Gas chromatography/tandem mass spectrometry as an analytical tool for the identification of fatty acids.

Structures of fatty acids present at very low quantities in mycobacteria are difficult to determine. A commonly used strategy is to introduce heteroatoms into functional groups by chemical means before subjecting them to gas chromatography/tandem mass spectrometry (GC/MS/MS) analysis. Routinely used methods give very low abundance diagnostic ions leading to ambiguities in structural conclusions. GC/MS/MS associated with electron capture ionization of pentafluorobenzyl esters was used to study very complex mixtures of fatty acids from Mycobacterium fallax and M. aurum. The charge-remote fragmentation of fatty acid carboxylate anions was used for structure determination at the nanogram level of a large number of unsaturated, branched, and cyclopropane-containing fatty acids. Some of them have not been observed previously in these Mycobacteria. On the basis of these studies, biosynthetic pathways of unsaturated, branched, and cyclopropane-containing fatty acid are proposed.