Biomedical Engineering Reference
In-Depth Information
4
Open source software for mass
spectrometry and metabolomics
Mark Earll
Abstract: This chapter introduces open source tools for mass
spectrometry (MS)-based metabolomics. The tools used include the
R language for statistical computing, mzMine and KNIME. A
typical MS-metabolomics data set is used for illustration and the
tasks of visualisation, peak detection, peak identifi cation, peak
collation and basic multivariate data analysis are covered. A
discussion of vendor formats and the role of open source software
in metabolomics is also included. Example R scripts and KNIME
R-nodes are shown, which should enable the reader to apply the
principles to their own data.
Key words: data visualisation; KNIME; mass spectrometry;
metabolomics; mzMine; R language.
￿ ￿ ￿ ￿ ￿
4.1 Introduction
Mass spectrometry has advanced enormously since the invention of the
fi rst mass spectrometer built in 1919 by Francis Aston at Cambridge
University [1, 2]. This fi rst instrument is reported to have had a mass
resolving power of 130. Less than a century later, many laboratories have
at their disposal instruments capable of resolving powers in excess of
60 000 and a few specialist instruments may reach as high as 200 000.
Technologies such as Time of Flight, Fourier Transform Ion Cyclotron
resonance (FTICR) mass spectrometry and the new generation of ion
 
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