Pre-Processing Mass Spectrometry Data

Mass spectrometry is actively being used to discover disease-related proteomic patterns in complex mixtures of proteins derived from tissue samples or from easily obtained biological fluids. The potential importance of these clinical applications has made the development of better methods for processing and analyzing the data an active area of research. In this chapter, we overview basic concepts of MALDI-TOF, describe the necessary preprocessing steps, and present our preferred method. We discuss the advantages and disadvantages of our approach relative to other alternatives in existing literature, and compare methods’ performance using real and simulated data.