Over 10 000 Peptide Identifications from the HeLa Proteome by Using Single-Shot Capillary Zone Electrophoresis Combined with Tandem Mass Spectrometry

• Published in: Angewandte Chemie (International ed.) Vol. 53; no. 50; pp. 13931 - 13933
• Main Authors: Sun, Liangliang, Hebert, Alexander S., Yan, Xiaojing, Zhao, Yimeng, Westphall, Michael S., Rush, Matthew J. P., Zhu, Guijie, Champion, Matthew M., Coon, Joshua J., Dovichi, Norman J.
• Format: Journal Article
• Language: English
• Published: Weinheim WILEY-VCH Verlag 08.12.2014; WILEY‐VCH Verlag
• Subjects: analytical methods; CZE-MS/MS; electrophoresis; Electrophoresis, Capillary - methods; HeLa Cells; Humans; mass spectrometry; Peptides - chemistry; Proteome; proteomics; Tandem Mass Spectrometry - methods; mass spectrometry; proteomics; electrophoresis; analytical methods; CZE-MS/MS
• ISSN: 1433-7851; 1521-3773
• DOI: 10.1002/anie.201409075

Capillary zone electrophoresis (CZE)–tandem mass spectrometry (MS/MS) has recently attracted attention as a tool for shotgun proteomics. However, its performance for this analysis has so far fallen far below that of reversed‐phase liquid chromatography (RPLC)–MS/MS. The use of a CZE method with a wide separation window (up to 90 min) and high peak capacity (ca. 300) is reported. This method was coupled to an Orbitrap Fusion mass spectrometer through an electrokinetically pumped sheath‐flow interface for the analysis of complex proteome digests. Single‐shot CZE–MS/MS lead to the identification of over 10 000 peptides and 2100 proteins from a HeLa cell proteome digest in approximately 100 min. This performance is nearly an order of magnitude better than earlier CZE studies and is within a factor of two to four of the state‐of‐the‐art nano ultrahigh‐pressure LC system. Let's see some ID: 2100 protein and 10 000 peptide identifications (IDs) from a HeLa cell proteome digest were obtained in a single 100 min capillary zone electrophoresis (CZE)–tandem mass spectrometry (MS/MS) analysis. These results represent an almost tenfold improvement in peptide and protein IDs compared with previous single‐shot analyses using this technology.