MALDI-TOF mass spectroscopy is a precious method to measuring the molecular size. But there was a problem during measuring fatty acid with DBH (2,5-dihysroxybenzoinc acid) matrix. In this method no signal detected and it seems that fatty acid couldn't flight with this matrix .
Try the sodium salts
Rapid Commun Mass Spectrom. 2001;15(21):2027-34.
Comparative quantitative fatty acid analysis of triacylglycerols using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and gas chromatography.
Hlongwane C1, Delves IG, Wan LW, Ayorinde FO.
We measured unsaturated fatty acids (oleic acid and elaidic acid) without matrix and salt and we detected H+, Na+ and K+ adducts. Measuring with matrix means you will have many peaks corresponding to the matrix in the same molecular weight range as your analyte, making analysis more difficult. Did you thought about ESI-TOF MS?
MALDI maybe not the best MS approach for fatty acid. I tried ESI LC-MS and the results were very impressive.
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