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