CLMSVault: A Software Suite for Protein Cross-Linking Mass- Spectrometry Data Analysis and Visualization

摘要

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 algorithrris 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 coniplex cross-linked under different conditions. CLMSVault is open-source software (available at https://gitlab.com/courcelni/clmsvault.git), and a live demo is available at http://democlmsvault.tyerslab.com/.