Discovery and Visualization of Uncharacterized Drug-Protein Adducts Using Mass Spectrometry.
Michael RiffleMichael R HoopmannDaniel JaschobGuo ZhongRobert L MoritzMichael J MacCossTrisha N DavisNina IsoherranenAlex ZelterPublished in: Analytical chemistry (2022)
Drugs are often metabolized to reactive intermediates that form protein adducts. Adducts can inhibit protein activity, elicit immune responses, and cause life-threatening adverse drug reactions. The masses of reactive metabolites are frequently unknown, rendering traditional mass spectrometry-based proteomics approaches incapable of adduct identification. Here, we present Magnum, an open-mass search algorithm optimized for adduct identification, and Limelight, a web-based data processing package for analysis and visualization of data from all existing algorithms. Limelight incorporates tools for sample comparisons and xenobiotic-adduct discovery. We validate our tools with three drug/protein combinations and apply our label-free workflow to identify novel xenobiotic-protein adducts in CYP3A4. Our new methods and software enable accurate identification of xenobiotic-protein adducts with no prior knowledge of adduct masses or protein targets. Magnum outperforms existing label-free tools in xenobiotic-protein adduct discovery, while Limelight fulfills a major need in the rapidly developing field of open-mass searching, which until now lacked comprehensive data visualization tools.
Keyphrases
- mass spectrometry
- label free
- protein protein
- small molecule
- immune response
- adverse drug
- binding protein
- electronic health record
- amino acid
- healthcare
- machine learning
- high resolution
- magnetic resonance imaging
- emergency department
- magnetic resonance
- liquid chromatography
- ms ms
- toll like receptor
- artificial intelligence
- drug induced
- high performance liquid chromatography
- fine needle aspiration
- ultrasound guided
- electron microscopy
- bioinformatics analysis