蛋白質體學是從基因質體學所衍生出的一門科學，著重於組成細胞的各類蛋白質，包含其鑑定、區域化及功能分析，故可應用於藥物評估、新藥開發、建立生物資訊資料庫等。
本論文利用串聯式質譜儀及穩定同位素二甲基標定法來觀察Cpd.1250先導藥物對於肺腺癌細胞A549的影響。為了了解癌細胞的存活與凋亡，故針對核蛋白質體進行定量分析。利用所改良的核萃取技術可將核蛋白質萃取量提升至3.7倍。經Cpd.1250處理與未經Cpd.1250處理的細胞之核蛋白溶解物，在胜肽層面分別標定穩定同位素H4、D4，觀察蛋白質表現量的變化。結合蛋白質體結果與生化分析發現經Cpd.1250處理後，會使得PA2G4增加，誘發PI3K/Akt途徑，使得Akt的磷酸化增加，減少細胞凋亡而增加細胞存活，但不影響細胞總數。
Cpd.1250在高濃度C型血管生長因子(150 ng/ml)下會減少G1/S的細胞數而抑制癌細胞增生，但可能不受PA2G4的影響，而與C型血管生長因子/血管內皮生長因子受體3有關。

Proteomics is a class of science developed from genomics. Identification, localization, and functionalization of every kind of proteins and protein interactions in cells are focused. Thus, proteomics can be applied for characterizing drug interactions and for establishing bioinformatics.
In this article, we used tandem MS and stable isotope dimethyl labeling to investigate the effects of compound 1250 on lung cancer cells (Lung Adenocarcinoma A549). In order to examine nuclear proteins that are related to the survival and apoptosis of cancer cells, we focused on the quantification for nuclear proteome.We attempted new nuclear extraction method that increases the number of identified nuclear proteins by 3.7 times. The lysate of nuclear extract with and without the treatment of compound 1250 were labeled with H2-formaldehyde and D2-formaldehyde, respectively, in order to profile the protein amount in two conditions. Base on the results of proteome analysis and bioassays, it was found that the amount of PA2G4 was increased 1.6 time upon the treatment of compound 1250 treatment. Such increase was believed to be related to cell apoptosis via PI3/Akt and Akt phosphorylation pathway. The activation of Akt inhibits cell apoptosis and promotes cell survival. From the results, we propose that compound 1250 encourages cell survival. Under a high concentration (150 ng/ml) of Vascular endothelial growth factor C (VEGFC), compound 1250 inhibits cell proliferation by reducing cell accumulation in G1/S phase. Such inhibition may be related to VEGFR3 pathway but not PA2G4.

1.Kahn, P., From Genome to Proteome: Looking at a Cell's Proteins. Science 1995, 270, (20), 369-370.
2.Swinbanks, D., Government backs proteome proposal Nature 1995, 378, (14), 378.
3.Abbott, A., And now for the proteome. Nature 2001, 409, (6822), 747.
4.Fields, S., Proteomics in Genomeland Science 2001, 291, (5507), 1221-1224.
5.陳玉如, 質譜技術與蛋白質體學. 醫藥基因生物技術教學資源中心 2003.
6.Huber, L. A.; Pfaller, K.; Vietor, I., Organelle proteomics: Implications for subcellular fractionation in proteomics. Circulation Research 2003, 92, (9), 962-968.
7.Dreger, M., Subcellular proteomics. Mass Spectrometry Reviews 2003, 22, (1), 27-56.
8.Brunet, S.; Thibault, P.; Gagnon, E.; Kearney, P.; Bergeron, J. J. M.; Desjardins, M., Organelle proteomics: Looking at less to see more. Trends in Cell Biology 2003, 13, (12), 629-638.
9.Taylor, S. W.; Fahy, E.; Ghosh, S. S., Global organellar proteomics. Trends in Biotechnology 2003, 21, (2), 82-88.
10.Pasquali, C.; Fialka, I.; Huber, L. A., Subcellular fractionation, electromigration analysis and mapping of organelles. Journal of Chromatography B 1999, 722, (1-2), 89-102.
11.Yates, J. R., III; Gilchrist, A.; Howell, K. E.; Bergeron, J. J. M., Proteomics of organelles and large cellular structures. Nature Reviews Molecular Cell Biology 2005, 6, (9), 702-714.
12.Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnology 1999, 17, (10), 994-999.
13.Y. Oda; K. Huanh; F. R. Cross; D.Cowburn, A.; Chait, B. T., Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. USA 1999, 96, 6591-6596.
