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.

1. Structure verification and elucidation
using the ChemSpider database
Antony J Williams, Valery Tkachenko and
Alexey Pshenichnov
SERMACS, November 16th 2012

2. 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. ?

3. ChemSpider
 28 million chemicals with associated data…linked
out to 400 data sources…

4. ChemSpider

5. What will ChemSpider give us??

6. What will ChemSpider give us??

7. What will ChemSpider give us??

8. What will ChemSpider give us??

9. Spectra Linked: e.g. Cholesterol

10. Spectra Linked

11. 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?

12. Pre-calculated data

13. Mass Spec Analysis
Jim Little, Eastman Chemical

14. ChemSpider Interface

16. Tinuvin 328

17. Position sorted by references

18. Position 1 only

19. Searching by Monoisotopic Mass

20. 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…

21. 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

22. Web Services

23. Results of the ChemSpider Search
in the MarkerLynx Worksheet

24. Hit Details in ChemSpider

25. Calculation of Elemental Composition &
ChemSpider Search of Lipid Maps
Database Performed via MarkerLynx

26. Commercial Database Access
 Recently deposited to ChemSpider
 EPA/NIST IR Database >5000 spectra
 Presently under development
 NIST MS database >200,000 MS spectra

27. Coming Soon – NIST DB in ChemSpider

28. 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”

29. SpectraSchool http://spectraschool.rsc.org/

32. Coming Soon
 Storage and display of ASSIGNED spectra –
already started with NMR spectral assignment

33. Crowdsourcing ChemSpider
 ChemSpider is crowdsourced
 Community deposition, annotation
and curation
 Anyone can “Leave Feedback”
 Registered users can add data

34. Ideas for Future Work
 Extended search capabilities
 Expand existing databases
 Integrate to metabolic
pathways tools

35. How long until Mobile StructureID?

36. 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!

37. Thank you
Email: williamsa@rsc.org
Twitter: ChemConnector
Personal Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams