Chemspider For Mass Spectrometrists Public Version

ChemSpider for Mass Spectrometrists Antony Williams

ChemSpider - A Search Engine for Chemists
Questions a chemist might ask…
What is the melting point of n-butanol?
What is the chemical structure of Xanax?
Chemically, what is phenolphthalein?
What are the stereocenters of cholesterol?
Where can I find publications about xylene?
What are the different trade names for Ketoconazole?
What is the NMR spectrum of Aspirin?
What are the safety handling issues for Thymol Blue?
ChemSpider can answer all of these questions

ChemSpider Data Content
Over 21.5 million unique chemical structures from ca. 150 data sources
Online Databases –PubChem, Drugbank, HMDB, Wikipedia
Chemical Vendors – over 40 different vendors and growing
Personal Depositions – individual contributions
Journal Publishers
Content database vendors
Analytical data collections
Patents (9 MILLION Structures being deposited now )
Web scraping
Content is generally linked back to the original data sources

ChemSpider for MS Spectrometrists
What would an MS spectrometrist want to do?
Search the database based on mass (various forms)
Search selected subsets of the database based on mass
Search based on mass and substructure(s)
Search for structure based on name(s) or database IDs
Search for structures based on elements/not elements
Download the structure/structures in standard format
Search literature for information
Identify related data sources – chemical vendors, pathway databases, etc

Tell me about Aspirin

Link outs

Tell me about Aspirin

Tell me About Aspirin

ChemSpider for MS Spectrometrists
What would an MS spectrometrist want to do?
Search the database based on mass (various forms)
Search selected subsets of the database based on mass
Search based on mass and substructure(s)
Search for structure based on name(s) or database IDs
Search for structures based on elements/not elements
Download the structure/structures in standard format
Search literature for information
Identify related data sources – chemical vendors, pathway databases, etc

Search Database Based on Mass

Search 309.08+/- 0.001 527 hits out of 21.5 MILLION Structures in 2 seconds

Include/Exclude Elements During a Search

Search based on Data Sources

Combined Searches
Search for a particular mass AND
Search a series of data sources only AND
Search inclusion/exclusion lists of elements AND
Search a particular substructure

Structure Searching

Substructure Searching

Outlinks – to vendors and other databases
Example databases of interest to MS Spectrometrists:
HMDB – Human Metabolome Database
KEGG – Kyoto Encyclopedia of Genes and Genomes
BioCyc - collection of Pathway/Genome Databases
Uni. Minnesota Biodegradation DB - information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds
WikiPathways – new initiative to build crowdsourced pathway data management

Links out to KEGG Kyoto Encyclopedia of Genes and Genomes

WikiPathways Link

Download Structure(s)
Download individual record – molfile
Download SDF file (group of structures)

Search Literature
Text indexing of >1/2 million Open Access Articles
Searching of Pubmed via the NCBI Entrez System
Potential directions include extension to focused searching- LCMS only, HPLC only etc. We can index based on Title and Abstracts and on chemical names

MassSpec API Web Services
http:// www.chemspider.com/MassSpecAPI.asmx

Web Services

Test Web Services for MassSpec
http:// www.chemspider.com/WebServices/WSMassSpecAPIDemo.aspx

Test results

Waters Integration

Outlinks from Table

Chemspider For Mass Spectrometrists Public Version

by Antony Williams, ChemConnector on Sep 19, 2008

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Chemspider For Mass Spectrometrists Public Version — Presentation Transcript