Ultraviolet photodissociation (UVPD) was evaluated as a technique for generating ion fragmentation information that is alternative and/or complementary to the information obtained by collision-induced dissociation (CID). Ions trapped in a pressurized linear ion trap were dissociated using a 355 nm or a 266 nm pulsed laser. Comparisons of UVPD and CID spectra using a set of aromatic chromophore-containing compounds (desmethyl bosentan, haloperidol, nelfinavir) demonstrated distinct characteristic fragmentation patterns resulting from photodissociation. The wavelength of light and the pressure of the buffer gas in the UVPD cell are important parameters that control fragmentation pathways. The wavelength effect is related to the absorption cross section, location of the chromophore and the energy carried by one photon. Thus, UV irradiation wavelength affects fragmentation pathways as well as the fragmentation rate. The pressure effect can be explained by collisional quenching of ‘slow’ fragmentation pathways. We observed that higher pressure of the buffer gas during UVPD experiments highlights unique fragment ions by suppressing slow fragmentation pathways responsible for CID-like fragmentation patterns. Copyright © 2010 John Wiley & Sons, Ltd.