ArticleNature methods2024
Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 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
- Mapping in-cell protein contact sites reveals hijacking of paraspeckles during influenza A virus infection.Nature microbiology · 2026Article
- FAIMS-GPF XL-MS: crosslinking-mass spectrometry based on gas-phase fractionation.Nature communications · 2026Article
- Integrative structural interactomics reveals protein organization and structure in a giant virus.Nature communications · 2026Article
- Oligomeric assemblies of plant biotin carboxylase revealed by cryo-EM and cross-linking.The Biochemical journal · 2026Article
- Black-box data: a new paradigm for biomedicine in the AI era.Chemical science · 2026Review
- Deciphering Membrane Protein Complexes in Plasmodium falciparum Gametocytes via Integrative Structural Systems Biology.Molecular & cellular proteomics : MCP · 2026Article
- Targeting protein protein interactions and their modulators to enable new therapeutic strategies for human diseases.NPJ systems biology and applications · 2026Review
- Molecular architecture of the ciliary base in mammalian multiciliated cells.bioRxiv : the preprint server for biology · 2026Article
- Phase separation of PGL-3 driven by structured domains that oligomerize and interact with RGG motifs.EMBO reports · 2026Article
- Loss-of-function variants in SAXO6, encoding a microtubule inner protein of photoreceptor cilia, cause a late-onset retinal dystrophy.American journal of human genetics · 2026Article
- A Brief Progress in Methods for Deciphering Protein-Protein Interaction Networks.International journal of molecular sciences · 2026Review
- XL-MSDigger: a deep learning-based, versatile solution for cross-linking mass spectrometry.Nature communications · 2026Article
- Optimized In-Solution and Gas-Phase Chemistry Enables High-Efficiency Interactome Mapping by DSBSO-Based Cross-Linking Mass Spectrometry.Angewandte Chemie (International ed. in English) · 2026Article
- Harnessing Ribonucleoprotein Granule Biology for Cancer Therapy: The Central Role of Protein Modifications.Research (Washington, D.C.) · 2026Review
- Towards a universal cross-linking mass spectrometry approach for protein structure analysis with homo-bi-functional photo-activatable cross-linkers.Communications biology · 2025Article
- AIRPred: A Deep Learning Model Predictor for Peptide Intensity Ratios in Cross-Linking Mass Spectrometry Improves Cross-Link Spectrum Matching.Analytical chemistry · 2025Article
- DMXL1 promotes recruitment of V1-ATPase to lysosomes upon TRPML1 activation.Nature structural & molecular biology · 2025Article
- Article
- Prosit-XL: enhanced cross-linked peptide identification by fragment intensity prediction to study protein interactions and structures.Nature communications · 2025Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
Advancing data analysis tools for proteome-wide cross-linking mass spectrometry (XL-MS) requires ground-truth standards that mimic biological complexity. Here we develop well-controlled XL-MS standards comprising hundreds of recombinant proteins that are systematically mixed for cross-linking. We use one standard dataset to guide the development of Scout, a search engine for XL-MS with MS-cleavable cross-linkers. Using other, independent standard datasets and published datasets, we benchmark the performance of Scout and existing XL-MS software. We find that Scout offers an excellent combination of speed, sensitivity and false discovery rate control. The results illustrate how our large recombinant standard can support the development of XL-MS analysis tools and evaluation of XL-MS results.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.