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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…

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.…

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,…

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.

MetExtract
Desktop

MetExtract

A software tool for scientists working with stable isotopic labelling and high…

A software tool for scientists working with stable isotopic labelling and high resolution liquid chromatography mass spectrometry.

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

An extension to the metabolomics analysis pipeline mzMatch R.

An extension to the metabolomics analysis pipeline mzMatch R.

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…

MetAlign
Desktop

MetAlign

A software programme for the pre-processing and comparison of full scan nominal…

A software programme for the pre-processing and comparison of full scan nominal or accurate mass LC-MS and GC-MS data.

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.

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
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…

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.…

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,…

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…

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…

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…

PUTMEDID-LCMS
Desktop

PUTMEDID-LCMS

A tool operating in the Taverna environment for putative identification of…

A tool operating in the Taverna environment for putative identification of metabolites from accurate mass data acquired in mass spectrometry-based metabolic profiling studies. Three workflows perform…

Ideom
Desktop

Ideom

An Excel template with many macros that enable user-friendly processing of…

An Excel template with many macros that enable user-friendly processing of metabolomics data from raw data files to annotated and hyperlinked metabolite lists.

FingerID
Desktop

FingerID

A metabolite identification software using tandem mass spectrometry and kernel…

A metabolite identification software using tandem mass spectrometry and kernel methods.

MPA-RF
Desktop

MPA-RF

A feature selection method, MPA-RF, for the identification of informative…

A feature selection method, MPA-RF, for the identification of informative biomarkers in complex metabolic datasets. The presented method provided the best use of both RF and MPA method. First, by…

PyMS
Desktop

PyMS

Comprises a library of functions for processing of instrument gas…

Comprises a library of functions for processing of instrument gas chromatography–mass spectrometry (GC-MS) data. PyMS currently provides a complete set of GC-MS processing functions, including…

MZedDB
Web

MZedDB

Tools for the annotation of High Resolution MS metabolomics data. The content…

Tools for the annotation of High Resolution MS metabolomics data. The content of MZedDB is derived largely from established repositories of curated information relating to metabolites. The databases…

MI-Pack
Desktop

MI-Pack

A semi-automated method to calculate a mass error surface associated with…

A semi-automated method to calculate a mass error surface associated with experimental peak-pair differences.

TNO-DECO
Desktop

TNO-DECO

Matlab code for preprocessing Gas Chromatography Mass Spectrometry Data.

Matlab code for preprocessing Gas Chromatography Mass Spectrometry Data.

El-Maven
Desktop

El-Maven

Allows large-scale metabolomic experiments. El-Maven allows completely…

Allows large-scale metabolomic experiments. El-Maven allows completely automated processing of raw Liquide Chromatography- Mass Spectrometry (LC-MS) data from isotopomer labeling and untargeted…

mzCloud
Dataset

mzCloud

An extensively curated database of high-resolution tandem mass spectra that are…

An extensively curated database of high-resolution tandem mass spectra that are arranged into spectral trees. mzCloud represents a key conceptual shift towards a modern mass spectral database. This…

SimMet
Web

SimMet

A robust high throughput informatics tool for qualitative and quantitative…

A robust high throughput informatics tool for qualitative and quantitative analysis of mass spectrometry metabolite data. SimMet® supports peak detection, peak picking, retention time alignment and…

SIEVE
Desktop

SIEVE

An automated, label-free differential analysis platform for proteomics and…

An automated, label-free differential analysis platform for proteomics and metabolomics biomarker discovery that enables comparison of LC/MSn spectra from healthy and diseased (or control and…

metaXCMS
Desktop

metaXCMS

Performs second-order ("meta") analysis of untargeted metabolomics…

Performs second-order ("meta") analysis of untargeted metabolomics data from multiple sample groups representing different models of the same phenotype. While the original version of XCMS…

MetaboNexus
Desktop

MetaboNexus

An interactive metabolomics data analysis platform that integrates…

An interactive metabolomics data analysis platform that integrates pre-processing of raw peak data with in-depth statistical analysis and metabolite identity search. MetaboNexus is designed to work…

metsamp
Desktop

metsamp

A probabilistic method for the assignment of empirical formulas to mass peaks…

A probabilistic method for the assignment of empirical formulas to mass peaks in high-throughput metabolomics mass spectrometry measurements. The method incorporates information about possible…

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