Combined proximity labeling and affinity purification−mass spectrometry workflow for mapping and visualizing protein interaction networks

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.

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SAINT-MS1: Protein–Protein Interaction Scoring Using Label-free Intensity Data in Affinity Purification-Mass Spectrometry Experiments

Journal of Proteome Research ◽

10.1021/pr201185r ◽

2012 ◽

Vol 11 (4) ◽

pp. 2619-2624 ◽

Cited By ~ 43

Author(s):

Hyungwon Choi ◽

Timo Glatter ◽

Mathias Gstaiger ◽

Alexey I. Nesvizhskii

Keyword(s):

Mass Spectrometry ◽

Protein Interaction ◽

Affinity Purification ◽

Intensity Data ◽

Label Free ◽

Protein Protein Interaction ◽

Affinity Purification Mass Spectrometry

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Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein–Protein Interaction Networks in Vivo

Journal of Proteome Research ◽

10.1021/acs.jproteome.0c00583 ◽

2020 ◽

Vol 20 (1) ◽

pp. 78-93

Author(s):

Manuel Matzinger ◽

Karl Mechtler

Keyword(s):

Mass Spectrometry ◽

Protein Interaction ◽

Protein Interaction Networks ◽

Interaction Networks ◽

Protein Protein Interaction ◽

Protein Protein Interaction Networks

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Regional Diversity in the Postsynaptic Proteome of the Mouse Brain

Proteomes ◽

10.3390/proteomes6030031 ◽

2018 ◽

Vol 6 (3) ◽

pp. 31 ◽

Cited By ~ 21

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.

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