Optimization of the discrete pulse sequence for two-dimensional FT-ICR mass spectrometry using infrared multiphoton dissociation

•2D FT-ICR MS shows potential as a data-independent analytical tool.•Increasing the observe pulse increases signal-to-noise ratio of fragment peaks.•Increasing the observe pulse does not affect signal-to-noise for precursor peaks.•Adjusting the encoding pulses to the fragmentation zone decreases harmonics.•Decreasing harmonics increases signal-to-noise ratio for all peaks.

2D FT-ICR MS, introduced by Pfändler et al. (Chem. Phys. Lett. 138 (1987) 195), allows one to correlate precursor and fragment ions in complex samples without requiring ion isolation. Recent advances in electronics, computer capacities, and gas-free in-cell fragmentation techniques open up new perspectives for 2D FT-ICR MS as an analytical technique. The pulse sequence consists of two encoding pulses separated by an incremental delay, followed by an observe pulse. In our previous 2D FT-ICR MS work we used three pulses of equal duration and amplitude. However, signal intensity was low because it was distributed over a series of intense harmonics. Using a simple theoretical model to analytically express ion fragmentation and 2D FT-ICR MS ion trajectories, we obtained a nearly pure signal when the maximum radius of the ions during the encoding pulses is within the laser beam. By adjusting the experimental parameters of the encoding pulses according to the calculation on the same cyclotron radius, we strongly decrease the intensity of harmonic peaks. We also discuss the effect of increasing the amplitude of the observe pulse, which affects precursor and fragment ion peaks differently in terms of signal-to-noise ratio. The 2D mass spectra obtained with the optimized pulse sequence show a much higher signal-to-noise ratio, even without using denoising algorithms.

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