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xiNET: cross-link network maps with residue resolution.

Combe CW, Fischer L, Rappsilber J - Mol. Cell Proteomics (2015)

Bottom Line: xiNET is a visualization tool for exploring cross-linking/mass spectrometry results.The interactive maps of the cross-link network that it generates are a type of node-link diagram.In these maps xiNET displays: (1) residue resolution positional information including linkage sites and linked peptides; (2) all types of cross-linking reaction product; (3) ambiguous results; and, (4) additional sequence information such as domains. xiNET runs in a browser and exports vector graphics which can be edited in common drawing packages to create publication quality figures. xiNET is open source, released under the Apache version 2 license.

View Article: PubMed Central - PubMed

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

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Example containing all three product types. The data pertains to the Human Nuclear Pore Complex, see Bui et al. (19), and xiNET distinguishes the three different product types present in the data. Note also, that the size of a circular node scales with the length of the protein sequence such that doubling the length of a protein leads to doubling the area of a circle. The interactive figure can be viewed at http://crosslinkviewer.org/figure6.html.
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Figure 6: Example containing all three product types. The data pertains to the Human Nuclear Pore Complex, see Bui et al. (19), and xiNET distinguishes the three different product types present in the data. Note also, that the size of a circular node scales with the length of the protein sequence such that doubling the length of a protein leads to doubling the area of a circle. The interactive figure can be viewed at http://crosslinkviewer.org/figure6.html.

Mentions: Network traffic is generated as sequences and annotations are downloaded but the cross-link data does not leave the local machine. The results are shown in Fig. 6, in which we see xiNET displaying and distinguishing all three product types. The live version of the figure is at http://crosslinkviewer.org/figure6.html.


xiNET: cross-link network maps with residue resolution.

Combe CW, Fischer L, Rappsilber J - Mol. Cell Proteomics (2015)

Example containing all three product types. The data pertains to the Human Nuclear Pore Complex, see Bui et al. (19), and xiNET distinguishes the three different product types present in the data. Note also, that the size of a circular node scales with the length of the protein sequence such that doubling the length of a protein leads to doubling the area of a circle. The interactive figure can be viewed at http://crosslinkviewer.org/figure6.html.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4390258&req=5

Figure 6: Example containing all three product types. The data pertains to the Human Nuclear Pore Complex, see Bui et al. (19), and xiNET distinguishes the three different product types present in the data. Note also, that the size of a circular node scales with the length of the protein sequence such that doubling the length of a protein leads to doubling the area of a circle. The interactive figure can be viewed at http://crosslinkviewer.org/figure6.html.
Mentions: Network traffic is generated as sequences and annotations are downloaded but the cross-link data does not leave the local machine. The results are shown in Fig. 6, in which we see xiNET displaying and distinguishing all three product types. The live version of the figure is at http://crosslinkviewer.org/figure6.html.

Bottom Line: xiNET is a visualization tool for exploring cross-linking/mass spectrometry results.The interactive maps of the cross-link network that it generates are a type of node-link diagram.In these maps xiNET displays: (1) residue resolution positional information including linkage sites and linked peptides; (2) all types of cross-linking reaction product; (3) ambiguous results; and, (4) additional sequence information such as domains. xiNET runs in a browser and exports vector graphics which can be edited in common drawing packages to create publication quality figures. xiNET is open source, released under the Apache version 2 license.

View Article: PubMed Central - PubMed

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

Show MeSH