ToolPurposeYear publicPublication
Chemical Translation Service
batch query for chemical names to DB identifiers across 200 DBs 2010 Bioinformatics (2010) 26(20):2647
MassBank of North America
integration of all freely available mass spectra, structures and metadata (> 200,000 spectra) 2015

Analytical Chemistry. (2016) 88(16):7946

Spectral Hash Key
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
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
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
Analytical Chemistry (2016), 88(16):7946