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Metabolite identification and quantification (MS-based metabolomic analysis)

MS profiling is a promising approach for the identification and quantification of metabolites from complex biological samples.

MetaboAnalyst
Web

MetaboAnalyst

Provides a user-friendly, web-based analytical pipeline for high-throughput…

Provides a user-friendly, web-based analytical pipeline for high-throughput metabolomics studies. In particular, MetaboAnalyst aims to offer a variety of commonly used procedures for metabolomic data…

MS-DIAL
Desktop

MS-DIAL

A total solution to deal with not only data dependent MS/MS but also data…

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…

MS2LDA SUPPORT
Web

MS2LDA SUPPORT

Allows users to explore fragment data. MS2LDA is based on the Latent Dirichlet…

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…

apLCMS
Desktop

apLCMS

Allows peaks detection from high-resolution…

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.…

eRah
Desktop

eRah

Enables users to execute a complete automated workflow for data analysis in…

Enables users to execute a complete automated workflow for data analysis in GC–MS untargeted metabolomics. eRah incorporates an innovative deconvolution process based on multivariate compound…

MetExtract
Desktop

MetExtract

Allows users to detect biologically derived compounds. MetExtract is a toolbox…

Allows users to detect biologically derived compounds. MetExtract is a toolbox for stable isotope labeling (SIL) -assisted and liquid chromatography high resolution mass spectrometry…

MIA
Desktop

MIA Mass Isotopolome Analyzer

A software tool to determine, visualize and analyze mass isotopomer…

A software tool to determine, visualize and analyze mass isotopomer distributions across multiple GC–EI-MS datasets in a non-targeted manner. MIA helps to reveal changes in metabolic fluxes,…

MetAlign
Desktop

MetAlign

Helps to process accurate mass data as nominal mass data. MetAlign is a…

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…

MAVEN
Desktop

MAVEN

An open source cross platform metabolomics data analyser.

An open source cross platform metabolomics data analyser.

Metabolite…
Desktop

Metabolite Detector

A QT4 based software package for the analysis of GC/MS based metabolomics data.

A QT4 based software package for the analysis of GC/MS based metabolomics data.

BinBase
Desktop

BinBase

An automated peak annotation and database system developed for the analysis of…

An automated peak annotation and database system developed for the analysis of GC-TOF-MS data derived from complex volatile mixtures.

FragmentAlign
Desktop

FragmentAlign

Allows gas chromatography - mass spectrometory (GC-MS) data analysis.…

Allows gas chromatography - mass spectrometory (GC-MS) data analysis. FragmentAlign provides functions for alignment and annotation of metabolite features. The software enables curation of peak…

FeatureFinderMe…
Desktop

FeatureFinderMetabo

Assembles metabolite features from singleton mass traces. FeatureFinderMetabo…

Assembles metabolite features from singleton mass traces. FeatureFinderMetabo is based on a sensitive detection of mass traces, which are then assembled into features based on mass-to-charge spacing,…

mzMatch–ISO
Desktop

mzMatch–ISO

Provides a convenient visual summary of the quality and quantity of labelling.…

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…

MS-FINDER
Desktop

MS-FINDER

Facilitates formula predictions and isomer structure selections from tandem…

Facilitates formula predictions and isomer structure selections from tandem mass spectrometry (MS/MS). MS-FINDER allows spectra elucidation of chemical structures from accurate mass precursor ions…

Metabomatching
Desktop

Metabomatching

Offers a method for identifying untargeted metabolites thanks to genetic…

Offers a method for identifying untargeted metabolites thanks to genetic spiking. Metabomatching is a standalone software developed in Matlab which permits users to annotate nuclear magnetic…

MetDIA
Desktop

MetDIA

Extracts targeted metabolites from multiplexed mass spectrometry (MS)/MS…

Extracts targeted metabolites from multiplexed mass spectrometry (MS)/MS spectra generated using data-independent acquisition (DIA) technique. MetDIA considers each metabolite in the spectral library…

geoRge
Desktop

geoRge

Analyzes untargeted Liquide Chromatography/Mass Spectrometry (LC/MS) data from…

Analyzes untargeted Liquide Chromatography/Mass Spectrometry (LC/MS) data from stable isotope-labeling experiments. geoRge uses unlabeled and labeled biologically equivalent samples to compare…

MFSearcher
Dataset

MFSearcher Molecular Formula Searcher

Improves the prediction of elemental compositions. MFSearcher is a RESTful web…

Improves the prediction of elemental compositions. MFSearcher is a RESTful web service for high-throughput prediction of elemental compositions from accurate mass values detected by high-resolution…

MetaboSearch
Dataset

MetaboSearch

A web-based software tool that enables simultaneous mass-based search and the…

A web-based software tool that enables simultaneous mass-based search and the integration of the results.

