Efficient topological identification of proteins has drawn significant attention in protein science and engineering because it is critical for studying topology-related biological activities of proteins and protein assemblies. Especially, structural/conformational characterizations of proteins remain challenging due to the lack of efficient methods to discover and identify protein topologies. However, identifying protein topologies is still tricky because the complexity of high-order protein structures, such as tertiary and quaternary structures, prevents proteins from finding the original topological features hidden under the complex structure. In the present work, we developed a new method based on supercharging electrospray ionization (ESI) and ion mobility spectrometry-mass spectrometry (IMS-MS) for quick topological identification of proteins. Electrospraying with supercharging reagents in protein samples results in the observation of proteins incorporating as many charges as possible. Therefore, the proteins' higher-order structures become untangled with the help of the extensive charge-charge repulsions. The degree of untangling indicates the topological information of the protein, regardless of its amino acid sequence. The chain-length-normalized maximum CCS values and charge states classified 21 model proteins into three protein topologies: the linear, the ring-containing (such as lasso, circuits), and the mechanically interlocked proteins. The approach suggested here has been successfully applied to monitor the topological transformation and identify any topological side product of synthetic proteins, providing a new tool for investigating protein topologies.