Evaluation of automatically generated substructure identification rules from tandem mass spectra

Substructure identification rules for phenothiazine and barbiturate substructures were generated by using a new version of the Method for Analyzing Patterns in Spectra (MAPS) software. This software uses tandem mass spectra and known substructure content of reference compounds to provide "feature-combination" rules. A feature-combination is a series of tandem mass spectral features which are completely unique to compounds containing a specified substructure. The current reference databases contain over 11,000 daughter spectra of 100 compounds acquired at two different collision gas pressures (i.e., single- and multiple-collision conditions). The results of rule evaluation procedures are presented and include a comparison of the spectral features developed in rule generation to those identified in documented fragmentation pathways of the indicated substructure. Two potential sources of error due to spectral feature and substructure "cross-correlation" were identified. If errors occur, they can be detected by calculating cross-correlation coefficients and edited from the rules. A beneficial cross-correlation involving feature-combinations was also discovered. The rules obtained by using single- and multiple-collision data were further evaluated by applying them to tandem mass spectra of 20 test compounds (compounds not in the reference database). The results of these evaluations give a good indication of the utility of the rules for use in an automated structure elucidation system for tandem mass spectrometry data.