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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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Overview of xiNET workflow. Three data sets form the input to a xiNET map: cross-link data (required); protein sequence data (can be omitted if UniProtKB accession numbers are used); and annotation data (optional, will be downloaded automatically if UniProtKB accession numbers are used for protein identifiers). Results can be communicated either by sharing the interactive map via the web or by exporting them as vector graphics that can be edited for use in publications.
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Figure 2: Overview of xiNET workflow. Three data sets form the input to a xiNET map: cross-link data (required); protein sequence data (can be omitted if UniProtKB accession numbers are used); and annotation data (optional, will be downloaded automatically if UniProtKB accession numbers are used for protein identifiers). Results can be communicated either by sharing the interactive map via the web or by exporting them as vector graphics that can be edited for use in publications.

Mentions: Fig. 2 provides an overview of the xiNET workflow. The input data sets for a cross-link map are: cross-link data; protein sequence data; and, optionally, annotation data. Sequence data can be omitted if UniProtKB (21) accession numbers are used as the protein identifiers, in this case protein sequences will be retrieved automatically using a web-service provided by UniProt1. If UniProtKB accession numbers are used then annotation data will also be retrieved from this web-service and from the SuperFamily (22) Distributed Annotation System (23) server2. Once data has been loaded into xiNET the CLMS network can be interactively explored and vector graphics can be exported for use in figures.


xiNET: cross-link network maps with residue resolution.

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

Overview of xiNET workflow. Three data sets form the input to a xiNET map: cross-link data (required); protein sequence data (can be omitted if UniProtKB accession numbers are used); and annotation data (optional, will be downloaded automatically if UniProtKB accession numbers are used for protein identifiers). Results can be communicated either by sharing the interactive map via the web or by exporting them as vector graphics that can be edited for use in publications.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Overview of xiNET workflow. Three data sets form the input to a xiNET map: cross-link data (required); protein sequence data (can be omitted if UniProtKB accession numbers are used); and annotation data (optional, will be downloaded automatically if UniProtKB accession numbers are used for protein identifiers). Results can be communicated either by sharing the interactive map via the web or by exporting them as vector graphics that can be edited for use in publications.
Mentions: Fig. 2 provides an overview of the xiNET workflow. The input data sets for a cross-link map are: cross-link data; protein sequence data; and, optionally, annotation data. Sequence data can be omitted if UniProtKB (21) accession numbers are used as the protein identifiers, in this case protein sequences will be retrieved automatically using a web-service provided by UniProt1. If UniProtKB accession numbers are used then annotation data will also be retrieved from this web-service and from the SuperFamily (22) Distributed Annotation System (23) server2. Once data has been loaded into xiNET the CLMS network can be interactively explored and vector graphics can be exported for use in figures.

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