Accurate Mass Measurements: Identifying “Known Unknowns” Using ChemSpider

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An unknown to an investigator, in many cases, is often known in the chemical literature.  We refer to these types of non-targeted species as "known unknowns."  The term originated in a much different context in a quote by Donald Rumsfeld.

ChemSpider is a very valuable source of known substances.  It contains >28 million compounds which can be searched by a variety of parameters and includes valuable links to other web-based resources.


Here is a graph showing the molecular weight distribution of species:


ChemSpider is owned by the Royal Society of Chemistry (RSC) and provided as a free resource to the community.  We refer to this type of database as “spectra-less” because it contains no computer-searchable EI or CID mass spectra.  However, very useful results can be obtained searching this database by molecular formula or monoisotopic mass.

Eastman collaborated in the modification of ChemSpider's web-based interface to facilitate the entry of monoisotopic molecular weight data and to sort the resulting search results by the number of associated references.  The use of monoisotopic mass does not require subjective limitations of the number of elements, types of elements, double bond equivalents or even the type of ion adduct in obtaining candidate structures.

Eastman had previously demonstrated the utility of using the number of associated references as a useful approach in the identification of unknowns with the CAS Registry.  The resulting candidates are further evaluated by their mass spectral fragmentation and a wide variety of other associated analytical information to arrive at the identification of the "known unknown."

ChemSpider Prepress Journal Article with Screenshots Illustrating Examples:


Journal of The American Society for Mass Spectrometry, Volume 23, Number 1, 179-185, DOI: 10.1007/s13361-011-0265-y

11/11/2022 Structure Search Refining Added: Recently, we began to refine searches in ChemSpider by substructure.  This is a very valuable addition to the search process.  Below is a brief video this refinement with and associated handout as used in the identification of a PCP-related drug unknown:

Brief Video Link to Substructure Limiting Searches
Associated Handout for Video
Using to Identify Seized Illegal Drugs (YouTube Video)

I am very impressed in MasterView software developed by Sciex to use ChemSpider in their work flow for the identification of unknowns, see:

Sciex Software Using ChemSpider

MasterView Videos

Link to ASMS Poster at ASMS Conference 2011, Denver, Colorado:


Additional Related Information:

A similar approach was previously demonstrated utilizing the CAS Registry which was searched by SciFinder.


NIST offers a similar approach as part of their NIST MS Search Software employing a somewhat smaller collection of compounds.


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