So far the most frequently used method for fatty acid (FA) analysis is GC coupled to flame ionization detector (FID). However, GC-FID does not allow profiling of FA synthesis and metabolism using stable isotopes. Here we present a rapid and sensitive GC-MS method for determination of fatty acid methyl esters (FAMEs). Fatty acid methylation was carried out by transesterification with acetyl-chloride and methanol. FAME separation applies a short and polar cyano-column resulting in an analysis time of 17.2min. Separation was achieved for positional and geometrical (cis/trans) isomers with chain lengths between C8 and C28. Partial overlap of FAMEs (e.g. for C20:2 (n-6) and C21:0) could be resolved using selected ion monitoring (SIM). The precisions for human plasma samples were better than 10% coefficient of variation (CV) except for very low abundant FAs and LODs were in the low femtomol range on column. The developed GC-MS method also allows quantification of conjugated FAs such as conjugated linoleic acid (CLA) isomers because lowering the derivatization temperature from 95 °C to room temperature prevented cis to trans double bond isomerization. Finally, profiling of fatty acid synthesis and metabolism was exemplified with stable isotope labeling of macrophages using fatty acid precursors or deuterated fatty acids. In summary, we present a fast and robust GC-MS method for fatty acid profiling of positional and geometrical isomers including CLAs as well as very long chain fatty acids (VLCFAs). The method is suitable for both clinical studies and basic research including application of stable isotope compounds.
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