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Tandem trapped ion mobility spectrometry.

Fanny C Liu1, Mark E Ridgeway, Melvin A Park

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Researchers developed a tandem trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) system to analyze protein structures. This new TIMS-TIMS instrument preserves ions and enables fragmentation for detailed structural insights.

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Area of Science:

  • Analytical Chemistry
  • Structural Biology
  • Biophysics

Background:

  • Ion mobility spectrometry-mass spectrometry (IMS-MS) is increasingly used for structural biology.
  • Momentum transfer cross sections from IMS-MS are key for reconstructing 3D analyte structures.
  • Extracting additional structural data by observing cross-section changes is a growing area of interest.

Purpose of the Study:

  • To develop and evaluate a novel tandem trapped ion mobility spectrometry analyser (TIMS-TIMS) coupled to a QqTOF mass spectrometer.
  • To assess the capability of the TIMS-TIMS system for preserving peptide and protein ions during analysis.
  • To demonstrate the potential of TIMS-TIMS for inducing conformational changes, fragmentation, and subsequent mobility analysis of ions.

Main Methods:

  • Construction of a TIMS-TIMS analyser by linking two TIMS analysers via an aperture-based interface region.
  • Incorporation of the TIMS-TIMS system into a QqTOF mass spectrometer.
  • Analysis of peptide oligomers (bradykinin) and protein ions (ubiquitin) using the TIMS-TIMS system.

Main Results:

  • Peptide oligomers and native-like protein ions were successfully preserved throughout TIMS-TIMS experiments.
  • The system demonstrated the ability to trap, collisionally activate, and perform subsequent mobility analysis on selected ions.
  • Low charge states of ubiquitin were fragmented between TIMS analysers, yielding significant sequence coverage and revealing multiple isomeric features in fragment ion spectra.

Conclusions:

  • The developed TIMS-TIMS system effectively preserves ion structures and allows for controlled fragmentation and mobility analysis.
  • The ability to dissociate mobility-selected protein ions and measure fragment ion cross sections opens new avenues for IMS-based structural elucidation.
  • This technology advances the field of structural biology by providing deeper insights into analyte structures and dynamics.