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.
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.
A software package which allows to perform quick quality control of raw LC/MS data through its fast visualization capabilities. BatMass also serves as a testbed for developers of LC/MS data processing algorithms by providing a data access library for open mass spectrometry file formats and a means of visually mapping processing results back to the original data.
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.
A quality control approach that is based on discrepancies between replicate samples. It suggests the optimal parameters of peak-picking procedure and detects local discrepancies of the chromatogram alignment.
Improves the quality of feature lists after initial processing. MS-FLO is a stand-alone web-based application that can be used for recognition and removal of erroneous features in liquid chromatography−tandem mass spectroscopy (LC-MS) datasets. The software is designed to examine datasets after initial processing and alert users to erroneous features, thus strengthening the statistical power of the dataset. It can be added to any untargeted LC-MS-based metabolomics workflow.
Serves for integration of metabolomic data from multiple batches, visualization and statistical analysis for non-targeted and targeted approaches of quantitative mass spectrometry-based omics data. StatTarget is based on the QC-RFSC algorithm to remove inter- and intra-unwanted variation. This tool aims to improve data quality of quantitative mass spectrometry-based omics data. It can be extended to perform on other biological data such as protein or peptide expression data.
Consists of a regression model for the quality control of samples from untargeted MS-based metabolomics. BatchCorrMetabolomics is a tool for batch correction and evaluation of batch effect sizes. This software permits a high-quality correction so that measurements across all batches are directly comparable.
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.
Can end-to-end metabolomics data analysis through a set of interchangeable modules. metaX automates analysis of untargeted metabolomics data acquired from Liquide chromatography coupled mass spectrometry (LC/MS) or gas chromatography coupled mass spectrometry (GC/MS). It is based upon the fast process and the optimized workflow to improve the interpretation of metabolomics data. The tool can deal with large-scale metabolomics datasets.
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.
Offers an assortment of features for metabolomics data processing. SECIMTools is available both as a standalone software or as a set of methods that can be run through the Galaxy platform. The software provides: (i) quality control metrics; (ii), visualization techniques including principal component analysis; (iii) basic statistical analysis methods; (iv) advanced classification methods such as random forest; and finally (v) variable selection tools.
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.
Aims to compare and evaluate various publicly available open source label-free data processing workflows. msCompare is a modular framework that allows the arbitrary combination of different feature detection/quantification and alignment/matching algorithms in conjunction with a scoring method to evaluate their overall performance. msCompare was used to assess the performance of workflows built from modules of publicly available data processing packages such as SuperHirn, OpenMS, and MZmine and in-house developed modules. It was found that the quality of results varied greatly among workflows, and interestingly, heterogeneous combinations of algorithms often performed better than the homogenous workflows. This scoring method showed that the union of feature matrices of different workflows outperformed the original homogenous workflows in some cases. msCompare is available as a standalone command line program or can be used through a Graphical User Interface (GUI) into the Galaxy framework.
Removes unwanted variations at feature-level in large-scale metabolomics and proteomics data. QC-RFSC is an algorithm that integrates the random forest (RF) based ensemble learning approach to learn the unwanted variations from quality control (QC) samples. It also predicts the correction factor in the neighboring real samples responses. Beside metabolomics data analysis, this method significantly improves the data quality for the proteomics.
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.
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