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

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 Analysis Jim 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”

SpectraSchool

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!

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