Protein complexes help to shape the structure of DNA which in turn regulates the expression of genes. Changes in protein-protein interactions (PPIs) can lead to disruptions in DNA structure and gene expression. Such disruptions are found in different types of cancer and diseases. Using mass spectrometry proteomics based techniques; I investigated the PPIs of two different DNA structures: chromatin and replication forks. To identify PPIs of chromatin, I optimized several different aspects of cross-linking mass spectrometry (XL-MS) for in situ cross-linking of a chromatin enriched fraction from cells. Score thresholds helped to improve false positive identification rate. Fragmentation methods and database size were investigated for effects on increasing cross-link identification. The use of multiple proteases increases cross-link peptide coverage. These optimizations were applied to XL-MS of in situ chromatin, which identified both known and new PPIs, including interactions of the nucleosome. Protein complexes are involved in stabilizing the replication fork. ATR is involved in the replication stress response pathway and its inhibition was reported to be synthetically lethal for cells expressing DNA transposase, PGBD5. To investigate the relationship between ATR, PGBD5 and the replication fork proteome, I applied iPOND SILAC-MS, a quantitative method to identify proteins at sites of nascent DNA, to cancer cells genetically engineered to manipulate PGBD5 expression levels. These cells exhibited changes in protein complexes at sites of nascent DNA, with enrichment of proteins involved in DNA damage and repair, and in post-translational modifications. PGBD5 shRNA control cells exhibited enrichment of proteins associated with the nuclear pore and RNA binding proteins at sites of nascent DNA. Another protein complex reported to stabilize replication forks is the Smc5/6 complex. I applied XL-MS on the 8-member γATP-bound Smc5/6 complex to determine its overall structure and architecture. From the cross-links, Nse5, Nse6 and Nse2 can be positioned along the head and coiled coil regions of Smc5 and Smc6, which suggests Nse5-Nse6 dimer interactions with Nse2 function and activity. Through the development and use of mass spectrometry proteomics methods, I have identified new PPIs and structures of DNA-binding protein complexes. Future studies will be needed to define the complex relations between DNA and protein structures.