ArticleNature protocols2018
Efficient and robust proteome-wide approaches for cross-linking mass spectrometry.
Article in Nature protocols, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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Who cites it
89 citing papers in PubMed.
- hnRNPK condensates facilitate enhancer-promoter looping and RNA polymerase II recruitment.Nature genetics · 2026Article
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- The phytoplasma effector, phyllogen, structurally mimics host plant MADS transcription factors.The Journal of biological chemistry · 2026Article
- FAIMS-GPF XL-MS: crosslinking-mass spectrometry based on gas-phase fractionation.Nature communications · 2026Article
- Investigating the relationship between ATP synthase and the TCA cycle by crosslinking mass spectrometry.Nature communications · 2026Article
- Deciphering photosynthetic protein networks: a crosslinking-MS strategy for studying functional thylakoid membranes.The Plant journal : for cell and molecular biology · 2026Article
- DMXL1 promotes recruitment of V1-ATPase to lysosomes upon TRPML1 activation.Nature structural & molecular biology · 2025Article
- Elucidating PTEN conformational dynamics and phosphatase regulation via integrative modeling and mutation prediction.Structure (London, England : 1993) · 2025Article
- Article
- A Photo-Caged Cross-Linker for Identifying Protein-Protein Interactions.Chembiochem : a European journal of chemical biology · 2024Article
- Targeted Analysis of Mitochondrial Protein Conformations and Interactions by Endogenous ROS-Triggered Cross-Linker Release.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics.Nature methods · 2024Article
- Remodelling of Rea1 linker domain drives the removal of assembly factors from pre-ribosomal particles.Nature communications · 2024Article
- Multi-adductomics: Advancing mass spectrometry techniques for comprehensive exposome characterization.Trends in analytical chemistry : TRAC · 2024Article
- Protein O-GlcNAcylation coupled to Hippo signaling drives vascular dysfunction in diabetic retinopathy.Nature communications · 2024Article
- Molecular mechanism of contactin 2 homophilic interaction.Structure (London, England : 1993) · 2024Article
- Cell fixation improves performance of in situ crosslinking mass spectrometry while preserving cellular ultrastructure.Nature communications · 2024Article
- High-Performance Workflow for Identifying Site-Specific Crosslinks Originating from a Genetically Incorporated, Photoreactive Amino Acid.Journal of proteome research · 2024Article
- Higher-order structure and proteoforms of co-occurring C4b-binding protein assemblies in human serum.The EMBO journal · 2024Article
- Noncanonical assembly, neddylation and chimeric cullin-RING/RBR ubiquitylation by the 1.8 MDa CUL9 E3 ligase complex.Nature structural & molecular biology · 2024Article
29 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cross-linking mass spectrometry (XL-MS) has received considerable interest, owing to its potential to investigate protein-protein interactions (PPIs) in an unbiased fashion in complex protein mixtures. Recent developments have enabled the detection of thousands of PPIs from a single experiment. A unique strength of XL-MS, in comparison with other methods for determining PPIs, is that it provides direct spatial information for the detected interactions. This is accomplished by the use of bifunctional cross-linking molecules that link two amino acids in close proximity with a covalent bond. Upon proteolytic digestion, this results in two newly linked peptides, which are identifiable by MS. XL-MS has received the required boost to tackle more-complex samples with recent advances in cross-linking chemistry with MS-cleavable or reporter-based cross-linkers and faster, more sensitive and more versatile MS platforms. This protocol provides a detailed description of our optimized conditions for a full-proteome native protein preparation followed by cross-linking using the gas-phase cleavable cross-linking reagent disuccinimidyl sulfoxide (DSSO). Following cross-linking, we demonstrate extensive sample fractionation and substantially simplified data analysis with XlinkX in Proteome Discoverer, as well as subsequent protein structure investigations with DisVis and HADDOCK. This protocol produces data of high confidence and can be performed within ~10 d, including structural investigations.
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