  MALDIquant and associated R packages provide a versatile and completely free
open-source platform for analyzing 2D mass spectrometry data as generated for
instance by MALDI and SELDI instruments. We first describe the various methods
and algorithms available in MALDIquant . Subsequently, we illustrate a typical
analysis workflow using MALDIquant by investigating an experimental cancer data
set, starting from raw mass spectrometry measurements and ending at
multivariate classification.
