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Axial ejection is found to be the principal cause of the loss of ions during Fourier transform mass spectrometry remeasurement experiments. Ion remeasurement improves to near unit efficiency when an open-ended cylindrical analyzer cell is used with capacitive coupling of the excitation signal to the adjacent trapping plates. With capacitive coupling enabled for the entire experiment, 100% remeasurement efficiency is observed over a narrow mass range (10 Da) for 200 scans of ions of poly(ethylene glycol) formed by internal matrix-assisted laser desorption/ionization. Greater than 99.5% efficiency per remeasurement cycle has been achieved for wide mass range (1000 Da) remeasurement with capacitive coupling enabled. Further evidence for axial ejection during remeasurement comes from a comparison of remeasurement efficiencies obtained at different trapping potentials.

Quadrupolar excitation is achieved over a wide mass range by using repetitive chirp excitation, filtered noise excitation, and high-amplitude, single-frequency excitation for matrix-assisted laser desorption FTICR mass spectrometry. These methods efficiently axialize ions over a wide range of masses in a 4.7 T FTICR spectrometer. Remeasurement efficiencies are >99.5% for broadband repetitive chirp excitation, 99% with filtered white noise, and 99.4% with high-amplitude, single-frequency broad-band quadrupolar excitation. Results indicate that z-axis ejection of ions during detection is the primary mechanism for ion loss during remeasurement experiments. Capacitive coupling of the excitation signal to the trapping plates of the open-ended cylindrical analyzer cell is required for high remeasurement efficiency.

Ions formed by a single laser desorption event can be remeasured more than 500 times in a Fourier transform ion cyclotron resonance spectrometer. Quadrupolar excitation and collisional axialization are used to move ions located in any region of the ICR cell to the center of the cell, where they can be effectively detected. With this method, the signal from ions formed by a single laser desorption event is averaged for 200 remeasurement cycles with an efficiency in excess of 99.5% per cycle. Collisions of ions with helium are found to give higher remeasurement efficiencies than collisions with methane, due to reduced scattering losses by the lighter collision gas. With this method, ions that are stored in the analyzer cell for more than 1 hour can be detected. This technique is shown to be compatible with high-resolution data acquisition. Ions formed by one laser desorption event are remeasured at eight bandwidths, demonstrating low-resolution, wide-mass-range analysis and high-resolution, narrow-mass-range analysis of the same group of ions.