Biological mass spectrometry analysis for traceability of production method and harvesting seasons of sea cucumber (Apostichopus japonicus)

The focus of this paper was to investigate the potential of distinguishing sea cucumbers from different production methods (farmed vs wild-caught) and different seasons (autumn vs summer) at the proteomic level. Based on biological mass spectrometry with sequential window acquisition of all the theoretical fragment ion mass spectra (SWATH) acquisition mode, the proteomes of Apostichopus japonicus under farmed and wild production methods were profiled and relatively quantified. The SWATH data were mined by chemometric tools aiming to screen protein biomarkers for the traceability of sea cucumbers in terms of production methods as well as harvesting seasons, respectively. In the end, 4 production-method-sensitive proteins regardless of harvesting seasons and 12 season-sensitive proteins regardless of production methods were unveiled. The protein biomarkers were visually validated by hierarchical clustering heatmap analysis, and gene ontology annotation of biomarkers provided more insight for understanding the intrinsic linkage between the traceability and function of Apostichopus japonicus.