xiNET: cross-link network maps with residue resolution.
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.
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
Mentions: We prefer the CLMS-CSV format to the XQuest output format because CLMS-CSV stores peptide sequences and link positions within peptides as separate columns. XQuest output concatenates this information together and records it as the identifier. However, for the convenience of XQuest users, xiNET reads XQuest output directly as it is very similar to its own CLMS-CSV format. Fig. 5 describes how the different product types are recorded in CLMS-CSV, though they can also be read from XQuest output directly.
Affiliation: From the ‡Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom;