Understanding protein–protein interactions (PPIs) and the architecture of protein complexes is essential for elucidating cellular functions and drug action mechanisms. Co-fractionation mass spectrometry (CF–MS) has emerged as an effective tool for ana-lyzing protein complexes under near-native conditions; however, its resolution and structural fidelity are often compromised by complex dissociation during biochemical processing. Here, we present an analytical strategy that integrates in vivo formalde-hyde cross-linking with reversed-phase co-fractionation mass spectrometry (XL–RP–CF–MS) to identify protein complexes in living cells. Cross-linking stabilizes native interactions, preserving complex integrity during denaturing separation. Reversed-phase liquid chromatography provides high-resolution, reproducible fractionation, enabling robust detection of co-elution pat-terns. Applying this platform to RS4;11 leukemia cells, we identified 5,983 proteins and detected 1,753 CORUM complexes together with 487 high-confidence EPIC-predicted assemblies. The workflow also demonstrated excellent quantitative perfor-mance, exhibiting highly linear correlations between chromatographic peak areas and protein loading (R² = 0.9972) as well as between MS signal intensities and loading amounts (R² = 0.9467). This strategy enables sensitive and physiologically relevant identification of protein complexes, offering a reliable approach for characterizing the composition of potential protein assem-blies within specific biological systems.