Characterizing the structure of biological compounds in metabonomics research utilizing tandem mass spectrometry

Metabonomics research involves the process of metabolic profiling to differentiate normal baseline profiles from profiles that are perturbed due to disease, genetic differences, or pharmaceutical intervention. Differences in the concentrations of known metabolites and characterizing previously unknown metabolites can be employed as diagnostic biomarkers for diseases and be utilized to identify toxicity.; Electrospray ionization (ESI) tandem mass spectrometry (MS/MS) methods are developed herein to characterize the structure of biological and pharmaceutical compounds that may be encountered in metabonomics research. The methods are based on four strategies: classifying product ions as primary or secondary, defining dissociation trends, probing dissociation mechanisms, and selectively identifying informative product ions for structural information.; Carbohydrate, peptide, and pharmaceutical product ions are classified as primary (originating directly from the precursor ion) or secondary (originating from primary product ions) based on their relative abundance in two tandem mass spectrometric experiments. The classification of ions is utilized to sequence a carbohydrate standard and construct genealogy diagrams for structural information of pharmaceuticals.; Structural information for pharmaceuticals is also gained through characterizing dissociation trends. A carboxylic acid library was analyzed to determine parent compound structural features that promoted the loss of the carboxylate group in MS/MS experiments. Hybridization of the alpha carbon and the presence of other carboxylic acid groups are predominant factors in the loss of this functional group. This information was applied to predict the neutral loss of the carboxylate group from pharmaceutical compounds.; Determining dissociation mechanisms is also useful for structural information. Structural information for alpha hydroxy acids is gained through characterizing the mechanism responsible for a specific neutral loss in MS/MS data. Identification of the specific atoms involved, such as beta hydrogens, can aid in identifying the structural features present when the precursor is unknown. Unknowns without the necessary structural features will not produce the characteristic neutral loss.; Although not classified as a metabolite, research indicates circulating DNA is present in the blood of cancer patients, and therefore, may be encountered in metabonomics research. The method developed in this research identifies sequence specific product ions and presents a strategy to elucidate the sequence of the parent compound.