Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports
dc.contributor.author
Khakzad, Hamed
dc.contributor.author
Vermeul, Swen
dc.contributor.author
Malmström, Lars
dc.date.accessioned
2022-01-25T11:08:18Z
dc.date.available
2021-12-07T09:28:48Z
dc.date.available
2022-01-25T11:08:18Z
dc.date.issued
2021-10
dc.identifier.issn
1940-087X
dc.identifier.other
10.3791/60311
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/519167
dc.identifier.doi
10.3929/ethz-b-000519167
dc.description.abstract
Protein-protein interactions can be challenging to study yet provide insights into how biological systems function. Targeted cross-linking mass spectrometry (TX-MS), a method combining quaternary protein structure modeling and chemical cross-linking mass spectrometry, creates high-accuracy structure models using data obtained from complex, unfractionated samples. This removes one of the major obstacles to protein complex structure analysis because the proteins of interest no longer need to be purified in large quantities. Cheetah-MS web server was developed to make the simplified version of the protocol more accessible to the community. Considering the tandem MS/MS data, Cheetah-MS generates a Jupyter Notebook, a graphical report summarizing the most important analysis results. Extending the Jupyter Notebook can yield more in-depth insights and better understand the model and the mass spectrometry data supporting it. The technical protocol presented here demonstrates some of the most common extensions and explains what information can be obtained. It contains blocks to help analyze tandem MS/MS acquisition data and the overall impact of the detected XLs on the reported quaternary models. The result of such analyses can be applied to structural models that are embedded in the notebook using NGLView.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
JoVE
en_US
dc.rights.uri
http://creativecommons.org/licenses/by-nc-nd/3.0/
dc.title
Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported
dc.date.published
2021-10-20
ethz.journal.title
Journal of Visualized Experiments. JoVE
ethz.journal.volume
176
en_US
ethz.journal.abbreviated
J Vis Exp
ethz.pages.start
e60311
en_US
ethz.size
8 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.scopus
ethz.publication.place
London
en_US
ethz.publication.status
published
en_US
ethz.date.deposited
2021-12-07T09:29:52Z
ethz.source
WOS
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2022-01-25T11:08:25Z
ethz.rosetta.lastUpdated
2023-02-06T23:55:26Z
ethz.rosetta.versionExported
true
ethz.COinS
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