| Tool | Purpose | Year public | Publication |
|---|---|---|---|
| Chemical Translation Service (CTS) |
batch query for chemical names to DB identifiers across 200 DBs | 2010 | Bioinformatics (2010) 26(20):2647 |
| MassBank of North America (MoNA) |
integration of all freely available mass spectra, structures and metadata (> 200,000 spectra) | 2015 | |
| Spectral Hash Key (SPLASH) |
online resource to create spectral identifiers, for MS library and DB exchanges | 2016 | Nature Biotechnology (2016) 34(11):1099 |
| LipidBlast | lipidomic ID, classes, templates, m/z lookups, MS/MS downloads, web search, MS/MS batch scores | 2013 | Nature Methods (2013);10(8):755 |
| MS-Feature List Optimizer (MS-FLO) |
to clean up errors from MS data processing (MZmine, XCMS, MS-DIAL), including isotopes, doublets and adducts | 2016 | Analytical Chemistry 89.6 (2017): 3250 |
| MSDialRest | REST service for batch online MS-DIAL data processing | 2017 | Bioinformatics (2017) in review |
| miniX (access with login) source code |
study design database as foundation for all WCMC studies, for biological species, organ, treatment data | 2006 | Pacific Symp. Biocomputing (2007): 169 |
| query of unknown GC/MS spectra against BinBase, the WCMC DB with 8,000 metabolites from 1600 studies, 110,000 samples | 2017 | Nature Methods (2017) in review |
|
| MS2Analyzer | Executable program download with tutorials; to analyze MS/MS spectra for neutral loss, product ion rules | 2014 | Analytical Chemistry 86.21 (2014): 10724 |
| Seven Golden Rules | Executable program download with tutorials; to calculate elemental formulas by accurate mass, isotopes | 2007 | BMC Bioinformatics (2007) 8(1):105 |
| MetaBox | R-based tool box for data normalization, statistics, pathway analysis with MetaMapp | 2016 | PloS ONE (2017) 12(1):e0171046 |
| ChemRICH | R-based comprehensive chemical clustering tool for Chemical Enrichment Analysis as alternative to metabolic pathway analysis | 2017 | SREP (2017) in review |
| ClassyFire batch | Online service to return chemical compound classes for lists of InChI key identifiers, based on the Wishart lab algorithm. | 2017 | J. Cheminformatics (2016), 8(1): 61 |
| MS-DIAL 2.0 | Software for data dependent and data independent LC-MS/MS and GC-MS data processing. Developed by Dr Hiroshi Tsugawa and Prof Masanori Arita in collaboration with the Fiehn laboratory | 2014 2017 |
Nature Methods (2015),1;12(6):523 |
| MS-FINDER 2.0 | Software for virtual mass spectra predictions from structure using bond energies, H-rearrangements, heuristic rules for LC-MS/MS and GC-MS spectra. Developed by Dr Hiroshi Tsugawa and Prof Masanori Arita in collaboration with the Fiehn laboratory | 2015 2017 |
Analytical Chemistry (2016), 88(16):7946 |