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Optimized Low-Field Differential Ion Mobility Separations with High-Resolution Mass Spectrometry for Top-Down

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Novel low-field differential ion mobility spectrometry (LODIMS) coupled with mass spectrometry effectively separates and analyzes smaller proteins like Concanavalin A. This advanced technique reveals new protein forms and provides insights into molecular structures.

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Area of Science:

  • Analytical Chemistry
  • Biophysical Chemistry
  • Proteomics

Background:

  • Ion mobility spectrometry coupled with mass spectrometry (IMS/MS) is crucial for analyzing complex biological mixtures, distinguishing isomers, and determining molecular geometries.
  • Traditional IMS methods (linear and FAIMS) have limitations in analyzing larger or more complex molecules, necessitating advancements for high-resolution applications in proteomics and structural biology.
  • Fourier-Transform (FT) MS coupled with IMS is essential for handling increasingly heavy macromolecules and complex samples requiring high resolution and accuracy.

Purpose of the Study:

  • To integrate a novel nonlinear low-field differential (LOD) IMS technique with Orbitrap MS/MS for enhanced analysis of smaller proteins.
  • To explore the capabilities of LODIMS in separating and characterizing noncovalent forms of Concanavalin A (ConA).
  • To identify novel proteoforms and assess molecular properties like directional cross sections and dipole moments of ConA.

Main Methods:

  • Integration of LODIMS using bisinusoidal or augmented flexible rectangular waveforms with Orbitrap MS and MS/MS.
  • Analysis of Concanavalin A (ConA, 25.6 kDa) to assess separation of intact and fragmented forms.
  • Characterization of molecular properties including directional cross sections and dipole moments using LODIMS waveforms.

Main Results:

  • The LODIMS/MS platform successfully disentangled isotopic envelopes and separated intact ConA from its noncovalent fragments across various charge states.
  • Consistent directional cross sections and dipole moments were obtained using rectangular and bis waveforms, indicating effective alignment of smaller proteins.
  • Discovery of two novel ConA forms resulting from endogenous cleavage at N162 (in addition to the known N118 cleavage site).

Conclusions:

  • LODIMS is capable of aligning smaller proteins, enabling reliable assessment of their directional cross sections and dipole moments.
  • The developed LODIMS/Orbitrap MS platform facilitates top-down proteomics by improving the detection and characterization of intact proteins and their isoforms.
  • This study demonstrates the potential of LODIMS for discovering novel proteoforms and advancing structural biology and proteomics research.