Sequence-specific fragmentation generated by matrix-assisted laser desorption/ionization in a quadrupole ion trap/reflectron time-of-flight device.

Sequence-specific fragmentation for structural analysis has been generated by activation of ions via matrix-assisted laser desorption/ionization (MALDI) in an ion trap storage/reflectron time-of-flight device (IT/reTOF). The key to this work is that ion decay can be induced by MALDI activation but requires an extended period of time to occur in large peptides. This extended decay period, which may be in excess of 20 ms, is provided in these experiments using the long storage times of the ion trap device. The ions are stored until decay is complete and then rapidly pulsed into a reflectron TOF for analysis. Since the ions decay within the trap, they ultimately appear as stable ions in the reTOF rather than as metastable decay peaks. The ion fragmentation was found to depend strongly on laser power and the rf voltage placed on the ring electrode of the trap. The fragmentation obtained was shown to be similar to but different from that observed in FAB-low-energy CAD. In particular, enhanced fragmentation was obtained in the lower mass range and large species could be more easily fragmented than with FAB-low-energy CAD. The types of fragmentation for several target peptides are discussed.