Label-free quantitative proteomics analysis of sea cucumber (Apostichopus japonicus) from different origins using...

Sea cucumbers (Apostichopus japonicus) from Liaoning, China command premium market value due to superior collagen integrity, yet the proteomic basis of this geographical differentiation remains unclear. Current geographic proteomic studies using data-dependent acquisition (DDA) mass spectrometry face stochastic ion selection bias, poor low-abundance reproducibility and limited coverage. Here, we established a custom label-free data-independent acquisition (DIA) workflow to characterize proteomic profiles of 200 sea cucumbers (80 Liaoning, 120 non-Liaoning). Our approach identified 6278 proteins and discovered 64 differentially expressed proteins (DEPs), including arginase (A0A141R8A8) and glutamine synthetase (A0A076VCY3) as potential authentication markers. Functional annotation highlighted arginine biosynthesis (P = 0.00034) as the pivotal pathway, alongside two-component system and necroptosis, indicating nitrogen homeostasis prioritization and stress adaptation in Liaoning specimens. This study provides a novel DIA-based framework for discovering the proteomic basis of geographical differentiation, linking nitrogen metabolism to regional quality differences in marine foods and identifying potential molecular targets for future authentication efforts.