the university of alabama at birmingham | uab - databases · 2016-08-09 · outline •...

Metabolomics Databases

Xiuxia Du, Stephen Barnes

Outline• Comprehensive metabolomics databases

• Compound databases

• Spectral databases

• Metabolic pathway databases

• Drug databases

• Disease & physiology databases

• Raw data databases

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• Drug databases



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Comprehensive databases• HMDB

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HMDB• Overview

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• Breakdown by mass

HMDB

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HMDB• One metabocard

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HMDB• One metabocard

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HMDB• Searches

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HMDB• Downloads

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HMDB• Download all metabolites

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• Drug databases



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Compound databases• PubChem

• ChemSpider

• ChEBI

• KEGG Glycan

• IIMDB

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Compound databases• PubChem

• ChemSpider

• ChEBI

• KEGG Glycan

• IIMDB

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PubChem• Website

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PubChem• Statistics (July 12, 2016)

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PubChem• Breakdown by mass

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PubChem• Information on one compound

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PubChem• Information on one compound

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PubChem• Search and FTP

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PubChem• FTP

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PubChem• Compound XML files

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PubChem• Download compound XML files

• Total number of XML files: 4,849

• Number of compounds in each XML file: 25,00023

ChemSpider• Website

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ChemSpider• Information

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ChemSpider• One compound

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ChemSpider• Compounds with the same molecular formula

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ChEBI• Chemical Entities of Biological Interest

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ChEBI• About

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ChEBI• One compound

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• Substructure search

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ChEBI• One compound





• Drug databases



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Spectral databases• NIST 14

• METLIN

• MassBank

• MoNA

• Gold Metabolome Database

• Feign GC-MS database

• HMDB

• BMRB

• Madison Metabolomics Consortium Database

• BML-NMR

• mzCloud

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Spectral databases• NIST 14

• METLIN

• MassBank

• MoNA

• Gold Metabolome Database

• Feign GC-MS database

• HMDB

• BMRB

• Madison Metabolomics Consortium Database

• BML-NMR

• mzCloud

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NIST 14• Electron ionization mass spectral library

- 276,259 spectra of 242,477 unique compounds

• MS/MS library: 234,284 spectra

- 51,216 ion trap spectra for 42,126 different ions of 8,171 compounds

- 183,068 collision cell spectra (QTOF and tandem quad) spectra for 14,835 different ions of 7,692 compounds

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NIST 14 EI library

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NIST 14 EI library

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• Focuses on

- Drugs, metabolites, and poisons

- Pesticides and fungicides

- Organics present in soil, water, and air

- Amino acids, di- and tai-peptides

- Common sample contaminants

- Common analytical derivatives of the above

NIST 14 EI library

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• Breakdown by mass

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NIST 14 MS/MS library

METLIN

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METLIN

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METLIN

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METLIN

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METLIN

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METLIN

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MassBank

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• About

MassBank

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• Database services

MassBank

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MassBank

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MassBank

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MassBank

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MassBank

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MoNA

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Metabolic pathway databases• KEGG

• MetaCyc

• HumanCyc

• BioCyc

• Reactome

• WikiPathways

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Drug databases• DrugBank

• Therapeutic target databases

• PharmGKB

• STITCH

• SuperTarget

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Disease & physiology databases• OMIM

• METAGENE

• OMMBID

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Raw data databases• Metabolomics Workbench

- Funded by the NIH Common Fund Metabolomics Program

- Serve as a national and international repository for metabolomics data and metadata

- Provide access to raw data, metabolite standards, protocols ……

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Raw data databases• Metabolomics Workbench

• MetaboLights

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Metabolomics orkbench• Website

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Raw data databases• Metabolomics Workbench: summary of all studies

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Raw data databases• Metabolomics Workbench: species

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Raw data databases• Metabolomics Workbench: sample sources

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Raw data databases• Metabolomics Workbench: diseases

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Raw data databases• MetaboLights

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PubChem, NIST, and HMDB, again

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3,412,370 2,000

471

59,621

1

PubChem NIST

HMDB

5,0834,647

3,481,721 66,269

10,202

• In terms of unique molecular formula

PubChem, NIST, and HMDB, again

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PubChem HMDB

91,101,371 26,65315,234

91,116,605 41,887

• In terms of unique InChi Key

Acknowledgement• Aleksandr Smirnov

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Thank you!

the university of alabama at birmingham | uab - databases · 2016-08-09 · outline •...

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