Fragmentation processes that occur very early during matrix-assisted laser desorption ionization (MALDI) of peptides are examined by utilization of delayed pulsed ion extraction with a linear time-of-flight mass spectrometer. The oxidized B chain of bovine insulin (MW=3495. 95 u), which produces a wide range of fragment ions, is utilized as a probe to examine the effects of several experimental parameters on this process. Experimental evidence suggests that this MALDI process is not prompt fragmentation and involves metastable ion decay that is quite different from that which is observed with postsource decay experiments. This conclusion is based upon the significant differences observed in the fragmentation products produced by the two techniques. This metastable ion decay process also appears to be over within the minimum pulse delay period (320 ns) that is possible with the current pulsed ion extraction hardware. These two observations suggest that either different activation processes are involved in the two techniques or that the much different time frame of the methods influences the observed ion decay pathways. This fast MALDI metastable ion fragmentation also is shown to be influenced by both the MALDI matrix and the laser fluence.

Initial results are presented for a novel experimental arrangement which allows the successful study of laser-desorbed neutral species under matrix isolation conditions. In the current work, a pulsed carbon dioxide laser (10.6 μm) is employed for laser desorption. With the combination of a previously described cryogenic trapping technique with coaxial matrix isolation gas (xenon or argon) introduction, laser-desorbed neutrals have been matrix isolated and their Fourier transform infrared spectra recorded. Two different cinnamic acid derivatives ( p-coumaric acid and sinapinic acid) typically employed for matrix-assisted laser ionization (MALDI) mass spectrometry were utilized to demonstrate this new technique. Experimental conditions were determined for optimal matrix isolation of the laser-desorbed species. Two different desorption geometries were examined with respect to their effectiveness for matrix isolation of desorbed neutrals. A covalent dimer of p-coumaric acid produced in an external UV photoreactor and thought to be a possible photoreaction product in UV MALDI was studied by this technique. Thermal degradation of this dimer is shown to occur above threshold irradiance for laser desorption.