請用此 Handle URI 來引用此文件:
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/59892
完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 翁啟惠 | |
dc.contributor.author | Chen-Chun Chen | en |
dc.contributor.author | 陳貞均 | zh_TW |
dc.date.accessioned | 2021-06-16T09:43:32Z | - |
dc.date.available | 2022-02-16 | |
dc.date.copyright | 2017-02-16 | |
dc.date.issued | 2017 | |
dc.date.submitted | 2017-02-01 | |
dc.identifier.citation | [1] B. J. Hollenbaugh D, Aruffo A, Bioorganic Chemistry: Carbohydrates. 1999, Oxford University Press: New York, 313-334.
[2] S. S. Pinho and C. A. Reis, Nature Reviews Cancer 2015. [3] K. W. Moremen, M. Tiemeyer and A. V. Nairn, Nature Reviews Molecular Cell Biology 2012, 13, 448-462. [4] a) J. Roth, Chemical Reviews 2002, 102, 285-304; b) S. Pan, R. Chen, R. Aebersold and T. A. Brentnall, Molecular & Cellular Proteomics 2011, 10, R110. 003251. [5] J. Hoseki, R. Ushioda and K. Nagata, Journal of Biochemistry 2010, 147, 19-25. [6] K. Ohtsubo and J. D. Marth, Cell 2006, 126, 855-867. [7] a) A. S. Vercoutter‐Edouart, M. C. Slomianny, O. Dekeyzer‐Beseme, J. F. Haeuw and J. C. Michalski, Proteomics 2008, 8, 3236-3256; b) A. Arcinas, T.-Y. Yen, E. Kebebew and B. A. Macher, Journal of proteome research 2009, 8, 3958-3968; c) S. A. Whelan, M. Lu, J. He, W. Yan, R. E. Saxton, K. F. Faull, J. P. Whitelegge and H. R. Chang, Journal of proteome research 2009, 8, 4151-4160. [8] J. A. Ludwig and J. N. Weinstein, Nature Reviews Cancer 2005, 5, 845-856. [9] a) H. Hwang, J. Zhang, K. A. Chung, J. B. Leverenz, C. P. Zabetian, E. R. Peskind, J. Jankovic, Z. Su, A. M. Hancock, C. Pan, T. J. Montine, S. Pan, J. Nutt, R. Albin, M. Gearing, R. P. Beyer, M. Shi and J. Zhang, Mass Spectrometry Reviews 2010, 29, 79-125; b) D. Meany and D. Chan, Clinical Proteomics 2011, 8, 7; c) H. H. Freeze, E. A. Eklund, B. G. Ng and M. C. Patterson, The Lancet Neurology 2012, 11, 453-466; d) T. Hennet, Biochimica et Biophysica Acta (BBA) - General Subjects 2012, 1820, 1306-1317. [10] a) J. Egrie, J. Browne, P. Lai and F. Lin, Progress in clinical and biological research 1984, 191, 339-350; b) J. C. Egrie, E. Dwyer, J. K. Browne, A. Hitz and M. A. Lykos, Experimental hematology 2003, 31, 290-299; c) I. C. Macdougall, S. J. Gray, O. Elston, C. Breen, B. Jenkins, J. Browne and J. Egrie, Journal of the American Society of Nephrology 1999, 10, 2392-2395. [11] H. Zhou, Y. Liu, J. Chui, K. Guo, Q. Shun, W. Lu, H. Jin, L. Wei and P. Yang, Archives of biochemistry and biophysics 2007, 459, 70-78. [12] Y. Tian and H. Zhang, PROTEOMICS – Clinical Applications 2010, 4, 124-132. [13] a) S. Ongay, A. Boichenko, N. Govorukhina and R. Bischoff, Journal of Separation Science 2012, 35, 2341-2372; b) D. S. Dalpathado and H. Desaire, Analyst 2008, 133, 731-738; c) I. M. Lazar, A. C. Lazar, D. F. Cortes and J. L. Kabulski, ELECTROPHORESIS 2011, 32, 3-13; d) F. Tousi, W. S. Hancock and M. Hincapie, Analytical Methods 2011, 3, 20-32. [14] J. Zhang and D. I. C. Wang, Journal of Chromatography B: Biomedical Sciences and Applications 1998, 712, 73-82. [15] B. Buszewski and S. Noga, Analytical and Bioanalytical Chemistry 2012, 402, 231-247. [16] a) S. Mysling, G. Palmisano, P. Højrup and M. Thaysen-Andersen, Analytical Chemistry 2010, 82, 5598-5609; b) A. Kondo, M. Thaysen-Andersen, K. Hjernø and O. N. Jensen, Journal of Separation Science 2010, 33, 891-902; c) J. Wohlgemuth, M. Karas, W. Jiang, R. Hendriks and S. Andrecht, Journal of Separation Science 2010, 33, 880-890; d) N. E. Scott, B. L. Parker, A. M. Connolly, J. Paulech, A. V. G. Edwards, B. Crossett, L. Falconer, D. Kolarich, S. P. Djordjevic, P. Højrup, N. H. Packer, M. R. Larsen and S. J. Cordwell, Molecular & Cellular Proteomics 2011, 10; e) K. Neue, M. Mormann, J. Peter-Katalinić and G. Pohlentz, Journal of Proteome Research 2011, 10, 2248-2260. [17] a) H. Zhang, T. Guo, X. Li, A. Datta, J. E. Park, J. Yang, S. K. Lim, J. P. Tam and S. K. Sze, Molecular & Cellular Proteomics 2010, 9, 635-647; b) P. Hao, T. Guo and S. K. Sze, PLoS ONE 2011, 6, e16884; c) T. H. H. Tran, In-Jae; Park, Jong-Moon; Kim, Jae-Bum; Lee, Hoo-Keun, Mass