蛋白質群組之辯識與交互關係分析系統

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姓名

李宗夷(Tzong-Yi Li) 查詢紙本館藏

畢業系所

資訊工程學系

論文名稱

蛋白質群組之辯識與交互關係分析系統
(A System to Identify Proteins Associated with Protein-Protein Interaction)

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摘要(中)

蛋白質辨識是蛋白質體學中一項很重要的研究，近年來質譜儀（Mass Spectrum）廣泛的應用在蛋白質體學相關的研究，尤其是應用在蛋白質辨識。蛋白質體學近年來成為生物科技領域的一股熱潮，主要原因是它改變過去只鑽研在一個蛋白質的研究，而著重在同時多個蛋白質之間的相互關係，因為蛋白質間通常會相互作用而產生它該有的功能。
雖然已經有許多的蛋白質辨識工具可以達到相當程度的辨識率（如Mascot），但是目前卻沒有任何蛋白質辨識工具可以讓使用者輸入多個MS spectra。因此在這個研究中設計了一個系統叫做MultiProtIdent，這個系統可以同時執行多組Peptide Mass Fingerprint（PMF）的辨識分析工作，並且利用蛋白質間的作用（Protein-Protein Interaction）和功能相關性（functional association）的資訊來分析每個PMF所對應的蛋白質間是否有某種關聯性。MultiProtIdent可以幫助蛋白質的研究者非常方便的交互作用分析。透過幾組protein complex實驗的測試，MultiProtIdent都可以提供非常好的結果。

摘要(英)

Protein identification is an important task in proteomics. Proteomic analyses based on the Mass Spectrum [1] are now key methods to determine the components in protein complexes. Proteins “work together” by actually binding to form multi-component complexes that carry out specific functions. Although several protein identification tools such as Mascot have high accuracy of identification, these tools do not have the facility of identifying multiple proteins simultaneously with the assistant of the protein-protein interaction or functional association information. In this study, we develop a novel tool, namely MultiProtIdent, which is able to identify proteins using additional information of protein-protein interactions and protein functional associations. The input of MultiProIdent is multiple PMFs and the identification results are proteins and possible relationships among identified proteins. Experiments using protein complexes as input show that MultiProtIdent is promising.

關鍵字(中)

★ 蛋白質與蛋白質的交互關係
★ 蛋白質辨識

關鍵字(英)

★ protein-protein interaction
★ protein identification

論文目次

Chapter 1 Introduction 1
1.1 Background 1
1.1.1 Protein Identification 1
1.1.2 Peptide Mass Fingerprinting 2
1.1.3 Scoring Function 5
1.2 Motivation 6
1.3 Goal 7
Chapter 2 Related Works 8
2.1 Protein Identification Tools using MS spectra 8
2.2 Protein Identification Using MS/MS spectra 10
2.3 Identifying the Components of Protein Complex 12
Chapter 3 Materials and Methods 14
3.1 Materials 14
3.1.1 Protein Sequence Database 14
3.1.2 Protein – Protein Interaction Databases 14
3.1.3 Gene and Protein Function Databases 17
3.2 Methods 19
3.2.1 System Flow of MultiProtIdent 20
3.2.2 Stage 1 of MultiProtIdent 21
3.2.3 Stage 2 of MultiProtIdent 23
3.2.4 Mining Associated Proteins 26
Chapter 4 Implementation 28
4.1 Data Preprocessing and Storage of Knowledgebase 28
4.2 Agent-based System 29
4.3 Web Interface 31
Chapter 5 Results and Case Study 36
5.1 MS Spectra 36
5.1.1 Result of Test_1 36
5.1.2 Result of Test_2 39
5.2 Known Cellular Complex 42
5.2.1 Simulation of Peptide Mass Fingerprint 42
5.2.2 Result of Second Test Data 44
Chapter 6 Summary 46
6.1 Discussion 46
6.2 Future Work 47
References 50
Appendix 52

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指導教授

洪炯宗、黃憲達
(Jorng-Tzong Horng、Hsien-Da Huang)

審核日期

2004-7-13

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