CLMSVault: A software suite for protein cross-linking mass-spectrometry data analysis and visualization
Open accessAbstract
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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Programs have been developed to analyze and visualize cross-linking data as a network of amino acid nodes, where edges represent a detected cross-link, and organizing clusters of nodes spatially according to subunit is one approach applied in these networks.
“For example, programs have been developed to analyze and visualize cross-linking data as a network of amino acid nodes, where edges represent a detected cross-link (Combe et al., 2015; Courcelles et al., 2017; Grimm et al., 2015; Riffle et al., 2016); organizing clusters of nodes spatially according to subunit is one approach that has been applied in these networks (Figure 5C).”
From Mapping the multiscale structure of biological systems (2021) · cites this paper as Courcelles et al., 2017
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Mapping the multiscale structure of biological systems
Schaffer, L. V., & Ideker, T. (2021) · Cell Systems · doi:10.1016/j.cels.2021.05.012 · Cited by 75 · see citing works
- Authors
- Courcelles, M., Coulombe-Huntington, J., Cossette, É., Gingras, A.-C., Thibault, P., & Tyers, M.
- Affiliations
- Institute for Research in Immunology and Cancer (CA)
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- University of Toronto (CA)
- Corresponding author
- Tyers, Mike
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2017-06-05
- Volume
- 16
- Issue
- 7
- Pages
- 2645-2652
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- PMC
- PMC5994346
- OpenAlex
- W2618922802
- Cited by
- 21
- References
- 42
- Citations by year
- 2026: 1 · 2024: 2 · 2023: 1 · 2021: 3 · 2020: 5 · 2019: 3 · 2018: 5 · 2017: 1
- FWCI
- 1.89
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Proteome Research (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Canadian Institutes of Health Research (MOP-126129)
- Minist?re de l'Enseignement Sup?rieur, de la Recherche, de la Science et de la Technologie
- Canada Research Chairs
- Genome Canada
- Canadian Cancer Society Research Institute
- Lea Reichmann Chair in Cancer Proteomics
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Keywords
- cross-linked peptide identification, protein-protein interaction, label-free quantification, open source software, data visualization tools
- MeSH terms
- Algorithms, Amino Acid Sequence, Binding Sites, Cross-Linking Reagents, Humans, Models, Molecular, Peptides, Protein Binding, Software, Mass Spectrometry, Protein Structure, Secondary, Ubiquitin, Protein Interaction Mapping, Ubiquitin-Conjugating Enzymes, Protein Interaction Domains and Motifs
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