Extensive Backbone Cleavage Coverage of Intact Proteoforms in a Mass Range of 10–70 kDa by Integrating Electron, Collision, and Photon-Based Fragmentation Techniques during an Electrophoretic Time Scale

Capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS) has been documented as a useful tool for top-down proteomics (TDP). However, CZE-MS/MS-based TDP typically has limited backbone cleavage coverage for identified proteoforms due to the use of traditional collision-based fragmentation methods (i.e., higher-energy collisional dissociation, HCD). Here, for the first time, we coupled CZE to an Orbitrap Ascend Tribrid mass spectrometer to investigate the performance of collision-, electron-, and photon-based fragmentation methods and their combinations for boosting the backbone cleavage coverage of proteoforms during the electrophoretic time scale using a standard protein mixture covering a mass range of about 10-70 kDa. CZE-MS achieved reproducible measurement of six proteins including three insulin-like growth factor (IGF) proteoforms with different modifications. Systematic investigations of HCD, electron-transfer dissociation (ETD), electron-transfer/HCD (EThcD), and ultraviolet photodissociation (UVPD) during CZE-MS/MS analysis revealed distinct yet complementary fragmentation characteristics. ETD, EThcD, and UVPD, in general, provided higher backbone cleavage coverage than HCD. The integration of HCD, ETD, EThcD, and UVPD data offered 67 and 98% sequence coverage for carbonic anhydrase (a 30 kDa protein) and thioredoxin (a 12 kDa protein), which is 158 and 100% higher than that produced by HCD alone. Adding internal fragments further boosted the backbone cleavage coverage substantially, for example, from 67 to 94% for 30 kDa carbonic anhydrase and from 21 to 82% for 50 kDa protein AG. The results demonstrate the capability of CZE-MS/MS with the integration of various fragmentation techniques for comprehensive characterization of proteoforms in a wide mass range.