McCool, Elijah N.Lubeckyj, Rachele A.Shen, XiaojingChen, DaoyangKou, QiangLiu, XiaowenSun, Liangliang2019-08-132019-08-132018-05-01McCool, E. N., Lubeckyj, R. A., Shen, X., Chen, D., Kou, Q., Liu, X., & Sun, L. (2018). Deep Top-Down Proteomics Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry: Identification of 5700 Proteoforms from the Escherichia coli Proteome. Analytical chemistry, 90(9), 5529–5533. doi:10.1021/acs.analchem.8b00693https://hdl.handle.net/1805/20342Capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS) has been recognized as a useful tool for top-down proteomics. However, its performance for deep top-down proteomics is still dramatically lower than widely used reversed-phase liquid chromatography (RPLC)-MS/MS. We present an orthogonal multidimensional separation platform that couples size exclusion chromatography (SEC) and RPLC based protein prefractionation to CZE-MS/MS for deep top-down proteomics of Escherichia coli. The platform generated high peak capacity (∼4000) for separation of intact proteins, leading to the identification of 5700 proteoforms from the Escherichia coli proteome. The data represents a 10-fold improvement in the number of proteoform identifications compared with previous CZE-MS/MS studies and represents the largest bacterial top-down proteomics data set reported to date. The performance of the CZE-MS/MS based platform is comparable to the state-of-the-art RPLC-MS/MS based systems in terms of the number of proteoform identifications and the instrument time.en-USPublisher PolicyElectrophoresis -- CapillaryEscherichia coli -- ChemistryEscherichia coli Proteins -- AnalysisProteome -- AnalysisProteomicsTandem Mass SpectrometryArticle