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!
| Tool | Purpose | Year public | Publication |
|---|---|---|---|
| Flash entropy search | to exploit large spectral libraries with little memory overhead for any mass spectrometry laboratory. | 2023 | Nature Methods (2023) |
| The BinDiscover database | to enable intuitive, rapid hypothesis generation for biologists based on these metabolomic samples. | 2023 | Journal of Cheminformatics (2023) |
| 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) |
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 |
| 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 | |
| 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 |
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 |
Specific WCMC data dictionaries and standard operating protocols (SOPs)
data dictionary lipidomics
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