Detection of oligonucleotides by external injection into an ion trap storage/reflection time-of-flight device.

The detection of oligonucleotides has been studied using external injection of Matrix-assisted laser desorption/ionization (MALDI) produced ions into a quadrupole ion trap storage device. The ions stored in the trap are then detected by pulsed DC injection into a reflection time-of-flight mass spectrometer. It is shown that by using a low acceleration voltage from the probe tip and external injection into the trap that 3-mers to 9-mers can be stored for 20-50 ms and detected as intact ions. In comparison, direct MALDI inside the trap resulted in extensive fragmentation as a function of storage time. Using the external injection with a He buffer gas in the trap yields a resolution of 250-400 in the ion trap storage/reflectron time-of-flight mass spectrometer. The resolution can be further enhanced to 400-800 using a bipolar extraction method. In addition, the trapping efficiency for the injection of externally produced ions into the trap can be enhanced using a dynamic trapping method. The MALDI mass spectra produced by this methodology result in excellent signal-to-noise ratio due to the capabilities of the trap for eliminating low mass matrix background from the spectra.