Capillary zone electrophoresis for bottom-up analysis of complex proteomes

Proteomics

Volumn 16, Issue 2, 2016, Pages 188-196

  Sun, Liangliang ^a   Zhu, Guijie ^a   Yan, Xiaojing ^a   Zhang, Zhenbin ^a   Wojcik, Roza ^a   Champion, Matthew M ^a   Dovichi, Norman J ^a  

^a UNIVERSITY OF NOTRE DAME   (United States)

Author keywords

Bottom up proteomics; Capillary electrophoresis; Cell biology; Electrokinetically pumped nanospray; Technology

Indexed keywords

PROTEOME;

CAPILLARY ZONE ELECTROPHORESIS; ELECTROPHORETIC MOBILITY; ELECTROSPRAY; HELA CELL LINE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; MASS SPECTROMETER; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; REVIEW; SENSITIVITY ANALYSIS; ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY; CAPILLARY ELECTROPHORESIS; ELECTROSPRAY MASS SPECTROMETRY; ISOLATION AND PURIFICATION; PROCEDURES; STANDARDS; TOTAL QUALITY MANAGEMENT;

ELECTROPHORESIS, CAPILLARY; HUMANS; PROTEOME; PROTEOMICS; QUALITY IMPROVEMENT; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION;

EID: 84956740748     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201500339     Document Type: Review

References (41)

1. Richards, A. L., Hebert, A. S., Ulbrich, A., Bailey, D. J. et al., One-hour proteome analysis in yeast. Nat. Protoc. 2015, 10, 701-714.
2. Sun, L., Hebert, A. S., Yan, X., Zhao, Y. et al., Over 10, 000 peptide identifications from the HeLa proteome by using single-shot capillary zone electrophoresis combined with tandem mass spectrometry. Angew. Chem. Int. Ed. Engl. 2014, 53, 13931-13933.
3. Jorgenson, J. W., Lukacs, K. D., Capillary zone electrophoresis. Science 1983, 222, 266-272.
4. Cheng, Y. F., Wu, S. L., Chen, D. Y., Dovichi, N. J., Interaction of capillary zone electrophoresis with a sheath flow cuvette detector. Anal. Chem. 1990, 62, 496-503.
5. Olivares, J. A., Nguyen, N. T., Yonker C. R., Smith, R. D. Online mass-spectrometric detection for capillary zone electrophoresis. Anal. Chem. 1987, 59, 1230-1232.
6. Smith, R. D., Olivares, J. A., Nguyen, N. T., Udseth, H. R. Capillary zone electrophoresis mass-spectrometry using an electrospray ionization interface. Anal. Chem. 1988, 60, 436-441.
7. Smith, R. D., Barinaga, C. J., Udseth, H. R., Improved electrospray ionization interface for capillary zone electrophoresis-mass-spectrometry. Anal. Chem. 1988, 60, 1948-1952.
8. Tong, W., Link, A., Eng, J. K., Yates, J. R., 3rd, Identification of proteins in complexes by solid-phase microextraction/multistep elution/capillary electrophoresis/tandem mass spectrometry. Anal. Chem. 1999, 71, 2270-2278.
9. n. Anal. Chem. 2006, 78, 7309-7316.
10. Faserl, K., Sarg, B., Kremser, L., Lindner, H. Optimization and evaluation of a sheathless capillary electrophoresis electrospray ionization mass spectrometry platform for peptide analysis: comparison to liquid chromatography electrospray ionization mass spectrometry. Anal. Chem. 2011, 83, 7297-7305.
11. Li, Y., Champion, M. M., Sun, L., Champion, P. A. et al., Capillary zone electrophoresis-electrospray ionization tandem mass spectrometry as an alternative proteomics platform to ultraperformance liquid chromatography electrospray ionization-tandem mass spectrometry for samples of intermediate complexity. Anal. Chem. 2012, 84, 1617-1622.
12. Wang, Y., Fonslow, B. R., Wong, C. C., Nakorchevsky, A., Yates, J. R., 3rd, Improving the comprehensiveness and sensitivity of sheathless capillary electrophoresis-tandem mass spectrometry for proteomic analysis. Anal. Chem. 2012, 84, 8505-8513.
13. Zhu, G., Sun, L., Yan, X., Dovichi, N. J., Single-shot proteomics using capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry with production of more than 1250 Escherichia coli peptide identifications in a 50 min separation. Anal. Chem. 2013, 85, 2569-2573.
14. Yan, X., Essaka, D. C., Sun, L., Zhu, G., Dovichi, N. J., Bottom-up proteome analysis of E. coli using capillary zone electrophoresis-tandem mass spectrometry with an electrokinetic sheath-flow electrospray interface. Proteomics 2013, 13, 2546-2551.
15. Sun, L., Li, Y., Champion, M. M., Zhu, G. et al., Capillary zone electrophoresis-multiple reaction monitoring from 100 pg of RAW 264.7 cell lysate digest. Analyst 2013, 138, 3181-3188.
16. Sun, L., Zhu, G., Dovichi, N. J., Integrated capillary zone electrophoresis-electrospray ionization tandem mass spectrometry system with an immobilized trypsin microreactor for online digestion and analysis of picogram amounts of RAW 264.7 cell lysate. Anal. Chem. 2013, 85, 4187-4194.
17. Sarg, B., Faserl, K., Kremser, L., Halfinger, B. et al., Comparing and combining capillary electrophoresis electrospray ionization mass spectrometry and nano-liquid chromatography electrospray ionization mass spectrometry for the characterization of post-translationally modified histones. Mol. Cell. Proteomics 2013, 12, 2640-2656.
18. Sun, L., Zhu, G., Zhao, Y., Yan, X. et al., Ultrasensitive and fast bottom-up analysis of femtogram amounts of complex proteome digests. Angew. Chem. Int. Ed. Engl. 2013, 52, 13661-13664.
19. Sun, L., Zhu, G., Mou, S., Zhao, Y. et al., Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry for quantitative parallel reaction monitoring of peptide abundance and single-shot proteomic analysis of a human cell line. J. Chromatogr. A. 2014, 1359, 303-308.
20. Sun, L., Zhu, G., Zhang, Z., Mou, S., Dovichi, N. J. 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. J. Proteome Res. 2015, 14, 2312-2321.
21. Faserl, K., Kremser, L., Müller, M., Teis, D., Lindner, H. H. Quantitative proteomics using ultralow flow capillary electrophoresis-mass spectrometry. Anal. Chem. 2015, 87, 4633-4640.
22. Mischak, H., Schanstra, J. P. CE-MS in biomarker discovery, validation, and clinical application. Proteomics Clin. Appl. 2011, 5, 9-23.
23. Gu, Y. M., Thijs, L., Liu, Y. P., Zhang, Z. et al., The urinary proteome as correlate and predictor of renal function in a population study. Nephrol. Dial. Transplant. 2014, 29, 2260-2268.
24. Pontillo, C., Filip, S., Borràs, D. M., Mullen, W. et al., CE-MS-based proteomics in biomarker discovery and clinical application. Proteomics Clin. Appl. 2015, 9, 322-334.
25. Lee, E. D., Muck W., Henion, J. D., Covey, T. R. On-line capillary zone electrophoresis-ion spray tandem mass spectrometry for the determination of dynorphins. J. Chromatogr. 1988, 458, 313-321.
26. Caprioli, R. M., Moore, W. T., Martin, M., Dague, B. B. et al., Coupling capillary zone electrophoresis and continuous-flow fast atom bombardment mass spectrometry for the analysis of peptide mixtures. J. Chromatogr. 1989, 480, 247-257.
27. Moini, M., Simplifying CE-MS operation. 2. Interfacing low flow separation techniques to mass spectrometry using a porous tip. Anal. Chem. 2007, 79, 4241-4246.
28. Wojcik, R., Dada, O. O., Sadilek, M., Dovichi, N. J., Simplified capillary electrophoresis nanospray sheath-flow interface for high efficiency and sensitive peptide analysis. Rapid Commun. Mass Spectrom. 2010, 24, 2554-2560.
29. Maxwell, E. J., Chen, D. D., Twenty years of interface development for capillary electrophoresis-electrospray ionization-mass spectrometry. Anal. Chim. Acta 2008, 627, 25-33.
30. Krenkova, J., Foret, F., On-line CE/ESI/MS interfacing: recent developments and applications in proteomics. Proteomics 2012, 12, 2978-2990.
31. Kleparnik, K., Recent advances in the combination of capillary electrophoresis with mass spectrometry: from element to single-cell analysis. Electrophoresis 2013, 34, 70-85.
32. Zhong, X., Zhang, Z., Jiang, S., Li, L., Recent advances in coupling capillary electrophoresis-based separation techniques to ESI and MALDI-MS. Electrophoresis 2014, 35, 1214-25
33. Heemskerk, A. A., Deelder, A. M., Mayboroda, O. A. CE-ESI-MS for bottom-up proteomics: advances in separation, interfacing and applications. Mass Spectrom. Rev. 2014, doi: 10.1002/mas.21432.
34. Sun, L., Zhu, G., Yan, X., Champion, M. M., Dovichi, N. J., Capillary zone electrophoresis for analysis of complex proteomes using an electrokinetically pumped sheath flow nanospray interface. Proteomics 2014, 14, 622-628.
35. Zhu, G., Sun, L., Dovichi, N. J., Thermally-initiated free radical polymerization for reproducible production of stable linear polyacrylamide coated capillaries, and their application to proteomic analysis using capillary zone electrophoresis-mass spectrometry. Talanta, in press (http://dx.doi.org/10.1016/j.talanta.2015.06.003).
36. Zhu, G., Sun, L., Yan, X., Dovichi, N. J., Bottom-up proteomics of Escherichia coli using dynamic pH junction preconcentration and capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry. Anal. Chem. 2014, 86, 6331-6336.
37. Zhang, Z., Sun, L., Zhu, G., Yan, X., Dovichi, N. J., Integrated strong cation-exchange hybrid monolith coupled with capillary zone electrophoresis and simultaneous dynamic pH junction for large-volume proteomic analysis by mass spectrometry. Talanta 2015, 138, 117-122.
38. Zhang, Z., Yan, X., Sun, L., Zhu, G., Dovichi, N. J., Detachable strong cation exchange monolith, integrated with capillary zone electrophoresis and coupled with ph gradient elution, produces improved sensitivity and numbers of peptide identifications during bottom-up analysis of complex proteomes. Anal. Chem. 2015, 87, 4572-4577.
39. Figeys, D., Corthals, G. L., Gallis, B., Goodlett, D. R. et al., Data-dependent modulation of solid-phase extraction capillary electrophoresis for the analysis of complex peptide and phosphopeptide mixtures by tandem mass spectrometry: application to endothelial nitric oxide synthase. Anal. Chem. 1999, 71, 2279-2287.
40. Onjiko, R. M., Moody, S. A., Nemes, P., Single-cell mass spectrometry reveals small molecules that affect cell fates in the 16-cell embryo. Proc. Natl. Acad. Sci. USA 2015, 112, 6545-50.
41. Sun, L., Bertke, M. M., Champion, M. M., Zhu, G. et al., Quantitative proteomics of Xenopus laevis embryos: expression kinetics of nearly 4000 proteins during early development. Sci. Rep. 2014, 4, 4365.