ArticleMolecular & cellular proteomics : MCP2016
High Sensitivity Crosslink Detection Coupled With Integrative Structure Modeling in the Mass Spec Studio.
Article in Molecular & cellular proteomics : MCP, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 57 citations in OpenAlex.
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- β-catenin functions as a molecular adapter for disordered cBAF interactions.Molecular cell · 2025Article
- HDXRank: A Deep Learning Framework for Ranking Protein Complex Predictions with Hydrogen-Deuterium Exchange Data.Journal of chemical theory and computation · 2025Article
- Chemical Protein Crosslinking-Coupled Mass Spectrometry Reveals Interaction of LHCI with LHCII and LHCSR3 inPlants (Basel, Switzerland) · 2024Article
- Structure of the human 20S U5 snRNP.Nature structural & molecular biology · 2024Article
- Structural basis for RAD18 regulation by MAGEA4 and its implications for RING ubiquitin ligase binding by MAGE family proteins.The EMBO journal · 2024Article
- MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows at High Sensitivity and Specificity.Journal of proteome research · 2023Article
- High-Sensitivity Proteome-Scale Searches for Crosslinked Peptides Using CRIMP 2.0.Analytical chemistry · 2023Article
- A combinatorial approach to uncover an additional Integrator subunit.Cell reports · 2023Article
- The augmin complex architecture reveals structural insights into microtubule branching.Nature communications · 2022Article
- Article
- In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology.Chemical reviews · 2022Review
- A Crosslinking Mass Spectrometry Protocol for the Structural Analysis of Microtubule-Associated Proteins.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The active DNA-PK holoenzyme occupies a tensed state in a staggered synaptic complex.Structure (London, England : 1993) · 2021Article
- Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein-Protein Interaction NetworksJournal of proteome research · 2021Review
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- The substrate specificity of the human TRAPPII complex's Rab-guanine nucleotide exchange factor activity.Communications biology · 2020Article
- Structural basis for loading and inhibition of a bacterial T6SS phospholipase effector by the VgrG spike.The EMBO journal · 2020Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Mass Spec Studio package was designed to support the extraction of hydrogen-deuterium exchange and covalent labeling data for a range of mass spectrometry (MS)-based workflows, to integrate with restraint-driven protein modeling activities. In this report, we present an extension of the underlying Studio framework and provide a plug-in for crosslink (XL) detection. To accommodate flexibility in XL methods and applications, while maintaining efficient data processing, the plug-in employs a peptide library reduction strategy via a presearch of the tandem-MS data. We demonstrate that prescoring linear unmodified peptide tags using a probabilistic approach substantially reduces search space by requiring both crosslinked peptides to generate sparse data attributable to their linear forms. The method demonstrates highly sensitive crosslink peptide identification with a low false positive rate. Integration with a Haddock plug-in provides a resource that can combine multiple sources of data for protein modeling activities. We generated a structural model of porcine transferrin bound to TbpB, a membrane-bound receptor essential for iron acquisition in Actinobacillus pleuropneumoniae Using mutational data and crosslinking restraints, we confirm the mechanism by which TbpB recognizes the iron-loaded form of transferrin, and note the requirement for disparate sources of restraint data for accurate model construction. The software plugin is freely available at www.msstudio.ca.
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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.