Development of an integrated multi-omic targeted workflow for <i>Gammarus fossarum</i>: a proof-of-concept application to study endocrine disruption in environmental species

However, mechanistic studies in ecologically relevant sentinel species often require organ-level investigation, which is hindered by extreme limitations in biomass and high inter-individual variability. In this context, we developed a targeted multi-omic workflow (proteomics, metabolomics, and lipidomics) optimised for low-mass sentinel species such as <i>Gammarus fossarum</i>.

A unified ‘metabolomics-first’ co-extraction protocol enabled the simultaneous recovery of proteins, metabolites, and lipids from identical caeca pools. To overcome data processing bottlenecks of high-resolution mass spectrometry (HRMS) and ensure high sensitivity, a fully targeted mass spectrometry strategy was adopted across all omics layers. Specifically, the Scout-MRM approach was implemented via the Scout-MRM Builder tool for metabolomics, providing an efficient alternative to untargeted HRMS.