Abstract Motivation: Although R packages exist for the pre-processing of metabolomic data, they currently do not incorporate additional analysis steps of summarization, filtering and normalization of aligned data. We developed the MSPrep R package to complement other packages by providing these additional steps, implementing a selection of popular normalization algorithms and generating diagnostics to help guide investigators in their analyses. Availability: http://www.sourceforge.net/projects/msprep Contact: [email protected] Supplementary Information: Supplementary materials are available at Bioinformatics online.