ArticleNature protocols2014
Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline.
Article in Nature protocols, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 174 papers.
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174 citing papers in PubMed.
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- Proteomic and structural comparison between cilia from primary ciliary dyskinesia patients with a DNAH5 defect.Frontiers in molecular biosciences · 2025Article
- Kinetic principles of chemical cross-link formation for protein-protein interactions.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A Photo-Caged Cross-Linker for Identifying Protein-Protein Interactions.Chembiochem : a European journal of chemical biology · 2024Article
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3 authors.
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Abstract
Chemical cross-linking in combination with LC-MS/MS (XL-MS) is an emerging technology to obtain low-resolution structural (distance) restraints of proteins and protein complexes. These restraints can also be used to characterize protein complexes by integrative modeling of the XL-MS data, either in combination with other types of structural information or by themselves, to establish spatial relationships of subunits in protein complexes. Here we present a protocol that has been successfully used to generate XL-MS data from a multitude of native proteins and protein complexes. It includes the experimental steps for performing the cross-linking reaction using disuccinimidyl suberate (a homobifunctional, lysine-reactive cross-linking reagent), the enrichment of cross-linked peptides by peptide size-exclusion chromatography (SEC; to remove smaller, non-cross-linked peptides), instructions for tandem MS analysis and the analysis of MS data via the open-source computational software pipeline xQuest and xProphet (available from http://proteomics.ethz.ch). Once established, this robust protocol should take ∼4 d to complete, and it is generally applicable to purified proteins and protein complexes.
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