Provides a web-based analytical pipeline for high-throughput metabolomics studies. MetaboAnalyst aims to offer a variety of commonly used procedures for metabolomic data processing, normalization, multivariate statistical analysis, as well as data annotation. The current implementation focuses on exploratory statistical analysis, functional interpretation, and advanced statistics for translational metabolomics studies. This tool is also available as desktop version.
A total solution to deal with not only data dependent MS/MS but also data independent MS/MS experiments for metabolomics and lipidomics. Its feature is 1) implementing de-convolution method for data independent MS/MS 2) using unified criteria for peak identification 3) supporting all data processing step from raw data import to statistical analysis 4) user-friendly graphic user interface. MS-DIAL deals with data independent acquisition MS/MS data (ex. SWATH) by means of two step algorithms (peak spotting and MS2Dec) for spectral deconvolution. Also, it supports compound identification, peak alignment, and principal component analysis on the graphical user interface. The spectrum information is outputted by MassBank, NIST, and Mascot formats. And the organized data matrix (sample vs metabolite) is exported as tab delimited text file.
Allows users to query the BinBase gas chromatography–mass spectrometry (GC-MS) metabolome database for exploring compounds. BinVestigate queries biological metadata for each metabolite. The software provides open access information about abundance, frequency, species, and organ origin. It can be used to query unknowns from metabolomics studies and to prioritize and select targeted unknowns for structural identification on the basis of their cross-study specificity and relevance.
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.
An LC/MS-based data analysis approach which incorporates novel nonlinear retention time alignment, feature detection, and feature matching. The XCMS software reads and processes LC/MS data stored in netcdf , mzXML, mzData and mzML files. It provides methods for feature detection, non-linear retention time alignment, visualization, relative quantization and statistics. XCMS is capable of simultaneously preprocessing, analyzing, and visualizing the raw data from hundreds of samples. XCMS is freely available under an open-source license.
Extracts metabolite information from raw. ADAP-GC is an automated computational pipeline for untargeted, gas chromatography mass spectrometry (GC/MS)-based metabolomics studies. This workflow is designed to preprocess raw, untargeted, GC/MS metabolomics data. It carries out a sequence of computational tasks that includes construction of extracted ion chromatograms (EICs), detection of peaks from EICs, spectral deconvolution, and alignment of analytes across samples.
Offers a platform dedicated to metabolite annotation. CEU Mass Mediator gives access to more than 270 000 real compounds extracted from four repositories including KEGG and LipidMaps as well as simulated compounds extracted from MINE. The application enables multiple query options, pathway displaying and the scoring of putative annotations, with a focus on reversed phase-liquid chromatography-electro spray ionization-mass spectrometry (RP-LC-ESI-MS) data.
Enables candidate substructure annotation of multistage accurate mass spectral trees. MAGMa is a web server that matches substructures of candidate molecules with multistage fragmentation data, resulting in a calculated candidate score allowing comparison of hundreds of candidates for a detected precursor mass. The software permits automated annotation of mass multistage mass spectrometry (LC−MSn) data with in silico generated metabolites.
An open-source software tool for mass-spectrometry data processing, with the main focus on LC-MS data. It is based on the original MZmine toolbox described in the 2006 Bioinformatics publication, but has been completely redesigned and rewritten since then. Our main goal is to provide a user-friendly, flexible and easily extendable software with a complete set of modules covering the entire LC-MS data analysis workflow.
Allows users to investigate molecular structure repositories starting from tandem mass spectrometry (MS/MS) data of small molecules. CSI:FingerID merges fragmentation trees and molecular fingerprints to elucidate a compound. It employs a Bayesian network to draw dependencies between molecular properties. This tool can find identity and connectivity of the atoms including bond multiplicities, but no spacial information.
Allows users to explore fragment data. MS2LDA is based on the Latent Dirichlet Allocation (LDA) method. It guides interpretation of comparative untargeted metabolomics experiments and prioritizes structural characterization of Mass2Motifs across large sample sets. This tool can find relevant substructures and/or substructures of both endogenous and exogenous origin in urine cohort samples where intragroup variance was suspected to arise from differential drug and/or food administration.
Allows peaks detection from high-resolution liquid-chromatography/mass-spectrometry (LC/MS) data. apLCMS is a machine learning approach designed for the processing of LC/MS based metabolomics data. The method learns directly from various data features of the extracted ion chromatograms (EICs) to differentiate between true peak regions from noise regions in the LC/MS profile. There are two major routes of data analysis: unsupervised analysis and hybrid analysis.
Permits comprehensive metabolomics data pre-processing, statistical analysis and interpretation. W4M includes computational modules for data normalization, multivariate analysis and annotation. It can create interactive web-based documents showing the results of the analyses, and users can share them with collaborators directly on the platform. This tool enables multi-omics analyses in a global systems-biology approach.
Aims to integrate and analyze metabolomics experiment data. MeltDB is a program that can be applied for the description and analysis of metabolomic experiments. This program hosts over 30 experiments predominantly from gas chromatography-mass spectrometry (GC/MS) measurements. Moreover, this tool includes an API allowing users to evaluate novel methods and algorithms for the preprocessing of metabolomic datasets.
Provides a convenient visual summary of the quality and quantity of labelling. mzMatch–ISO is an extension to mzMatch, an open-source Java toolbox for mass spectrometry (MS) data processing and visualization. It provides an efficient and user-friendly output for the analysis and compact visualization of isotope-labelled metabolomics datasets without the need for specialist bioinformatics skills, allowing rapid, precise and meaningful biological interpretation.
Allows users to detect biologically derived compounds. MetExtract is a toolbox for stable isotope labeling (SIL) -assisted and liquid chromatography high resolution mass spectrometry LC-HRMS(/MS)-based untargeted metabolomics. The software consists of three modules: AllExtract, TracExtract and FragExtract and supports experiments using native and highly isotope-enriched biological material or tracer compounds.
Combines statistical analysis modules into pipelines to deal with heterogenous big data. T-BioInfo is an application that can be used for: (1) next-generation sequencing (NGS) data (transcriptomics, genomics/epigenetics, and DNA/RNA); (2) mass-spectroscopy; (3) structural biology; and (4) data integration and modeling (virology, data association, and data mining).
A computational platform entitled MetSign for high-resolution mass spectrometry-based metabolomics. By converting the instrument raw data into mzXML format as its input data, MetSign provides a suite of bioinformatics tools to perform raw data deconvolution, metabolite putative assignment, peak list alignment, normalization, statistical significance tests, unsupervised pattern recognition, and time course analysis. MetSign uses a modular design and an interactive visual data mining approach to enable efficient extraction of useful patterns from data sets.
Provides an application for daily routine and emergency toxicology. AMDIS is a software developed to identify of even low-abundant peaks in the total ion chromatograms (TIC) and the reduction of the evaluation time by half. This method first deconvolutes pure component spectra and related information such as peak shape and retention time from complex chromatograms and subsequently matches the obtained spectra with those of a reference library.
Helps to process accurate mass data as nominal mass data. MetAlign is a software program for the pre-processing and comparison of full scan nominal or accurate mass Liquid chromatography-mass spectrometry (LC–MS) and Gas chromatography-mass spectrometry (GC–MS) data. It involves running multiple threads simultaneously so that a one thread per core situation is established in which memory between threads is not shared.