proteins are proteolyzed, and the resulting peptides are resolved via reverse-phase liquid chromatography and identified by high-resolution tandem mass spectrometry. The data analysis makes it possible to establish a list of animal proteins and their abundances. Herein, we describe a sample preparation method for protein extraction from small aquatic invertebrates and for performing shotgun proteogenomics suitable for crustaceans and mollusks, which are the most common aquatic invertebrates.
水生无脊椎动物占已知动物物种的很大比例。它们在形态和生活方式上的多样性以及对各种生境的适应性都很突出。其中一些动物被认为是流域健康的可靠指标，因此经常被用作生态毒理学计划中的环境哨兵。虽然水生无脊椎动物涵盖了生命之树的很大一部分，但很少有代表在最亲密的分子水平上得到充分研究，因此被认为是参考模型。蛋白质基因组学完全改变了这种局面，因为可以直接获得任何无脊椎动物的蛋白质组的全面分子特征，从而有助于定义不同进化群的保守特征或特定特征，并提出用于环境监测的生物标志物。通常，为了获得最全面的分析，通过测序全长转录本来通知包含假定蛋白质序列的数据库。提取的蛋白质被蛋白酶解，所得肽通过反相液相色谱分离，并通过高分辨率串联质谱进行鉴定。数据分析可以建立动物蛋白质及其丰度的列表。在此，我们描述了一种适用于甲壳类动物和软体动物的从小型水生无脊椎动物中提取蛋白质并进行鸟枪法蛋白质基因组学的样品制备方法，这两种动物是最常见的水生无脊椎动物。