Spectrometry Letters 2012, 3, 39-42. [18] A. J. Alpert, Analytical Chemistry 2007, 80, 62-76. [19] a) R. D. Cummings in Use of lectins in analysis of glycoconjugates, Vol. Volume 230 (Ed. G. W. H. William J. Lennarz), Academic Press, 1994, pp. 66-86; b) P. Gravel, C. Walzer, C. Aubry, L. P. Balant, B. Yersin, D. F. Hochstrasser and J. Guimon, Biochemical and Biophysical Research Communications 1996, 220, 78-85. [20] K. Matsumura, K. Higashida, H. Ishida, Y. Hata, K. Yamamoto, M. Shigeta, Y. Mizuno-Horikawa, X. Wang, E. Miyoshi, J. Gu and N. Taniguchi, Journal of Biological Chemistry 2007, 282, 15700-15708. [21] M. Hedlund, E. Ng, A. Varki and N. M. Varki, Cancer Research 2008, 68, 388-394. [22] W. I. Weis and K. Drickamer, Annual Review of Biochemistry 1996, 65, 441-473. [23] S. Feng, N. Yang, S. Pennathur, S. Goodison and D. M. Lubman, Analytical Chemistry 2009, 81, 3776-3783. [24] a) Y. H. Ahn, Y.-S. Kim, E. S. Ji, J. Y. Lee, J.-A. Jung, J. H. Ko and J. S. Yoo, Analytical Chemistry 2010, 82, 4441-4447; b) K. L. Abbott, K. Aoki, J.-M. Lim, M. Porterfield, R. Johnson, R. M. O’Regan, L. Wells, M. Tiemeyer and M. Pierce, Journal of Proteome Research 2008, 7, 1470-1480. [25] M. C. Roque-Barreira and A. Campos-Neto, The Journal of Immunology 1985, 134, 1740-1743. [26] M. Madera, B. Mann, Y. Mechref and M. V. Novotny, Journal of Separation Science 2008, 31, 2722-2732. [27] a) R. D. Cummings and S. Kornfeld, Journal of Biological Chemistry 1982, 257, 11235-11240; b) M. Madera, Y. Mechref, I. Klouckova and M. V. Novotny, Journal of Chromatography B 2007, 845, 121-137. [28] a) Z. Yang and W. S. Hancock, Journal of Chromatography A 2004, 1053, 79-88; b) P. Hao, Y. Ren and Y. Xie, Journal of Chromatography B 2009, 877, 1657-1666. [29] M. Kullolli, W. S. Hancock and M. Hincapie, Journal of Separation Science 2008, 31, 2733-2739. [30] a) B. Xu, L. Zhou, F. Wang, H. Qin, J. Zhu and H. Zou, Chemical Communications 2012, 48, 1802-1804; b) W.-F. Ma, Y. Zhang, L.-L. Li, L.-J. You, P. Zhang, Y.-T. Zhang, J.-M. Li, M. Yu, J. Guo, H.-J. Lu and C.-C. Wang, ACS Nano 2012, 6, 3179-3188; c) J. Yan, X. Li, L. Yu, Y. Jin, X. Zhang, X. Xue, Y. Ke and X. Liang, Chemical Communications 2010, 46, 5488-5490. [31] a) M. R. Larsen, T. E. Thingholm, O. N. Jensen, P. Roepstorff and T. J. D. Jørgensen, Molecular & Cellular Proteomics 2005, 4, 873-886; b) M. R. Larsen, S. S. Jensen, L. A. Jakobsen and N. H. H. Heegaard, Molecular & Cellular Proteomics 2007, 6, 1778-1787; c) B. Zhang, Q. Sheng, X. Li, Q. Liang, J. Yan and X. Liang, Journal of Separation Science 2011, 34, 2745-2750. [32] a) H. G. Kuivila, A. H. Keough and E. J. Soboczenski, The Journal of Organic Chemistry 1954, 19, 780-783; b) Q. Zhang, N. Tang, J. W. C. Brock, H. M. Mottaz, J. M. Ames, J. W. Baynes, R. D. Smith and T. O. Metz, Journal of Proteome Research 2007, 6, 2323-2330; c) Q. Zhang, A. A. Schepmoes, J. W. C. Brock, S. Wu, R. J. Moore, S. O. Purvine, J. W. Baynes, R. D. Smith and T. O. Metz, Analytical Chemistry 2008, 80, 9822-9829; d) A. Takátsy, K. Böddi, L. Nagy, G. Nagy, S. Szabó, L. Markó, I. Wittmann, R. Ohmacht, T. Ringer, G. K. Bonn, D. Gjerde and Z. Szabó, Analytical Biochemistry 2009, 393, 8-22. [33] S. Feng, M. Ye, X. Jiang, W. Jin and H. Zou, Journal of Proteome Research 2006, 5, 422-428. [34] H. Zhang, X.-j. Li, D. B. Martin and R. Aebersold, Nature Biotechnology 2003, 21, 660-666. [35] J. Nilsson, U. Ruetschi, A. Halim, C. Hesse, E. Carlsohn, G. Brinkmalm and G. Larson, Nature Methods 2009, 6, 809-811. [36] a) M. Wuhrer, M. I. Catalina, A. M. Deelder and C. H. Hokke, Journal of Chromatography B 2007, 849, 115-128; b) A. L. Burlingame, Current opinion in biotechnology 1996, 7, 4-10; c) D. J. Harvey, Expert Review of Proteomics 2005, 2, 87-101. [37] a) N. L. Kelleher, Analytical chemistry 2004, 76, 196 A-203 A; b) A. D. Catherman, O. S. Skinner and N. L. Kelleher, Biochemical and biophysical research communications 2014, 445, 683-693; c) E. Balaguer and C. Neusüss, Analytical Chemistry 2006, 78, 5384-5393. [38] a) S. A. Carr, M. J. Huddleston and M. F. Bean, Protein Sci 1993, 2, 183-196; b) M. J. Huddleston, M. F. Bean and S. A. Carr, Anal Chem 1993, 65, 877-884; c) M. J. Kieliszewski, M. O'Neill, J. Leykam and R. Orlando, Journal of Biological Chemistry 1995, 270, 2541-2549. [39] a) B. Sullivan, T. A. Addona and S. A. Carr, Analytical chemistry 2004, 76, 3112-3118; b) N. Hashii, N. Kawasaki, S. Itoh, Y. Nakajima, A. Harazono, T. Kawanishi and T. Yamaguchi, Journal of proteome research 2009, 8, 3415-3429; c) S. M. Peterman and J. J. Mulholland, Journal of the American Society for Mass Spectrometry 2006, 17, 168-179. [40] a) Y. Satomi, Y. Shimonishi, T. Hase and T. Takao, Rapid Commun Mass Spectrom 2004, 18, 2983-2988; b) T. Imre, G. Schlosser, G. Pocsfalvi, R. Siciliano, É. Molnár‐Szöllősi, T. Kremmer, A. Malorni and K. Vékey, Journal of mass spectrometry 2005, 40, 1472-1483. [41] M. Wuhrer, C. I. Balog, C. A. Koeleman, A. M. Deelder and C. H. Hokke, Biochimica et Biophysica Acta (BBA)-General Subjects 2005, 1723, 229-239. [42] a) J. T. Adamson and K. Håkansson, Journal of proteome research 2006, 5, 493-501; b) R. R. Seipert, E. D. Dodds and C. B. Lebrilla, Journal of proteome research 2008, 8, 493-501; c) K. Håkansson, M. J. Chalmers, J. P. Quinn, M. A. McFarland, C. L. Hendrickson and A. G. Marshall, Analytical chemistry 2003, 75, 3256-3262. [43] a) J. V. Olsen, B. Macek, O. Lange, A. Makarov, S. Horning and M. Mann, Nature methods 2007, 4, 709-712; b) Z. M. Segu and Y. Mechref, Rapid communications in mass spectrometry 2010, 24, 1217-1225; c) C. Singh, C. G. Zampronio, A. J. Creese and H. J. Cooper, Journal of proteome research 2012, 11, 4517-4525. [44] a) M. Mormann, H. Paulsen and J. Peter-Katalinic, European Journal of Mass Spectrometry 2005, 11, 497-512; b) M. B. Renfrow, H. J. Cooper, M. Tomana, R. Kulhavy, Y. Hiki, K. Toma, M. R. Emmett, J. Mestecky, A. G. Marshall and J. Novak, Journal of Biological Chemistry 2005, 280, 19136-19145. [45] a) Z. Darula and K. F. Medzihradszky, Molecular & Cellular Proteomics 2009, 8, 2515-2526; b) W. R. Alley, Y. Mechref and M. V. Novotny, Rapid Communications in Mass Spectrometry 2009, 23, 161-170. [46] a) S. H. Kaji H., Yamauchi Y., Shinkawa T., Taoka M., Hirabayashi J, Kasai K., Takahashi N., Isobe T., Nat. Biotechnol. 2003, 21, 667-672; b) D. F. Zielinska, F. Gnad, J. R. Wiśniewski and M. Mann, Cell 2010, 141, 897-907. [47] P. M. Angel, J. M. Lim, L. Wells, C. Bergmann and R. Orlando, Rapid communications in mass spectrometry 2007, 21, 674-682. [48] G. Palmisano, M. N. Melo-Braga, K. Engholm-Keller, B. L. Parker and M. R. Larsen, Journal of proteome research 2012, 11, 1949-1957. [49] X. Yin, M. Bern, Q. Xing, J. Ho, R. Viner and M. Mayr, Molecular & Cellular Proteomics 2013, mcp. M112. 024018. [50] a) S.-F. Chien, R. Weinburg, S.-C. Li and Y.-T. Li, Biochemical and biophysical research communications 1977, 76, 317-323; b) H. Muramatsu, H. Tachikui, H. Ushida, X.-j. Song, Y. Qiu, S. Yamamoto and T. Muramatsu, Journal of biochemistry 2001, 129, 923-928. [51] a) F. G. Hanisch, S. Teitz, T. Schwientek and S. Müller, Proteomics 2009, 9, 710-719; b) Y. Huang, T. Konse, Y. Mechref and M. V. Novotny, Rapid communications in mass spectrometry 2002, 16, 1199-1204. [52] C. A. Cooper, E. Gasteiger and N. H. Packer, Proteomics 2001, 1, 340-349. [53] E. P. Go, K. R. Rebecchi, D. S. Dalpathado, M. L. Bandu, Y. Zhang and H. Desaire, Anal Chem 2007, 79, 1708-1713. [54] J. M. Ren, T. Rejtar, L. Li and B. L. Karger, J Proteome Res 2007, 6, 3162-3173. [55] N. Deshpande, P. H. Jensen, N. H. Packer and D. Kolarich, J Proteome Res 2010, 9, 1063-1075. [56] J. Irungu, E. P. Go, D. S. Dalpathado and H. Desaire, Anal Chem 2007, 79, 3065-3074. [57] C. L. Woodin, D. Hua, M. Maxon, K. R. Rebecchi, E. P. Go and H. Desaire, Anal Chem 2012, 84, 4821-4829. [58] P. Pompach, K. B. Chandler, R. Lan, N. Edwards and R. Goldman, J Proteome Res 2012, 11, 1728-1740. [59] D. Goldberg, M. Bern, S. Parry, M. Sutton-Smith, M. Panico, H. R. Morris and A. Dell, J Proteome Res 2007, 6, 3995-4005. [60] M. Bern, Y. J. Kil and C. Becker, Curr