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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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Related in: MedlinePlus

Example of ambiguous CLMS results. Ambiguity regarding the linkage site can occur if, for example, an identified cross-linked peptide belongs to more than one protein in the search space. xiNET uses a dashed line to represent ambiguous linkage sites while highlights on mouse-over are used to show the possible alternatives. The example data shows cross-links between microtubules and the human kinetochore Ska complex (18). The links from SKA1 to residues in the 110–120 range of Tubulin beta-3 chain isoforms TBB3 and TBB2B are all ambiguous; the same identified peptide (highlighted in orange) occurs in both isoforms. The links from SKA1 to residues around 160 in TBB3 and TBB2B are all unambiguous; for these links, all the identified peptides contained residue 155, which distinguishes TBB3 and TBB2B. In the interactive figures (for example http://crosslinkviewer.org/figure7.html), the peptide attached to a particular cross-link is highlighted in orange when the mouse is moved over a link and the highlight is accompanied by a tool-tip giving protein names or ID's, linked residue numbers and the number of supporting peptide-spectrum matches.
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Figure 7: Example of ambiguous CLMS results. Ambiguity regarding the linkage site can occur if, for example, an identified cross-linked peptide belongs to more than one protein in the search space. xiNET uses a dashed line to represent ambiguous linkage sites while highlights on mouse-over are used to show the possible alternatives. The example data shows cross-links between microtubules and the human kinetochore Ska complex (18). The links from SKA1 to residues in the 110–120 range of Tubulin beta-3 chain isoforms TBB3 and TBB2B are all ambiguous; the same identified peptide (highlighted in orange) occurs in both isoforms. The links from SKA1 to residues around 160 in TBB3 and TBB2B are all unambiguous; for these links, all the identified peptides contained residue 155, which distinguishes TBB3 and TBB2B. In the interactive figures (for example http://crosslinkviewer.org/figure7.html), the peptide attached to a particular cross-link is highlighted in orange when the mouse is moved over a link and the highlight is accompanied by a tool-tip giving protein names or ID's, linked residue numbers and the number of supporting peptide-spectrum matches.

Mentions: Fig. 7 shows ambiguous data displayed in xiNET. Dashed lines are used to indicate the ambiguous links and highlights on mouse-over show the possible alternatives. In Fig. 7 the numbered bars have been expanded (see Table I for user controls) until the sequence of the protein is visible. When xiNET has information on the peptide sequence, its highlights both the link and the linked peptide on mouse-over. Hence, in Fig. 7 we can see the specific recurring peptide that is the source of ambiguity. (Interactive figure at http://crosslinkviewer.org/figure7.html.)


xiNET: cross-link network maps with residue resolution.

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

Example of ambiguous CLMS results. Ambiguity regarding the linkage site can occur if, for example, an identified cross-linked peptide belongs to more than one protein in the search space. xiNET uses a dashed line to represent ambiguous linkage sites while highlights on mouse-over are used to show the possible alternatives. The example data shows cross-links between microtubules and the human kinetochore Ska complex (18). The links from SKA1 to residues in the 110–120 range of Tubulin beta-3 chain isoforms TBB3 and TBB2B are all ambiguous; the same identified peptide (highlighted in orange) occurs in both isoforms. The links from SKA1 to residues around 160 in TBB3 and TBB2B are all unambiguous; for these links, all the identified peptides contained residue 155, which distinguishes TBB3 and TBB2B. In the interactive figures (for example http://crosslinkviewer.org/figure7.html), the peptide attached to a particular cross-link is highlighted in orange when the mouse is moved over a link and the highlight is accompanied by a tool-tip giving protein names or ID's, linked residue numbers and the number of supporting peptide-spectrum matches.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Figure 7: Example of ambiguous CLMS results. Ambiguity regarding the linkage site can occur if, for example, an identified cross-linked peptide belongs to more than one protein in the search space. xiNET uses a dashed line to represent ambiguous linkage sites while highlights on mouse-over are used to show the possible alternatives. The example data shows cross-links between microtubules and the human kinetochore Ska complex (18). The links from SKA1 to residues in the 110–120 range of Tubulin beta-3 chain isoforms TBB3 and TBB2B are all ambiguous; the same identified peptide (highlighted in orange) occurs in both isoforms. The links from SKA1 to residues around 160 in TBB3 and TBB2B are all unambiguous; for these links, all the identified peptides contained residue 155, which distinguishes TBB3 and TBB2B. In the interactive figures (for example http://crosslinkviewer.org/figure7.html), the peptide attached to a particular cross-link is highlighted in orange when the mouse is moved over a link and the highlight is accompanied by a tool-tip giving protein names or ID's, linked residue numbers and the number of supporting peptide-spectrum matches.
Mentions: Fig. 7 shows ambiguous data displayed in xiNET. Dashed lines are used to indicate the ambiguous links and highlights on mouse-over show the possible alternatives. In Fig. 7 the numbered bars have been expanded (see Table I for user controls) until the sequence of the protein is visible. When xiNET has information on the peptide sequence, its highlights both the link and the linked peptide on mouse-over. Hence, in Fig. 7 we can see the specific recurring peptide that is the source of ambiguity. (Interactive figure at http://crosslinkviewer.org/figure7.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
Related in: MedlinePlus