Abstract: A method for generating a searchable small-molecule tandem mass spectrometry library comprises: (a) generating, by theoretical calculation and for each of a plurality of small-molecule compounds, a list of ion species, including fragment-ion species that are predicted, by the theoretical calculations, to be generated by tandem mass spectrometry (MSn) analyses, where n?2; (b) comparing at least a subset of the predicted ion species to entries in a database that includes a list of experimentally observed ion species; (c) matching a predicted mass-to-charge ratio (m/z) value of each of one or more of the predicted fragment-ion species to a respective experimentally measured m/z value of an experimentally observed fragment-ion species for which information is tabulated in the database; and (d) updating the predicted list of ion species based on information derived from the matched predicted and experimentally measured m/z values.

Abstract: Methods for determining the chemical structures, substructures and/or ionic structural arrangements of unknown or partially structurally characterized compounds from mass spectrometric data are disclosed. The methods of the invention are directed to elucidating the molecular structures of compounds by identifying the structures of ions generated from those compounds through the use of tandem mass spectrometry and subsequently conducting a library search of structurally characterized tandem product spectra from known ions for specific matches. The collective structural information and/or alternative structural candidates are then constructed from the determined ion structures and other structural characteristics using a structure generator and/or a structure assembly and/or a structure reduction system. The structure or substructure determination process can be continuously improved by adding additional data, e.g., information obtained from molecules previously structurally characterized using this method.