mzMatch is a modular, open source and platform independent data processing pipeline for metabolomics LC/MS data written in the Java language. It was designed to provide small tools for the common processing tasks for LC/MS data. The mzMatch environment was based entirely on the PeakML file format and core library, which provides a common framework for all the tools.

With the introduction of the PeakML file format, the tools can share their data output with the other software. This means that we can integrate with other tools, for which we provide a first implementation integration mzMatch with XCMS.

Features

The mzMatch environment tries to provide a jumping board for the further development of metabolomics data analysis. However it already features a number of essential tools (for more information see the mzmatch documentation):

Publications

Please cite the following publication if you use mzMatch or mzmatch.R to analyze your data:

PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis

2011

Related publications:

Separating the wheat from the chaff: a prioritisation pipeline for the analysis of metabolomics datasets

2012

IDEOM: An Excel interface for analysis of LC-MS based metabolomics data
Darren J. Creek, Andris Jankevics, Karl E.V. Burgess, Rainer Breitling and Michael P. Barrett
Bioinformatics 2012 In Press

Towards Global Metabolomics Analysis with Liquid Chromatography–Mass Spectrometry: Improved Metabolite Identification by Retention Time Prediction
Darren J. Creek , Andris Jankevics , Rainer Breitling , David G. Watson , Michael P. Barrett , and Karl E.V. Burgess
Analytical Chemistry 2011 83 (22), pp 8703-8710

Metabolomic analysis of a synthetic metabolic switch in Streptomyces coelicolor A3(2)
Andris Jankevics, M. Elena Merlo, Marcel de Vries, Roel J. Vonk, Eriko Takano, Rainer Breitling
Proteomics 2011 11 (24), pp 4622-4631

Pipeline

Design based on the SWT pages.