Protoc Bioinformatics 2012, Chapter 13, Unit13 20. [61] L. He, L. Xin, B. Shan, G. A. Lajoie and B. Ma, J Proteome Res 2014, 13, 3881-3895. [62] O. Ozohanics, J. Krenyacz, K. Ludanyi, F. Pollreisz, K. Vekey and L. Drahos, Rapid Commun Mass Spectrom 2008, 22, 3245-3254. [63] Y. Wu, Y. Mechref, I. Klouckova, A. Mayampurath, M. V. Novotny and H. Tang, Rapid Commun Mass Spectrom 2010, 24, 965-972. [64] a) C. C. Nwosu, R. R. Seipert, J. S. Strum, S. S. Hua, H. J. An, A. M. Zivkovic, B. J. German and C. B. Lebrilla, J Proteome Res 2011, 10, 2612-2624; b) J. S. Strum, C. C. Nwosu, S. Hua, S. R. Kronewitter, R. R. Seipert, R. J. Bachelor, H. J. An and C. B. Lebrilla, Anal Chem 2013, 85, 5666-5675. [65] S. W. Wu, S. Y. Liang, T. H. Pu, F. Y. Chang and K. H. Khoo, J Proteomics 2013, 84, 1-16. [66] a) B. Wollscheid, D. Bausch-Fluck, C. Henderson, R. O'Brien, M. Bibel, R. Schiess, R. Aebersold and J. D. Watts, Nature biotechnology 2009, 27, 378-386; b) K. J. Reynolds, X. Yao and C. Fenselau, Journal of proteome research 2002, 1, 27-33; c) B. B. Quazi Shakey, and Jiang Wu, Anal. Chem. 2010, 82, 7722-7728. [67] B. Mann, M. Madera, I. Klouckova, Y. Mechref, L. E. Dobrolecki, R. J. Hickey, Z. T. Hammoud and M. V. Novotny, Electrophoresis 2010, 31, 1833-1841. [68] Y. Li, Y. Tian, T. Rezai, A. Prakash, M. F. Lopez, D. W. Chan and H. Zhang, Analytical chemistry 2011, 83, 240. [69] H. Baumann, E. Nudelman, K. Watanabe and S.-i. Hakomori, Cancer research 1979, 39, 2637-2643. [70] a) K. F. Medzihradszky, Methods Enzymol 2005, 405, 116-138; b) M. V. Novotny and Y. Mechref, J Sep Sci 2005, 28, 1956-1968. [71] B. Domon and C. E. Costello, Glycoconjugate Journal 1988, 5, 397-409. [72] F. Li, O. V. Glinskii and V. V. Glinsky, Proteomics 2013, 13, 341-354. [73] a) D. C. Dallas, W. F. Martin, S. Hua and J. B. German, Brief Bioinform 2013, 14, 361-374; b) C. L. Woodin, M. Maxon and H. Desaire, Analyst 2013, 138, 2793-2803; c) H. Hu, K. Khatri and J. Zaia, Mass spectrometry reviews 2016. [74] Z. M. Segu and Y. Mechref, Rapid Communications in Mass Spectrometry 2010, 24, 1217-1225. [75] a) A. Helenius and M. Aebi, Science 2001, 291, 2364-2369; b) J. C. Trinidad, R. Schoepfer, A. L. Burlingame and K. F. Medzihradszky, Mol Cell Proteomics 2013, 12, 3474-3488. [76] a) P. Zhao, R. Viner, C. F. Teo, G. J. Boons, D. Horn and L. Wells, J Proteome Res 2011, 10, 4088-4104; b) C. I. A. Balog, O. A. Mayboroda, M. Wuhrer, C. H. Hokke, A. M. Deelder and P. J. Hensbergen, Molecular & Cellular Proteomics 2010, 9, 667-681; c) C. W. Lin, J. M. Chen, Y. M. Wang, S. W. Wu, I. H. Tsai and K. H. Khoo, Glycobiology 2011, 21, 530-542. [77] K. Fiedler and K. Simons, Cell 1995, 81, 309-312. [78] a) B. Y. Yang, J. S. Gray and R. Montgomery, Carbohydr Res 1996, 287, 203-212; b) W. Zhou, N. Yao, G. Yao, C. Deng, X. Zhang and P. Yang, Chem Commun (Camb) 2008, 5577-5579. [79] a) Z. Q. Ma, M. C. Chambers, A. J. Ham, K. L. Cheek, C. W. Whitwell, H. R. Aerni, B. Schilling, A. W. Miller, R. M. Caprioli and D. L. Tabb, J Proteome Res 2011, 10, 2896-2904; b) D. Schluesener, F. Fischer, J. Kruip, M. Rogner and A. Poetsch, Proteomics 2005, 5, 1317-1330. [80] M. Thaysen-Andersen, S. Mysling and P. Hojrup, Analytical Chemistry 2009, 81, 3933-3943. [81] R. Apweiler, A. Bateman, M. J. Martin, C. O'Donovan, M. Magrane, Y. Alam-Faruque, E. Alpi, R. Antunes, J. Arganiska, E. B. Casanova, B. Bely, M. Bingley, C. Bonilla, R. Britto, B. Bursteinas, W. M. Chan, G. Chavali, E. Cibrian-Uhalte, A. Da Silva, M. De Giorgi, F. Fazzini, P. Gane, L. G. Castro, P. Garmiri, E. Hatton-Ellis, R. Hieta, R. Huntley, D. Legge, W. D. Liu, J. Luo, A. MacDougall, P. Mutowo, A. Nightingale, S. Orchard, K. Pichler, D. Poggioli, S. Pundir, L. Pureza, G. Y. Qi, S. Rosanoff, T. Sawford, A. Shypitsyna, E. Turner, V. Volynkin, T. Wardell, X. Watkins, H. Zellner, M. Corbett, M. Donnelly, P. Van Rensburg, M. Goujon, H. McWilliam, R. Lopez, I. Xenarios, L. Bougueleret, A. Bridge, S. Poux, N. Redaschi, L. Aimo, A. Auchincloss, K. Axelsen, P. Bansal, D. Baratin, P. A. Binz, M. C. Blatter, B. Boeckmann, J. Bolleman, E. Boutet, L. Breuza, C. Casal-Casas, E. de