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Analysis of conjugated fatty acids (CFA) is both convenient and challenging. Convenient, because CFA have a unique double bond system with chemical properties not common to other fatty acids (FA) that can be used for their selective analysis. Challenging, because CFA exist in many isomeric forms just as other unsaturated FAs, and most FAs have different biological properties. Therefore, the choice of method used depends on whether a selective or a complete analysis of all FAs in any given matrix is desired. For routine analysis, gas chromatography (GC) as their fatty acid methyl esters (FAME) is the method of choice. The choice of the separation column depends on the FA complexity of the matrix and how well CFA isomers separate from other FAMEs and among themselves. Currently, there is no single GC method to analyse all geometric/positional isomers of FAMEs that might occur in natural fats or synthetic mixtures. Analytical techniques can be combined considering the complexity of the matrix, the selectivity of GC columns, choice of supportive techniques, and keeping analyses per sample to a minimum. In this review, the benefits and limitations of different GC columns are evaluated and supported by selective techniques. Combinations of methods are suggested to obtain a comprehensive analysis of as many conjugated and non-conjugated FAs as possible.

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