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:

• MALDIquant contains the base functionality for processing mass spectrometry data.
• MALDIquantForeign contains routines for importing and exporting data.

Furthermore,

• MALDIquantExamples provides examples of real case studies using MALDIquant.

Additionally,

Please visit the binda page for corresponding example R scripts.

• binda implements a binary discriminant approach useful for classification with mass spectrometry data as described in Gibb and Strimmer (2015).

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:

• Overview over MALDIquant mass spectrometry analysis pipeline - vignette (PDF) .
• Example workflow with multiple spectra and alignment - demo R code.
• Preprocessing and peak detection example for a single spectrum - demo R code:
  
• Comparison of different baseline corrections - demo R code.
• Illustration of peak alignment by warping - demo R code.

Examples from MALDIquantForeign:

• Overview over functions for data import - vignette (PDF).

Examples contained in MALDIquantExamples:

1. Mass Spectrometry Imaging (MSI) example - 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 using SDA) - see the vignette (PDF) and corresponding R code. For an alternative analysis script using binary discriminant analysis see the binda page.
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 1.18 (published July 2018) :

• Release history.
• Manual and vignette (pdf files).
• Download of MALDIquant version 1.18 source package.
• Archive of previous versions of MALDIquant.

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

The current version of MALDIquantForeign is 0.11.1 (published December 2017):

• Release history.
• Manual and vignette (pdf files).
• Download of MALDIquantForeign version 0.11.1 source package.
• Archive of previous versions of MALDIquantForeign.
• Associated R packages for data import: readBrukerFlexData and readMzXmlData.

Reference Publication:

• Please cite this paper if you use MALDIquant:
  S. Gibb and K. Strimmer. 2012. MALDIquant: a versatile R package for the analysis of mass spectrometry data. Bioinformatics 28: 2270-2271 (arXiv:1203.5885)
• R code to reproduce Figure 1 (color version).
  

Further material:

• Talk at the 29th European Meeting of Statisticians (Budapest July 2013): Quantitative Analysis of Proteomics Mass Spectrometry Data (size of PDF: 3.5 MB) .
• S. Gibb and K. Strimmer. 2011. Analysis of proteomic data using MALDIquant. Proceedings of the 8th International Workshop on Computational Systems Biology, WCSB 2011 (June 6-8, 2011, Zurich, Switzerland), pp. 49-52.
• S. Gibb and K. Strimmer. 2015. Differential protein expression and peak selection in mass spectrometry data by binary discriminant analysis. Bioinformatics 31: 3156-3162. (arXiv:1502.07959)
• S. Gibb and K. Strimmer. 2016. Mass spectrometry analysis using MALDIquant. To appear in: Datta, S., and Mertens, B. (eds). 2016. Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry. Springer, New York.

Related Software:

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

The MALDIrppa package provides quality control and robust preprocessing methods for MALDIquant.

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

MASSyPup - The Mass Spectrometry Live Linux developed by Robert Winkler comes with many useful free software for mass spectrometry analysis and also includes MALDIquant and MALDIquantForeign.

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

Back to software page.