A data acquisition system and method are described that may be used with various spectrometers. The data acquisition system may include an ion detector, an initial processing module, and a spectra processing module. The initial processing module is provided for processing the ion detection signals and for supplying processed signals to the spectra processing module. The spectra processing module generates spectra from the processed signals and supplies the generated spectra to an external processor for post-processing. The spectra processing module may include one or more of: a cross-spectra filter for filtering data in each spectra as a function of data in at least one prior spectra; a shaping filter for removing skew and shoulders from the processed signals; a sharpening filter for sharpening the peaks of the processed signals to effectively deconvolve and separate overlapping peaks; an ion statistics filter; and a peak histogram filtering circuit.