MALDIquant: a versatile R package for the analysis of mass spectrometry data

Bioinformatics. 2012 Sep 1;28(17):2270-1. doi: 10.1093/bioinformatics/bts447. Epub 2012 Jul 12.


MALDIquant is an R package providing a complete and modular analysis pipeline for quantitative analysis of mass spectrometry data. MALDIquant is specifically designed with application in clinical diagnostics in mind and implements sophisticated routines for importing raw data, preprocessing, non-linear peak alignment and calibration. It also handles technical replicates as well as spectra with unequal resolution.

Availability: MALDIquant and its associated R packages readBrukerFlexData and readMzXmlData are freely available from the R archive CRAN ( The software is distributed under the GNU General Public License (version 3 or later) and is accompanied by example files and data. Additional documentation is available from

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Data Interpretation, Statistical*
  • Humans
  • Software*
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / methods*