MetiTree
Desktop

MetiTree Metabolite Identification Tree

Identifies metabolites from multi-stage mass spectrometry (MSn) data. MetiTree…

Identifies metabolites from multi-stage mass spectrometry (MSn) data. MetiTree aims to assist in designation of chemical compounds by providing a set of tools for compute, visualize, compare and…

CFM-ID
Web

CFM-ID

Provides a method for accurately and efficiently identifying metabolites in…

Provides a method for accurately and efficiently identifying metabolites in spectra generated by electrospray tandem mass spectrometry (ESI-MS/MS).

PROFANCY
Desktop

PROFANCY PRioritization of candidate metabOlites using Functional relAtioNships in the Context of metabolic pathwaY

A pathway-based random walk method for prioritization of candidate disease…

A pathway-based random walk method for prioritization of candidate disease metabolites. PROFANCY is used to prioritize candidate disease-related metabolites based on the assumption that metabolites…

NP-StructurePre…
Desktop

NP-StructurePredictor

Finds possible structures for each targeted molecular weights (MW) in…

Finds possible structures for each targeted molecular weights (MW) in users' peak tables. NP-StructurePredictor is a computational method that can accelerate the process of identifying chemical…

AssayR
Desktop

AssayR

Allows users to the measure metabolite usage. Assay R is an open source…

Allows users to the measure metabolite usage. Assay R is an open source software that investigate high resolution liquid chromatography−mass spectrometry (LC-MS) data. The application uses…

AntDAS
Desktop

AntDAS Automatic Data Analysis Strategy

Provides nontargeted data analysis strategy (AntDAS) for ultraperformance…

Provides nontargeted data analysis strategy (AntDAS) for ultraperformance liquid chromatography hyphenated with high resolution time-of-flight mass spectrometer (UPLC-QTOF)-based nontargeted…

MAGI
Web
Desktop

MAGI Metabolite, Annotation, and Gene Integration

Generates metabolite-gene associations. MAGI finds and scores consensus between…

Generates metabolite-gene associations. MAGI finds and scores consensus between metabolite identifications and gene annotations. It associates input sequences to biochemical reactions by assessing…

PiMP
Web
Desktop

PiMP Polyomics integrated Metabolomics Pipeline

Allows users to analyze and visualize liquid chromatography – mass spectrometry…

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…

compMS2Miner
Web

compMS2Miner Comprehensive MS2 Miner

Integrates many useful tools in a single workflow for metabolite annotation.…

Integrates many useful tools in a single workflow for metabolite annotation. compMS2Miner workflow consists of the following steps: i) matching unknown MS1 features to precursor MS2 scans, ii)…

peakANOVA
Desktop

peakANOVA

Integrates data of multiple detected peaks that come from one compound. The…

Integrates data of multiple detected peaks that come from one compound. The PeakANOVA package is used for extending statistical analysis to all available peaks and demonstrate that the additional…

PowerGet
Desktop

PowerGet

Detects, aligns, and annotates metabolite features from data obtained using…

Detects, aligns, and annotates metabolite features from data obtained using liquid chromatography (LC) high-resolution mass spectrometry (HRMS). PowerGet consists of two modules: (i) PowerFT for…

mAPV
Desktop

mAPV modified Asymmetric Pseudo-Voigt

Incorporates DT-CWT (Dual-Tree Complex Wavelet Transformation) along with SURE…

Incorporates DT-CWT (Dual-Tree Complex Wavelet Transformation) along with SURE for spectra smoothing thus avoiding the overhead of customizing the method for different datasets by setting parameters.…

MbIdent
Desktop

MbIdent MbIdentification

Evaluates similarity score distribution to improve the accuracy of metabolite…

Evaluates similarity score distribution to improve the accuracy of metabolite identifications and their confidence measures for two-dimensional gas chromatography time-of-flight mass spectrometry…

MassTRIX
Web

MassTRIX

Annotates metabolites in high precision mass spectrometry data. MassTRIX marks…

Annotates metabolites in high precision mass spectrometry data. MassTRIX marks the identified chemical compounds on KEGG pathway maps using the KEGG/API. Selected genes or enzymes can be highlighted,…

