ArticleMolecular & cellular proteomics : MCP2016
Cross-linking immunoprecipitation-MS (xIP-MS): Topological Analysis of Chromatin-associated Protein Complexes Using Single Affinity Purification.
Article in Molecular & cellular proteomics : MCP, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Application of Proximity-Labeling Techniques in Plants: A Review of Successful Cases.International journal of molecular sciences · 2026Review
- A practical guide to sample preparation for immunoprecipitation coupled with mass spectrometry analysis ofmicroPublication biology · 2026Article
- Identification of Plant Chromatin Interaction Networks Using IP-MS and co-IP.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Site-specific crosslinking reveals Phosphofructokinase-L inhibition drives self-assembly and attenuation of protein interactions.Advances in biological regulation · 2023Article
- Site-Specific Crosslinking Reveals Phosphofructokinase-L Inhibition Drives Self-Assembly and Attenuation of Protein Interactions.bioRxiv : the preprint server for biology · 2023Article
- Cross-Linking Mass Spectrometry on P-Glycoprotein.International journal of molecular sciences · 2023Article
- Characterizing Endogenous Protein Complexes with Biological Mass Spectrometry.Chemical reviews · 2022Review
- Target Discovery for Host-Directed Antiviral Therapies: Application of Proteomics Approaches.mSystems · 2021Article
- FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington's disease.Cell reports · 2021Article
- Off-the-shelf proximity biotinylation for interaction proteomics.Nature communications · 2021Article
- From Affinity to Proximity Techniques to Investigate Protein Complexes in Plants.International journal of molecular sciences · 2021Review
- The Ku complex: recent advances and emerging roles outside of non-homologous end-joining.Cellular and molecular life sciences : CMLS · 2021Review
- Cross-linking mass spectrometry reveals the structural topology of peripheral NuRD subunits relative to the core complex.The FEBS journal · 2021Article
- The Role of Ku70 as a Cytosolic DNA Sensor in Innate Immunity and Beyond.Frontiers in cellular and infection microbiology · 2021Review
- Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein-Protein Interaction NetworksJournal of proteome research · 2021Review
- Identifying and characterising Thrap3, Bclaf1 and Erh interactions using cross-linking mass spectrometry.Wellcome open research · 2021Article
- Mapping the native interaction surfaces of PREP1 with PBX1 by cross-linking mass-spectrometry and mutagenesis.Scientific reports · 2020Article
- On the Detection and Functional Significance of the Protein-Protein Interactions of Mitochondrial Transport Proteins.Biomolecules · 2020Review
- An Integrative Computational Approach for the Prediction of Human-BioMed research international · 2020Article
- Growth inhibition by bacterial Cas2Em proteins expressed in mammalian cells.American journal of translational research · 2020Article
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In recent years, cross-linking mass spectrometry has proven to be a robust and effective method of interrogating macromolecular protein complex topologies at peptide resolution. Traditionally, cross-linking mass spectrometry workflows have utilized homogenous complexes obtained through time-limiting reconstitution, tandem affinity purification, and conventional chromatography workflows. Here, we present cross-linking immunoprecipitation-MS (xIP-MS), a simple, rapid, and efficient method for structurally probing chromatin-associated protein complexes using small volumes of mammalian whole cell lysates, single affinity purification, and on-bead cross-linking followed by LC-MS/MS analysis. We first benchmarked xIP-MS using the structurally well-characterized phosphoribosyl pyrophosphate synthetase complex. We then applied xIP-MS to the chromatin-associated cohesin (SMC1A/3), XRCC5/6 (Ku70/86), and MCM complexes, and we provide novel structural and biological insights into their architectures and molecular function. Of note, we use xIP-MS to perform topological studies under cell cycle perturbations, showing that the xIP-MS protocol is sufficiently straightforward and efficient to allow comparative cross-linking experiments. This work, therefore, demonstrates that xIP-MS is a robust, flexible, and widely applicable methodology for interrogating chromatin-associated protein complex architectures.
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