| 摘要: | 在生命體中蛋白質是基因表達的最終形態，而其中胺基酸排序和結構則成為決定蛋白質功能的關鍵。生物學中有關蛋白質的研究至今已經累積了許多知識和資訊，因此利用生物資訊工具整合與蛋白質的相關研究成果則成為蛋白質組學和其相關的代謝組學的重要方法，如此進而能夠了解一些未知功能的蛋白質的生物活性和其在代謝中所扮演的角色。傳統上，利用液相層析與串聯質譜 (LC-MS/MS) 來分離和識別目標化合物 （例如蛋白質和代謝物） 是實驗室常用的方法，然而，目標化合物的有效定量則存在一些挑戰。在這裡，我們提出了一個名為 MS-Picker 的軟體工具，用於精確的化合物定量，是專為代謝組學的準確波峰偵測而設計。我們的軟體工具是用 Java 編程語言編寫的，因此可以實現跨平台操作。MS-Picker 與當前可用的定量工具 （如 MZmine3 和 XCMS）相比，由於大多數工具僅使用質荷比和滯留時間萃取離子層析圖 (Extracted Ion Chromatogram, EIC)，而 MS-Picker 除了以上功能外，更特別生成理論同位素模式，並將生成的模式與質譜儀資料中觀察到的同位素模式進行質譜原始文件的比對，不僅有利於同位素峰的去除，還可用於噪聲估計，可進一步改善定量的結果。MS-Picker 將 mzML 文件格式的質譜原始文件作為輸入文件，通過幾個步驟處理文件，包括去噪、去同位素、提取離子層析圖構建和電荷狀態確定，並以文本文件導出峰列表，具有質荷比 (mass-to-charge ratio, m/z)、滯留時間 (retention time, rt)、同位素比、電荷狀態和峰訊號強度的格式，之後可以通過後續的對齊軟體工具和下游統計分析來處理輸出結果。;Metabolomics has increasingly become an important research for the understanding of biological activities. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) is a conventional platform for the identification and quantification of compounds of interests (e.g., proteins and metabolites). Here we propose a, software tool, called MS-Picker, for accurate compound quantitation. Our software tool is written in Java programming language and thus enables cross-platform operations. Comparing with current available quantitation tools, such as MZmine3 and XCMS, most of which simply extract ion chromatograms using m/z and retention time, MS-Picker particularly generates theoretical isotope patterns and compares the generated patterns with the observed isotope patterns in LC-MS/MS raw files, which not only is beneficial for isotope peak removal, but also can be used for the estimation of noises and further improve quantitation results. MS-Picker takes LC-MS/MS raw files in mzML file format as input files, processes the files with several common steps, including noise removal, deisotoping, extracted ion chromatogram construction, and charge state determination, and exports peak lists in text file format with the peak information of m/z, retention time, isotope ratio, charge state, and abundance. The output results can then be processed by subsequent alignment software tool and downstream statistical analysis. MS-Picker is designed for accurate peak detection of metabolomics. |
