A database of chromatographic properties and mass spectra of fatty acid methyl esters from omega-3 products

• Fatty acid methyl esters from selected omega-3 products were analyzed by GC–MS.
• Samples were analyzed on polyethylene glycol and cyanopropyl stationary phases.
• Novel methodology for combining mass spectra and retention indices is described.
• Mass spectra and retention indices are combined into a single score value.
• Equivalent chain lengths are provided for approximately 100 compounds.

Fatty acids in products claimed to contain oils with the omega-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) were analyzed as fatty acid methyl esters by gas chromatography–mass spectrometry using electron impact ionization. To cover the variation in products on the market, the 20 products that were studied in detail were selected from a larger sample set by statistical methodology. The samples were analyzed on two different stationary phases (polyethylene glycol and cyanopropyl) and the fatty acid methyl esters were identified by methodology that combines the mass spectra and retention indices into a single score value. More that 100 fatty acids had a chromatographic area above 0.1% of the total, in at least one product. Retention indices are reported as equivalent chain lengths, and overlap patterns on the two columns are discussed. Both columns were found suitable for analysis of major and nutritionally important fatty acids, but the large number of minor compounds that may act as interferents will be problematic if low limits of quantification are required in analyses of similar sample types. A database of mass spectral libraries and equivalent chain lengths of the detected compounds has been compiled and is available online.