Lipidomic Characterization of Marine By-Product Oils: Impact of Species and Extraction Methods on Lipid Profile and Antioxidant Potential

Marine by-products represent an important source of bioactive lipids with potential applications in nutraceuticals and functional foods. This study provides a biochemical and lipidomic characterization of oils derived from sardine, monkfish, grey mullet roe, squid, and anchovy by-products, assessing how the extraction method influences their lipid and antioxidant profiles. Fatty acids were quantified by GC-FID, antioxidant compounds by HPLC-DAD, and untargeted lipidomics by TIMS-HRMS. A total of 228 lipid species were identified, predominantly triglycerides (TGs) and diglycerides (DGs), accounting for approximately 69% of the annotated lipidome. Grey mullet roe oils exhibited the highest levels of long-chain PUFAs (EPA, DHA) and antioxidants (α-tocopherol 205–469 mg/Kg, lutein 10–125 mg/Kg, and squalene 1004–6049 mg/Kg), whereas squid oils showed high n-3/n-6 proportions. The extraction method strongly affected lipid integrity. Supercritical CO2 extraction with ethanol (SFE–SE) preserved the greatest proportion of PUFA-rich TGs, yielding ~27–28 g EPA + DHA per 100 g oil, while wet reduction and mechanical pressing produced lower PUFA levels (~22 g/100 g) and increased hydrolysis/oxidation-associated lipids. PCA and PLS-DA revealed clear clustering driven by species and extraction class, with PUFA-containing TGs and DGs identified as major discriminating lipids. These results highlight the critical role of extraction conditions in determining the nutritional and functional value of marine oils and support the valorization of marine by-products in high-value applications.