ArticleNature methods2012
Identification of cross-linked peptides from complex samples.
Article in Nature methods, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 348 papers.
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Who cites it
348 citing papers in PubMed.
- To cleave or not to cleave: a systemic evaluation of DSS versus DSSO for cross-linking mass spectrometry analysis.Molecular systems biology · 2026Article
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- Library-based, multiplexed strategy for mapping protein interaction networks via crosslinking.BMC biotechnology · 2026Article
- 4-Oxo-2-Nonenal Crosslinks Vicinal Cysteine-Lysine Pairs in Cellular Proteins.Molecular & cellular proteomics : MCP · 2026Article
- Improved Peptide Search for Identification of SUMO and Sequence-Based Modifiers, in MaxSBM.Molecular & cellular proteomics : MCP · 2026Article
- Chromatin context-dependent deacetylation by the asymmetric Rpd3L.Nucleic acids research · 2026Article
- Assembly of two functionally-distinct protein import complexes in the outer membrane of plant chloroplasts.Nature communications · 2026Article
- A Brief Progress in Methods for Deciphering Protein-Protein Interaction Networks.International journal of molecular sciences · 2026Review
- A practical guide to sample preparation for immunoprecipitation coupled with mass spectrometry analysis ofmicroPublication biology · 2026Article
- Stepped collisional energy improves protein acylation identification by eliminating positional bias of cyclic immonium ions.Communications chemistry · 2025Article
- AIRPred: A Deep Learning Model Predictor for Peptide Intensity Ratios in Cross-Linking Mass Spectrometry Improves Cross-Link Spectrum Matching.Analytical chemistry · 2025Article
- ULK1-dependent phosphorylation of OGT instructs the tumorigenicity of O-GlcNAcylation.Science China. Life sciences · 2025Article
- Molecular mechanism of co-transcriptional H3K36 methylation by SETD2.Nature communications · 2025Article
- A DNA-containing phase-separated compartment links the nuclear envelope to chromosome axes to promote homolog pairing inScience advances · 2025Article
- Proteomic characterization of type I collagen N-terminal crosslinked peptides.Matrix biology plus · 2025Article
- The RNA-binding protein RRP1 brakes macrophage one-carbon metabolism to suppress autoinflammation.Nature communications · 2025Article
- Prosit-XL: enhanced cross-linked peptide identification by fragment intensity prediction to study protein interactions and structures.Nature communications · 2025Article
- Molecular basis for the regulation of human phosphorylase kinase by phosphorylation and CaNature communications · 2025Article
- Structural basis for the asymmetric binding of coactivator SRC1 to FXR-RXRα and allosteric communication within the complex.Communications biology · 2025Article
- Article
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Authors and funding
19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have developed pLink, software for data analysis of cross-linked proteins coupled with mass-spectrometry analysis. pLink reliably estimates false discovery rate in cross-link identification and is compatible with multiple homo- or hetero-bifunctional cross-linkers. We validated the program with proteins of known structures, and we further tested it on protein complexes, crude immunoprecipitates and whole-cell lysates. We show that it is a robust tool for protein-structure and protein-protein-interaction studies.
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