Download to read offline
Using online chemistry databases to facilitate structure identification in mass spectral data
The document discusses the use of ChemSpider, an online chemistry database, for structure identification in mass spectral data, providing free access to over 34 million chemicals. It highlights the database's capabilities in searching by mass, linking structure-based data, and offering programming interfaces for integration. Future developments aim to expand spectral data availability, including the transformation of text and figures into spectral formats.
More Related Content
Similar to Using online chemistry databases to facilitate structure identification in mass spectral data
Using online chemistry databases to facilitate structure identification in mass spectral data
- 1. Using online chemistrydatabases to facilitate structure identification in mass spectral data Antony Williams, Valery Tkachenko, Alexey Pshenichnov ACS Denver, March 2015
- 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 be available at: www.slideshare.net/AntonyWilliams/
- 3.
- 4.
- 5. What will ChemSpidergive us?
- 6. What will ChemSpidergive us?
- 7. 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?
- 8.
- 9. Data Source Selection •>34 million chemicals include • Vendor collections • Government databases • Individual/Lab data • Publication data • All segregated allowing for data source selection
- 10. Data Source Selection- Type
- 11. Data Source Selection- Individual
- 12. Mass Spec Analysis JimLittle, Eastman Chemical
- 13.
- 14. 1287 Hits Rankedby Defect
- 15. 1287 Hits Rankedby # of References
- 16.
- 17.
- 18. What can Ifind on ChemSpider?
- 19. What can Ifind?
- 20. What can Ifind?
- 21.
- 22. What can Ifind on ChemSpider?
- 23.
- 24. What can Ifind on ChemSpider?
- 25. …and in theRSC Databases..
- 26. Linked to thePublisher
- 27. What can Ifind?
- 28. And out toGoogle Patents
- 29. What About theEntire Web?
- 30.
- 31. InChIStrings Hash toInChIKeys
- 32. Searching Internet byStructure
- 33. Extended Study Sorting byreferences
- 34. Position sorted byreferences
- 35.
- 36. Web Services ForCollaboration • Many instrument vendors are using or investigating our web-based services for compound lookup • Many academic sites integrating directly – metabonomics, name lookup, mass-based searching
- 37. Results of theChemSpider Search in the MarkerLynx Worksheet
- 38. Hit Details inChemSpider
- 39. “REAL Spectral Data” •Masses on ChemSpider are clearly valuable! • We’d like to host “spectral curves” • But we’re a publisher so what can we do?
- 40.
- 41. ChemSpider ID 24528095H1 NMR
- 42. ChemSpider ID 24528095HHCOSY
- 43. Publications & “RealSpectra” • We are turning text into spectra • We are turning figures into spectra
- 44. ESI – TextSpectra
- 45. 1H NMR (CDCl3,400 MHz): δ = 2.57 (m, 4H, Me, C(5a)H), 4.24 (d, 1H, J = 4.8 Hz, C(11b)H), 4.35 (t, 1H, Jb = 10.8 Hz, C(6)H), 4.47 (m, 2H, C(5)H), 4.57 (dd, 1H, J = 2.8 Hz, C(6)H), 6.95 (d, 1H, J = 8.4 Hz, ArH), 7.18–7.94 (m, 11H, ArH)
- 46. “Where is thereal data please?” FIGURE DATA
- 47. Future Developments • Wehave extracted 100s of 1000s of text strings from patents – next we go into our archive • We estimate many 1000s of figures with spectral data in our ESI and articles • We are aiming for a million spectra online… • But YOU can submit your data today and share it
- 48. We want this…weneed YOU!
- 49. Data Mining –it’s mine, mine!
- 50. New Repository Architecture doi:10.1007/s10822-014-9784-5
- 51. Acknowledgments • Jim Little,Eastman Chemical Company • Daniel Lowe – NextMove Software • Bill Brouwer – Plot2Txt Development • Carlos Cobas and Stan Sykora– MestreLabs • Patrick Wheeler - ACD/Labs
- 52. Thank you Email: williamsa@rsc.org ORCID:0000-0002-2668-4821 Twitter: @ChemConnector Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams