SE132:/MS1
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" |
The raw data files are available at DROP Met web site in PRIMe database of RIKEN.
Analytical Method Details Information
| ID | MS1 |
|---|---|
| Title | GC-TOF MS |
| Instrument | Agilent 6890 gas chromatograph - Leco Pegasus 2 time-of-flight mass spectrometer (LECO) |
| Instrument Type | |
| Ionization | EI |
| Ion Mode | Positive |
| Description | Metabolites were extracted from pools of seedlings in a total of four biological replicates. Extraction and derivatisation of metabolites from leaves using GC-MS were performed as outlined by Lisec et al. GC-MS data were obtained using an Agilent 7683 series autosampler (Agilent Technologies GmbH, Waldbronn, Germany), coupled to an Agilent 6890 gas chromatograph - Leco Pegasus 2 time-of-flight mass spectrometer (LECO, St. Joseph, MI, USA). Identical chromatogram acquisition parameters were used as those previously described by Weckwerth et al. |
| Comment_of_details | Lisec et al. Nat Protoc. (2006) 1(1):387-96. Weckwerth et al. Proteomics. (2004) Jan;4(1):78-83. |