Castro, L. Cerutti, E. Coudert, B. Cuche, M. Doche, D. Dornevil, S. Duvaud, A. Estreicher, L. Famiglietti, M. Feuermann, E. Gasteiger, S. Gehant, V. Gerritsen, A. Gos, N. Gruaz-Gumowski, U. Hinz, C. Hulo, J. James, F. Jungo, G. Keller, V. Lara, P. Lemercier, J. Lew, D. Lieberherr, T. Lombardot, X. Martin, P. Masson, A. Morgat, T. Neto, S. Paesano, I. Pedruzzi, S. Pilbout, M. Pozzato, M. Pruess, C. Rivoire, B. Roechert, M. Schneider, C. Sigrist, K. Sonesson, S. Staehli, A. Stutz, S. Sundaram, M. Tognolli, L. Verbregue, A. L. Veuthey, C. H. Wu, C. N. Arighi, L. Arminski, C. M. Chen, Y. X. Chen, J. S. Garavelli, H. Z. Huang, K. Laiho, P. McGarvey, D. A. Natale, B. E. Suzek, C. R. Vinayaka, Q. H. Wang, Y. Q. Wang, L. S. Yeh, M. S. Yerramalla, J. Zhang and U. Consortium, Nucleic Acids Research 2014, 42, D191-D198. [82] H. Malerod, R. L. Graham, M. J. Sweredoski and S. Hess, J Proteome Res 2013, 12, 248-259. [83] M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, G. M. Rubin and G. Sherlock, Nat Genet 2000, 25, 25-29. [84] CFG Functionalglycomicsgateway. [85] M. P. Campbell, R. Peterson, J. Mariethoz, E. Gasteiger, Y. Akune, K. F. Aoki-Kinoshita, F. Lisacek and N. H. Packer, Nucleic Acids Res 2014, 42, D215-221. [86] a) N. M. English, J. F. Lesley and R. Hyman, Cancer Research 1998, 58, 3736-3742; b) D. Naor, S. Nedvetzki, I. Golan, L. Melnik and Y. Faitelson, Crit Rev Clin Lab Sci 2002, 39, 527-579. [87] a) A. Bartolazzi, A. Nocks, A. Aruffo, F. Spring and I. Stamenkovic, Journal of Cell Biology 1996, 132, 1199-1208; b) J. Lesley, N. English, A. Perschl, J. Gregoroff and R. Hyman, J Exp Med 1995, 182, 431-437. [88] H. e. a. Han, Anal Bioanal Chem 2012, 404, 373-388. [89] P. Ponka and C. N. Lok, Int J Biochem Cell Biol 1999, 31, 1111-1137. [90] G. R. Hayes, A. Williams, C. E. Costello, C. A. Enns and J. J. Lucas, Glycobiology 1995, 5, 227-232. [91] A. Apte and N. S. Meitei, Functional Glycomics: Methods and Protocols 2010, 269-281. [92] P. Shah, X. Wang, W. Yang, S. T. Eshghi, S. Sun, N. Hoti, L. Chen, S. Yang, J. Pasay and A. Rubin, Molecular & Cellular Proteomics 2015, 14, 2753-2763. [93] E. Suzuki, R. Niwa, S. Saji, M. Muta, M. Hirose, S. Iida, Y. Shiotsu, M. Satoh, K. Shitara, M. Kondo and M. Toi, Clin Cancer Res 2007, 13, 1875-1882. [94] P. M. Drake, W. Cho, B. Li, A. Prakobphol, E. Johansen, N. L. Anderson, F. E. Regnier, B. W. Gibson and S. J. Fisher, Clin Chem 2010, 56, 223-236. [95] T. M. Lih, W.-K. Choong, C.-C. Chen, C.-W. Cheng, H.-N. Lin, C.-T. Chen, H.-Y. Chang, W.-L. Hsu and T.-Y. Sung, Nucleic acids research 2016, gkw254. [96] G. Durand and N. Seta, Clin Chem 2000, 46, 795-805. [97] M. Polanski and N. L. Anderson, Biomarker insights 2006, 1, 1. [98] L. Wang, M. Yao, Z. Dong, Y. Zhang and D. Yao, Tumor Biology 2014, 35, 9-20. [99] S.-S. Wang, R.-H. Lu, F.-Y. Lee, Y. Chao, Y.-S. Huang, C.-C. Chen and S.-D. Lee, Journal of hepatology 1996, 25, 166-171. [100] a) K. Taketa, Electrophoresis 1998, 19, 2595-2602; b) P. Johnson, T. Poon, N. Hjelm, C. Ho, S. Ho, C. Welby, D. Stevenson, T. Patel and R. Parekh, British journal of cancer 1999, 81, 1188; c) K. Yamashita, K. Taketa, S. Nishi, K. Fukushima and T. Ohkura, Cancer research 1993, 53, 2970-2975. [101] a) B. Campion, D. LÉGER, J. M. WIERUSZESKI, J. MONTREUIL and G. SPIK, European Journal of Biochemistry 1989, 184, 405-413; b) M. Blohm, D. Vesterling-Hörner, G. Calaminus and U. Göbel, Pediatric hematology and oncology 1998, 15, 135-142; c) R. Goldman, H. W. Ressom, R. S. Varghese, L. Goldman, G. Bascug, C. A. Loffredo, M. Abdel-Hamid, I. Gouda, S. Ezzat and Z. Kyselova, Clinical Cancer Research 2009, 15, 1808-1813; d) S. Zhang, H. Shu, K. Luo, X. Kang, Y. Zhang, H. Lu and Y. Liu, Molecular BioSystems 2011, 7, 1621-1628. [102] D. C. Dallas, W. F. Martin, S. Hua and J. B. German, Briefings in Bioinformatics 2013, 14, 361-374. [103] R. Apweiler, H. Hermjakob and N. Sharon, Biochim Biophys Acta 1999, 1473, 4-8. [104] a) P. Alves, R. J. Arnold, D. E. Clemmer, Y. Li, J. P. Reilly, Q. Sheng, H. Tang, Z. Xun, R. Zeng