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Mass spectrometry is a widely used method for the identification of small molecules in complex samples. Current tools for database search of experimental spectra against libraries of small molecules are not scalable. Moreover, these tools are limited to known small molecules and they cannot identify novel variants of molecules in the database. Chemia has developed a proprietary mass spectral database search algorithm for the identification of novel variants of small molecules. This database search engine removes false identifications by estimating the statistical significance of matches between spectra and molecular structures. Benchmarking this database search on 483,537,388 spectra from GNPS against 87,032,328 molecules from PubChem revealed tens of thousands of novel variants of small molecules that were previously unreported.