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Software and tools

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West Coast Metabolomics Center Tools

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

All WCMC data and protocols available from the metabolomicsworkbench.org

For linking to scientists and events in North America, please check out
the newly founded Metabolomics Association of North America !

ToolPurpose
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

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

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 query of 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

BinVestigate

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
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 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

Wohlgemuth at server

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

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