Matrix-assisted laser desorption ionization time-of-flight (MALDl-TOF) mass spectrometers are simple and robust instruments for analysis of biologically relevant peptides and proteins including pathogen identification. Despite high nominal resolution and implied accuracy, we have observed mass accuracy deviations in internally calibrated spectra significantly in excess of instrument specifications. Increasing the number of laser pulses for each spectrum improved signal/noise, but did not resolve the observed accuracy variations. Using a modern MALDl-TOF/TOF instrument, we evaluated contributions to the observed variability in accuracy. These data suggest accuracy variability is attributable to differences in the flight time measurements for ions from both the minor inconsistencies in laser pulse timing (also known as jitter) and, more significantly, binning of data into discrete signal packets defined by the clock speed of the analog-to-digital (AD) detection system. While increased number of laser pulses may rectify minor laser timing issues, it cannot rectify parsing the raw data signal into discrete bins defined at the start of acquisition by the AD detection system. The resulting discontinuous intensity-versus-time measurement produces a discontinuous mass spectrum that requires interpolation by automated peak fitting procedures. Importantly, the variation imparted by these factors is predominantly normal in distribution, which implies a simple method to mitigate this variability through spectrum averaging. Restarting the acquisition for each spectrum resets the bins within the electronic error of the AD detector system. Therefore, increasing the number of independent spectra, not the number of laser pulses, leverages this inherent binning error to improve instrument accuracy.