Discovery and Visualization of Uncharacterized Drug-Protein Adducts Using Mass Spectrometry

Drugs are often metabolized to reactive intermedi-ates that form protein adducts. Adducts can inhibit protein activity,elicit immune responses, and cause life-threatening adverse drugreactions. The masses of reactive metabolites are frequentlyunknown, rendering traditional mass spectrometry-based proteo-mics approaches incapable of adduct identification. Here, wepresent Magnum, an open-mass search algorithm optimized foradduct identification, and Limelight, a web-based data processingpackage for analysis and visualization of data from all existingalgorithms. Limelight incorporates tools for sample comparisonsand xenobiotic-adduct discovery. We validate our tools with threedrug/protein combinations and apply our label-free workflow toidentify novel xenobiotic-protein adducts in CYP3A4. Our newmethods and software enable accurate identification of xenobiotic-protein adducts with no prior knowledge of adduct masses orprotein targets. Magnum outperforms existing label-free tools in xenobiotic-protein adduct discovery, while Limelight fulfills a majorneed in the rapidly developingfield of open-mass searching, which until now lacked comprehensive data visualization tools.