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Tandem Mass Spectrometry01:21

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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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Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.Matrix-assisted laser desorption ionization (MALDI) is a commonly...
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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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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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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: Apr 23, 2026

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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Mass spec studio for integrative structural biology.

Martial Rey1, Vladimir Sarpe1, Kyle M Burns1

  • 1Department of Biochemistry and Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.

Structure (London, England : 1993)
|September 23, 2014
PubMed
Summary
This summary is machine-generated.

This study introduces Mass Spec Studio, a software platform for integrating mass spectrometry (MS) data with protein modeling. It enables accurate structural modeling of complex biological systems, like microtubule interactions.

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

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Accurate structural models of large multiprotein systems are essential.
  • Mass spectrometry (MS) provides valuable biophysical data but requires integration for modeling.
  • Existing methods struggle to integrate diverse MS data types for complex systems.

Purpose of the Study:

  • To develop a software platform for integrating mass spectrometry data analysis with protein modeling.
  • To enable the analysis of various labeling data from any mass spectrometer.
  • To facilitate data-directed protein interaction modeling using HADDOCK.

Main Methods:

  • Developed Mass Spec Studio software platform.
  • Integrated analysis of label-based MS and tandem MS (MS(2)) data.
  • Supported hydrogen/deuterium exchange (HX) and covalent labeling chemistries.
  • Implemented novel HX-MS(2) acquisition strategies (targeted and data-independent).

Main Results:

  • Mass Spec Studio can mine labeling data in a proteomics-grade manner.
  • Successfully linked labeling methods with HADDOCK for protein interaction modeling.
  • Demonstrated the modeling of complex systems, including microtubule interactions, using data-independent HX-MS(2).

Conclusions:

  • Mass Spec Studio provides a unified platform for MS data analysis and protein modeling.
  • The software facilitates the structural modeling of large, complex biological systems.
  • Novel HX-MS(2) strategies enable advanced analysis of challenging systems like microtubule interactions.