Mass spectrometry analysis using MALDIquant. 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.