Challenges and perspectives in MS-based omics approaches for ecotoxicology studies: An insight on Gammarids sentinel amphipods

Abstract

The aquatic environment is one of the most complex biosystems, as organism at all trophic levels may be exposed to a multitude of pollutants. As major goals, ecotoxicology typically investigates the impact of toxic pollutants on the ecosystems through the study of sentinel organisms. Over the past decades, Mass Spectrometry (MS)-based omics approaches have been extended to sentinel species both in laboratory and field exposure conditions. Single-omics approaches enable the discovery of biomarkers mirroring the health status of an organism. By covering a restricted set of the molecular cascade, they turn out to only partially satisfy the understanding of complex ecotoxicological effects. In contrast, a more complete understanding of the ecotoxicity pathways can be accessed through multi-omics approaches. In this perspective, we provide a state-of-the-art and a critical evaluation on further developments in MS-based single and multi-omics studies in aquatic ecotoxicology. As case example, literature regarding Gammarids freshwater amphipods, non-model sentinel organisms sensitive to pollutants and environmental changes and crucial species for downstream ecosystems, will be reviewed.

Concomitant investigation of crustacean amphipods lipidome and metabolome during molting stage by Zeno SWATH Data-Independent Acquisition coupled with Electron Activated Dissociation and machine learning

“…Concerning the other relevant features, those partially identified lipids were further confirmed and elucidated using EAD. Specifically, PC O-34:3 was identified as PC O-16:0/18:3 (9,12,15), PC O-36:5 as PC O-16:0/20:5 (5,8,11,14,17), PC O-36:1 as PC O-18:0/18:1(9), and TG 45:0 as TG 14:0/16:0/15:0. However, the unknown features that did not match any CID MS/MS spectra in MS-DIAL remained unidentified even after MS/MS EAD spectral database, that can be attributed to the limited comprehensiveness of the database.…”

“…SWATH guarantees comprehensive acquisition of a wide range of compounds in complex biological samples, as each precursor is assigned to a reconstructed fragmentation spectrum. While SWATH has demonstrated its efficacy in proteomics [7][8][9], it has also been recently explored in the field of metabolomics [10][11][12] and applied to lipidomics [13,14].…”

Electron-activated dissociation (EAD) for the complementary annotation of metabolites and lipids through data-dependent acquisition analysis and feature-based molecular networking, applied to the sentinel amphipod Gammarus fossarum

“…In the last 20 years, research on G. fossarum has been pushed to study the biological perturbations caused by environmental contaminants. Mass spectrometry-based proteomics and proteogenomics have contributed to fostering the knowledge of the molecular physiology of reproduction in G. fossarum and to investigating the mechanisms of action of some contaminants, such as pesticides or metal ions [56][57][58][59][60][61][62][63][64]. More recently, shotgun lipidomics or mass spectrometry imaging have been integrated to gain extensive knowledge on G. fossarum lipid composition and on their spatial distribution in different organ sections [65,66].…”