Dual Apodization Maximizes Charge Resolution and Frequency Precision in Charge Detection Mass Spectrometry

Charge detection mass spectrometry (CD-MS) is a single-particle technique in which the masses of individual ions are determined from simultaneous measurements of their <i>m</i>/<i>z</i> ratio and charge. Ions are trapped in an electrostatic linear ion trap and oscillate back and forth through a detection cylinder coupled to a low noise charge sensitive amplifier. The resulting signal is analyzed using short-time Fourier transforms (STFTs) to determine the <i>m</i>/<i>z</i> ratio and charge. The <i>m</i>/<i>z</i> ratio is determined from the oscillation frequency, and the charge is obtained from the magnitude of the fundamental. Here we compare the methods used to analyze time domain data for single ion measurements including STORI plots. We conclude that the original STFT approach remains the best method for the analysis of CD-MS data. However, there are many ways of implementing the STFT approach. We compare the options with the goal of maximizing precision of the charge and <i>m</i>/<i>z</i> determinations while simultaneously maximizing the number of ions that are detected. A variety of apodization methods are compared, and the effects of scalloping loss, equivalent noise bandwidth, computation time, window length, and step size are evaluated. Maximizing the precision of the charge and <i>m</i>/<i>z</i> determinations places conflicting constraints on the window length, and we conclude that a dual apodization strategy, with different window lengths, provides the most robust approach to analyzing results for the broad range of different samples that can be measured by CD-MS.