Microporous sol-gels prepared from a tetramethyl orthosilicate precursor with 5-hydroxytryptophan, 5-HTPP, as a dopant were investigated by matrix-assisted laser desorption/ionization mass spectrometry (MALDI). Spectra of 5-HTPP and its oxidation products were obtained when (a) the matrix, α-hydroxycinnamic acid, was included in the sol, (b) thin wafers of silica were used, and (c) the surface of the gel was abraded after mounting the sol-gel on the MALDI sample puck so that laser reflection was minimized. The methodology permitted elucidation of the 5-HTPP oxidation pathway. In microporous silica a low molecular product, the dione, was obtained whereas in a mesoporous matrix, dimeric products were formed.