Databases, tools and software developed and hosted by the West Coast Metabolomics Center

For other tools, check out 'resources' in the Metabolomics Association of North America website!

ToolPurposeYear publicPublication
MS/MS spectral entropy similarity to reduce the number of false positives when performing MS/MS library searches 2021 Nature Methods (2021)
Metabolome atlas of the aging mouse brain to build a background database for 1,547 identified compounds in 10 brain microdissection of 3 to 92 weeks old mice 2021 Nature Communications (2021)
Blood Exposome DB to build a database for all chemicals that are reported in literature as detected in blood 2019 Environmental Health Perspectives (2019)
Systematic Error Removal by Random Forest (SERRF) to normalize metabolomic and lipidomic data sets using QC pool samples 2019 Analytical Chemistry (2019)
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 (> 640,000 spectra)

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) 
LipidBlast lipidomic ID, classes, templates, m/z lookups, 
MS/MS downloads, web search, MS/MS batch scores
2013 Nature Methods (2013);
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
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 (2018) 15: 53
BinDiscoverer query organs, species of all GC/MS Bins against BinBase, using ontologies, the WCMC DB with 8,000 metabolites from 2,000 studies, 156,000 samples 2023 J. Cheminformatics
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
MetaMapp Chemical and biochemical mapping of metabolomics datasets 2012 BMC Bioinformatics (2012) 13(1):99
ChemRICH R-based comprehensive chemical clustering tool 
for Chemical Enrichment Analysis as alternative 
to metabolic pathway analysis
2017 Scientific Reports (2017) 
ClassyFire batch Online service to return chemical compound classes for lists of InChI key identifiers, based on the Yannick Djoumbou Feunang's algorithm (Wishart lab) 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
Nature Methods (2015),
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
Analytical Chemistry (2016), 88(16):7946


Specific WCMC data dictionaries and standard operating protocols (SOPs)

data dictionary lipidomics

6cde9183 34fd 4650 a345 57adbd4f4fa1

SOP biofluid extraction lipidomics  
SOP data acquisition lipidomics   
SOP data processing lipidomics

data dictionary primary metabolomics

SOP biofluid extraction primary metabolism 
SOP data acquisition primary metabolites   
SOP data processing primary metabolites

data dictionary biogenic amines / specialized metabolites

SOP biofluid extraction biogenic amines / specialized metabolites
SOP biofluid data acquisition biogenic amines / specialized metabolites
SOP biofluid data processing biogenic amines / specialized metabolites

data dictionary bile acids

SOP bile acids

data dictionary eicosanoids

SOP eicosanoids

data dictionary steroids

SOP steroids

data dictionary flux analysis

SOP flux analysis