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Related Concept Videos

Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and signal-to-noise ratio for the analyte. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.
Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called collision-induced...
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The molecular ion peak of a molecule in the mass spectrum provides vital information for molecular identification. However, conventional electron impact ionization can lead to the rapid dissociation of some molecular ions before they reach the detector. A milder ionization method is required to increase the lifetime of such ionized analyte molecules. Chemical ionization (CI) is a gas-phase protonation reaction useful for mass-analyzing analyte molecules that are easily protonated to yield the...
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Mass Spectrometry: Overview01:19

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Mass spectrometry is an analytical technique used to determine the molecular mass and molecular formula of a compound. The basic principle of mass spectrometry is to generate ions from the analyte molecule and measure these ion abundances against their molecular mass.  One common type of ionization, known as electrospray ionization or EI, bombards the analyte molecules in the gas phase with high-energy electron beams. The electron beams displace an electron from the molecule and leave...
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The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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Updated: Oct 27, 2025

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
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Combined Chemical Modification and Collision Induced Unfolding Using Native Ion Mobility-Mass Spectrometry Provides

Asia Al-Jabiry1, Martin Palmer2, James Langridge2

  • 1School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.

Chemistry (Weinheim an Der Bergstrasse, Germany)
|July 21, 2021
PubMed
Summary

This study reveals key interactions stabilizing protein structures in a vacuum using chemical modification and collision-induced unfolding. These findings advance our understanding of gas-phase protein structure and stability.

Keywords:
collision induced unfoldingion mobility-mass spectrometrynative mass spectrometryprotein chemical modificationprotein molecular dynamics

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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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Area of Science:

  • Structural Biology
  • Biophysics
  • Mass Spectrometry

Background:

  • Native mass spectrometry is crucial for studying protein structure in the gas phase.
  • Understanding the stability of higher protein structures in a vacuum is a significant research area.
  • Identifying the role of individual amino acid residues in stabilizing protein structures is a key goal.

Purpose of the Study:

  • To investigate the stabilizing role of intramolecular interactions in compact gas-phase protein ions.
  • To develop and apply a novel strategy combining chemical modification and collision-induced unfolding (CIU) for structural probing.
  • To infer the importance of specific interactions for gas-phase protein stability.

Main Methods:

  • Developed a strategy combining chemical modification of amino acid residues with collision-induced unfolding (CIU).
  • Utilized ion mobility-mass spectrometry (IM-MS) to monitor unfolding extent as a function of chemical modification.
  • Employed molecular dynamics simulations to aid in structural interpretation.

Main Results:

  • Identified a crucial stabilizing interaction between lysine 6 (K6) and histidine 68 (H68) in ubiquitin.
  • Discovered a stabilizing contact between the N-terminus and glutamic acid 22 (E22) in the ubiquitin-binding protein UBA2.
  • Demonstrated the utility of chemical modification coupled with IM-MS for probing gas-phase protein structure.

Conclusions:

  • Specific intramolecular interactions significantly contribute to the stability of compact gas-phase protein structures.
  • The developed methodology provides insights into residue-level contributions to protein stability in the absence of solvent.
  • This approach enhances the understanding of protein structure and dynamics in mass spectrometry-based studies.