Data processing programs for MS-based metabolomic analysis.

yamss
Desktop

yamss Yet Another Mass Spectrometry Software

Analyzes and visualizes high-throughput metabolomics data aquired using…

Analyzes and visualizes high-throughput metabolomics data aquired using chromatography-mass spectrometry. yamss preprocess data in a way that enables reliable and powerful differential analysis.…

BatMass
Desktop

BatMass

A software package which allows to perform quick quality control of raw LC/MS…

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…

iMet-Q
Desktop

iMet-Q intelligent Metabolomic Quantitation

An automated tool with friendly user interfaces for quantifying metabolites in…

An automated tool with friendly user interfaces for quantifying metabolites in full-scan liquid chromatography-mass spectrometry (LC-MS) data. iMet-Q has a complete quantitation procedure for noise…

MIDcor
Desktop

MIDcor

Performs a primary analysis of isotopic isomers (isotopomers) distribution…

Performs a primary analysis of isotopic isomers (isotopomers) distribution obtained by Gas Chromatography coupled with Mass Spectrometry (GCMS). The aim of MIDcor is to have a correct distribution of…

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…

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…

QCScreen
Desktop

QCScreen

Offers a quick and easy data quality check of liquid chromatography-high…

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…

IsoCor
Desktop

IsoCor

A scientific software tool designed for the purpose of isotope labeling…

A scientific software tool designed for the purpose of isotope labeling experiments (ILE). IsoCor correct raw MS data (isotopic clusters) for the contribution of all naturally abundant isotopes. The…

ICT
Desktop

ICT Isotope Correction Toolbox

A program that corrects tandem mass isotopomer data from tandem mass…

A program that corrects tandem mass isotopomer data from tandem mass spectrometry experiments. ICT supports numerous features, including but not limited to batch processing, considering the purity of…

TargetSearch
Desktop

TargetSearch

An open source tool which is a flexible and accurate method for pre-processing…

An open source tool which is a flexible and accurate method for pre-processing very large numbers of GC-MS samples within hours. A novel strategy was developed to iteratively correct and update…

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.…

TagFinder
Desktop

TagFinder

A software tool for the alignment of large GC-MS-based metabolite profiling…

A software tool for the alignment of large GC-MS-based metabolite profiling experiments into statistically accessible data matrices. The matrix generation is directed by co-analysis of retention…

MzJava
Library

MzJava

An open-source Java library for the analysis of mass spectrometry data from…

An open-source Java library for the analysis of mass spectrometry data from large scale proteomics and glycomics experiments. MzJava provides data structures and algorithms for representing and…

GridMass
Desktop

GridMass

An efficient algorithm for 2D feature detection. GridMass is based on landing…

An efficient algorithm for 2D feature detection. GridMass is based on landing probes across the chromatographic space that are moved to find local maxima providing accurate boundary estimations.…

MetTailor
Desktop

MetTailor

A software package which implements two post-extraction processing steps…

A software package which implements two post-extraction processing steps including a method for block-wise quantitative summary and a novel normalization procedure. There are a number of experimental…

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…

IPO
Desktop

IPO Isotopologue Parameter Optimization

Optimizes XCMS peak picking parameters by using natural, stable 13C isotopic…

Optimizes XCMS peak picking parameters by using natural, stable 13C isotopic peaks to calculate a peak picking score. Retention time correction is optimized by minimizing relative retention time…

MetMSLine
Desktop

MetMSLine

Represents a complete collection of functions in the R programming language as…

Represents a complete collection of functions in the R programming language as an accessible GUI for biomarker discovery in large-scale liquid-chromatography high-resolution mass spectral datasets…

X13CMS
Desktop

X13CMS

An extension of the widely used mass spectrometry-based metabolomic software…

An extension of the widely used mass spectrometry-based metabolomic software package XCMS. X(13)CMS uses the XCMS platform to detect metabolite peaks and perform retention-time alignment in liquid…

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.…

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…

MET-IDEA
Desktop

MET-IDEA Metabolomics Ion-based Data Extraction Algorithm

A current and significant limitation to metabolomics is the large-scale,…

A current and significant limitation to metabolomics is the large-scale, high-throughput conversion of raw chromatographically coupled mass spectrometry datasets into organized data matrices…

Normalyzer
Desktop
Web

Normalyzer

Normalizes the uploaded data using twelve different well known normalization…

Normalizes the uploaded data using twelve different well known normalization methods and compares the resulting data based on quantitative and qualitative parameters. Normalyzer is completely…

Metab
Desktop

Metab

An R package for high-throughput processing of metabolomics data analysed by…

An R package for high-throughput processing of metabolomics data analysed by the Automated Mass Spectral Deconvolution and Identification System (AMDIS). In addition, it performs statistical…

MetabR
Desktop

MetabR

A simple menu-driven program designed to aid researchers with no programming…

A simple menu-driven program designed to aid researchers with no programming background in statistical analysis of metabolomic data. MetabR implements linear mixed models to normalize metabolomic…

MetaboQC
Desktop

MetaboQC

A quality control approach that is based on discrepancies between replicate…

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…

XCMS
Desktop

XCMS

An LC/MS-based data analysis approach which incorporates novel nonlinear…

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…

xMSanalyzer
Desktop

xMSanalyzer

A package of utilities for data extraction, quality control assessment,…

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…

Ionwinze
Desktop

Ionwinze

Tool to pick out ion signals that discriminate two groups of samples (e.g.…

Tool to pick out ion signals that discriminate two groups of samples (e.g. diseased/healthy, resistant/susceptible) by quasi-datapoint-wise comparison using univariate statistic procedures.

apLCMS
Desktop

apLCMS

Designed for the processing of LC/MS based metabolomics data.

Designed for the processing of LC/MS based metabolomics data.

MarkerLynx
Desktop

MarkerLynx

Process Complex Metabonomic and Metabolomic Multivariate Data.

Process Complex Metabonomic and Metabolomic Multivariate Data.

XCMS Online
Web

XCMS Online

A cloud-based metabolomic data processing platform that provides high-quality…

A cloud-based metabolomic data processing platform that provides high-quality metabolomic analysis in a user-friendly, web-based format.

MZmine
Desktop

MZmine

An open-source software tool for mass-spectrometry data processing, with the…

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…

MetaPre
Web

MetaPre

Evaluates the performance of 16 methods specifically for normalizing liquid…

Evaluates the performance of 16 methods specifically for normalizing liquid chromatography/mass spectrometry (LC/MS) based metabolomics data. MetaPre provides 4 steps: (1) uploading the dataset; (2)…

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…

Curators for Data preprocessing

  • Biswapriya Biswavas Misra's avatar image
    Biswapriya Biswavas Misra
    Department of Biology, Genetics…
Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.