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

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/ 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.comwww.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliamswww.slideshare.net/AntonyWilliams