The glycoprotein, human Factor IX, from recombinant and natural sources was analyzed for monosaccharide composition by preparing the TMS derivatives of the methylglycosides followed by GC and combined GC/MS analyses. TMS methylglycosides were prepared from the sample by methanolysis in 1 M HCl in methanol followed by N-acetylation with pyridine and acetic anhydride. Inositol was added to the sample before derivatization as an internal standard, and a number of n-alkanes were co-injected as retention standards for the GC analysis. The monosaccharides were identified by their retention times in comparison to standards, and their carbohydrate character was authenticated by their mass spectra.