We developed an in situ cross-linking coupled reversed-phase liquid chromatography-based co-fractionation mass spectrometry (XL-CoFrac-MS) platform to analyze drug-induced protein complex changes. A software tool, ChromaQuant, was built to automate chromatographic peak quantification. Using RS4;11 leukemia cells treated with the BCL-2 inhibitor ABT-199, we demonstrated the ability of the platform to detect BCL-2-associated protein complexes and characterize signaling pathway alterations. This approach enables efficient protein complex profiling and provides mechanistic insights into drug-induced apoptosis.