To functionalize the surface of nanoparticles with phenyl groups for subsequent cross-linking with aromatic molecules by mutual interactions, we prepared functional nanoparticles (d = 3 nm) by silanization with phenyl-triethoxysilane. The nanoparticles had Fe(2)O(3) cores conjugated to phenyl groups; this was confirmed by Fourier transform infrared (FT-IR) spectroscopy and absorption spectrophotometry. The typical C-H and C-C peaks and the absorption at 240 nm, which corresponds to aromatic rings, were detected in the spectroscopic results for the phenyl group-modified nanoparticles. The nanoparticles could ionize aromatic (colchicine, reserpine, and bradykinin peptide) and nonaromatic (L-α-phosphatidylethanolamine,dioleoyl, and polyethylene glycol) molecules by nanoparticle-assisted laser desorption/ionization mass spectrometry. The nanoparticles worked as a selective trap and an ionization-assisting reagent in mass spectrometry for the aromatic molecular targets.