Home › Analytical Chem › Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports
Analytical Chem JoVE (Open Access) Citable · DOI

Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports

DOI: 10.3791/60311-v
What you'll learn
  • ✓ Explain targeted cross-linking mass spectrometry workflow
  • ✓ Extend TX-MS Jupyter reports for in-depth analysis
  • ✓ Install JupyterHub for running TX-MS workflows
  • ✓ Interpret structural models with cross-linked peptides
Protocol

Biopharma Insights Targeted cross-linking mass spectrometry creates quaternary protein structure models using mass spectrometry data acquired using up to three different acquisition protocols. When executed as a simplified workflow on the Cheetah-MS web server, the results are reported in a Jupyter Notebook. Here, we demonstrate the technical aspects of how the Jupyter Notebook can be extended for a more in-depth analysis.

Difficulty
intermediate
Total time
~1-2 days per sample

Steps

1
Understand TX-MS principles

Learn about targeted cross-linking mass spectrometry for quaternary protein structure modeling.

▶ 00:47
2
Install JupyterHub environment

Set up JupyterHub to run the TX-MS workflow and report generation.

▶ 02:21
3
Download the TX-MS report

Download the generated Jupyter Notebook report from the Cheetah-MS server.

▶ 02:51
4
Extend and upload report

Modify the Jupyter Notebook to add custom analyses and upload it back for further processing.

▶ 03:30
5
Analyze representative structural models

Inspect the extended report showing cross-links mapped on structures of Streptococcus pyogenes protein M1 and human albumin.

▶ 03:50
💬 Comments coming soon