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In recent years, isotope analysis is becoming a key instrument in food products authentication. This work reviews the use of isotope analysis to trace the production sources (wild or farmed) and geographic origins of aquatic products. The assay has studied the isotope values of freshwater fish to Atlantic salmon, sea bass, rainbow trout, and other commercial fish and shellfish. The predictable confidence of isotope analysis can be enhanced in combination with other analytical techniques, such as fatty acids and multi-element profiling. Moreover, future research to combine isotope analysis with data fusion and multivariate data evaluation is recommended.