Molecular ion fragmentation and its effects on mass isotopomer abundances of fatty acid methyl esters ionized by electron impact

We have analyzed the isotopomer abundance ratios of an equimolar mixture of nine fatty acid methyl esters (decanoate, undecanoate, laurate, tridecanoate, myristate, pentadecanoate, palmitate, heptadecanoate, and stearate) by selected-ion monitoring gas chromatography/electron impact/mass spectrometry (GC/EI/MS). The abundance of the second lowest m/z isotopomer (IM1) increased disproportionately compared with the abundance of the lowest m/z isotopomer (IM0) as a function of: (1) increasing sample size; (2) decreasing repeller voltage; and (3) decreasing alkyl chain length. We also compared the abundance of the third lowest m/z isotopomer (IM2) and the abundance of the second lowest m/z isotopomer (IM1) of methyl palmitate and [4,4-2H2]methyl palmitate. We observed that the IM2/IM1 for methyl palmitate was significantly lower than IM2/IM1 for [4,4-2H2]methyl palmitate. From these results, as well as a consideration of basic principles of ion chemistry and ion physics, we conclude that gas-phase chemistry, specifically proton (or deuteron) transfer from fragment ions to molecules, is a major contributor to the sample size dependence observed in mass isotopomer abundance measurements of fatty acid methyl esters ionized by EI. Our results and analysis do not support hydrogen abstraction as the reaction mechanism. In addition, we calculate that rearranged molecular ions are unlikely to contribute significantly to intermolecular proton transfer because of their relatively brief lifetime. We also discuss alternative analytical techniques which might improve the precision and accuracy of isotopomer measurements by reducing molecular ion fragmentation.