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TargetSearch - a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data

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http://pubman.mpdl.mpg.de/cone/persons/resource/persons97111

Cuadros-Inostroza,  A.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97097

Caldana,  C.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97348

Redestig,  H.
BioinformaticsCRG, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97274

Lisec,  J.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97481

Willmitzer,  L.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97182

Hannah,  M. A.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Citation

Cuadros-Inostroza, A., Caldana, C., Redestig, H., Kusano, M., Lisec, J., Pena-Cortes, H., et al. (2009). TargetSearch - a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data. BMC Bioinformatics, 10, 428. doi:10.1186/1471-2105-10-428.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0014-2602-C
Abstract
Background: Metabolite profiling, the simultaneous quantification of multiple metabolites in an experiment, is becoming increasingly popular, particularly with the rise of systems-level biology. The workhorse in this field is gas-chromatography hyphenated with mass spectrometry (GC-MS). The high-throughput of this technology coupled with a demand for large experiments has led to data pre-processing, i.e. the quantification of metabolites across samples, becoming a major bottleneck. Existing software has several limitations, including restricted maximum sample size, systematic errors and low flexibility. However, the biggest limitation is that the resulting data usually require extensive hand-curation, which is subjective and can typically take several days to weeks. Results: We introduce the TargetSearch package, an open source tool which is a flexible and accurate method for pre-processing even very large numbers of GC-MS samples within hours. We developed a novel strategy to iteratively correct and update retention time indices for searching and identifying metabolites. The package is written in the R programming language with computationally intensive functions written in C for speed and performance. The package includes a graphical user interface to allow easy use by those unfamiliar with R. Conclusions: TargetSearch allows fast and accurate data pre-processing for GC-MS experiments and overcomes the sample number limitations and manual curation requirements of existing software. We validate our method by carrying out an analysis against both a set of known chemical standard mixtures and of a biological experiment. In addition we demonstrate its capabilities and speed by comparing it with other GC-MS pre-processing tools. We believe this package will greatly ease current bottlenecks and facilitate the analysis of metabolic profiling data.