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Updated: May 28, 2026

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
Published on: November 17, 2019
Cross-linking mass spectrometry: Workflow enhancements for mapping large-scale interactomes
Shenbaga Moorthy Balakrishnan1, Taoufik Nedjadi1, Rawiah Alsiary1
1King Abdullah International Medical Research Center, P.O. Box 9515, Jeddah 21423, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, P.O. Box 9515, Jeddah 21423, Saudi Arabia; Ministry of the National Guard-Health Affairs, P.O. Box 9515, Jeddah 21423, Saudi Arabia.
In-vivo chemical cross-linking with mass spectrometry (XL-MS) captures protein-protein interactions directly in cells. Innovations in cross-linkers and MS analysis enhance the study of these vital biological networks.
Area of Science:
- Biochemistry
- Proteomics
- Molecular Biology
Background:
- Protein-protein interactions (PPIs) are crucial for cellular functions.
- Existing methods may miss transient or weak PPIs during sample processing.
- In-vivo methods preserve native cellular interactions.
Purpose of the Study:
- To review the workflow and recent innovations in in-vivo chemical cross-linking with mass spectrometry (XL-MS).
- To highlight strategies for proteome-wide PPI mapping using XL-MS.
- To discuss the potential of standardized XL-MS for biological research.
Main Methods:
- In-vivo chemical cross-linking to stabilize PPIs in native environments (cells, tissues).
- Sample preparation and high-resolution mass spectrometry (MS) analysis.
- Computational identification of cross-linked peptides.
Main Results:
- XL-MS captures weak or transient PPIs in near-native contexts.
- Advancements in cross-linker design (multifunctional, MS-cleavable) improve efficiency.
- Innovations in MS instrumentation and software increase identification depth and reliability.
Conclusions:
- In-vivo XL-MS is a powerful technique for studying PPIs within their native cellular environment.
- Ongoing technological advancements are enhancing the sensitivity, throughput, and accuracy of XL-MS.
- Standardization of XL-MS methodology will facilitate its broader application in biological research.
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