Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Accurate quantification in proteomics with QuantUMS.

Nature biotechnology·2026
Same author

5'-Triphosphate guanosine RNAs recruit GTP-binding proteins to suppress RIG-I/IFN type I signaling.

Molecular cell·2026
Same author

Rapid photo-crosslinking in living cells reveals protein-nucleic acid dynamics on a timescale of minutes.

Nucleic acids research·2026
Same author

Cold Orthogonal Translation: A Psychrophilic Pyrrolysyl-tRNA Synthetase Boosts Genetic Code Expansion in E. coli.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same author

The evolution of a Na<sup>+</sup>-sensitive <i>Vibrio cholerae</i> mutant unmasks the moonlighting aminopeptidase PepA as a regulator of <i>nhaB</i> Na<sup>+</sup>/H<sup>+</sup> antiporter gene expression.

bioRxiv : the preprint server for biology·2026
Same author

Defining the chromatin-associated protein landscapes on <i>Trypanosoma brucei</i> repetitive elements using synthetic TALE proteins.

eLife·2026
Same journal

Platelet proteome links metabolism to reactivity in Essential Thrombocythemia.

Molecular & cellular proteomics : MCP·2026
Same journal

Genetic rescue of disrupted synaptic protein interaction network dynamics following SYNGAP1 reactivation.

Molecular & cellular proteomics : MCP·2026
Same journal

ASAP-ID: Proximity labelling with small tags.

Molecular & cellular proteomics : MCP·2026
Same journal

Proteome profiling reveals NQO2 activity contributing to proteasome inhibitor resistance in multiple myeloma cell lines.

Molecular & cellular proteomics : MCP·2026
Same journal

Depletion-Free Automated Enrichment of Serum Glycopeptides for High-Throughput Clinical Glycoproteomics.

Molecular & cellular proteomics : MCP·2026
Same journal

Extracellular Vesicles from Glioblastoma Cells Reflect 2D vs. 3D Culture Adaptation and Resistance to Temozolomide.

Molecular & cellular proteomics : MCP·2026
See all related articles

Related Experiment Video

Updated: Apr 17, 2026

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
10:01

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

20.7K

xiNET: cross-link network maps with residue resolution.

Colin W Combe1, Lutz Fischer1, Juri Rappsilber2

  • 1From the ‡Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom;

Molecular & Cellular Proteomics : MCP
|February 5, 2015
PubMed
Summary
This summary is machine-generated.

xiNET visualizes cross-linking/mass spectrometry data, creating interactive network maps. This tool aids researchers in analyzing complex protein interactions and generating publication-quality figures from experimental results.

More Related Videos

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

2.7K
Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

2.4K

Related Experiment Videos

Last Updated: Apr 17, 2026

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
10:01

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

20.7K
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

2.7K
Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

2.4K

Area of Science:

  • Proteomics
  • Biotechnology
  • Bioinformatics

Background:

  • Cross-linking/mass spectrometry (XL-MS) is a powerful technique for studying protein interactions.
  • Analyzing XL-MS data can be complex due to the nature of the results.

Purpose of the Study:

  • To introduce xiNET, a novel visualization tool for exploring XL-MS data.
  • To provide a user-friendly platform for interactive analysis and interpretation of cross-linking networks.

Main Methods:

  • xiNET generates interactive node-link diagrams representing cross-link networks.
  • The tool displays residue-level positional information, linkage sites, and linked peptides.
  • It accommodates all cross-linking reaction products, ambiguous results, and additional sequence data.

Main Results:

  • xiNET provides residue-resolution positional information for cross-linked peptides.
  • The visualization tool effectively displays various cross-linking products and ambiguous data.
  • Generated vector graphics are easily editable for publication.

Conclusions:

  • xiNET is an effective open-source tool for visualizing and analyzing complex XL-MS data.
  • The software facilitates the generation of high-quality figures for scientific publications.
  • xiNET is accessible via a web browser or local download.