Chapter

Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry

Part of the series Frontiers in Probability and the Statistical Sciences pp 101-124

Date:

Mass Spectrometry Analysis Using MALDIquant

  • Sebastian GibbAffiliated withAnesthesiology and Intensive Care Medicine, University Hospital Greifswald, Ferdinand-Sauerbruch-Straße
  • , Korbinian StrimmerAffiliated withEpidemiology and Biostatistics, School of Public Health, Imperial College London Email author 

Abstract

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.