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We developed a new proteomics platform (sCIP-TMT) to map protein druggability faster. This method enables high-throughput screening of chemical probes, identifying numerous liganded cysteines for drug discovery.

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Area of Science:

  • Proteomics
  • Chemical Biology
  • Drug Discovery

Background:

  • Mapping protein ligandability is crucial for drug discovery.
  • Current methods require high throughput and coverage for chemical probe analysis.
  • Technical innovations are needed to increase sample preparation throughput.

Purpose of the Study:

  • To establish a novel proteomics platform for high-throughput covalent chemoproteomic screening.
  • To improve sample preparation efficiency for mapping protein druggability across the human proteome.

Main Methods:

  • Developed the silane-based cleavable linkers for isotopically-labeled proteomics-tandem mass tag (sCIP-TMT) platform.
  • Utilized early sample pooling to increase throughput.
  • Functionalized custom click-compatible sCIP capture reagents with TMT reagents.
  • Synthesized and benchmarked a 10-plex sCIP-TMT set.

Main Results:

  • The sCIP-TMT platform significantly reduces sample preparation time.
  • Achieved high coverage and accurate quantification in proteomic analysis.
  • Identified 789 total liganded cysteines using four cysteine-reactive electrophiles.
  • Demonstrated utility for chemoproteomic target hunting.

Conclusions:

  • sCIP-TMT enhances sample preparation throughput for covalent chemoproteomics.
  • The platform is compatible with established enrichment and quantification protocols.
  • sCIP-TMT is expected to accelerate covalent chemoproteomic applications and drug discovery efforts.