H-D exchange reactions of methanol-d, with protonated amino acids were performed in an external-source Fourier transform mass spectrometer. Absolute rate constants were determined for the group which included glycine, alanine, valine, leucine, isoleucine and proline. By comparing reactivities with selected methyl esters, it was found that exchange on the carboxylic acid occurs 3-10 times faster than exchange on the amino group. No simple correlation is observed between the rates of H-D exchange on the acid group and the size of the alkyl group. However, the rates of exchange on the amine decrease with increasing gas-phase basicity. Glycine, the least basic amino acid, exchanges its amine hydrogens the fastest. These results are useful for determining the interaction of methanol with protonated amino acids and can provide insight into the H-D exchange reactions observed with polyprotonated proteins produced by electrospray ionization.