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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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Optimized In-Solution and Gas-Phase Chemistry Enables High-Efficiency Interactome Mapping by DSBSO-Based

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Summary

Optimized cross-linking mass spectrometry (XL-MS) with azide-A-DSBSO reduces sample prep time to 10 hours. This streamlined workflow enhances protein interaction identification in complex samples, improving speed and efficiency.

Keywords:
Cross‐linking mass spectrometryProtein‐protein interactionsProteomics

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Area of Science:

  • Biochemistry
  • Proteomics
  • Molecular Biology

Background:

  • Cross-linking mass spectrometry (XL-MS) is vital for characterizing protein structures and interactions in complex biological samples.
  • The disuccinimidyl bissulfoxide (DSBSO) cross-linker has facilitated comprehensive XL-MS studies.
  • Existing DSBSO workflows are time-consuming, require high sample input, and lack detection sensitivity.

Purpose of the Study:

  • To systematically optimize the chemistry of azide-A-DSBSO-based XL-MS.
  • To reduce sample preparation time and improve detection sensitivity.
  • To develop a resource-efficient workflow for high-throughput interactome profiling.

Main Methods:

  • Optimization of in-solution and gas-phase chemistry for azide-A-DSBSO-based XL-MS.
  • Implementation of StageTip-based strong cation exchange (SCX) separation for salt and contaminant removal.
  • Application of the optimized workflow to intact Bacillus subtilis.

Main Results:

  • Sample preparation time reduced to 10 hours.
  • 15-fold reduction in sample consumption compared to conventional methods.
  • Doubled protein interaction identification numbers, yielding 3,209 interactions at a 1% false-discovery rate.

Conclusions:

  • The optimized azide-A-DSBSO XL-MS workflow significantly enhances speed, analytical depth, and resource efficiency.
  • This streamlined approach makes XL-MS more amenable to high-throughput interactome profiling.
  • The method enables comprehensive protein interaction characterization in complex biological samples with reduced resources.