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CLMSVault: a software suite for protein cross-linking mass spectrometry data analysis and visualization.

Courcelles M, Coulombe-Huntington J, Cossette É, Gingras AC, Thibault P, Tyers M

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 inter-protein contact sites and/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 analysis of a non-covalent 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/.

J. Proteome Res. 2017.

Pubmed ID: 28537071

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