Methods for combining predicted and observed mass spectral fragmentation data

A method for generating a searchable small-molecule tandem mass spectrometry library comprising:

• (a) generating, by theoretical calculation and for each of a plurality of small-molecule compounds, a list of predicted ion species, each said list including a predicted precursor-ion species and a corresponding list of fragment-ion species that are predicted, by the theoretical calculations, to be generated by fragmentation of the respective precursor-ion species;
• (b) comparing at least a subset of the predicted precursor-ion species and predicted fragment ion species to entries in a database that includes a list of experimentally observed precursor-ion species and that further includes, for each of said experimentally observed precursor-ion species, a list of fragment-ion species that are experimentally observed to be generated by fragmentation of the respective precursor-ion species;
• (c) matching a pair of predicted ion species, said pair comprising a predicted precursor-ion species and a predicted corresponding fragment ion species to a pair of experimentally observed ion species comprising an experimentally observed precursor ion species and a corresponding experimentally observed fragment-ion species;
• (d) identifying at least one other predicted fragment-ion species in the list of predicted fragment-ion species corresponding to the matched precursor-ion species for which there is no match in the list of experimentally observed fragment-ion species that correspond to the matched experimentally observed fragment ion species;
• and
• (e) updating the predicted list of ion species by deleting or otherwise marking as invalid the entry or entries corresponding to the at least one other predicted fragment-ion species.