Tools for 3D Interactome Visualization

In cells, intra- and inter-molecular interactions of proteins confer function and the dynamic modulation of this interactome is critical to meet changing needs required to support life. Cross-linking and mass spectrometry (XL-MS) enable detection of both intra- and inter-molecular protein interactions in organelles, cells, tissues and organs. Quantitative XL-MS enables detection of interactome changes in cells due to environmental, phenotypic, pharmacological, or genetic perturbations. We have developed new informatics capabilities, the first to enable three-dimensional visualization of multiple quantitative interactome datasets, acquired over time or with varied perturbation levels, to reveal relevant dynamic interactome changes. These new tools are integrated within release 3.0 of our online cross-linked peptide database and analysis tool suite XLinkDB. With the recent rapid expansion in XL-MS for protein structural studies and the extension to quantitative XL-MS measurements, 3D interactome visualizati...