Quality assessment software tools | Mass spectrometry-based untargeted metabolomics
Metabolomics experiments often comprise large numbers of biological samples resulting in huge amounts of data. This data needs to be inspected for plausibility before data evaluation to detect putative sources of error e.g. retention time or mass accuracy shifts. Especially in liquid chromatography-high resolution mass spectrometry (LC-HRMS) based metabolomics research, proper quality control checks (e.g. for precision, signal drifts or offsets) are crucial prerequisites to achieve reliable and comparable results within and across experimental measurement sequences. Software tools can support this process.
A package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. xMSanalyzer comprises of utilities that can be classified into five main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat.
Allows users to analyze and visualize liquid chromatography – mass spectrometry (LC-MS) data. PiMP is a comprehensive and integrated web enabled pipeline that consists of five tasks: (1) project administration, (2) data upload, (3) quality control, (4) analysis parameters and (5) data interpretation. Users can define the experimental design, specify metadata and share the project with collaborators with a chosen level of permission. It aims at automatization and standardization of metabolomics analysis.
Allows analysis of direct infusion and liquid chromatography mass spectrometry-based metabolomics data. Galaxy-M consists of a metabolomics tool for Galaxy, developed for both direct infusion mass spectrometry (DIMS) and liquid chromatography mass spectrometry (LC-MS) metabolomics. This tool aims to enable biologists without programming skills to construct and execute next generation sequencing (NGS) data analyses.
Assist users in processing, visualization and re-analysis of publicly-submitted raw and processed Gas Chromatography-Mass Spectrometry (GC-MS) metabolomics datasets. MetabolomeExpress performs three main functions: (i) store complete GC/MS metabolomics datasets in a way that makes them highly accessible, (ii) provide researchers with cost-free online access to a powerful raw data processing pipeline and (iii) store metabolite response statistics in a central database.
Assists with analyze and management of multiple types of spectral and chemical data. KnowItAll Informatics System is an application that integrates toolsets for: spectral search, spectral identification, mixture analysis, multi-technique spectral data management, nuclear magnetic resonance (NMR) prediction, processing and subtraction, quality control analysis, reporting and publishing tools among others.
Offers a quick and easy data quality check of liquid chromatography-high resolution mass spectrometry (LC-HRMS) derived data. QCScreen allows a flexible investigation and comparison of basic quality-related parameters within user-defined target features and the possibility to automatically evaluate multiple sample types within or across different measurement sequences in a short time. It offers a user-friendly interface that allows an easy selection of processing steps and parameter settings. The generated results include a coloured overview plot of data quality across all analysed samples and targets and, in addition, detailed illustrations of the stability and precision of the chromatographic separation, the mass accuracy and the detector sensitivity. It accepts the generic mzXML format and thus can be used with many different LC-HRMS platforms to process both multiple quality control sample types as well as experimental samples in one or more measurement sequences.