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Related Concept Videos

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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Identification of cross-linked peptides from large sequence databases.

Oliver Rinner1, Jan Seebacher, Thomas Walzthoeni

  • 1Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Wolfgang-Pauli Strasse 16, 8093 Zurich, Switzerland.

Nature Methods
|March 11, 2008
PubMed
Summary

A new method and software, xQuest, efficiently identifies cross-linked peptides in complex biological samples. This approach uses isotopically tagged cross-linkers and targeted proteomics for accurate protein interaction analysis.

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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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Published on: November 28, 2017

Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports
05:18

Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports

Published on: October 20, 2021

Area of Science:

  • Proteomics
  • Biochemistry
  • Computational Biology

Background:

  • Identifying cross-linked peptides is crucial for understanding protein structure and interactions.
  • Existing methods face challenges with complex samples and large protein databases.

Purpose of the Study:

  • To develop a robust method for identifying cross-linked peptides.
  • To introduce a novel software tool, xQuest, for enhanced cross-linked peptide identification.

Main Methods:

  • Combined isotopically tagged cross-linkers, chromatographic enrichment, and targeted proteomics.
  • Developed the xQuest search engine with an upstream candidate-peptide search to reduce the search space.

Main Results:

  • Successfully identified cross-linked peptides from a complex Escherichia coli lysate.
  • Demonstrated the efficacy of xQuest with an unrestricted database search.

Conclusions:

  • The described method and xQuest software provide an efficient and accurate approach for cross-linked peptide identification.
  • This advancement facilitates deeper insights into protein interactions and cellular mechanisms.