A mass spectrometer system includes an ion detector, a plurality of analog-to-digital (A/D) converters, an adder, and a controller. The A/D converters are configured to sample an analog signal from the ion detector at different times, and the A/D converters introduce sampling errors to digital samples generated by the A/D converters. The adder is configured to sum the digital samples, and the summed digital samples define a mass spectrum. The controller is configured to compensate for the sampling errors introduced by the A/D converters.