ArticleNature communications2022
Mimicked synthetic ribosomal protein complex for benchmarking crosslinking mass spectrometry workflows.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Structural proteomics reveals the functional docking interface of ferredoxin-NADPThe Plant journal : for cell and molecular biology · 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
- Breaking barriers in crosslinking mass spectrometry with enhanced throughput and sensitivity using Orbitrap Astral.Nature communications · 2025Article
- In vivo crosslinking and effective 2D enrichment for proteome wide interactome studies.Communications chemistry · 2025Article
- Prosit-XL: enhanced cross-linked peptide identification by fragment intensity prediction to study protein interactions and structures.Nature communications · 2025Article
- Transient Cross-linking Mass Spectrometry: Taking Conformational Snapshots of Proteins.Analytical chemistry · 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
- Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics.Nature methods · 2024Article
- A Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline.Analytical chemistry · 2024Article
- Cleavable Cross-Linkers Redefined by a Novel MSAnalytical chemistry · 2023Article
- New advances in cross-linking mass spectrometry toward structural systems biology.Current opinion in chemical biology · 2023Review
- MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows at High Sensitivity and Specificity.Journal of proteome research · 2023Article
- Article
- Cross-linking mass spectrometry discovers, evaluates, and corroborates structures and protein-protein interactions in the human cell.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- High-Sensitivity Proteome-Scale Searches for Crosslinked Peptides Using CRIMP 2.0.Analytical chemistry · 2023Article
- Cross-linking mass spectrometry for mapping protein complex topologies in situ.Essays in biochemistry · 2023Article
- Real-Time Library Search Increases Cross-Link Identification Depth across All Levels of Sample Complexity.Analytical chemistry · 2023Article
- Deep Proteome Profiling with Reduced Carryover Using Superficially Porous Microfabricated nanoLC Columns.Analytical chemistry · 2022Article
- Mimicked synthetic ribosomal protein complex for benchmarking crosslinking mass spectrometry workflows.Nature communications · 2022Article
- Mass Spectrometry-Based Proteomics Technologies to Define Endogenous Protein-Protein Interactions and Their Applications to Cancer and Viral Infectious Diseases.Mass spectrometry reviewsReview
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Cross-linking mass spectrometry has matured to a frequently used tool for the investigation of protein structures as well as interactome studies up to a system-wide level. The growing community generated a broad spectrum of applications, linker types, acquisition strategies and specialized data analysis tools, which makes it challenging to decide for an appropriate analysis workflow. Here, we report a large and flexible synthetic peptide library as reliable instrument to benchmark crosslink workflows. Additionally, we provide a tool, IMP-X-FDR, that calculates the real, experimentally validated, FDR, compares results across search engine platforms and analyses crosslink properties in an automated manner. We apply the library with 6 commonly used linker reagents and analyse the data with 6 established search engines. We thereby show that the correct algorithm and search setting choice is highly important to improve identification rate and reliability. We reach identification rates of up to ~70 % of the theoretical maximum (i.e. 700 unique lysine-lysine cross-links) while maintaining a real false-discovery-rate of <3 % at cross-link level with high reproducibility, representatively showing that our test system delivers valuable and statistically solid 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.