A data acquisition system for acquiring a digitized time-domain signal and corresponding mass spectra from a mass spectrometer. The system comprises a signal conditioning device including an amplifier and an analog low-pass filter, to amplify and filter an analog signal generated by the mass spectrometer, and to output a conditioned analog signal; an analog-to-digital converter to convert in real time the conditioned analog signal into a digital data stream; a digital signal processing device having an in-line digital signal processing device for processing the digital data stream to generate the digitized time-domain signal, and to digitally decode a digital triggering signal from the mass spectrometer; and a host device having a data processing device to receive the digitized time-domain signal from the digital signal processing device, and to construct a corresponding mass spectra from the digitized time-domain signal.