A data acquisition system for acquiring a digitized time-domain signal from a mass spectrometer, the system comprising: a signal conditioning device including an amplifier (21, 22, 23) and an analog low-pass filter (24, 25, 26), configured to amplify and filter an analog signal generated by the mass spectrometer, and to output a conditioned analog signal; an analog-to-digital converter configured to convert in real time the conditioned analog signal into a digital data stream; and a digital signal processing device having an in-line digital signal processing device configured to process the digital data stream to generate the digitized time-domain signal, and to digitally decode a digital triggering signal from the mass spectrometer; a host device having a data processing device configured to receive the digitized time-domain signal from the digital signal processing device, and to construct corresponding mass spectra from the digitized time-domain signal; wherein the in-line digital signal processing device comprises: a digital decoder configured to decode a start event and a stop event when generating each individual digitized transient signal in the mass spectrometer, wherein a detection of the stop event is performed by using the digital triggering signal from the mass spectrometer; a digital valve configured to distinguish individual digitized transient signals in the digital data stream, according to the start event and the stop event; and a digital downsampler based on a digital low-pass finite-impulse response filter configured to reduce data of the individual digitized transient signals, the digital low-pass finite-impulse response filter providing a phase function close to a linear function of frequency. a signal conditioning device including an amplifier (21, 22, 23) and an analog low-pass filter (24, 25, 26), configured to amplify and filter an analog signal generated by the mass spectrometer, and to output a conditioned analog signal; an analog-to-digital converter configured to convert in real time the conditioned analog signal into a digital data stream; and a digital signal processing device having an in-line digital signal processing device configured to process the digital data stream to generate the digitized time-domain signal, and to digitally decode a digital triggering signal from the mass spectrometer; a host device having a data processing device configured to receive the digitized time-domain signal from the digital signal processing device, and to construct corresponding mass spectra from the digitized time-domain signal; wherein the in-line digital signal processing device comprises: a digital decoder configured to decode a start event and a stop event when generating each individual digitized transient signal in the mass spectrometer, wherein a detection of the stop event is performed by using the digital triggering signal from the mass spectrometer; a digital valve configured to distinguish individual digitized transient signals in the digital data stream, according to the start event and the stop event; and a digital downsampler based on a digital low-pass finite-impulse response filter configured to reduce data of the individual digitized transient signals, the digital low-pass finite-impulse response filter providing a phase function close to a linear function of frequency.