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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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TFIIF dimerization domain. Here we see xiNET displaying the data from Fig. 1, this time with self links included. xiNET uses the same numbered bar representation as is found in a variety of cross-linking publications (1, 17, 18, 19). A homomultimeric link (in red) occurs in the data set and xiNET highlights this - this link does not actually help support the conclusions of the original paper and it may be a false identification. The interactive figure can be viewed at http://crosslinkviewer.org/figure4.html.
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Figure 4: TFIIF dimerization domain. Here we see xiNET displaying the data from Fig. 1, this time with self links included. xiNET uses the same numbered bar representation as is found in a variety of cross-linking publications (1, 17, 18, 19). A homomultimeric link (in red) occurs in the data set and xiNET highlights this - this link does not actually help support the conclusions of the original paper and it may be a false identification. The interactive figure can be viewed at http://crosslinkviewer.org/figure4.html.

Mentions: Both the CLMS-CSV file and annotation CSV file are then uploaded. The result is shown in Fig. 4. An online, interactive version is available at http:/crosslinkviewer.org/figure4.html.


xiNET: cross-link network maps with residue resolution.

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

TFIIF dimerization domain. Here we see xiNET displaying the data from Fig. 1, this time with self links included. xiNET uses the same numbered bar representation as is found in a variety of cross-linking publications (1, 17, 18, 19). A homomultimeric link (in red) occurs in the data set and xiNET highlights this - this link does not actually help support the conclusions of the original paper and it may be a false identification. The interactive figure can be viewed at http://crosslinkviewer.org/figure4.html.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: TFIIF dimerization domain. Here we see xiNET displaying the data from Fig. 1, this time with self links included. xiNET uses the same numbered bar representation as is found in a variety of cross-linking publications (1, 17, 18, 19). A homomultimeric link (in red) occurs in the data set and xiNET highlights this - this link does not actually help support the conclusions of the original paper and it may be a false identification. The interactive figure can be viewed at http://crosslinkviewer.org/figure4.html.
Mentions: Both the CLMS-CSV file and annotation CSV file are then uploaded. The result is shown in Fig. 4. An online, interactive version is available at http:/crosslinkviewer.org/figure4.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