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Method Article
Using XlinkCyNET to visualize protein cross-links in Cytoscape software
Diogo Borges Lima
Department of Chemical Biology, Leibniz - Forschungsinstitut für Molekulare Pharmakologie (FMP),13125, Berlin, Germany
Corresponding Author
ORCiD: https://orcid.org/0000-0001-6056-0825
Fan Liu
Department of Chemical Biology, Leibniz - Forschungsinstitut für Molekulare Pharmakologie (FMP),13125, Berlin, Germany
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
We present a high-performance app for Cytoscape to visualize cross-linking mass-spectrometry (XL-MS) data. XlinkCyNET is an open-source Java plugin that generates residue-to-residue connections provided by XL-MS in protein interaction networks. Importantly, it provides an interactive interface for the exploration of cross-links and offers various options to display protein domains. XlinkCyNET works well in complex networks containing thousands of proteins.
Keywords
cytoscape, protein-protein interaction, cross-linking mass spectrometry
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This is a preprint. It has not completed peer review.
Method Article
Using XlinkCyNET to visualize protein cross-links in Cytoscape software
Diogo Borges Lima
Department of Chemical Biology, Leibniz - Forschungsinstitut für Molekulare Pharmakologie (FMP),13125, Berlin, Germany
Corresponding Author
ORCiD: https://orcid.org/0000-0001-6056-0825
Fan Liu
Department of Chemical Biology, Leibniz - Forschungsinstitut für Molekulare Pharmakologie (FMP),13125, Berlin, Germany
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 30 Nov, 2020
No community comments so far
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
We present a high-performance app for Cytoscape to visualize cross-linking mass-spectrometry (XL-MS) data. XlinkCyNET is an open-source Java plugin that generates residue-to-residue connections provided by XL-MS in protein interaction networks. Importantly, it provides an interactive interface for the exploration of cross-links and offers various options to display protein domains. XlinkCyNET works well in complex networks containing thousands of proteins.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8