An R package that allows the selection of the optimal set of fragments and retention time windows for target analytes in GC-SIM-MS based analysis. SIMAT provides guidance in choosing fragments for a list of targets. This is accomplished through an optimization algorithm that has the capability to select the most appropriate fragments from overlapping chromatographic peaks based on a pre-specified library of background analytes. The tool also allows visualization of the total ion chromatograms (TIC) of runs and extracted ion chromatograms (EIC) of analytes of interest. Moreover, retention index (RI) calibration can be performed and raw GC-SIM-MS data can be imported in netCDF or NIST mass spectral library (MSL) formats.
A software tool for the efficient and automatic analysis of GC/MS-based metabolomics data. Starting with raw MS data, MetaboliteDetector detects and subsequently identifies potential metabolites. Moreover, a comparative analysis of a large number of chromatograms can be performed in either a targeted or nontargeted approach. It automatically determines appropriate quantification ions and performs an integration of single ion peaks. The analysis results can directly be visualized with a principal component analysis. Since the manual input is limited to absolutely necessary parameters, the program is also usable for the analysis of high-throughput data. However, the intuitive graphical user interface of MetaboliteDetector additionally allows for a detailed examination of a single GC/MS chromatogram including single ion chromatograms, recorded mass spectra, and identified metabolite spectra in combination with the corresponding reference spectra obtained from a reference library. MetaboliteDetector is able to import GC/MS data in NetCDF and FastFlight format.
An open source tool which is a flexible and accurate method for pre-processing very large numbers of GC-MS samples within hours. A novel strategy was developed to iteratively correct and update retention time indices for searching and identifying metabolites. TargetSearch includes a graphical user interface to allow easy use by those unfamiliar with R. It allows fast and accurate data pre-processing for GC-MS experiments and overcomes the sample number limitations and manual curation requirements of existing software.