Identification of dynamic protein-protein interactions at the peptide level on a proteomic scale is a challenging approach that is still in its infancy. We have developed a system to rapidly cross-link cells in culture with the special lysine cross-linker bis(succinimidyl)-3-azidomethyl-glutarate (BAMG). Using the Gram positive model bacterium Bacillus subtilis we were able to identify 82 unique inter-protein cross-linked peptides with less than a 1% false discovery rate by mass spectrometry and genome-wide data base searching. Nearly 60% of the inter-protein cross-links occur in assemblies involved in transcription and translation. Several of these interactions are new, and we identified a binding site between the δ and βʹ subunit of RNA polymerase close to the downstream DNA channel, providing insight into how δ regulates promoter selectivity and promotes RNA polymerase recycling. Our methodology opens new avenues to investigate the functional dynamic organization of complex protein assemblies involved in bacterial growth.