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FAIMS-IMS-QTOF MS Combined with TSPSO Deconvolution Algorithm for Effectively Probing Protein Conformation Changes

Kaiqun Wu1,2,3, Rong Liu1,2,3, Zhonghan Hu1,2,3

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Researchers used a novel r-FAIMS-IMS-QTOF MS system to identify different protein conformations of carbonic anhydrase (CA) induced by dipole locking. This method aids in structural elucidation of large biomolecules.

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Area of Science:

  • Biochemistry
  • Analytical Chemistry
  • Proteomics

Background:

  • Carbonic anhydrase (CA) is a crucial enzyme involved in various physiological processes.
  • Understanding protein conformational changes is vital for elucidating biological functions.
  • Existing mass spectrometry techniques may face challenges in resolving complex protein structures.

Purpose of the Study:

  • To investigate conformational changes in carbonic anhydrase (CA) induced by dipole locking using r-FAIMS-IMS-QTOF MS.
  • To evaluate the capability of the developed system for distinguishing protein conformers.
  • To establish a powerful platform for the structural elucidation of large biomolecules.

Main Methods:

  • Utilized a radio-frequency planar waveform field asymmetric ion mobility spectrometry-ion mobility spectrometry-quadrupole time-of-flight mass spectrometry (r-FAIMS-IMS-QTOF MS) system.
  • Employed dipole locking and unlocked modes in FAIMS to separate CA ions.
  • Applied a two-step particle swarm optimization (TSPSO) algorithm for deconvolution of overlapping IMS peaks.

Main Results:

  • Identified distinct CA FAIMS peaks corresponding to dipole-locked and unlocked states for specific charge states.
  • Observed significantly different ion mobility drift times for CA ions from locked and unlocked states, indicating different conformers.
  • MS/MS fragmentation analysis revealed distinct product ion spectra for CA ions from different FAIMS peaks, confirming conformational heterogeneity.

Conclusions:

  • The r-FAIMS-IMS-QTOF MS system effectively distinguishes between different conformers of carbonic anhydrase.
  • Dipole locking in FAIMS can induce or reveal distinct protein conformations.
  • The combination of r-FAIMS-IMS-QTOF MS and TSPSO deconvolution offers a robust approach for large biomolecule structural analysis.