MALDIquant: Quantitative Analysis of Mass Spectrometry Data

MALDIquant and
MALDIquantForeign pages on CRAN.

MALDIquant provides a complete analysis pipeline for MALDI-TOF and other mass spectrometry data. Distinctive features include baseline subtraction methods such as TopHat or SNIP, peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.

Quick install:
enter at the R console:
install.packages(c("MALDIquant", "MALDIquantForeign"))

The MALDIquant pipeline consists of two main R packages:

Debian GNU/Linux:
install the Debian packages
r-cran-maldiquant and r-cran-maldiquantforeign.

All softwares are licensed under the GNU GPL version 3 (or any later version).

Author: Sebastian Gibb.

Example R Code:

To illustrate the application of MALDIquant for analyzis of mass spectrometry data please find below a number of example R scripts - see also the corresponding github page. In each example click on the "Raw" button to get the actual R file:

The MALDIquant and MALDIquantForeign packages are also part of the Bioconductor RforProteomics analysis pipeline developed by Laurent Gatto.


The MALDIquant R package offers the core functions for mass spectrometry analysis, including base classes, plotting, base-line correction, peak identification, alignment etc.

The current version of MALDIquant is 1.10 (published April 2014) :

The MALDIquantForeign package provides additional functions for reading (tab, csv, fid, mzXML, mzML, imzML, Analyze 7.5) and writing common file formats for mass spectrometry data into/from MALDIquant objects.

The current version of MALDIquantForeign is 0.7 (published April 2014):

Reference Publication:

Further material:

Related Software:

The Mass-Up software developed at the University of Vigo uses some functions of MALDIquant.

See also our list of open source tools for mass spectrometry analysis (mostly in R).

Back to software page.