Base-catalyzed transesterification of acyl lipids with methanol in the presence of trimethylsulfonium hydroxide (TMSH) is an easy and convenient method for the preparation of fatty acid methyl esters for gas chromatography (GC) analyses. Free fatty acids are converted to fatty acid methyl esters by the pyrolytic reaction with TMSH as well. We have found that lipids and other compounds containing thiol groups are also converted easily to the corresponding methyl sulfides (methyl thioethers) by the pyrolytic reaction with TMSH occurring in the injector of the gas chromatograph. For example, alkane thiols such as dodecane thiol and octadecane thiol are converted to the corresponding alkyl methyl sulfides, whereas bis(methylthio) derivatives are formed from alpha,omega-alkane dithiols, e.g., 1,8-octanedithiol, and from 2,3-dimercaptopropan-1-ol (dimercaprol). Furthermore, 3beta-mercaptocholest-5-ene (thiocholesterol) is converted to 3-methylthiocholest-5-ene by the same reaction. The S-methylation reactions which finally lead to the corresponding methylthio derivatives of lipids and other compounds with thiol groups may be of diagnostic value for the structural analysis of such compounds by GC and GC/mass spectrometry.