Database Commons

a catalog of worldwide biological databases

Proxl is an open source web application for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data and results. Proxl's core features include comparing datasets, structural analysis, customizable and interactive data visualizations, access to all underlying mass spectrometry data, and quality control tools. All features of Proxl are designed to be independent of specific cross-linker chemistry or software analysis pipelines. Proxl's sharing tools allow users to share their data with the public or securely restrict access to trusted collaborators. Since being published in 2016, Proxl has continued to be expanded and improved through active development and collaboration with cross-linking researchers. Some of Proxl's new features include a centralized, public site for sharing data, greatly expanded quality control tools and visualizations, support for stable isotope labelled peptides, and general improvements that make Proxl easier to use, data easier to share and import, and data visualizations more customizable. Source code and more information may be found at http://proxl-ms.org/.

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app .