qXL-MS raw data for "Capturing the Hierarchically Assorted Modules of Protein-protein Interaction in the Organized Nucleome"

To decipher the global connectivity of nuclear proteins and the hierarchically organized modules of nuclear protein interactions, the double chemical-crosslinking coupled with mass spectrometry (in vivo XL-MS) analysis was integrated with the dimethyl-labelling to generate a qXL-MS workflow, which consequently identified 5,340 cross-linked peptides (or crosslinks) from the nuclei of soybean seedlings.

These crosslinks were converted into 1,297 nuclear protein-protein interactions (PPIs), 1220 (94%) of which were non-confirmative (or novel) nuclear PPIs compared to those in repositories. There were 250 and 26 novel interactors of histones and nucleolar box C/D snoRNP complex, respectively. Modulomic analysis of the Arabidopsis orthoglous PPIs constructed 27 and 24 master nuclear protein-protein interaction modules (NPIMs) that contain the condensate-forming protein(s) and the intrinsically disordered region (IDR)-containing proteins, respectively.