Quantitative Analysis of Mass Spectrometry Data

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.

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:

• Preprocessing and peak detection example:
  
  (click on image to enlarge).
• Comparison of different baseline corrections.
• Illustration of peak alignment by warping.
• Peak detection and labeling.
• Mass calibration.
• Example workflow.
• Data import using MALDIquantForeign.
• Direct Infusion/Orbitrap workflow (thanks to Victor J. Nesatyy).
• Imaging mass spectrometry (IMS) example - import of imzML data and image display.

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

Documentation:

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

• Manual (pdf file) and release history.
• Download of MALDIquant version 1.7 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) and writing common file formats for mass spectrometry data into/from MALDIquant objects:

• Manual (pdf file) and release history.
• Download of MALDIquantForeign version 0.4 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 (reprint, arXiv:1203.5885)
• R code to reproduce Figure 1.

Further material:

• Talk at Inselspital Bern (March 2013): Analysis of Mass Spectrometry Data using MALDIquant.
• 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.

Related Software:

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

Back to software page.