A strategy for the characterization of protein interaction networks by mass spectrometry

1999 ◽  
Vol 27 (4) ◽  
pp. 549-554 ◽  
Author(s):  
A. Shevchenko ◽  
W. Zachariae ◽  
A. Shevchenko
Keyword(s):  
Mass Spectrometry ◽  
Protein Interaction ◽  
Protein Interaction Networks ◽  
Interaction Networks

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

2020 ◽  
Author(s):  
Diogo Borges Lima ◽  
Ying Zhu ◽  
Fan Liu
Keyword(s):  
Mass Spectrometry ◽  
Protein Interaction ◽  
Large Scale ◽  
Interaction Network ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Cross Linking ◽  
Protein Interaction Data ◽  
Interaction Data ◽  
Link Type

ABSTRACTSoftware 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.

scholarly journals Characterization of protein-interaction networks in tumors

2007 ◽  
Vol 8 (1) ◽  
pp. 224 ◽  
Author(s):  
Alexander Platzer ◽  
Paul Perco ◽  
Arno Lukas ◽  
Bernd Mayer
Keyword(s):  
Protein Interaction ◽  
Protein Interaction Networks ◽  
Interaction Networks

scholarly journals Regional Diversity in the Postsynaptic Proteome of the Mouse Brain

Proteomes ◽  
2018 ◽  
Vol 6 (3) ◽  
pp. 31 ◽  
Author(s):  
Marcia Roy ◽  
Oksana Sorokina ◽  
Colin McLean ◽  
Silvia Tapia-González ◽  
Javier DeFelipe ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Human Brain ◽  
Protein Interaction ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Excitatory Synapses ◽  
Vertebrate Species ◽  
Biochemical Pathways ◽  
Disease Protein ◽  
The Brain

The proteome of the postsynaptic terminal of excitatory synapses comprises over one thousand proteins in vertebrate species and plays a central role in behavior and brain disease. The brain is organized into anatomically distinct regions and whether the synapse proteome differs across these regions is poorly understood. Postsynaptic proteomes were isolated from seven forebrain and hindbrain regions in mice and their composition determined using proteomic mass spectrometry. Seventy-four percent of proteins showed differential expression and each region displayed a unique compositional signature. These signatures correlated with the anatomical divisions of the brain and their embryological origins. Biochemical pathways controlling plasticity and disease, protein interaction networks and individual proteins involved with cognition all showed differential regional expression. Combining proteomic and connectomic data shows that interconnected regions have specific proteome signatures. Diversity in synapse proteome composition is key feature of mouse and human brain structure.

Analysis of protein interaction networks using mass spectrometry compatible techniques

2006 ◽  
Vol 564 (1) ◽  
pp. 10-18 ◽  
Author(s):  
Martin Ethier ◽  
Jean-Philippe Lambert ◽  
Julian Vasilescu ◽  
Daniel Figeys
Keyword(s):  
Mass Spectrometry ◽  
Protein Interaction ◽  
Protein Interaction Networks ◽  
Interaction Networks
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