MALDIquant Examples

This R package provides some some examples to demonstrate how to analyze mass spectrometry data using MALDIquant.

Description

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.

Please visit: https://strimmerlab.github.io/software/maldiquant/index.html

Details

MALDIquant examples

• MALDIquant vignette

• Preprocessing and peak detection example - single spectrum.

• Analysis of Fiedler et al. 2009 using MALDIquant vignette, R code

• Bacterial Species Determination using MALDIquant vignette, R code

• R code to reproduce figure 1 used in Gibb and Strimmer 2012 ([colorized version] (https://github.com/sgibb/MALDIquantExamples/blob/master/R/createFigure1_color.R)).

MALDIquantForeign examples

• MALDIquantForeign vignette

Mass Spectrometry Imaging (MSI) examples

• Mass Spectrometry Imaging using MALDIquant.

• MALDIquant IMS + shiny example.

Demo files distributed with the MALDIquant R package

• Comparison of different baseline corrections.
• Peak detection and labeling.
• Illustration of peak alignment by warping.
• Example workflow.

Installation

GitHub is not supported by the basic install.packages command. You could use the devtools package to install MALDIquantExamples.

install.packages("devtools")
library("devtools")
install_github("sgibb/MALDIquantExamples")

Contact

You are welcome to:

• submit suggestions and bug-reports at: https://github.com/sgibb/MALDIquantExamples/issues
• send a pull request on: https://github.com/sgibb/MALDIquantExamples/
• compose an e-mail to: mail@sebastiangibb.de