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。 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.
