ArticleJournal of proteome research2017
CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization.
Article in Journal of proteome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
10 citing papers in PubMed.
- Characterizing lysinoalanine crosslinks in food systems: Discovery of a diagnostic ion in model peptides using MALDI mass spectrometry.Food chemistry: X · 2023Article
- Mapping the multiscale structure of biological systems.Cell systems · 2021Review
- Quantitative Cross-Linking of Proteins and Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2021Article
- The Smc5/6 Core Complex Is a Structure-Specific DNA Binding and Compacting Machine.Molecular cell · 2020Article
- Chemical Cross-Linking and Mass Spectrometric Analysis of the Endogenous Yeast Exosome Complexes.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Cross-ID: Analysis and Visualization of Complex XL-MS-Driven Protein Interaction Networks.Journal of proteome research · 2019Article
- Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology.Nature structural & molecular biology · 2018Review
- Chemical cross-linking in the structural analysis of protein assemblies.Methods (San Diego, Calif.) · 2018Review
- Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology.Analytical chemistry · 2018Review
- Mass Spectrometry Structural Proteomics Enabled by Limited Proteolysis and Cross-Linking.Mass spectrometry reviewsReview
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Protein cross-linking mass spectrometry (CL-MS) enables the sensitive detection of protein interactions and the inference of protein complex topology. The detection of chemical cross-links between protein residues can identify intra- and interprotein contact sites or provide physical constraints for molecular modeling of protein structure. Recent innovations in cross-linker design, sample preparation, mass spectrometry, and software tools have significantly improved CL-MS approaches. Although a number of algorithms now exist for the identification of cross-linked peptides from mass spectral data, a dearth of user-friendly analysis tools represent a practical bottleneck to the broad adoption of the approach. To facilitate the analysis of CL-MS data, we developed CLMSVault, a software suite designed to leverage existing CL-MS algorithms and provide intuitive and flexible tools for cross-platform data interpretation. CLMSVault stores and combines complementary information obtained from different cross-linkers and search algorithms. CLMSVault provides filtering, comparison, and visualization tools to support CL-MS analyses and includes a workflow for label-free quantification of cross-linked peptides. An embedded 3D viewer enables the visualization of quantitative data and the mapping of cross-linked sites onto PDB structural models. We demonstrate the application of CLMSVault for the analysis of a noncovalent Cdc34-ubiquitin protein complex cross-linked under different conditions. CLMSVault is open-source software (available at https://gitlab.com/courcelm/clmsvault.git ), and a live demo is available at http://democlmsvault.tyerslab.com/ .
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