A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry

Area of Science:

• Structural Biology
• Proteomics
• Biochemistry

Background:

• Chemical cross-linking mass spectrometry (XL-MS) reveals protein structure by identifying linked amino acid residues.
• XL-MS data complements other structural biology techniques like X-ray crystallography, NMR, and cryo-electron microscopy.
• Quantitative proteomics combined with XL-MS can offer insights into protein structural dynamics and complex formation.

Purpose of the Study:

• To develop a general method for targeted quantitative mass spectrometric analysis of cross-linked peptide pairs.
• To adapt the open-source software Skyline for analyzing quantitative XL-MS data, facilitating data sharing and method dissemination.
• To demonstrate the robustness and utility of the developed method through a cross-laboratory study.

Main Methods:

• Adaptation of the Skyline software package for the targeted quantitative analysis of cross-linked peptides.
• Implementation of a general method for quantitative mass spectrometric analysis of cross-linked peptide pairs.
• Validation of the method through a cross-laboratory study, comparing results with previously published data.

Main Results:

• Successful adaptation of Skyline for quantitative XL-MS data analysis, enabling easier data interpretation and sharing.
• Demonstration of the method's utility and robustness across different laboratories.
• Validation of quantified cross-linked peptide pairs, confirming the accuracy and reliability of the approach.

Conclusions:

• The developed method provides an accessible resource for quantitative XL-MS analysis.
• Laboratories with LC-MS systems can now readily and accurately measure dynamic changes in protein structure and interactions.
• This advance lowers the barrier for widespread adoption of quantitative XL-MS techniques in structural biology research.