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Comparison of 2-D RP-RP MS/MS with 1-D RP MS/MS for Proteomic Analysis  

Moon, Pyong-Gon (Department of Molecular Medicine, School of Medicine, Kyungpook National University)
Cho, Young-Eun (Department of Molecular Medicine, School of Medicine, Kyungpook National University)
Baek, Moon-Chang (Department of Molecular Medicine, School of Medicine, Kyungpook National University)
Publication Information
YAKHAK HOEJI / v.54, no.5, 2010 , pp. 377-386 More about this Journal
Abstract
Single-dimensional (1-D) and two-dimensional (2-D) LC methods were utilized to separate peptides from various sources followed by MS/MS analysis. Two-dimensional ultra-high performance liquid chromatography is a useful tool for proteome analysis, providing a greater peak capacity than 1-D LC. The most popular 2-D LC approach used today for proteomic research combines strong cation exchange and reversed-phase LC. We have evaluated an alternative mode for 2-D LC of peptides using 2-D RP-RP nano UPLC Q-TOF Mass Spectrometry, employing reversed-phase columns in both separation dimensions. As control experiments, we identified 129 proteins in 1-D LC and 322 proteins in 2-D LC from E. coli extract peptides. Furthermore, we applied this method to rat primary hepatocyte and a total of 170 proteins were identified from 1-D LC, and 527 proteins were identified from all 2-D LC system. The in-depth protein profiling established by this 2-D LC MS/MS from rat primary hepatocyte could be a very useful reference for future applications in regards to drug induced liver toxicity.
Keywords
2-D LC MS/MS; RP-RP; hepatocyte;
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1 Korolainen, M. A., Nyman, T. A., Nyyssonen, P., Hartikainen, E. S. and Pirttila, T. : Multiplexed proteomic analysis of oxidation and concentrations of cerebrospinal fluid proteins in Alzheimer disease. Clin. Chem. 53, 657 (2007).   DOI   ScienceOn
2 Beigel, J., Fella, K., Kramer, P. J., Kroeger, M. and Hewitt, P. : Genomics and proteomics analysis of cultured primary rat hepatocytes. Toxicol. In Vitro 22, 171 (2008).   DOI   ScienceOn
3 Zolotarjova, N., Martosella, J., Nicol, G., Bailey, J., Boyes, B. E. and Barrett, W. C. : Differences among techniques for highabundant protein depletion. Proteomics. 5, 3304 (2005).   DOI   ScienceOn
4 Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J. and Gygi, S. P. : Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for largescale protein analysis: the yeast proteome. J. Proteome. Res. 2, 43 (2003).   DOI   ScienceOn
5 Weatherly, D. B., Atwood, J. A., 3rd, Minning, T. A., Cavola, C., Tarleton, R. L. and Orlando, R. : A Heuristic method for assigning a false-discovery rate for protein identifications from Mascot database search results. Mol. Cell. Proteomics. 4, 762 (2005).   DOI   ScienceOn
6 Bargagli, E., Penza, F., Vagaggini, C., Magi, B., Perari, M. G. and Rottoli, P. : Analysis of carbonylated proteins in bronchoalveolar lavage of patients with diffuse lung diseases. Lung. 185, 139 (2007).   DOI   ScienceOn
7 Gilar, M., Olivova, P., Chakraborty, A. B., Jaworski, A., Geromanos, S. J. and Gebler, J. C. : Comparison of 1-D and 2- D LC MS/MS methods for proteomic analysis of human serum. Electrophoresis 30, 1157 (2009).   DOI   ScienceOn
8 Omenn, G. S., States, D. J., Adamski, M., Blackwell, T. W., Menon, R., Hermjakob, H., Apweiler, R., Haab, B. B., Simpson, R. J., Eddes, J. S., Kapp, E. A., Moritz, R. L., Chan, D. W., Rai, A. J., Admon, A., Aebersold, R., Eng, J., Hancock, W. S., Hefta, S. A., Meyer, H., Paik, Y. K., Yoo, J. S., Ping, P., Pounds, J., Adkins, J., Qian, X., Wang, R., Wasinger, V., Wu, C. Y., Zhao, X., Zeng, R., Archakov, A., Tsugita, A., Beer, I., Pandey, A., Pisano, M., Andrews, P., Tammen, H., Speicher, D. W. and Hanash, S. M. : Overview of the HUPO plasma proteome project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics. 5, 3226 (2005).   DOI   ScienceOn
9 Toll, H., Oberacher, H., Swart, R. and Huber, C. G. : Separation, detection, and identification of peptides by ion-pair reversed-phase high-performance liquid chromatographyelectrospray ionization mass spectrometry at high and low pH. J. Chromatogr. A 1079, 274 (2005).   DOI   ScienceOn
10 Liu, H., Li, G. Finch, J. W., Geromanos, S. J. and Gebler, J. C. : Development of an Automated RP/RP 2D Nano LC/MS Method for Proteomic Analysis. ABRF P57-T (2007).
