Enhancing MALDI time-of-flight mass spectrometer performance through spectrum averaging.

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometers are simple and robust mass spectrometers used for analysis of biologically relevant molecules in diverse fields including pathogen identification, imaging mass spectrometry, and natural products chemistry. Despite high nominal resolution and accuracy, we have observed significant variability where 30-50% of individual replicate measurements have errors in excess of 5 parts-per-million, even when using 5-point internal calibration. Increasing the number of laser shots for each spectrum did not resolve this observed variability. What is responsible for our observed variation? Using a modern MALDI-TOF/TOF instrument, we evaluated contributions to variability. Our data suggest a major component of variability is binning of the raw flight time data by the electronics and clock speed of the analog-to-digital (AD) detection system, which requires interpolation by automated peak fitting algorithms and impacts both calibration and the observed mass spectrum. Importantly, the variation observed is predominantly normal in distribution, which implies multiple components contribute to the observed variation and suggests a method to mitigate this variability through spectrum averaging. Restarting the acquisition impacts each spectrum within the electronic error of the AD detector system and defines a new calibration function. Therefore, averaging multiple independent spectra and not a larger number of laser shots leverages this inherent binning error to mitigate variability in accurate MALDI-TOF mass measurements.