As scientists we now have online a number of domain specific databases in chemistry for us to use. While there are hundreds of these “compound databases” available for us to access there are very few developed with the concerns of the analytical scientist in mind. ChemSpider is a free resource from the Royal Society of Chemistry hosting over 28 million chemicals from over 400 data sources and is already utilized by the mass spectrometry community in particular to aid in the process of structure verification. This presentation will give an overview of how ChemSpider has become one of the internets’ primary resources for chemists providing access to chemicals, experimental and predicted properties, patents, publications and analytical data and ultimately acting as a structure-centric hub. The importance of programming interfaces to allow for integration and how the primary mass spectrometry vendors are already utilizing ChemSpider will be discussed. The progress towards providing a dereplication platform for natural products using a combination of mass spectrometry and NMR spectroscopy data will be outlined and the path forward to a fully chemical structure-enabled internet and the importance of data interchange standards to enable this will be discussed.

1. Utilizing Online Databases for the Purpose
of Structure Identification – Approaches
Utilizing the ChemSpider Resource
Antony Williams
Triangle Chromatography Discussion Group
May 16th
2013

2. Free and Easy
• Everything I will show in terms of ChemSpider is
available for free online today
• To make it easy to “take notes” these slides will
go online tonight for you to download
www.slideshare.net/AntonyWilliams/

3. 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. ?

4. ChemSpider
• > 28 million chemicals with associated data
• Linked out to 400 data sources…

5. ChemSpider

6. What will ChemSpider give us??

7. What will ChemSpider give us??

8. What will ChemSpider give us??

9. What will ChemSpider give us??

10. Spectra: e.g. Cholesterol

11. Spectra

12. 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?

13. Pre-calculated data

14. Data Source Selection
• >28 million chemicals include
– Vendor collections
– Government databases
– Individual/Lab data
– Publication data
– All segregated allowing for data source selection

15. Data Source Selection - Type

16. Data Source Selection - Individual

17. Mass Spec Analysis
Jim Little, Eastman Chemical

18. ChemSpider Interface

19. 1287 Hits Ranked by Defect

20. 1287 Hits Ranked by # of References

21. Top Ranked Hit

22. Tinuvin 328

23. What can I find on ChemSpider?

24. What can I find on ChemSpider?

25. What can I find on ChemSpider?

26. Source and Purchase…

27. What can I find on ChemSpider?

28. External Calculation Engines

29. What can I find on ChemSpider?

30. and in the RSC Databases..

31. Linked to the Publisher

32. What can I find on ChemSpider?

33. And out to Google Patents

34. And is it “Dangerous”

35. And What About the Entire Web?

36. The InChI Identifier

37. InChIStrings Hash to InChIKeys

38. Searching the Internet by Structure

39. What can I find on ChemSpider?
• Experimental properties
• Predicted properties
• Literature links
• Book Links
• Database links
• Where to Buy
• Patent links
• Spectral data
• Toxicity data
• Virtual screening data
• ……….and a hub for
searching the entire
internet!!!

40. Extended Study
Sorting by references

41. Position sorted by references

42. Position 1 only

43. Searching by Monoisotopic Mass

44. Improved Searches
• Substructure Search with Mass Filter
352.239 +/- 0.0018

45. 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…

46. • FP7 Initiative. PharmaSea: increasing value and flow in
the marine biodiscovery pipeline

47. The PharmaSea Project
• PharmaSea project for the identification of
natural products – dereplication approaches
– Use MS searches of natural product slices to identify
– Natural product data include from RSC databases
(NPU) and ChemSpider data sources

48. What about ID’ing “Unknowns”?
• Bring together various spectroscopic techniques
for structure elucidation – primarily NMR and
Mass Spectrometry
• Work to identify substructural fragments
• Use Computer-Assisted Structure Elucidation

49. CASE Systems

50. Blind Trials of CASE
http://www.jcheminf.com/content/4/1/5

51. The PharmaSea Project
• PharmaSea project for the identification of
natural products – dereplication approaches
– Use MS searches of natural product slices to identify
– Natural product data include from RSC databases
(NPU) and ChemSpider data sources
– Pre-fragment compounds and develop searches
– Dereplication using NMR data
• NMR features
• Predicted spectra and “Verification approaches”
• CASE based approaches

52. Web Services Open Up Collaboration
• Agilent, Bruker, Waters and Thermo all using or
investigating our web-based services for
compound lookup
• Many academic sites integrating directly –
metabonomics, name lookup, mass-based
searching

53. Web Services

54. Results of the ChemSpider Search
in the MarkerLynx Worksheet

55. Hit Details in ChemSpider

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

57. Some usage statistics
• ca. 200 visitors at any one time, ~30,000 visits per day
• Mar 4-Apr 3, 2013
– Visits = 731,656
– Unique Visitors = 527,008
• Independent servers to support other projects

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

59. Future Developments
• Support for Multiple Substructures
• Mass to formula conversion
• Expand data sources with MS focus
• Hosting reference data for Metabonomics
• Investigating how to serve chromatographers
• What can we do for you???
• Anybody in the audience teach spectroscopy??

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

63. Presently in Beta
• Storage and display of ASSIGNED spectra –
already started with NMR spectral assignment

64. Coming Soon – NIST DB in ChemSpider

65. How long until Mobile StructureID?

66. Formula Generation

67. NMR Prediction

68. 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!

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