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.
A software tool for the alignment of large GC-MS-based metabolite profiling experiments into statistically accessible data matrices. The matrix generation is directed by co-analysis of retention index (RI) marker substances within each chromatogram and the simultaneous in-parallel analysis of mixtures of reference compounds is recommended. In addition, we offer automated extraction of quantitative data from predefined mass fragments, time groups of mass fragments or clusters of intensity-correlated mass fragments. TagFinder is freely available for academic use.
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.
Determines isotopologues for a wide variety of metabolites detected by gas chromatography-mass spectrometry (GC-MS). DExSI offers to users automated identification annotation and quantitation of stable-isotope labelled metabolites identifies by GC-MS. This software can detect all isotopomers of multiple metabolites in complex biological mixtures irrespective of variation in the extent of labelling.
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.
A web-based tool that objectively quantifies every metabolite peak detected in a set of samples and aligns peaks across multiple samples to enable quantitative comparison of each metabolite between samples. The analysis incorporates quantification of multiple peaks/ions that have different chromatographic retention times but are detected within a single SRM transition.
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.
An R package for metabolic network analysis to perform targeted metabolome-wide association study of specific metabolites to facilitate detection of their related metabolic pathways and network structures. MetabNet can be useful to simplify data analysis and enhance the utility of high-resolution data by improved documentation of chemical identities and discovery of network structures and substructures that contribute to disease risk and responses to therapies.
Aims to formalize the analysis of gas chromatography-mass spectrometry (GC/MS) data. PYQUAN uses the AMDIS data to align the individual samples against the personal retention time (RT) library. It offers the possibility to backfill expected peaks in samples where AMDIS did not recognize those peaks. Moreover, this program utilizes AMDIS for producing for each peak a list of all possible identifications, based on a personally managed mass spectra library.
An industry standard mass spectrometer data system for acquiring, processing, and reporting data. Uniquely designed to meet the needs of today’s laboratory professionals in the food/flavor/fragrance, metabolomics, environmental, and petrochemical industries. ChromaTOF® offers seamless control of both the instrument and accessories, as well as an intuitive acquisition queue with built-in data processing.
Offers library searching of data generated from any Liquid Chromatography-Mass Spectrometry (LC-MS) and Gas chromatography-mass spectrometry (GC-MS) platform. AnalyzerPro is a commercial and comprehensive post-processing utility for low and high-resolution LC-MS and GC-MS data with multi-vendor data support. It also provides optimized workflows for sample-to-sample comparison, target component analysis, quantification.
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