The invention provides a data acquisition system and method for detecting ions in a mass spectrometer, comprising: a detection system for detecting ions comprising two or more detectors for outputting two or more detection signals in separate channels in response to ions arriving at the detection system; and a data processing system for receiving and processing the detection signals in separate channels of the data processing system and for merging the processed detection signals to construct a mass spectrum; wherein the processing in separate channels comprises removing noise from the detection signals by applying a threshold to the detection signals. The detection signals are preferably produced in response to the same ions, the signals being shifted in time relative to each other. The invention is suitable for a TOF mass spectrometer.