and P. Radivojac, Bioinformatics 2008, 24, 102-109; b) P. Hagglund, J. Bunkenborg, F. Elortza, O. N. Jensen and P. Roepstorff, J Proteome Res 2004, 3, 556-566; c) M. B. Strader, D. L. Tabb, W. J. Hervey, C. Pan and G. B. Hurst, Anal Chem 2006, 78, 125-134; d) D. Tsur, S. Tanner, E. Zandi, V. Bafna and P. A. Pevzner, Nature Biotechnology 2005, 23, 1562-1567. [105] D. M. Parkin, F. Bray, J. Ferlay and P. Pisani, CA: a cancer journal for clinicians 2005, 55, 74-108. [106] a) T. D. Boyer, T. L. Wright and M. P. Manns, Zakim and Boyer's hepatology: a textbook of liver disease, Elsevier Health Sciences, 2011, p; b) C. Bosetti, F. Levi, P. Boffetta, F. Lucchini, E. Negri and C. La Vecchia, Hepatology 2008, 48, 137-145. [107] T. M. Block, A. S. Mehta, C. J. Fimmel and R. Jordan, Oncogene 2003, 22, 5093-5107. [108] a) D. Y. Kim, Y. H. Paik, S. H. Ahn, Y. J. Youn, J. W. Choi, J. K. Kim, K. S. Lee, C. Y. Chon and K. H. Han, Oncology 2007, 72, 52-57; b) K. Okuda, Hepatology 1986, 6, 729-738. [109] a) Z. Lin, H. Yin, A. Lo, M. T. Ruffin, M. A. Anderson, D. M. Simeone and D. M. Lubman, Electrophoresis 2014, 35, 2108-2115; b) J.-M. Ahn, H.-J. Sung, Y.-H. Yoon, B.-G. Kim, W. S. Yang, C. Lee, H.-M. Park, B.-J. Kim, B.-G. Kim and S.-Y. Lee, Molecular & Cellular Proteomics 2014, 13, 30-48; c) Y. Sato, K. Nakata, Y. Kato, M. Shima, N. Ishii, T. Koji, K. Taketa, Y. Endo and S. Nagataki, New England Journal of Medicine 1993, 328, 1802-1806. [110] T. Nakagawa, E. Miyoshi, T. Yakushijin, N. Hiramatsu, T. Igura, N. Hayashi, N. Taniguchi and A. Kondo, Journal of proteome research 2008, 7, 2222-2233. [111] K. Shimizu, T. Taniichi, S. Satomura, S. Matsuura, H. Taga and K. Taketa, Clinica chimica acta 1993, 214, 3-12. [112] a) K. Nakamura, N. Imajo, Y. Yamagata, H. Katoh, K. Fujio, T. Tanaka, S. Satomura and S. Matsuura, Analytical chemistry 1998, 70, 954-957; b) H. Katoh, K. Nakamura, T. Tanaka, S. Satomura and S. Matsuura, Analytical chemistry 1998, 70, 2110-2114; c) D. Li, T. Mallory and S. Satomura, Clin Chim Acta 2001, 313, 15-19. [113] C. Kagebayashi, I. Yamaguchi, A. Akinaga, H. Kitano, K. Yokoyama, M. Satomura, T. Kurosawa, M. Watanabe, T. Kawabata and W. Chang, Analytical biochemistry 2009, 388, 306-311. [114] a) E. Hadziyannis, K. Sialevris, A. Georgiou and J. Koskinas, Oncology reports 2013, 29, 835-839; b) M. Ueno, S. Hayami, Y. Shigekawa, M. Kawai, S. Hirono, K.-i. Okada, H. Tamai, N. Shingaki, Y. Mori and M. Ichinose, Journal of hepatology 2015, 63, 1352-1359; c) G. P. Caviglia, M. L. Abate, E. Petrini, S. Gaia, M. Rizzetto and A. Smedile, Hepatology Research 2015. [115] a) L. Anderson and C. L. Hunter, Molecular & Cellular Proteomics 2006, 5, 573-588; b) T. A. Addona, S. E. Abbatiello, B. Schilling, S. J. Skates, D. Mani, D. M. Bunk, C. H. Spiegelman, L. J. Zimmerman, A.-J. L. Ham and H. Keshishian, Nature biotechnology 2009, 27, 633-641. [116] J. Cao, C. Shen, H. Wang, H. Shen, Y. Chen, A. Nie, G. Yan, H. Lu, Y. Liu and P. Yang, Journal of proteome research 2009, 8, 662-672. [117] P. J. Boersema, R. Raijmakers, S. Lemeer, S. Mohammed and A. J. Heck, Nature protocols 2009, 4, 484-494. [118] R. Pieper, C. L. Gatlin, A. J. Makusky, P. S. Russo, C. R. Schatz, S. S. Miller, Q. Su, A. M. McGrath, M. A. Estock and P. P. Parmar, Proteomics 2003, 3, 1345-1364. [119] a) M. Collin and A. Olsén, The EMBO Journal 2001, 20, 3046-3055; b) M. Allhorn, J. G. Briceño, L. Baudino, C. Lood, M. L. Olsson, S. Izui and M. Collin, Blood 2010, 115, 5080-5088. [120] J. Sjögren, E. F. Cosgrave, M. Allhorn, M. Nordgren, S. Björk, F. Olsson, S. Fredriksson and M. Collin, Glycobiology 2015, cwv047. [121] S. Yanagidani, N. Uozumi, Y. Ihara, E. Miyoshi, N. Yamaguchi and N. Taniguchi, Journal of Biochemistry 1997, 121, 626-632. [122] a) S. Lee, T. Wyttenbach and M. T. Bowers, International Journal of Mass Spectrometry and Ion Processes 1997, 167–168, 605-614; b) Y. Liu and D. E. Clemmer, Analytical Chemistry 1997, 69, 2504-2509; c) L. S. Fenn and J. A. McLean, Methods in molecular biology (Clifton, N.J.) 2013, 951, 171-194. [123] a) C. Przybylski and V. Bonnet, Rapid Communications in Mass Spectrometry 2013, 27, 75-87; b) H. Desaire, Molecular & Cellular Proteomics 2013, 12, 893-901. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/59892 | - |
