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ISO 12966-3:2009 specifies a rapid base-catalysed transesterification method for fats and oils with trimethylsulfonium hydroxide to prepare fatty acid methyl esters. The method is exclusively applicable to the preparation of methyl esters of fats and oils for gas liquid chromatographic analysis. It is applicable to all fats and oils including milk fat and blends containing milk fat. Isomerization of unsaturated fatty acids only occurs to a minor extent and isomerized fatty acids are only present at the determination limit. As isomerization takes place the procedure is not recommended for conjugated linoleic acid (CLA). As CLA is not correctly analysed, this method is not applicable to the determination of the complete fatty acid composition of milk fat samples.

Only about 70 % to 80 % of the free fatty acids are esterified. In the case of conjugated cyclopropyl and cyclopropenyl fatty acids, side reactions may occur, but these do not interfere with the determination of the fatty acids.