MALDIquant: Quantitative Analysis of Mass Spectrometry Data


MALDIquant and
MALDIquantForeign pages on CRAN.

MALDIquantExamples page on GitHub.

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.

The MALDIquant pipeline consists of two main R packages:

Additionally,

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:

Demos contained in MALDIquant package:

Examples from MALDIquantForeign:

To run these analyses without installing MALDIquantExamples use the following R scripts:
  1. ims-standalone.R,
  2. fiedler2009-standalone.R,
  3. species-standalone.R.

Examples contained in MALDIquantExamples:

  1. Imaging mass spectrometry (IMS) example (import of imzML data and image display) - see the vignette (PDF) and corresponding R code.
  2. Example analysis of Fiedler et al. (2009) pancreas cancer data (including peak filtering, feature selection and classification) - see the vignette (PDF) and corresponding R code.
  3. Example cluster analysis of 96 MALDI-TOF mass spectra of four different bacteria species (incl. peak selection) - see the vignette (PDF) and corresponding R code.

Installation:

On Debian GNU/Linux install r-cran-maldiquant and r-cran-maldiquantforeign.

For installing the two main packages simply enter at the R console:

install.packages(c("MALDIquant", "MALDIquantForeign"))

To install devtools run:
install.packages("devtools")

For MALDIquantExamples you need to use the devtools R package:

library("devtools")
install_github("sgibb/MALDIquantExamples")

Note that you can run the examples provided in MALDIquantExamples also without installing the actual package (see above).

Documentation:

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 1.11 (published August 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 0.9 (published August 2014):

Reference Publication:

Further material:

Related Software:

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

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.