14.Steven P. Gygi; Beate Rist; Scott A. Gerber; Frantisek Turecek; Michael H. Gelb, a.; Aebersold, R., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17, 994-999.
15.L., P.; Ross; N., Y.; Huang; N., J.; Marchese; Brian Williamson; Kenneth Parker; Stephen Hattan; Nikita Khainovski; Sasi Pillai; Subhakar Dey; Scott Daniels; Subhasish Purkayastha; Peter Juhasz; Stephen Martin; Michael Bartlet-Jones; Feng He, A.; Jacobson, a.; Pappin, D. J., Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents Mol Cell Proteomics 3, 1154-1169.
16.Masood, R.; Cai, J.; Zheng, T.; Smith, D. L.; Hinton, D. R.; Gill, P. S., Vascular endothelial growth factor (VEGF) is an autocrine growth factor for VEGF receptor-positive human tumors. Blood 2001, 98, (6), 1904-1913.
17.Su, J.-L.; Yang, P.-C.; Shih, J.-Y.; Yang, C.-Y.; Wei, L.-H.; Hsieh, C.-Y.; Chou, C.-H.; Jeng, Y.-M.; Wang, M.-Y.; Chang, K.-J.; Hung, M.-C.; Kuo, M.-L., The VEGF-C/Flt-4 axis promotes invasion and metastasis of cancer cells. Cancer Cell 2006, 9, (3), 209-223.
18.Alitalo, K.; Carmeliet, P., Molecular mechanisms of lymphangiogenesis in health and disease. Cancer Cell 2002, 1, (3), 219-227.
19.Skobe, M.; Hawighorst, T.; Jackson, D. G.; Prevo, R.; Janes, L.; Velasco, P.; Riccardi, L.; Alitalo, K.; Claffey, K.; Detmar, M., Induction of tumor lymphangiogenesis by VEGF-C promotes breast cancer metastass. Nature Medicine 2001, 7, (2), 192-198.
20.Li, Q., Dong, X., Gu, W., Qiu, X., and Wang, E., Clinical significance of
co-expression of VEGF-C and VEGFR-3 in non-small cell lung cancer. Chin.Med. J.
2003, 116, 727–730.
21.Squatrito, M.; Mancino, M.; Donzelli, M.; Areces, L. B.; Draetta, G. F., EBP1 is a nucleolar growth-regulating protein that is part of pre-ribosomal ribonucleoprotein complexes. Oncogene 2004, 23, (25), 4454-4465.
22.Bose, S. K.; Sengupta, T. K.; Bandyopadhyay, S.; Spicer, E. K., Identification of Ebp1 as a component of cytoplasmic bcl-2 mRNP (messenger ribonucleoprotein particle) complexes. Biochemical Journal 2006, 396, (Part 1), 99-107.
23.Yoo, J. Y.; Wang, X. W.; Rishi, A. K.; Lessor, T.; Xia, X. M.; Gustafson, T. A.; Hamburger, A. W., Interaction of the PA2G4 (EBP1) protein with ErbB-3 and regulation of this binding by heregulin. British Journal of Cancer 2000, 82, (3), 683-690.
24.Ahn, J.-Y.; Liu, X.; Liu, Z.; Pereira, L.; Cheng, D.; Peng, J.; Wade, P. A.; Hamburger, A. W.; Ye, K., Nuclear Akt associates with PKC-phosphorylated Ebp1, preventing DNA fragmentation by inhibition of caspase-activated DNase. EMBO (European Molecular Biology Organization) Journal 2006, 25, (10), 2083-2095.
25.Kaelin, W. G., Jr., Functions of the retinoblastoma protein. Bioessays 1999, 21, (11), 950-958.
26.Weintraub SJ; Prater CA; DC., D., Retinoblastoma protein
switches the E2F site from positive to negative element. Nature 1992, 358, 259-261.
27.Xia, X.; Cheng, A.; Lessor, T.; Zhang, Y.; Hamburger, A. W., Ebp1, an ErbB-3 binding protein, interacts with Rb and affects Rb transcriptional regulation. Journal of Cellular Physiology 2001, 187, (2), 209-217.
28.Chan, G. K. T.; Jablonski, S. A.; Starr, D. A.; Goldberg, M. L.; Yen, T. J., Human Zw10 and ROD are mitotic checkpoint proteins that bind to kinetochores. Nature Cell Biology 2000, 2, (12), 944-947.