Identification of unknowns in atmospheric pressure ionization mass spectrometry using a mass to structure Search Engine

This study evaluates a new model for identifying unknown compounds in atmospheric pressure ionization mass spectrometry based on a mass-to-structure (MTS) paradigm. In this method, rudimentary ESI spectrum interpretation is required to recognize key spectral features such as MH+, MNa+, and MNH4+, which lead to the unknown's monoisotopic mass. The unknown's mass is associated directly with known organic compounds using an Access 2003 database containing records of 19 438 substances assembled from common sources such as the Merck Index, pesticide and pharmaceutical compilations, and chemical catalogues. A user-defined mass tolerance (+/- 0.001-0.5 Da) is set according to the instrument mass accuracy-unit mass resolution data require a wide mass tolerance (similar to 0.5 Da) while tolerances for accurate mass data can be as narrow as +/- 0.001 Da. Candidate structures retrieved with the MTS Search Engine appear in a report window providing formulas, mass error, and Internet links. This paper provides examples of structure elucidation with 15 organic compounds based on ESI mass spectra from both unit mass resolution (e.g., quadrupole ion trap and triple-stage quadrupole) and accurate mass instruments (e.g., TOF and Q-TOF). Orthogonal information (e.g., isotope ratios and fragmentation data) is complementary and useful for ranking candidates and confirming assignments. The MTS Search Engine identifies unknowns quickly and efficiently, and supplements existing interpretation schemes for unknown identification.