SE132:/S1

Sample Set Information

ID	SE132
Title	TargetSearch - a bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data
Description	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. 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.
Authors	Álvaro Cuadros-Inostroza, Camila Caldana, Henning Redestig, Miyako Kusano, Jan Lisec, Hugo Peña-Cortés, Lothar Willmitzer and Matthew A Hannah
Reference	Cuadros-Inostroza et al. (2009) BMC Bioinformatics 10:428
Comment	Total of 27 chromatograms with replicates of three different standard mixtures. Provided for validation of the Bioconductor package. The raw files were stored in DROP Met as "Mixture Dilution Series for Pre-processing Validation"

PubMed

The original paper is available at BMC Bioinformatics.

The raw data files are available at DROP Met web site in PRIMe database of RIKEN.

Sample Information

ID	S1
Title	wild-type Col-0 Arabidopsis thaliana seedling
Organism - Scientific Name	Arabidopsis thaliana
Organism - ID	NCBI taxonomy 3702
Compound - ID
Compound - Source
Preparation	The biological dataset consisted of wild-type Col-0 Arabidopsis thaliana seedling samples. Three week old seedlings, grown on solid MS medium with 1% sucrose, were kept for 4h under either continuous light or darkness.
Sample Preparation Details ID
Comment