Native Proteomics by Capillary Zone Electrophoresis‐Mass Spectrometry

Native proteomics measures endogenous proteoforms and protein complexes under a near physiological condition using native mass spectrometry (nMS) coupled with liquid‐phase separations. Native proteomics should provide the most accurate bird's‐eye view of proteome dynamics within cells, which is fundamental for understanding almost all biological processes. nMS has been widely employed to characterize well‐purified protein complexes. However, there are only very few trials of utilizing nMS to measure proteoforms and protein complexes in a complex sample (i.e., a whole cell lysate). Here, we pioneer the native proteomics measurement of large proteoforms or protein complexes up to 400 kDa from a complex proteome via online coupling of native capillary zone electrophoresis (nCZE) to an ultra‐high mass range (UHMR) Orbitrap mass spectrometer. The nCZE‐MS technique enabled the measurement of a 115‐kDa standard protein complex while consuming only about 0.1 ng of protein material. nCZE‐MS analysis of an E.coli cell lysate detected 72 proteoforms or protein complexes in a mass range of 30–400 kDa in a single run while consuming only 50‐ng protein material. The mass distribution of detected proteoforms or protein complexes agreed well with that from mass photometry measurement. This work represents a technical breakthrough in native proteomics for measuring complex proteomes. Native proteomics enabled the measurement of protein complexes up to 400 kDa from a complex proteome, via online coupling of native capillary zone electrophoresis to an ultra‐high mass range Orbitrap mass spectrometer. Mass spectrometry‐based native proteomics agreed well with native mass photometry regarding the mass distribution of detected proteins.