“…Structure-oriented monitoring methods are employed for the detection of multiple classes of toxicologically or pharmacologically relevant compounds. In contrast to unbiased-shotgun methodologies, structure-oriented monitoring utilizes prior knowledge of the elemental composition, structural moiety, or functional group characteristics to develop an analytical pipeline honed for the detection of a subset of compounds. , Fragmentation-based LC–MS/MS methods are routinely used to characterize phase I and phase II metabolites such as cysteinyl, ,− sulfate, ,, or glucuronide conjugated products. ,, Additionally, discovery methods have been developed to monitor for specific classes of clinically relevant molecules by diagnostic fragmentation patterns, including steroid hormones, − covalently modified DNA and RNA nucleosides, ,− and small molecules or peptides exhibiting glycosylated, phosphorylated, or other distinct functional groups modifications. − Early stage drug discovery requires extensive characterization of drug metabolism, including description of drug-related metabolites, potential reactive intermediaries, and degradation products. ,, To characterize this array of metabolically diverse drug intermediates, structure-oriented monitoring approaches were developed to screen predictable transformations frequently occurring in vivo , such as hydroxylation, dehydrogenation, and demethylation, among other common phase I or II conjugation reactions. , These approaches have been used to discover numerous drug biproducts − and nerve agents and their degradation products. , …”