We here present select software systems that have been tested by MANA members. For 'compound ID' software, we require showcasing the software using test data sets from recent CASMI contests. For all other software, we require programs to be demonstrated on publicly available data sets on the MetabolomicsWorkbench.

Suggestions by MANA members to add further software are most welcome ('contact us')!
Corporate MANA members may suggest adding select licensed software systems to the list.


Raw data processing


The free MS-DIAL software uses LC-MS/MS or GC-MS raw data from any vendor, including deconvolution, alignment and compound identification.


The free XCMS software is the most popular tool for LC-MS raw data processing, including alignment of mz / retention time features.


The open source, free MZmine software provides an alternative solution for LC-MS raw data processing, and alignement of mz / ret. time features.


Cleaning errors from raw data processing results


This free software enables finding clusters of mz / ret. time features from XCMS and has been built to remove erroneous feature reports.

MS-Feature List Optimizer (MS-FLO)

The free MS-FLO tool uses result reports from XCMS, MZmine or MS-DIAL to remove erroneous peak findings, including isotopes and adducts.


Compound identification


The free MS-FINDER software uses bond strengths, the 7-Golden Rules, product ion rules and H-rearrangements to predict mass spectra.


MAGMa is a free online tool for structure annotations of multistage MSn spectral data using PubChem compounds and enzymatic predictions.


The free CFM-ID tool predicts mass spectra from chemical structures using trained machine learning algorithms.

CSI:Finger ID

The free CSI:Finger ID tool uses MS fragmentation trees to predict structure fingerprints of unknown compounds using machine learning.


The new MetFrag software predicts MS/MS spectra from chemical bond energies, in addition to external data sources and InChIKey filtering.


Result data statistics


MetaboAnalyst is a free online tool for univariate and multivariate statistics, including data normalizations and transformations.


Result data visualization, networks, pathway mapping, integration


The free MetaboAnalyst application uses pathway enrichments statistics based on KEGG pathways and hypergeometric tests.


The free Galaxy 'worflow4metabolomics' tool uses XCMS and CAMERA for data processing, statistics and visualization of results.


The free MetScape tool uses metabolite and gene expression results to build networks and calculate enriched pathways.


The free MetaMapp software diplays differential network graphs using chemical similarity matrices and KEGG Rpair relationships.


The free ChemRich tool using chemical structure similarities and MeSH ontologies for chemical enrichment statistics using KS-tests.