Table 1.
List of tools available for metabolomics spectral processing and data analysis.
| Tool | Type | Target | Featuresa | Website | Reference |
|---|---|---|---|---|---|
| MetaboAnalyst2 | Web | MS and NMR | 1–7 | http://www.metaboanalyst.ca/ | Xia et al. (2012) |
| XCMS | R | MS | 1–3 | http://metlin.scripps.edu/xcms/ | Smith et al. (2006) |
| MetSign | MatLab | MS | 1–3 | http://metaopen.sourceforge.net/ | Lommen and Kools (2012) |
| XCMS online | Web | LC-MS | 1–4 | https://xcmsonline.scripps.edu/ | Tautenhahn et al. (2012b) |
| MAVEN | Application | LC-MS | 1–7 | http://genomics-pubs.princeton.edu/mzroll | Melamud et al. (2010) |
| mzMine2 | Application | LC-MS | 1–5 | http://mzmine.sourceforge.net/ | Pluskal et al. (2010) |
| MAIT | R | LC-MS | 1–5 | http://b2slab.upc.edu/software-and-downloads | Fernández-Albert et al. (2014) |
| OpenMS | Application | LC-MS | 1–3 | http://open-ms.sourceforge.net/ | Sturm et al. (2008) |
| Metabolome express | Web | GC-MS | 1–5 | https://www.metabolome-express.org/ | Carroll et al. (2010) |
| Metabolite detector | Application | GC-MS | 1–4 | http://md.tu-bs.de/ | Hiller et al. (2009) |
| MetDAT | Web | MS | 1–5 | http://smbl.nus.edu.sg/METDAT2/ | Biswas et al. (2010) |
| FOCUS | MatLab | NMR | 1–4 | http://www.urr.cat/FOCUS/ | Alonso et al. (2013) |
| Automics | Application | NMR | 1–2, 5 | https://code.google.com/p/automics/ | Wang et al. (2009) |
| Bayesil | Web | NMR | 1–4 | http://bayesil.ca/ | Ravanbakhsh et al. (2014) |
| Speaq | Application | NMR | 1–2, 5 | https://code.google.com/p/speaq/ | Vu et al. (2011) |
| MetaboLab | Application | NMR | 1–2, 5 | http://www.nmrlab.org.uk/ | Ludwig and Gunther (2011) |
| rNMR | R | NMR | 8 | http://rnmr.nmrfam.wisc.edu/ | Lewis et al. (2009) |
| MetaboMiner | Application | NMR | 8 | http://wishart.biology.ualberta.ca/metabominer/ | Xia et al. (2008) |
| Muma | R | – | 5 | http://cran.r-project.org/web/packages/muma | Gaude et al. (2013) |
| MetaXCMS | R | MS and NMR | 5 | http://metlin.scripps.edu/metaxcms/ | Tautenhahn et al. (2010) |
| BATMAN | R | NMR | 3–4 | http://batman.r-forge.r-project.org/ | Hao et al. (2012) |
| AStream | R | LC-MS | 4 | http://www.urr.cat/AStream/AStream.html | Alonso et al. (2011) |
| Camera | R | LC-MS | 4 | http://metlin.scripps.edu/xcms/ | Kuhl et al. (2011) |
| MetaboHunter | Web | NMR | 4 | http://www.nrcbioinformatics.ca/metabohunter/ | Tulpan et al. (2011) |
| MetScape | Application | – | 6–7 | http://metscape.ncibi.org/ | Gao et al. (2010) |
| IMPaLA | Web | – | 6–7 | http://impala.molgen.mpg.de/ | Kamburov et al. (2011) |
| MetExplore | Web | – | 6–7 | http://metexplore.toulouse.inra.fr/ | Cottret et al. (2010) |
| MetPA | Web | – | 6–7 | http://metpa.metabolomics.ca/ | Xia and Wishart (2010a) |
| Cytoscape | Application | – | 7 | http://www.cytoscape.org/ | Smoot et al. (2011) |
| Vanted | Application | – | 7 | http://vanted.ipk-gatersleben.de/ | Rohn et al. (2012) |
| Paintomics | Web | – | 7 | http://www.paintomics.org/ | García-Alcalde et al. (2011) |
This table provides a complete and updated list of the open-source software that is commonly used in the untargeted analysis of metabolomic data.
aThis column refers to the features included in the tool: spectral pre-processing (1), spectral/peak alignment (2), peak detection (3), metabolite identification (4), data analysis (5), pathway analysis (6), pathway visualization (7), and 2D-NMR analysis (8).