dc.description.abstract | 蛋白質醣基化為一個相當普遍的後轉譯修飾,並且在生物體中扮演著許多重要的角色,例如:細胞辨識、免疫細胞自我調節功能等,近年來,蛋白質醣基化被廣泛的研究,其中醣基化程度的異常表現被認為與人類癌症發展具有高度關聯性。隨著質譜技術的發展與演進,質譜儀成為研究蛋白質體不可或缺的分析工具,然而,由於醣基化蛋白質在細胞中的低含量及其醣型結構的複雜程度,以質譜技術為基礎的醣蛋白分析仍面臨許多挑戰。基於上述原因,我們發展一整合型的醣胜肽分析策略結合生物資訊的技術平台分析及酵素輔助質譜定量技術,期許此一研究平台可加速我們對於蛋白質醣基化生物意義上的了解。
在本論文第二章,我們藉由高解析度及高靈敏度的串聯式質譜技術結合生物資訊方法發展準確的醣胜肽鑑定軟體,利用搜尋串聯質譜圖中特有的醣胜肽碎片,自動產生可用於蛋白質資料庫作鑑定的檔案格式,最後全面性的對醣胜肽之定序、特定位點的醣結構、及蛋白質作完整分析並依其候選醣型型式提供分數以供使用者參考。我們將此分析工具分別鑑定不同樣品複雜度的串聯式質譜圖以確認其實際應用上的表現,其結果顯示,此一平台提供快速且精準的分析,預期能應用於未來大規模醣蛋白質體的研究。 此外,於本論文第三章,我們開發以質譜為基礎的醣蛋白定量技術。由於岩藻醣化(core-fucosylated)的甲種胎兒蛋白為美國食品藥品管理局(Food and Drug Administration 簡稱FDA)認可的肝癌生物標記分子,因此我們以其此蛋白質作為方法開發的分析標的。然而,醣型結構的多樣性造成醣胜肽游離程度的極大差異,直接定量醣胜肽在實際應用上並不可行,因此,我們利用切醣酵素使醣胜肽統一化做僅一至兩顆醣修飾的胜肽片段,這樣的方法使得其目標分子離子的質荷比變為已知,也使得定量質譜術可充分用於特定位點的醣胜肽的定量分析。此一方法預期在未來可應用於實際臨床樣品的分析。 | zh_TW |
dc.description.abstract | Protein glycosylation is one of the most common post-translational modifications and has received increased attention for its critical role in cell biology and diseases. Despite its biological significance, the delineation of intact glycopeptides and site-specific glycopeptide quantification still await exploration. In this dissertation, we established an analytical workflow integrating a newly-designed automated tool for glycopeptide profiling and an enzyme-assisted targeted glycopeptide quantification to facilitate the understanding of glycosylation in diseases.
First, Mass-spectrometry-based Automated Glyco-peptide IdentifiCation platform (MAGIC), an in-house automated computational tool was developed to accurately characterize the intact glycopeptides without prior knowledge of the proteins and glycans present in the sample. Using a novel “Trident” strategy that detects a triplet pattern corresponding to [Y0, Y1, Y2] or [Y0−NH3, Y0, Y1] from the fragmentation of the common trimannosyl core of N-linked glycopeptides, the Y1 (i.e. peptide+GlcNAc) ion was identified from beam-type collision-induced dissociation tandem mass spectra. After Y1 assignment, the software generates in silico spectra by overwriting the original precursor with the naked peptide m/z and removing all of the glycan-related ions to identify the peptide sequence by common database search engines. Finally, MAGIC computes the glycan compositions and ranks them. Result from several datasets with various sample complexity from single protein to cell lysate implied that MAGIC enables to identify N-linked intact glycopeptide at a high speed and with high accuracy. In the second part, we developed a mass spectrometry based methodology to study the altered core-fucosylation in human sera. In this study, we selected alpha-fetoprotein (AFP) as a model target analyte since its core-fucosylated isoform has been used as a diagnostic and prognostic marker for hepatocellular carcinoma (HCC). To overcome the limitation on quantitative mass spectrometry, we took an advantage of endoglycosidase, which specifically cleaves the glycosidic bond between two GlcNAc residues, to reduce the microheterogeneity of the glycan on peptide backbone. This will result in truncated glycopeptides, e.g. peptide with GlcNAc or peptide with coreFuc GlcNAc, which can be directly analyzed by LC-MS/MS and quantified by extracting the peak area of target m/z. We evaluated the analytical figures of merit of the proposed method by following the guideline of the US Food and Drugs Administration (US FDA) for bioanalytical method validation. The targeted glycopeptide quantitation had good linearity from 15.6-1000 ng/mL (r2=0.9930 for interday experiments) and a limit of detection of 15.6 ng/mL. We anticipate applying the proposed protocol to understand the correlation between glycosylation and liver diseases by calculating the ratio of core-fucosylated to non-core-fucosylated glycopeptides in different patient groups. | en |
