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Peptide Identification Using Tandem Mass Spectrometry01:33

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Updated: May 23, 2025

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
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TargetSeeker-MS: A Bayesian Inference Approach for Drug-Target Discovery Using Protein Fractionation Coupled to Mass

Mathieu Lavallée-Adam1, Alexander Pelletier1, Jolene K Diedrich1,2

  • 1Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States.

Journal of the American Society for Mass Spectrometry
|March 11, 2025
PubMed
Summary
This summary is machine-generated.

TargetSeeker-MS is a new Bayesian inference method that identifies drug targets using mass spectrometry. This approach works across different experimental techniques, enabling confident drug-target identification for better drug development.

Keywords:
BioinformaticsDrug target discoveryMass spectrometryProteomicsThermal shift assay

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Area of Science:

  • Proteomics
  • Pharmacology
  • Computational Biology

Background:

  • Determining drug-target affinity is crucial for understanding drug mechanisms and clinical viability.
  • Energetics-based protein separation coupled with mass spectrometry (EBPS-MS) shows promise for proteome-wide drug target identification.
  • Current computational analyses for EBPS-MS are often protocol-specific, limiting their broad applicability.

Purpose of the Study:

  • To develop a flexible computational approach for identifying drug targets across diverse EBPS-MS techniques.
  • To introduce TargetSeeker-MS, a novel Bayesian inference method for robust drug-target prediction.
  • To validate the efficacy and reproducibility of TargetSeeker-MS in identifying drug targets.

Main Methods:

  • Developed TargetSeeker-MS, a flexible Bayesian inference computational approach.
  • Applied TargetSeeker-MS to analyze proteomic data from *Caenorhabditis elegans* and HEK 293 cells treated with benomyl.
  • Validated identified drug targets through in vitro enzymatic activity assays.

Main Results:

  • TargetSeeker-MS successfully identified known and novel benomyl drug targets in both *C. elegans* and HEK 293 samples.
  • Drug-target identifications by TargetSeeker-MS were reproducible across different EBPS techniques (thermal shift assay and DiffPOP) in *C. elegans*.
  • A novel benomyl target was experimentally validated by demonstrating altered enzymatic activity upon drug treatment.

Conclusions:

  • TargetSeeker-MS provides a versatile and confident method for proteome-scale drug target identification.
  • The approach enhances understanding of drug mechanisms of action.
  • TargetSeeker-MS facilitates the evaluation of drug clinical viability and facilitates drug discovery.