AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction
AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction
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DOI：
10.1186/1471-2105-8-15
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发表时间：
2007-01-18
影响因子：
3
通讯作者：
Miyano, Satoru
中科院分区：
文献类型：
--
作者：
Saito, Ayumu;Nagasaki, Masao;Miyano, Satoru
背景资料：以定量的方式全面描述细胞组分的行为对于系统地理解生物事件是必不可少的。最近的LC-MS/MS（串联质谱与液相色谱法相结合）技术，结合SILAC（细胞培养物中氨基酸的稳定同位素标记）方法，使我们能够在蛋白质组水平上进行相对定量。Blagoev等人（Nat.Biotechnol.，22，1139-1145，2004）表明该方法也适用于细胞信号传导事件的时程分析。通过计算MS光谱中差异标记肽对应的峰强度比，可以容易地进行相对定量。由于目前可用的软件需要一些GUI应用程序，是耗时的，它不适合处理大规模的蛋白质组data.Results：为了解决这个困难，我们开发了一种算法，自动检测每个光谱中的峰。使用这种算法，我们开发了一个名为AYUMS的软件工具，它可以自动识别对应于差异标记肽的峰，比较这些峰，计算混合样品中的每个峰的比率，并将它们整合到一个数据表中。结论：AYUMS是一个非常有用的软件工具，可用于LC-MS/MS分析所产生的蛋白质组数据的全面定量。该软件使用Java开发，可在Linux、Windows和Mac OSX上运行。
Background: Comprehensive description of the behavior of cellular components in a quantitative manner is essential for systematic understanding of biological events. Recent LC-MS/MS (tandem mass spectrometry coupled with liquid chromatography) technology, in combination with the SILAC (Stable Isotope Labeling by Amino acids in Cell culture) method, has enabled us to make relative quantitation at the proteome level. The recent report by Blagoev et al. (Nat. Biotechnol., 22, 1139-1145, 2004) indicated that this method was also applicable for the time-course analysis of cellular signaling events. Relative quatitation can easily be performed by calculating the ratio of peak intensities corresponding to differentially labeled peptides in the MS spectrum. As currently available software requires some GUI applications and is time-consuming, it is not suitable for processing large-scale proteome data.Results: To resolve this difficulty, we developed an algorithm that automatically detects the peaks in each spectrum. Using this algorithm, we developed a software tool named AYUMS that automatically identifies the peaks corresponding to differentially labeled peptides, compares these peaks, calculates each of the peak ratios in mixed samples, and integrates them into one data sheet. This software has enabled us to dramatically save time for generation of the final report.Conclusion: AYUMS is a useful software tool for comprehensive quantitation of the proteome data generated by LC-MS/MS analysis. This software was developed using Java and runs on Linux, Windows, and Mac OSX.