R: Quantitative Analysis of MALDI-TOF MS Data

Quantitative Analysis of MALDI-TOF MS Data

MALDIquant page on CRAN.

This package is intended to provide an easy-to-use framework for quantitative analysis of MALDI-TOF mass spectrometry data. Currently, it provides methods for importing mass spectrometric data, for preprocessing (smoothing and baseline removal) and for peak detection.

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

MALDIquant is currently under active development. Features available in future versions include quantitative calibration and classification so that MALDIquant is useful for clinical diagnostics.

Current Version: 0.5

Authors: Sebastian Gibb.

Documentation and Installation:

Quick install:
enter at the R console:
install.packages( "MALDIquant", dependencies=TRUE)

Manual (pdf file) and release history.
Download of MALDIquant version 0.5 source package.
Archive of previous versions of MALDIquant.
Licensed under the GNU GPL version 3 (or any later version).
Related R packages: readBrukerFlexData and readMzXmlData.

Additional Information and Relevant Papers:

Overview paper: Gibb, S., 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. (reprint)
MALDIquant poster: download the poster presented at WCSB 2011.
MALDIquant talk: download the talk presented at useR 2011.
Preprocessing and peak detection example (click on image to enlarge and see here for the R code):
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