ArticleAnalytical chemistry2016
Differential Tandem Mass Spectrometry-Based Cross-Linker: A New Approach for High Confidence in Identifying Protein Cross-Linking.
Article in Analytical chemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Strategies for Acid and Amine Cross-linking and Labeling for Protein Structural Characterization Using Mass Spectrometry.Analytical chemistry · 2025Article
- Protein-Protein Interaction Network Mapping by Affinity Purification Cross-Linking Mass Spectrometry (AP-XL-MS) based Proteomics.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Identification of Inflammatory Proteomics Networks of Toll-like Receptor 4 through Immunoprecipitation-Based Chemical Cross-Linking Proteomics.Proteomes · 2022Article
- Evaluating the performance of an ETD-cleavable cross-linking strategy for elucidating protein structures.Journal of proteomics · 2020Article
- Use of Multiple Ion Fragmentation Methods to Identify Protein Cross-Links and Facilitate Comparison of Data Interpretation Algorithms.Journal of proteome research · 2020Article
- Ion Activation Methods for Peptides and Proteins.Analytical chemistry · 2020Review
- Cross-linking Proteomics Indicates Effects of Simvastatin on the TLR2 Interactome and Reveals ACTR1A as a Novel Regulator of the TLR2 Signal Cascade.Molecular & cellular proteomics : MCP · 2019Article
- ETD-Cleavable Linker for Confident Cross-linked Peptide Identifications.Journal of the American Society for Mass Spectrometry · 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
- Development of a Novel Sulfoxide-Containing MS-Cleavable Homobifunctional Cysteine-Reactive Cross-Linker for Studying Protein-Protein Interactions.Analytical chemistry · 2018Article
- Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data.Nature protocols · 2018Article
- Inflammatory Proteomic Network Analysis of Statin-treated and Lipopolysaccharide-activated Macrophages.Scientific reports · 2018Article
- Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology.Analytical chemistry · 2018Review
- Comparative and network-based proteomic analysis of low dose ethanol- and lipopolysaccharide-induced macrophages.PloS one · 2018Article
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Authors and funding
5 authors.
Funding
Abstract
Chemical cross-linking and mass spectrometry are now widely used to analyze large-scale protein-protein interactions. The major challenge in cross-linking approaches is the complexity of the mass spectrometric data. New approaches are required that can identify cross-linked peptides with high-confidence and establish a user-friendly analysis protocol for the biomedical scientific community. Here, we introduce a novel cross-linker that can be selectively cleaved in the gas phase using two differential tandem mass-spectrometric fragmentation methods, such as collision-induced or electron transfer dissociation (CID and ETD). This technique produces two signature mass spectra of the same cross-linked peptide, thereby producing high confidence in identifying the sites of interaction. Further tandem mass spectrometry can also give additional confidence on the peptide sequences. We demonstrate a proof-of-concept for this method using standard peptides and proteins. Peptides and proteins were cross-linked and their fragmentation characteristics were analyzed using CID and ETD tandem mass spectrometry. Two sequential cleavages unambiguously identified cross-linked peptides. In addition, the labeling efficiency of the new cross-linker was evaluated in macrophage immune cells after stimulation with the microbial ligand lipopolysaccharide and subsequent pulldown experiments with biotin-avidin affinity chromatography. We believe this strategy will help advance insights into the structural biology and systems biology of cell signaling.
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