Methotrexate has been a clinical agent used in cancer, immunosuppression, rheumatoid arthritis and other highly proliferative diseases for many years, yet its underlying molecular mechanism of action in these therapeutic areas is still unclear. We present a chemical proteomics approach that uses ultra-sensitive mass spectrometry coupled to an inverse protein-ligand docking computational technique to unravel the mechanism of action of this drug. Using methotrexate tethered to a solid support we were able to isolate a signficant number of proteins. We effectively captured a large portion of the de novo purine metaolome and propose a pathway architecture similar to that seen in signaling pathways and consistent with substrate channeling. More importantly, we were able to capture protein targets that could potentially provide new insights into the mechanism of action of methotrexate in rheumatoid arthritis and immunosuppression. The application of this approach to other drugs and drug candidates may facilitate the prediction of unknown and secondary therapeutic target proteins and those related to the side effects and toxicity. These results demonstrate that this proteomics technology could play an important role in drug discovery and development since it allows monitoring of the interactions between a drug and the protein content of a cell.