Photodissociation studies of small peptide ions by Fourier transform mass spectrometry

Fourier transform mass spectrometry was used to study the 193 nm photodissociation of laser‐desorbed peptide ions. The output of an excimer laser was split and the two beams were directed sequentially at a sample probe to form ions, and through an aperture in the analyzer cell, to cause photodissociation of trapped ions. A solenoid‐driven shutter that is capable of rapid switching (30 ms) between the open and closed states allowed a single laser to be used for both desorption/ionization and photodissociation. Multiple laser pulses were required to fragment a significant fraction of the precursor ions (five pulses yielded 40% dissociation). Collisionally activated dissociation (CAD) mass spectra of the peptides were recorded and compared with the photodissociation mass spectra. Photo‐activation of peptide ions produced lower yields of fragment ions formed by loss of small molecules (H2O, NH3, CO, CO2) than did CAD, and produced higher yields of structurally informative sequence ions. For most peptides, the efficiency of ion fragmentaton by photodissociation paralleled the condensed‐phase molar absorptivity of the peptide at 193 nm. A comparison of these data with those of previous studies suggested that both the ionization method and the observation time (dictated by the type of mass spectrometer) influence the appearance of the photodissociation mass spectrum.