Traceability of Wild and Farmed Four Major Chinese Carps Using High-Resolution Mass Spectrometry-Based Proteomics Combined with Multivariate Statistical Analysis

The escalating demand for traceability and authentication of aquatic products, driven by significant quality and commercial value differences between wild and farmed fish, necessitates applicable analytical strategies. Sequential window acquisition of all theoretical fragment ion mass spectra (SWATH-MS)-based proteomics, along with multivariate statistical analysis, was employed to discriminate wild and farmed populations of the Four Major Chinese Carps: <i>Mylopharyngodon piceus</i>, <i>Ctenopharyngodon idellus</i>, <i>Hypophthalmichthys molitrix</i>, and <i>Hypophthalmichthys nobilis</i>. As a consequence, 24 proteins were identified as discriminators with the model of orthogonal partial least-squares-discriminant analysis (OPLS-DA) and validated by hierarchical clustering analysis (HCA) with visually significant abundance variations between wild and farmed populations. Gene Ontology (GO) annotation additionally revealed that these biomarkers were predominantly involved in energy metabolism and structural development, reflecting molecular adaptations to distinct habitat environments. The applicability of the developed OPLS-DA models to traceability of wild and farmed populations of the Four Major Chinese Carps was also verified by the commercial real-life samples.