In this chapter, we demonstrate how to analyze MALDI-TOF/SELDI-TOF mass spectrometry data using the wavelet-based functional mixed model introduced by Morris and Carroll (2006), which generalizes the linear mixed models to the case of functional data. This approach models each spectrum as a function, and is very general, accommodating a broad class of experimental designs and allowing one to model nonparametric functional effects for various factors, which can be conditions of interest (e.g. cancer/normal) or experimental factors (blocking factors). Inference on these functional effects allows us to identify protein peaks related to various outcomes of interest, including dichotomous outcomes, categorical outcomes, continuous outcomes, and any interactions among factors. Functional random effects make it possible to account for correlation between spectra from the same individual or block in a flexible manner. After fitting this model using an MCMC, the output can be used to perform peak detection and identify the peaks that are related to factors of interest, while automatically adjusting for nonlinear block effects that are characteristic of these data. We apply this method to mass spectrometry data from an University of Texas MD Anderson Cancer Center experiment studying the serum proteome of mice injected with one of two cell lines in one of two organs. This methodology ap-1