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研究生:林育新
研究生(外文):Yu-Hsing Lin
論文名稱:發展以片段氨基酸序列資訊鑑定蛋白質的工具
論文名稱(外文):Development of Protein Identification Tool Using Partial Amino Acid Sequences
指導教授:林照雄林照雄引用關係
指導教授(外文):Chao-Hsiung Lin
學位類別:碩士
校院名稱:國立陽明大學
系所名稱:生物化學研究所
學門:生命科學學門
學類:生物化學學類
論文種類:學術論文
論文出版年:2004
畢業學年度:92
語文別:中文
中文關鍵詞:生物資訊
外文關鍵詞:Proteomics
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近代研究中指出,細胞研究中真正的主角不是 gene ,而是由 gene 所決定的 protein 。在不同的細胞中,儘管有著幾乎一樣的 DNA ,但在 gene 表現的產物 protein 上,卻仍然可以有非常大的差異;甚至是相同的 protein ,就因為其數量的不同,而可以產生不同的影響力。因此將所有蛋白質分門別類並且研究蛋白質之間的相互作用,已成為現在研究主要的方向,即所謂的 proteomics 。
Proteomics 裡主要的研究方法如下:由 Two-Dimensional Gel Electrophoresis 挑選出目標 protein ,經過 protein digestion 將protein 切成小片段 peptides 送進 mass spectrometry 分析,因為由 6 到 20 個 amino acids 組成的 peptides 對於 mass spectrometry 和 database 的解讀最為有利。
本研究建構一系統用以鑑定由 mass spectrometry 分析所得的短peptide ,判斷是屬於哪種 protein 。由 mass spectrometry 得出的資料中,較長的 peptide 較容易由 protein database 比對出來,但是短的 peptide 卻難以比對。在實際由 mass spectrometry 分析有得的資料中,常會因為許多因素而無法得到完整 peptide 的 amino acid sequence ,只能得到不完整的 peptide ,也就是短的 amino acid sequence 。本研究使用同時對多個短的 peptide 進行比對,以解決短 peptide 無法從 database 中找到的情形;並使用 genome database 作為比對的 database ,以期能找到未知 protein 的來源 gene 資訊或相對應的 genome 位置;另外,本研究並且使用切割所輸入的短 peptide 轉換產生出的 nucleotide sequences 來避免因為輸入的短 peptide 正好落於 splicing site 上,因而無法在 database 中找到符合的資料的問題。
Recent studies have shown that the most important topic in the cell researches is not the gene itself but the proteins that it controls. Although the DNA in different cells are very similar to each other, but the proteins, the product of their gene expression, can still vary a lot. Even the different amounts of the same protein can make a crucial difference. Therefore, proteomics, which is the research field to categorize the proteins and to study the interactions between the proteins, has already become the most important research field now.
The typical research method in Proteomics studies is to use Two-Dimensional Gel Electrophoresis to select the target protein, and cut the protein into small segments of peptides through protein digestion, then using mass spectrometry to analyze it. Previous studies have indicated that peptides which consist of 6 to 20 amino acids are the optimal materials for mass spectrometry and database analysis.
Using mass spectrometry, it is much easier to identify the longer peptides from searching the protein database than to identify the short peptides. From the mass spectrometry analysis, the results are usually the amino acid sequences of the incomplete peptide (short amino acid sequences). The present study constructed a new system to identify the protein form the short peptides derived from mass spectrometry analysis. This method identifies several short peptides at the same time and using genome database as the searching database to identify the source gene information or correspondent genome location of the unknown proteins. In addition, we used the short peptide to transform the nucleotide sequences to avoid the problem that we could not identify the protein from the database because of the short peptides were locating at the splicing site.
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