Identifying “Unknown Unknowns”

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There will be many non-targeted species found in environmental and commercial samples which are "unknown unknowns."  In other words, compounds which are not found in any spectral databases or even large "spectra-less" databases such as the CAS Registry or ChemSpider.  These species are noted as yielding "No Results" in our process flowchart.

Many of the these will be "transformation products" formed by oxidation, dealkylation, hydrolysis, etc. of "known unknowns" identified in the sample of interest.   It is much more difficult to identify these components, but information obtained in the identification of other components in the sample will often yield information that facilitates their identification.

For example, many components will be metabolites formed from other components.  Thus software designed to identify metabolites by generating possible molecular formula from expected biotransformations will prove useful.  Furthermore, using the mass defect filter technique [1-3] to search for related compounds of identified components could be utilized.

In most of our commercial samples, "unknown unknowns" are routinely identified from common fragment ions and neutral losses noted for components identified in the sample.  With this data and accurate mass information, additional components can often be easily identified.  These newly identified components are then added to our in-house mass spectral/structural database for future reference.


1.  Mass defect filter technique and its applications to drug metabolite identification by high-resolution mass spectrometry, J Mass Spectrom,  2009 Jul;44(7):999-1016. doi: 10.1002/jms.1610

2.  Metabolite Identification Using Multiple Mass Defect Filters and Higher Energy Collisional Dissociation on a Hybrid Mass Spectrometer, Spectroscopy 2008.

3.  Mass Defect Filtering:  a New Toot to Expedite Screening, Dereplication, and Identification of Natural Products, poster, XenoBiotic Laboratories Poster

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