ArticleJournal of proteome research2011
Xlink-identifier: an automated data analysis platform for confident identifications of chemically cross-linked peptides using tandem mass spectrometry.
Article in Journal of proteome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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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
29 citing papers in PubMed.
- Alzheimer's-specific brain amyloid interactome: Neural-network analysis of intra-aggregate crosslinking identifies novel drug targets.iScience · 2024Article
- "Protein aggregates" contain RNA and DNA, entrapped by misfolded proteins but largely rescued by slowing translational elongation.Aging cell · 2021Article
- Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein-Protein Interaction NetworksJournal of proteome research · 2021Review
- Alternative proteins are functional regulators in cell reprogramming by PKA activation.Nucleic acids research · 2020Article
- Covalent Labeling with an α,β-Unsaturated Carbonyl Scaffold for Studying Protein Structure and Interactions by Mass Spectrometry.Analytical chemistry · 2020Article
- Computational methods in mass spectrometry-based structural proteomics for studying protein structure, dynamics, and interactions.Computational and structural biotechnology journal · 2020Review
- Article
- Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers.Nature communications · 2019Article
- Evaluation of Different Stationary Phases in the Separation of Inter-Cross-Linked Peptides.Journal of proteome research · 2019Article
- Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology.Nature structural & molecular biology · 2018Review
- Chemical cross-linking in the structural analysis of protein assemblies.Methods (San Diego, Calif.) · 2018Review
- Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus.Journal of proteome research · 2018Article
- Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins.Nature protocols · 2018Article
- Differential Tandem Mass Spectrometry-Based Cross-Linker: A New Approach for High Confidence in Identifying Protein Cross-Linking.Analytical chemistry · 2016Article
- ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database.BMC bioinformatics · 2016Article
- A Study into the Collision-induced Dissociation (CID) Behavior of Cross-Linked Peptides.Molecular & cellular proteomics : MCP · 2016Article
- Protein Structural Analysis via Mass Spectrometry-Based Proteomics.Advances in experimental medicine and biology · 2016Review
- Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology.Protein science : a publication of the Protein Society · 2015Review
- Kojak: efficient analysis of chemically cross-linked protein complexes.Journal of proteome research · 2015Article
- Automated assignment of MS/MS cleavable cross-links in protein 3D-structure analysis.Journal of the American Society for Mass Spectrometry · 2015Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Chemical cross-linking combined with mass spectrometry provides a powerful method for identifying protein-protein interactions and probing the structure of protein complexes. A number of strategies have been reported that take advantage of the high sensitivity and high resolution of modern mass spectrometers. Approaches typically include synthesis of novel cross-linking compounds, and/or isotopic labeling of the cross-linking reagent and/or protein, and label-free methods. We report Xlink-Identifier, a comprehensive data analysis platform that has been developed to support label-free analyses. It can identify interpeptide, intrapeptide, and deadend cross-links as well as underivatized peptides. The software streamlines data preprocessing, peptide scoring, and visualization and provides an overall data analysis strategy for studying protein-protein interactions and protein structure using mass spectrometry. The software has been evaluated using a custom synthesized cross-linking reagent that features an enrichment tag. Xlink-Identifier offers the potential to perform large-scale identifications of protein-protein interactions using tandem mass spectrometry.
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Registered trials
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