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Related Concept Videos

Cytoskeletal Linker Proteins - Plakins01:09

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Plakins are large proteins with binding domains for microtubules, microfilaments, intermediate filaments, and membrane-associated protein complexes at cell junctions. Plakin functions are evolutionarily conserved and are primarily involved in organizing the different components of the cytoskeleton by crosslinking them to each other and connecting them to the cell-matrix and cell adhesion complexes. They are also known to interact with signal transducers, serve as scaffolds for signaling...
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Related Experiment Video

Updated: Apr 16, 2026

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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Using pLink to Analyze Cross-Linked Peptides.

Sheng-Bo Fan1,2, Jia-Ming Meng1,2, Shan Lu3

  • 1Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.

Current Protocols in Bioinformatics
|March 11, 2015
PubMed
Summary
This summary is machine-generated.

The pLink software identifies cross-linked peptides using mass spectrometry. The updated version is faster, more versatile, and identifies new cross-linking sites like disulfide bonds and SUMO modifications.

Keywords:
cross-linkingmass spectrometrypLink

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Area of Science:

  • Biochemistry
  • Proteomics
  • Computational Biology

Background:

  • Chemical cross-linking coupled with mass spectrometry (MS) analysis is crucial for studying protein interactions.
  • pLink is a widely used search engine for identifying cross-linked peptides from tandem mass spectra.
  • The initial release of pLink in 2012 has garnered over 200 international users.

Purpose of the Study:

  • To introduce the significantly enhanced 2014 version of the pLink software.
  • To detail the expanded capabilities for identifying various protein cross-linking sites.
  • To provide guidance on utilizing pLink for protein cross-link identification.

Main Methods:

  • Development of a new, faster, and more user-friendly version of the pLink search engine.
  • Expansion of pLink's functionality to include identification of endogenous cross-linking sites.
  • Integration of accessory tools: pLabel for spectral annotation and pConfig for parameter setup.

Main Results:

  • The new pLink version demonstrates at least a 40-fold increase in speed compared to previous versions.
  • The software now identifies endogenous protein cross-linking sites, including disulfide bonds and SUMOylation sites.
  • Enhanced versatility and user-friendliness streamline the analysis of cross-linked peptides.

Conclusions:

  • The updated pLink software offers a substantial improvement in speed, versatility, and user experience for cross-linked peptide identification.
  • The expanded functionality enables the detection of a broader range of biologically relevant cross-linking events.
  • This release provides comprehensive guidance for researchers utilizing pLink in proteomics studies.