11 Masuda, J., Maynard, D. M., Nishimura, M., Ueda, T., Kowalak, J. A. and Markey, S. P. : Fully automated micro- and nanoscale one- or two-dimensional high-performance liquid chromatography system for liquid chromatography-mass spectrometry compatible with non-volatile salts for ion exchange chromatography. J. Chromatogr. A 1063, 57 (2005).   DOI   ScienceOn
12 Shen, Y., Zhang, R., Moore, R. J., Kim, J., Metz, T. O., Hixson, K. K., Zhao, R., Livesay, E. A., Udseth, H. R. and Smith, R. D. : Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomics. Anal. Chem. 77, 3090 (2005).   DOI   ScienceOn
13 Echan, L. A., Tang, H. Y., Ali-Khan, N., Lee, K. and Speicher, D. W. : Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma. Proteomics. 5, 3292 (2005).   DOI   ScienceOn
14 Gilar, M., Olivova, P., Daly, A. E. and Gebler, J. C. : Twodimensional separation of peptides using RP-RP-HPLC system with different pH in first and second separation dimensions. J. Sep. Sci. 28, 1694 (2005).   DOI   ScienceOn
15 Adkins, J. N., Monroe, M. E., Auberry, K. J., Shen, Y., Jacobs, J. M., Camp, D. G., 2nd, Vitzthum, F., Rodland, K. D., Zangar, R. C., Smith, R. D. and Pounds, J. G. : A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy. Proteomics. 5, 3454 (2005).   DOI   ScienceOn
16 Eriksson, J. and Fenyo, D. : Protein identification in complex mixtures. J. Proteome. Res. 4, 387 (2005).   DOI   ScienceOn
17 Wolters, D. A., Washburn, M. P. and Yates, J. R., 3rd : An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73, 5683 (2001).   DOI   ScienceOn
18 Figliomeni, M. L. and Abdel-Rahman, M. S. : Ethanol does not increase the hepatotoxicity of cocaine in primary rat hepatocyte culture. Toxicology 129, 25 (1998).
19 Washburn, M. P., Wolters, D. and Yates, J. R. 3rd. : Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242 (2001).   DOI   ScienceOn
20 Schley, C., Altmeyer, M. O., Swart, R., Muller, R. and Huber, C. G. : Proteome analysis of Myxococcus xanthus by off-line two-dimensional chromatographic separation using monolithic poly-(styrene-divinylbenzene) columns combined with ion-trap tandem mass spectrometry. J. Proteome. Res. 5, 2760 (2006).   DOI   ScienceOn
21 Han, C. L., Chien, C. W., Chen, W. C., Chen, Y. R., Wu, C. P., Li, H. and Chen, Y. J. : A multiplexed quantitative strategy for membrane proteomics: opportunities for mining therapeutic targets for autosomal dominant polycystic kidney disease. Mol. Cell. Proteomics. 7, 1983 (2008).   DOI   ScienceOn
22 Nakamura, T., Kuromitsu, J. and Oda, Y. : Evaluation of comprehensive multidimensional separations using reversedphase, reversed-phase liquid chromatography/mass spectrometry for shotgun proteomics. J. Proteome. Res. 7, 1007 (2008).   DOI   ScienceOn
23 Rowe, C., Goldring, C. E., Kitteringham, N. R., Jenkins, R. E., Lane, B. S., Sanderson, C., Elliott, V., Platt, V., Metcalfe, P. and Park, B. K. : Network analysis of primary hepatocyte dedifferentiation using a shotgun proteomics approach. J. Proteome. Res. 9, 2658 (2010).   DOI   ScienceOn
24 Dennis, G., Jr., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C.and Lempicki, R. A. : DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome. Biol. 4, P3 (2003).   DOI
25 Dowell, J. A., Frost, D. C., Zhang, J. and Li, L. : Comparison of two-dimensional fractionation techniques for shotgun proteomics. Anal. Chem. 80, 6715 (2008).   DOI   ScienceOn