Strong cation exchange-reversed phase liquid chromatography-capillary zone electrophoresis-tandem mass spectrometry platform with high peak capacity for deep bottom-up proteomics

Analytica Chimica Acta
Daoyang ChenLiangliang Sun

Abstract

Two-dimensional (2D) liquid chromatography (LC)-tandem mass spectrometry (MS/MS) are typically employed for deep bottom-up proteomics, and the state-of-the-art 2D-LC-MS/MS has approached over 8000 protein identifications (IDs) from mammalian cell lines or tissues in 1-3 days of mass spectrometer time. Capillary zone electrophoresis (CZE)-MS/MS has been suggested as an alternative to LC-MS/MS for bottom-up proteomics. CZE-MS/MS and LC-MS/MS are complementary in protein/peptide ID from complex proteome digests because CZE and LC are orthogonal for peptide separation. In addition, the migration time of peptides from CZE-MS can be predicted accurately, which is invaluable for evaluating the confidence of peptide ID from the database search and even guiding the database search. However, the number of protein IDs from complex proteomes using CZE-MS/MS is still much lower than the state of the art using 2D-LC-MS/MS. In this work, for the first time, we established a strong cation exchange (SCX)-reversed phase LC (RPLC)-CZE-MS/MS platform for deep bottom-up proteomics. The platform identified around 8200 protein groups and 65,000 unique peptides from a mouse brain proteome digest in 70 h. The data represents the largest bottom-up prote...Continue Reading

Citations

Aug 4, 2018·Electrophoresis·Andrea ŠlampováPetr Gebauer
Sep 22, 2018·Journal of Separation Science·Ivan Mikšík
Aug 14, 2019·Mass Spectrometry Reviews·Fabio P Gomes, John R Yates
Feb 28, 2020·International Journal of Molecular Sciences·Van-An DuongHookeun Lee
Jul 8, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Goyeun YunHookeun Lee
Apr 21, 2021·Chemical Reviews·Noor AbdulhussainPeter Schoenmakers
Nov 9, 2019·Analytical Chemistry·Courtney J KristoffLisa A Holland

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