Sample Preparation for Proteogenomics of Aquatic Invertebrates.

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.
(© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)