MALDI, while providing advantages such as the ability to do in-depth and repeated exploration of the sample, challenges the existing performance capabilities of Fourier transform mass spectrometry (FTMS). The challenge arises because MALDI-produced ions have high mass-to-charge ratios and uncertain kinetic-energy distributions. We demonstrate that a combination of a gated trapping event, a RF-only mode pressure focusing event, and an electrically compensated trap provides a compelling advantage in meeting these challenges. Removal of any of the above combination elements significantly degrades the detection performance of substance P from 850 K resolving power at 34.9 kHz and of melittin from 278 K resolving power at 16.5 kHz when using a 3-Tesla magnet-based spectrometer. atrix-assisted laser desorption ionization (MALDI), when interfaced to Fourier transform mass spectrometry (FTMS) in principle has advantages with respect to electrospray ionization (ESI). First, MALDI places a lower vacuum load than does ESI on the instrument, permitting a simplified high vacuum system. Second, the low charge-state ions that are produced by MALDI allow more ions in the trap for a given charge capacity and give better utilization of the limited dynamic range of FTMS. Third, when the sample probe is located at the trap, a simple instrument results, negating the use of an external ion source, transmission ion optics, and associated pumping. The combination of random access and retrieval, a general characteristic of MALDI, and the versatility of FTMS (e.g., accurate mass, ion manipulation and activation) facilitate in-depth and repeated exploration of unknown samples.The shortcomings of FTMS, however, are more apparent with MALDI-produced than ESI-produced ions. The principal problem is that the former ions have higher m/z, lower frequency than do corresponding ESI ions. The former ions often have a lower charge state, causing poor performance because magnetic forces decrease as m/z increases. Use of higher B fields reduces the problem while shifting it to higher m/z. Furthermore, distributions of initially formed MALDI ions are variable and broad with high velocities (up to Ïł 660 m/s) [1], resulting in inefficient "catching" and unreliable and often poor detection.An effective and logical plan to improve MALDI/ FTMS could include three general approaches. The first is to modify the MALDI desorption to attenuate the translational velocities and internal energies of the desorbed ions. Examples of these efforts include the use of a comatrix [2] or a "waiting room," [3] which in the limit becomes high-pressure MALDI [4]. An alternative is the use of an external source [5], which permits the use of quadrupole and higher order traps or ion guides to focus and thermalize the MALDI-produced ions before introducing them into the FTMS trap. The second approach is to introduce efficiently the MALDI ions, whether produced externally or in-field, into the trap. The third is to improve the trap for detection of the high-m/z ions that are oft...