ArticleJournal of proteome research2019
Optimized Cross-Linking Mass Spectrometry for in Situ Interaction Proteomics.
Article in Journal of proteome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed.
- Identification of Key Genes Regulated by Lactylation Modification and Associated with Tumor Immune Microenvironment in Breast Cancer.Current issues in molecular biology · 2026Article
- State-of-the-Art and Future Directions in Structural Proteomics.Molecular & cellular proteomics : MCP · 2025Review
- GAPDH heme delivery to Indoleamine 2,3-dioxygenase 1 involves their complex formation and complementary charge pairing at the protein-protein interface.The Journal of biological chemistry · 2025Article
- Rational Modification of a Cross-Linker for Improved Flexible Protein Structure Modeling.Analytical chemistry · 2025Article
- Cross-Linking Mass Spectrometry to Capture Protein Network Dynamics of Cell Membranome.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex.Communications chemistry · 2024Article
- High-Performance Workflow for Identifying Site-Specific Crosslinks Originating from a Genetically Incorporated, Photoreactive Amino Acid.Journal of proteome research · 2024Article
- Hybrid structural modeling of alloantibody binding to human leukocyte antigen with rapid and reproducible cross-linking mass spectrometry.Cell reports methods · 2023Article
- MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows at High Sensitivity and Specificity.Journal of proteome research · 2023Article
- The emerging role of mass spectrometry-based proteomics in drug discovery.Nature reviews. Drug discovery · 2022Review
- Dynamic Interactions of Post Cleaved NS2B Cofactor and NS3 Protease Identified by Integrative Structural Approaches.Viruses · 2022Article
- In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology.Chemical reviews · 2022Review
- Integrative analysis reveals unique structural and functional features of the Smc5/6 complex.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- MS Annika: A New Cross-Linking Search Engine.Journal of proteome research · 2021Article
- Identifying and characterising Thrap3, Bclaf1 and Erh interactions using cross-linking mass spectrometry.Wellcome open research · 2021Article
- Leveraging the Entirety of the Protein Data Bank to Enable Improved Structure Prediction Based on Cross-Link Data.Journal of proteome research · 2021Article
- Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein-Protein Interaction NetworksJournal of proteome research · 2021Review
- Exploring Spacer Arm Structures for Designs of Asymmetric Sulfoxide-Containing MS-Cleavable Cross-Linkers.Analytical chemistry · 2020Article
- MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity.Molecular & cellular proteomics : MCP · 2020Article
- A synthetic peptide library for benchmarking crosslinking-mass spectrometry search engines for proteins and protein complexes.Nature communications · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Recent development of mass spectrometer cleavable protein cross-linkers and algorithms for their spectral identification now permits large-scale cross-linking mass spectrometry (XL-MS). Here, we optimized the use of cleavable disuccinimidyl sulfoxide (DSSO) cross-linker for labeling native protein complexes in live human cells. We applied a generalized linear mixture model to calibrate cross-link peptide-spectra matching (CSM) scores to control the sensitivity and specificity of large-scale XL-MS. Using specific CSM score thresholds to control the false discovery rate, we found that higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD) can both be effective for large-scale XL-MS protein interaction mapping. We found that the coverage of protein-protein interaction maps is significantly improved through the use of multiple proteases. In addition, the use of focused sample-specific search databases can be used to improve the specificity of cross-linked peptide spectral matching. Application of this approach to human chromatin labeled in live cells recapitulated known and revealed new protein interactions of nucleosomes and other chromatin-associated complexes in situ. This optimized approach for mapping native protein interactions should be useful for a wide range of biological problems.
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Registered trials
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