structure verification and elucidation using the chemspider database
DESCRIPTION
The ChemSpider database is an online resource containing >26 million chemicals sourced from over 400 data sources. As a result the database is a rich resource supporting the verification and elucidation of chemical structures and is utilized by mass spectrometrists around the world using the online user interface as well as the application programming interface. This presentation will provide an overview of how ChemSpider can be used for the purpose of structure identification and will include (1) direct interaction with the online interface; (2) integration to mass spectrometry vendor software; (3) applications to the identification of “known unknowns” and a comparison with the capabilities of CAS Scifinder and (4) the hosting of online mass spectral data.TRANSCRIPT
Structure verification and elucidation using the ChemSpider database
Antony J Williams, Valery Tkachenko and Alexey Pshenichnov
SERMACS, November 16th 2012
Mass Spectrometry for Structure ID
Many applications of mass spectrometry are the identification of “knowns”
Known structures, previously characterized, previously identified and, increasingly, online
Dereplication, identification of “other manufacturers” materials, metabolites, lipids analysis – can be supported by existing databases
What large database could serve mass spec. ?
ChemSpider
28 million chemicals with associated data…linked out to 400 data sources…
ChemSpider
What will ChemSpider give us??
What will ChemSpider give us??
What will ChemSpider give us??
What will ChemSpider give us??
Spectra Linked: e.g. Cholesterol
Spectra Linked
For Mass Spectrometrists Valuable searches for Mass Spec would be:
Search the database by mass or formula for structure identification
Search subsets of data – e.g. “metabolism”, pesticides etc
Link structure-based data across the internet Provide “programming interfaces” to integrate
Does ChemSpider provide value to Mass Spectrometrists?
Pre-calculated data
Mass Spec AnalysisJim Little, Eastman Chemical
ChemSpider Interface
Tinuvin 328
Position sorted by references
Position 1 only
Searching by Monoisotopic Mass
Identification of “Known Unknowns”
“Known Unknowns” can be identified by searching in ChemSpider
Searching of “segregated” datasets can be performed
Datasets can be expanded for specific projects – for example, natural products ID…
Web Services Open Up Collaboration
Agilent, Bruker, Waters and Thermo all use our web-based services for compound lookup
Many academic sites integrating directly – metabonomics, name lookup, semantic markup
Web Services
Results of the ChemSpider Search in the MarkerLynx Worksheet
Hit Details in ChemSpider
Calculation of Elemental Composition & ChemSpider Search of Lipid Maps Database Performed via MarkerLynx
Commercial Database Access
Recently deposited to ChemSpider EPA/NIST IR Database >5000 spectra
Presently under development NIST MS database >200,000 MS spectra
Coming Soon – NIST DB in ChemSpider
Where next with Analytical Support? PharmaSea project for the identification of natural
products – dereplication approaches Use mass spectrometry searches of natural
product slices to identify Natural product data include from RSC
databases (NPU) and ChemSpider data sources – MarinLit for example
Pre-fragment compounds and develop searches Dereplication using NMR data
NMR features Predicted spectra and “Verification approaches”
Coming Soon Storage and display of ASSIGNED spectra –
already started with NMR spectral assignment
Crowdsourcing ChemSpider
ChemSpider is crowdsourced
Community deposition, annotation and curation
Anyone can “Leave Feedback”
Registered users can add data
Ideas for Future Work
Extended search capabilities
Expand existing databases
Integrate to metabolic pathways tools
How long until Mobile StructureID?
Acknowledgments RSC eScience Team
James Little, Eastman Chemical Company
Alexey Pshenichnov, University of Leicester – SpectraSchool
ACD/Labs – Assigned Spectra Display Widget
Depositors of data – there are many!
Thank you
Email: [email protected] Twitter: ChemConnectorPersonal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams