ArticleNature protocols2018
A cross-linking/mass spectrometry workflow based on MS-cleavable cross-linkers and the MeroX software for studying protein structures and protein-protein interactions.
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 122 papers.
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Who cites it
122 citing papers in PubMed, 240 citations in OpenAlex.
- Unified down-stream analysis of crosslinking mass spectrometry results with pyXLMS.Nature communications · 2026Article
- FAF1 and FAF2 enhance unfolding by p97-UFD1-NPL4 complex enabling rational design of p97 activators.The EMBO journal · 2026Article
- FAIMS-GPF XL-MS: crosslinking-mass spectrometry based on gas-phase fractionation.Nature communications · 2026Article
- Revisiting the p53:Sirt1 interaction in light of controlling p53 acetylation levels.Communications chemistry · 2026Article
- Enzymatic Encoding of Topology in an Intrinsically Disordered Single-Chain Protein.Angewandte Chemie (International ed. in English) · 2026Article
- Inherent MS-cleavability of diazirine photo-cross-links enables residue-level structural analysis.Nature communications · 2026Article
- Oligomeric assemblies of plant biotin carboxylase revealed by cryo-EM and cross-linking.The Biochemical journal · 2026Article
- Mavacamten inhibits myosin activity by stabilizing the myosin interacting-heads motif and stalling motor force generation.Science advances · 2026Article
- Structural interactions of TLP18.3 and Psb27-H1 to the luminal CP43 and rubredoxin-ENH1 to the stromal side of photosystem II in higher plants.The Journal of biological chemistry · 2026Article
- Integrative structural analysis of the human LRP2-LRPAP1 complex reveals multiple regulatory sites.Communications biology · 2026Article
- The oncogenic CCDC6-RET fusion protein is a dual ATP- and ADP-dependent kinase.Nature communications · 2026Article
- Evaluation of Cleavable Crosslinking for Characterization of Proteoform Structural Differences by Top-Down Mass Spectrometry.International journal of mass spectrometry · 2026Article
- A Brief Progress in Methods for Deciphering Protein-Protein Interaction Networks.International journal of molecular sciences · 2026Review
- Methods for the Investigation of Protein-Ligands Interactions.Advances in experimental medicine and biology · 2026Review
- Towards a universal cross-linking mass spectrometry approach for protein structure analysis with homo-bi-functional photo-activatable cross-linkers.Communications biology · 2025Article
- Cysteine-enabled cleavability to advance cross-linking mass spectrometry for global analysis of endogenous protein-protein interactions.Nature communications · 2025Article
- AIRPred: A Deep Learning Model Predictor for Peptide Intensity Ratios in Cross-Linking Mass Spectrometry Improves Cross-Link Spectrum Matching.Analytical chemistry · 2025Article
- A combined biochemical and computational approach provides evidence for membrane remodelling by the structural scaffold of the endocytic TPLATE complex.Nature plants · 2025Article
- Sample Preparation for Multi-Omics Analysis: Considerations and Guidance for Identifying the Ideal Workflow.Proteomics · 2025Review
- The multimerization pathway of the glucocorticoid receptor.Nucleic acids research · 2025Article
62 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chemical cross-linking in combination with mass spectrometric analysis of the created cross-linked products is an emerging technology aimed at deriving valuable structural information from proteins and protein complexes. The goal of our protocol is to obtain distance constraints for structure determination of proteins and to investigate protein-protein interactions. We present an integrated workflow for cross-linking/mass spectrometry (MS) based on protein cross-linking with MS-cleavable reagents, followed by enzymatic digestion, enrichment of cross-linked peptides by strong cation-exchange chromatography (SCX), and LC/MS/MS analysis. To exploit the full potential of MS-cleavable cross-linkers, we developed an updated version of the freely available MeroX software for automated data analysis. The commercially available, MS-cleavable cross-linkers (DSBU and CDI) used herein possess different lengths and react with amine as well as hydroxy groups. Owing to the formation of two characteristic 26-u doublets in their MS/MS spectra, many fewer false positives are found than when using classic, non-cleavable cross-linkers. The protocol, exemplified herein for BSA and the whole Escherichia coli ribosome, is robust and widely applicable, and it allows facile identification of cross-links for deriving spatial constraints from purified proteins and protein complexes. The cross-linking/MS procedure takes 2-3 days to complete.
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