Top-down proteomics (TDP) aims to characterize the proteome samples in a proteoform-specific manner and accomplish the human proteoform project (PMID: 34767442), which requires highly efficient separation and sensitive detection of proteoforms due to the extremely high sample complexity. Capillary electrophoresis-mass spectrometry (CE-MS) for top-down MS analysis of intact proteins/proteoforms is pioneered by the McLafferty, Lee, and Smith groups in 1990s. CE-MS is a powerful analytical technique for proteoform measurements due to its extremely high efficiency and sensitivity for proteoform separation and detection. However, due to the limitations of MS instrumentation and robustness of CE-MS interface, CE-MS had not been widely adopted until the recent 10 years. During the last decade, CE-MS interface has tremendous improvement in terms of sensitivity and robustness and several interfaces have been commercialized. MS instrumentation has impressive improvement in terms of mass resolution, gas-phase fragmentation performance, speed, and sensitivity. Using the modern instrumentation, it is straightforward to achieve the identification of thousands of proteoforms from whole cell lysates using CE-MS/MS with high reproducibility. For example, our group recently demonstrated the identification of over 23,000 proteoforms from colorectal cancer cells and documented drastically different proteoform profiles between metastatic and non-metastatic colorectal cancer cells using CE-MS/MS (PMID: 36542699). It is also approachable to delineate large proteoforms (e.g., monoclonal antibodies) and membrane proteoforms using CE-MS and MS/MS. We expect that CE-MS will be a powerful analytical tool for high-throughput TDP of various complex biological samples in the next several years.


Liangliang Sun (Michigan State University)