Many of the steps we have been discussing today are common to almost all software solutions availabe for tha analysis of metabolomics data:

1. Commercial suites
2. Open source solutions which can be run locally (e.g. xcms,MzMine,MSDial)
3. Freely available web services

1 - Allow the use of xcms through a web interface

xcms online

2 - Allows to use xcms through Galaxy

The French metabolomics network also provide software for pathway analysis and visualization

Metabohub - Workflow-4-metabolomics

Linked to the Human Metabolome Database

MetaboAnalyst - statistical, functional and integrative analysis of metabolomics data

Metaboanalyst

Python Based

As part of the deNBI Center for integrative Bioinformatics, OpenMS offers an open-source software C++ library (+ python bindings) for LC/MS data management and analyses

OpenMS

In Galaxy and Knime

KNIME Analytics Platform is the open source software for creating data science

knime

PhenoMeNal (Phenome and Metabolome aNalysis) is a comprehensive and standardised e-infrastructure that supports the data processing and analysis pipelines for molecular phenotype data generated by metabolomics applications

PhenoMeNal

MZmine

MZmine 3 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data.

MZmine3

MS-DIAL was launched as a universal program for untargeted metabolomics that supports multiple instruments (GC/MS, GC/MS/MS, LC/MS, and LC/MS/MS) and MS vendors (Agilent, Bruker, LECO, Sciex, Shimadzu, Thermo, and Waters)

MS-Dial