High-resolution, Ultrasensitive, and Native Proteomics

Liangliang Sun

Assistant Professor

229 CEM


Primary Research Area

Analytical (An)

Other Area(s) of Interest

Biological (Bi)

Material (Ma)


(Research Description PDF)

Proteomics aims to comprehensively identify and quantify proteins in a biological system, including protein expression, localization, interaction, post-translational modifications (PTMs) and turn over. It routinely employs reversed-phase liquid chromatography (RPLC)-electrospray ionization (ESI)-tandem mass spectrometry (MS/ MS) for protein identification. Capillary zone electrophoresis (CZE)-ESI-MS/MS has also attracted great attentions for proteomics due to its advantageous features. First, CZE-MS and RPLC-MS can produce complementary identifications and the combination of these two techniques can improve proteomic scale, and especially enhance protein isoform identifications. Second, CZE can produce much better intact protein separation than RPLC. Third, CZE-MS can yield higher sensitivity than RPLC-MS. Fourth, CZE can separate proteins in their native conditions (close to pH 7), and CZE-native MS is invaluable for native proteomics.

Our research focuses on development of new techniques for exploring CZE-MS for high-resolution, ultrasensitive and native proteomics, and also applications of the new techniques for answering important questions in developmental biology and cancer.

(I) Couple multi-dimensional LC and/or electrophoresis-based protein prefractionation with CZE-MS/MS to improve the resolution of protein isoform separation and identification. The long-term goal is to generate a complete protein isoform database for human cells. We also collaborate with biologists to apply our proteomic techniques for understanding embryo early development using Zebrafish and fruit fly as model systems.

(II) Couple magnetic beads and monolithic materials-based immobilized enzymes with CZE-MS for highly efficient digestion and ultrasensitive detection of proteins from single cells. Single cell proteomics is invaluable for understanding cellular heterogeneity, and is particularly useful for the fields of stem cell biology, neuroscience and developmental biology. This work focuses on understanding how a particular cell (blastomere) develops into the final cell type or organ during embryo development. The long-term goal is to approach deep proteomics on individual cancer cells, which can provide new insights on cancer heterogeneity and cancer therapies.

(III) Develop a microdialysis interface using a hollow fiber membrane for highly efficient and rapid removal of detergents and salts from native proteins. We will couple the interface with CZE-MS for online native protein cleanup, separation and native mass spectrometry detection. The long-term goal is to apply this system for native proteomics, which aims to achieve large-scale analysis of protein complexes in native conditions.

Selected Publications

Over 10,000 peptide identifications from the HeLa proteome by using single-shot capillary zone electrophoresis combined with tandem mass spectrometry, Sun L, Hebert AS, Yan X, Zhao Y, Westphall MS, Rush MJ, Zhu G, Champion MM, Coon JJ, Dovichi NJ., Angew. Chem. Int. Ed. 2014, 53, 13931.

Ultrasensitive and fast bottom-up analysis of femtogram amounts of complex proteome digests, Sun L, Zhu G, Zhao Y, Yan X, Mou S, Dovichi NJ., Angew. Chem. Int. Ed. 2013, 52, 13661.

Quantitative proteomics of Xenopus laevis embryos: expression kinetics of nearly 4000 proteins during early development, Sun L, Bertke MM, Champion MM, Zhu G, Huber PW, Dovichi NJ., Sci. Rep. 2014, 4, 4365.

Fast top-down intact protein characterization with capillary zone electrophoresis- electrospray ionization tandem mass spectrometry. Sun L, Knierman MD, Zhu G, Dovichi NJ., Anal. Chem. 2013, 85, 5989.

Third-generation electrokinetically pumped sheath-flow nanospray interface with improved stability and sensitivity for automated capillary zone electrophoresis- mass spectrometry analysis of complex proteome digests, Sun L, Zhu G, Zhang Z, Mou S, Dovichi NJ., J. Proteome Res. 2015, 14, 2312.


B.S., 2005, Dalian University of Technology;

Ph.D., 2011, Dalian Institute of Chemical Physics, Chinese Academy of Sciences

Postdoctoral Fellow (2011-12) and Research Assistant Professor (2013-16), Univ. of Notre Dame