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Related Concept Videos

Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

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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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Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
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Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
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Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

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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.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can...
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High-Resolution Mass Spectrometry (HRMS)01:15

High-Resolution Mass Spectrometry (HRMS)

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The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For...
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Updated: Oct 22, 2025

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

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Protein-Small Molecule Interactions in Native Mass Spectrometry.

Jack L Bennett1, Giang T H Nguyen1, William A Donald1

  • 1School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia.

Chemical Reviews
|August 27, 2021
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Summary

Native mass spectrometry (MS) offers a rapid and sensitive method for studying drug interactions with complex protein systems. This technique provides unique insights into drug discovery, overcoming limitations of traditional biophysical approaches.

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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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Analyzing Large Protein Complexes by Structural Mass Spectrometry
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Area of Science:

  • Biochemistry and Biophysics
  • Chemical Biology
  • Drug Discovery and Development

Background:

  • Traditional biophysical methods for studying drug action are often slow, low-throughput, and struggle with complex biological systems.
  • Heterogeneous systems like dynamic protein assemblies and post-translationally modified proteins present significant challenges for conventional analysis.
  • There is a need for advanced techniques to efficiently probe protein-small molecule interactions in drug discovery.

Purpose of the Study:

  • To review the applications of native mass spectrometry (MS) in understanding protein-small molecule interactions.
  • To highlight the advantages of native MS for analyzing complex and dynamic biological systems in drug discovery.
  • To discuss methods for quantifying binding thermodynamics and kinetics, and interrogating complex structures.

Main Methods:

  • Native mass spectrometry (native MS) is employed to analyze protein-small molecule interactions.
  • Gas-phase ion activation techniques are used to interrogate the structure of protein-small molecule complexes.
  • Thermodynamic and kinetic properties of ligand binding are quantified.

Main Results:

  • Native MS provides high speed and sensitivity for probing interactions in polydisperse biomolecular systems.
  • The technique is effective for studying large multiprotein complexes and membrane proteins, common in drug discovery.
  • Native MS has demonstrated significant advances in key areas of modern drug design.

Conclusions:

  • Native MS is a powerful tool for studying protein-small molecule interactions, overcoming limitations of traditional methods.
  • It offers unique insights into complex biological systems relevant to drug discovery.
  • Future applications include whole-proteome scale analysis of drug-target interactions.