SmetSearch
Desktop

SmetSearch

Automatically identifies the presence of S-metabolites in ultra-high-resolution…

Automatically identifies the presence of S-metabolites in ultra-high-resolution metabolome data. SmetSearch is useful for rapidly qualifying the presence of known and unknown S-metabolites in a…

MetFamily
Web

MetFamily

Allows users to analyze metabolomics data from untargeted liquid chromatography…

Allows users to analyze metabolomics data from untargeted liquid chromatography tandem mass spectra (LC-MS/MS) measurements. MetFamily is an open source application that identifies metabolite…

IsoMS
Desktop

IsoMS

Processes the raw data generated from one or multiple LC-MS runs by peak…

Processes the raw data generated from one or multiple LC-MS runs by peak picking, peak pairing, peak-pair filtering, and peak-pair intensity ratio calculation. IsoMS is a data processing method and a…

RAMClustR
Desktop

RAMClustR

Clusters non-targeted mass spectrometric metabolomics data. With RAMClustR,…

Clusters non-targeted mass spectrometric metabolomics data. With RAMClustR, feature detection is performed on both MS and idMS/MS (indiscriminant MS/MS) data and feature-feature relationships are…

MetSign
Desktop

MetSign

A computational platform entitled MetSign for high-resolution mass…

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…

MET-COFEA
Desktop

MET-COFEA METabolite COmpound Feature Extraction and Annotation

A liquid chromatography/mass spectrometry (LC/MS) data processing and analysis…

A liquid chromatography/mass spectrometry (LC/MS) data processing and analysis platform. MET-COFEA detects and clusters chromatographic peak features for each metabolite compound by first…

MSPrep
Desktop

MSPrep

An R package for post-processing of metabolomic data. The primary functions of…

An R package for post-processing of metabolomic data. The primary functions of the MSPrep package are summarization of replicates, filtering, imputation of missing data, normalization and/or batch…

AMDORAP
Desktop

AMDORAP Accurate M/z Detection method for LC-Orbitrap

Detects m/z values of biological samples for high-resolution mass spectrometry…

Detects m/z values of biological samples for high-resolution mass spectrometry (MS). AMDORAP allows to address the relationships between biological effects and cellular metabolites based on accurate…

Metabolome…
Web

Metabolome searcher

Provides an automated tool to identify metabolites from MS analyses from…

Provides an automated tool to identify metabolites from MS analyses from metabolic reconstruction of specific genomes. This approach couples long lists of masses to specific genomic-based metabolites…

ALLocator
Web

ALLocator

A web-platform for the analysis of LC-ESI-MS experiments. ALLocator covers the…

A web-platform for the analysis of LC-ESI-MS experiments. ALLocator covers the workflow from raw data processing to metabolite identification and mass isotopomer ratio analysis. The integrated…

MINE
Web

MINE Metabolic In silico Network Expansion Databases

An extension of known metabolite databases to include molecules that have not…

An extension of known metabolite databases to include molecules that have not been observed, but are likely to occur based on known metabolites and common biochemical reactions. We utilize an…

SpectConnect
Web

SpectConnect

Analysis of metabolomic profiling data from gas chromatography-mass…

Analysis of metabolomic profiling data from gas chromatography-mass spectrometry (GC/MS) measurements. SpectConnect allows for systematic, automated analysis of GC/MS metabolite profiling data sets…

MetaboliteDetec…
Desktop

MetaboliteDetector

A software tool for the efficient and automatic analysis of GC/MS-based…

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.…

decoMS2
Desktop

decoMS2

A two-part approach for performing metabolomic identifications. First, MS(2)…

A two-part approach for performing metabolomic identifications. First, MS(2) scans are collected with less stringent isolation settings to obtain improved sensitivity at the expense of specificity.…

EMP
Desktop

EMP Expertomica Metabolite Profiling

Uses probalistic methods for the filtration of liquid chromatography–mass…

Uses probalistic methods for the filtration of liquid chromatography–mass spectrometry or gas chromatography-mass spectrometry. EMP evaluates the given instrument, detects compounds and calculates…

DECOMP
Desktop

DECOMP

Calculates the sum formula of all molecules whose mass equals the input mass.…

Calculates the sum formula of all molecules whose mass equals the input mass. DECOMP is a program to compute decompositions of an input query. Its two primary applications are (i) computing sum…

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