Table 2.
Selected Platforms for Metabolomics Analysis and Interpretation
| Name | Link | Access | Input | Databases Used | Functions | Comments |
|---|---|---|---|---|---|---|
| MetExplore [28] | http://metexplore.toulouse.inra.fr | Web-based | Compound IDs, Mass IDs | Generally BioCyc related | Compound mapping, graph analysis of metabolism maps. | Choice of organism database, filtering options, multiple graph analysis tools, Cytoscape integration. |
| PAPi [24] | http://www.4shared.com/file/0v5zSobM/PAPi_10.html | R Package | KEGG Compound IDs | KEGG | Compares activity of metabolic pathways between sample types. | Non organism specific, more difficult/powerful command line R interface. Usable with spent media results. |
| MBRole [27] | http://csbg.cnb.csic.es/mbrole/ | Web-based | Compound IDs | KEGG, HMDB, PubChem, ChEBI, SMILES | Enrichment analysis of metabolites’ annotations. | Background set from known organisms or custom set. Metabolite ID converter. |
| MetaboAnalyst[57] | http://www.metaboanalyst.ca/MetaboAnalyst/ | Web-based | Raw Spectra (GC and LC MS), peak lists and spectral bins (MS and NMR) | Custom, KEGG, HMDB | Full processing, Statistical Analysis | Comprehensive metabolomics analysis platform with easy interface, tutorials, help. Human focused though some model organisms or custom metabolite set option. |
| MetaboAnalyst(MSEA) [58] | http://www.metaboanalyst.ca/MetaboAnalyst/ | Web-based. | Compound IDs and abundances | Custom, KEGG, HMDB | Enrichment Analysis | Comprehensive metabolomics analysis platform with easy interface, tutorials, help. Human focused though some model organisms or custom metabolite set option. |
| MetaboAnalyst (MetPa [59]) | http://www.metaboanalyst.ca/MetaboAnalyst/ | Web-based | Compound IDs and abundances | KEGG | Pathway Analysis | Select model organisms. Network topology analysis. Intuitive network visualization. |
| MPEA [29] | http://ekhidna.biocenter.helsinki.fi/poxo/mpea/ | Web-based | Compound IDs, GC-MS Spectrum as ranked list | KEGG, GMD, SMPDB | Pathway enrichment analysis. | Optional background set. Limited to top-down/bottom-up analysis. |
| MeltDB (MSEA) [30, 60] | http://www.cebitec.uni-bielefeld.de/groups/brf/software/meltdb_info/ | Web-based, login required | Raw GC/LC-MS spectra, processed spectra, compound IDs and abundances | GMD, KEGG, ChEBI, CAS | Comprehensive preprocessing, statistical analysis and metabolite mapping, enrichment analysis. | Integrated comprehensive online system, accessible by multiple users. Many statistical tools, custom metrics and sets for enrichment analysis. |
| Meta P-server [61] | http://metabolomics.helmholtz-muenchen.de/metap2/ | Web-based | Compound IDs, sample meta-data | KEGG, HMDB, LipidMaps, PubChem | Data quality control, statistical analysis, hypothesis testing. | No use of organismal databases. Focus mainly on global statistical analysis. |
| MassTrix [62, 63] | http://metabolomics.helmholtz-muenchen.de/masstrix2/ | Web-based | MS spectra | KEGG, HMDB, LipidMaps | Compound mapping | Choice of KEGG organism. Optional background set. Color-coding. |
| BioCyc (Pathway Tools) [52] | http://biocyc.org/ | Installation required | Annotated genome, ‘omics data | MetaCyc | Network exploration, genome annotation, ‘omics data painting. | Comprehensive systems biology network analysis. |
| Pathos [64] | http://motif.gla.ac.uk/Pathos/index.html | Web-based | Simple m/z values, Compound IDs | KEGG | Compound mapping | Choice of limited organism databases. |
| PaintOmics [65] | http://www.paintomics.org | Web-based | KEGG formatted metabolites and/or genes | KEGG | Compound mapping | Choice of 100 hundred top species. Colours pathway metabolites and genes according to increase/decrease. |
| IMPaLA [66] | http://impala.molgen.mpg.de/ | Web-based | Gene IDs and/or Compound IDs | KEGG, HMDB, CAS, ChEBI, PubChem, Reactome, Wikipathways | Enrichment Analysis | Combined analysis with proteins or transcripts. Organism independent. Optional background set. |
| MetaMapp [25] | http://uranus.fiehnlab.ucdavis.edu:8080/MetaMapp/homePage | Web-based | Compound IDs | KEGG | Metabolite networking | Organism independent. Network construction based on chemical similarity. |
| VANTED [67] | http://vanted.ipk-gatersleben.de/ | Installation required | Compound abundances | KEGG | Metabolite networking, compound mapping, statistical analysis | Combined analysis with proteins and transcripts. Organism independent. Direct visualization of results on networks. Time course analysis. Statistical analysis. |
| TICL [68] | http://mips.helmholtz-muenchen.de/proj/cmp/home.html | Web-based | Compound IDs | KEGG | Enrichment analysis. | No choice of organism. Currently non-functional |