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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 reduce chemical noise during analyte detection. 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...
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Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Peptide Identification Using Tandem Mass Spectrometry01:33

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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

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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.
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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 electron 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 behind a...
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Mass Spectrometry: Complex Analysis01:21

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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.
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Related Experiment Video

Updated: Dec 15, 2025

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
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Computational methods in mass spectrometry-based structural proteomics for studying protein structure, dynamics, and

Seungjin Na1, Eunok Paek1

  • 1Dept. of Computer Science, Hanyang University, Seoul 04763, Republic of Korea.

Computational and Structural Biotechnology Journal
|July 9, 2020
PubMed
Summary

Mass spectrometry (MS) is revolutionizing structural biology by analyzing protein structure, dynamics, and interactions. Specialized data analysis methods are crucial for interpreting MS data to understand protein conformation.

Keywords:
Bioinformatics softwareChemical cross-linkingComputational proteomicsCovalent labelingHydrogen/deuterium exchangeMass spectrometryStructural biology

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Last Updated: Dec 15, 2025

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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:

  • Biochemistry
  • Structural Biology
  • Proteomics

Background:

  • Mass spectrometry (MS) is a powerful tool for protein identification and quantification in proteomics.
  • MS is increasingly utilized in structural biology, complementing traditional methods.
  • Characterizing protein structure, dynamics, and interactions is vital in biological research.

Purpose of the Study:

  • To review MS-based techniques for structural biology.
  • To focus on data analysis methods for structural MS.
  • To highlight challenges in large-scale proteome analysis.

Main Methods:

  • Hydrogen/deuterium exchange (HDX-MS)
  • Covalent labeling
  • Chemical cross-linking
  • Peptide sequencing and isotopic distribution analysis

Main Results:

  • MS-based techniques provide insights into local conformational and dynamic changes in proteins.
  • Structural information is decoded by interpreting MS data at the peptide level.
  • Dedicated computational methods are required for structural MS data analysis.

Conclusions:

  • MS-based approaches offer unique capabilities for characterizing protein structure and dynamics.
  • Advanced computational tools are essential for unlocking the full potential of structural MS.
  • Addressing challenges in large-scale analysis will further advance the field.