dc.description.provenance | Made available in DSpace on 2021-06-16T09:43:32Z (GMT). No. of bitstreams: 1 ntu-106-F99223146-1.pdf: 3918254 bytes, checksum: e41e04cbb01d27798a70e2d4f7c47c30 (MD5) Previous issue date: 2017 | en |
dc.description.tableofcontents | 口試委員會審定書 #
誌謝 i 中文摘要 ii ABSTRACT iii CONTENTS v LIST OF FIGURES ix LIST OF TABLES xi LIST OF APPENDIX xii ABBREVIATIONS xiii Chapter 1 Introduction 1 1.1 Protein Glycosylation 1 1.2 Significance of Protein Glycosylation 1 1.3 Overview of Glycoproteomic Analysis 3 1.3.1 Enrichment of the Glycoproteome 3 1.3.2 MS-based Glycopeptide Analysis 9 1.3.3 Bioinformatic Data Analysis 15 1.3.4 Quantitative Glycoproteomics 16 1.4 Objectives and Outline of the Dissertation 17 Chapter 2 An Automated Tool for N-linked Glycopeptide Identification 19 2.1 Introduction 19 2.2 Materials and Methods 22 2.2.1 Materials 22 2.2.2 Cell Culture 23 2.2.3 Membrane Protein Purification 23 2.2.4 Protein Purification from Human Serum 24 2.2.5 Protein Digestion Methods 24 2.2.6 Glycopeptide Enrichment by ZIC®-HILIC StageTips 25 2.2.7 Protein and Peptide Assays 26 2.2.8 C18 ZipTip® Pipette Tips Desalting 26 2.2.9 Reverse-phase LC MS/MS Analysis 27 2.2.10 Data processing and Database Search 29 2.2.11 Software Description and Avaliability of MAGIC and MAGIC-web 30 2.3 Result and Discussion 30 2.3.1 Workflow of automated glycopeptide identification 30 2.3.1.1 Glycopeptide spectrum filtering 31 2.3.1.2 Trident pattern matching for Y1-ion detection 32 2.3.1.3 Detection of glycopeptide fragment ions 34 2.3.1.4 In silico peptide spectrum generation for peptide identification 35 2.3.1.5 Glycan composition determination 36 2.3.2 Performance evaluation of MAGIC 38 2.3.2.1 Performance evaluation on the HRP dataset 38 2.3.2.2 Performance evaluation on the mixture dataset 46 2.3.2.3 Performance evaluation on the large-scale HeLa cell dataset 48 2.3.3 Escherichia Coli as negative control dataset 50 2.3.4 Performance comparison with other conventional tools 51 2.3.5 User interfaces of MAGIC 53 2.3.6 Targeted glycoprotein analysis in MAGIC+ 55 2.3.7 Case study of human alpha-fetoprotein (AFP) 57 2.4 Summary and Conclusion 62 Chapter 3 Development of an Enzyme-assisted Targeted Quantitative Approach for Core-fucosylated Glycopeptide in AFP-L3 66 3.1 Introduction 66 3.2 Materials and Methods 68 3.2.1 Materials 68 3.2.2 Cell Culture 68 3.2.3 Plasmid 68 3.2.4 Transfection 69 3.2.5 Protein Purification 69 3.2.6 Trypsin digestion and Endoglycosidase Tandem Digestion 70 3.2.7 Stable isotope labeling for relative quantification 70 3.2.8 Mass spectrometry analysis 71 3.2.9 Data Intepretation 72 3.2.10 Method Validation 73 3.3 Result and Discussion 74 3.3.1 Experimental design and workflow 74 3.3.2 Enrichment of AFP from human plasma 75 3.3.3 Performance evaluation of endoglycosidase treatment 77 3.3.4 Labeling efficiency of stable isotope dimethyl labeling 79 3.3.5 Determination of detection sensitivity 80 3.3.6 Proof of concept on a model study 84 3.3.7 Validation of the proposed analytical pipeline in human plasma 87 3.4 Summary and Future Perspective 88 Chapter 4 Conclusion and Future Perspective 90 REFERENCE 93 APPENDIX 1 | |
dc.language.iso | en | |
dc.title | 開發整合型醣胜肽分析策略應用於探討血清生物標記蛋白質 | zh_TW |
dc.title | Development of an Integrated Glycopeptide Analytical Strategy for Serum Protein Biomarker Analysis | en |
dc.type | Thesis | |
dc.date.schoolyear | 105-1 | |
dc.description.degree | 博士 | |
dc.contributor.oralexamcommittee | 陳玉如,陳仲瑄,宋定懿,楊懷壹 | |
dc.subject.keyword | 蛋白質醣基化,串聯式質譜技術,醣胜?定量,甲種胎兒蛋白,肝癌, | zh_TW |
dc.subject.keyword | N-linked glycosylation,intact glycopeptide identification,mass spectrometry,targeted quantification,alpha-fetoprotein,hepatocellular carcinoma, | en |
dc.relation.page | 128 | |
dc.identifier.doi | 10.6342/NTU201700296 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2017-02-04 | |
dc.contributor.author-college | 理學院 | zh_TW |
dc.contributor.author-dept | 化學研究所 | zh_TW |
顯示於系所單位: | 化學系 |
文件中的檔案:
檔案 | 大小 | 格式 | |
---|---|---|---|
ntu-106-1.pdf 目前未授權公開取用 | 3.83 MB | Adobe PDF |
系統中的文件,除了特別指名其著作權條款之外,均受到著作權保護,並且保留所有的權利。