Borges Lima, D. | bioRxiv Science

bioRxiv2021

TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics

MotivationWe present a new software-tool allowing an easy visualization of fragment ions and thus a rapid evaluation of key experimental parameters on the sequence coverage obtained for the MS/MS analysis of intact proteins. Our tool can deal with multiple fragmentation methods. ResultsWe demonstrate that TDFragMapper can rapidly highlight the experimental fragmentation parameters that are critical to the characterization of intact proteins of various size using top-down proteomics. AvailabilityTDFragMapper, a demonstration video and user tutorial are freely available at https://msbio.pas-teur.fr/tdfragmapper, for academic use; all data are thus available from the ProteomeXchange consortium (identifier PXD024643). Contactdiogobor@gmail.com or julia.chamot-rooke@pasteur.fr

biochemistry↗

bioRxiv2020

XlinkCyNET: a Cytoscape application for visualization of protein interaction networks based on cross-linking mass-spectrometry identifications

Software tools that allow visualization and analysis of protein interaction networks are essential for studies in systems biology. One of the most popular network visualization tools in biology is Cytoscape, which offers a large selection of plugins for interpretation of protein interaction data. Chemical cross-linking coupled to mass spectrometry (XL-MS) is an increasingly important source for such interaction data, but there are currently no Cytoscape tools to analyze XL-MS results. In light of the suitability of Cytoscape platform but also to expand its toolbox, here we introduce XlinkCyNET, an open-source Cytoscape Java plugin for exploring large-scale XL-MS-based protein interaction networks. XlinkCyNET offers rapid and easy visualization of intra and intermolecular cross-links and the locations of protein domains in a rectangular bar style, allowing subdomain-level interrogation of the interaction network. XlinkCyNET is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/xlinkcynet and at https://www.theliulab.com/software/xlinkcynet.

bioinformatics↗