Quality assessment software tools | Mass spectrometry based targeted metabolomics

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.

Allows metabolome analysis of large-scale multiple reaction monitoring (MRM) assays. MRMPROBS is a universal program for targeted metabolomics using multiple reaction monitoring (MRM)- or selected reaction monitoring (SRM), as well as SCAN and data independent tandem mass spectrometry (MS/MS) acquisition (DIA) data. The software was developed for metabolomics but can also be applied to lipidomics and proteomics studies.

Performs calculation of the chemical properties of derivative compounds. MetaboloDerivatizer is an in silico derivatization software that can filter out remaining false positive candidates.

Processes targeted mass spectrometry (MS) data. XCMS-MRM is a cloud-based data-analysis platform that integrates the repository METLIN-MRM for streamline experimental design, data processing, analysis and data sharing for targeted small-molecule analysis by MS. The software integrates quantitative and statistical data analyses that can facilitate the translational and cooperative use of MS.