Software

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This page contains a list of the most widely used freely available software and tools that are used primarily in metabolomics based on the review article by Spicer et al[1].

Software tools for data preprocessing

XCMS for LC-MS and GC-MS

MetAlign for LC-MS

MS-DIAL for LC-MS

mzMatch for LC-MS

IDEOM for LC-MS

AMDIS for GC-MS

MetaboliteDetector for GC-MS

MeltDB for LC-MS and GC-MS

metaMS for GC-MS

SpectConnect for GC-MS

rNMR for NMR

Software tools for data post-processing

batchCorr for LC-MS

crmn for LC-MS and GC-MS

EigenMS for LC-MS

KMDA for MS

metabomxtr for LC-MS and GC-MS

Metabnorm for NMR

MetabR for LC-MS

MetNorm for LC-MS, GC-MS and NMR

MSPrep for LC-MS

muma for MS and NMR


Software tools for statistical analysis

Ionwinze for LC-MS

MetabolAnalyze for MS and NMR

muma for MS and NMR

ropls for MS and NMR

MetaboAnalyst for LC-MS and NMR


Software tools for metabolite annotation

CAMERA, Level 4

Rdisop, Level 4

SIRIUS and CSI Finger ID, Level 4

ProbMetab, Level 3

MetAssign–mzMatch, Level 3

MetFrag, Level 2a

CFM-ID, Level 2a

FingerID, Level 2a

MAGMa, Level 2a

MyCompoundID, Level 2a

BATMAN, NMR

Bayesil, NMR

MetaboMiner, NMR

SpinAssign, NMR

COLMAR, NMR

MassBank

MetFusion

CDM-ID

MS2LDA

GNPS


Workflows for the analysis of metabolomics data

Galaxy-M for LC-MS

GNPS for LC-MS

MetaboAnalyst 4.0 for LC-MS and NMR

MAVEN for LC-MS

MAIT for LC-MS

MZmine 2 for LC-MS

Workflow4metabolomics for LC-MS, GC-MS and NMR

XCMS Online for LC-MS and GC-MS

References

  1. Spicer R, Salek RM, Moreno P, Cañueto D, Steinbeck C., "Navigating freely-available software tools for metabolomics analysis", Metabolomics. 2017;13(9):106. doi: 10.1007/s11306-017-1242-7.