Introduction

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.

Publications

  1. TargetSearch--a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data.
    Cite this
    Cuadros-Inostroza A, Caldana C, Redestig H, Kusano M, Lisec J, Peña-Cortés H, Willmitzer L, Hannah MA, 2009-01-01 - BMC bioinformatics

Credits

  1. Alvaro Cuadros-Inostroza
    Developer

  2. Camila Caldana
    Developer

  3. Henning Redestig
    Developer

  4. Miyako Kusano
    Developer

  5. Jan Lisec
    Developer

  6. Hugo Peña-Cortés
    Developer

  7. Lothar Willmitzer
    Developer

  8. Matthew A Hannah
    Investigator

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Summary
AccessionBT004051
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, R
User InterfaceTerminal Command Line
Download Count0
Submitted ByMatthew A Hannah