Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37027, USA.
Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
Biomed Res Int. 2014;2014:971857. doi: 10.1155/2014/971857. Epub 2014 May 11.
Proteolytic (18)O-labeling has been widely used in quantitative proteomics since it can uniformly label all peptides from different kinds of proteins. There have been multiple algorithms and tools developed over the last few years to analyze high-resolution proteolytic (16)O/(18)O labeled mass spectra. We have developed a software package, O18Quant, which addresses two major issues in the previously developed algorithms. First, O18Quant uses a robust linear model (RLM) for peptide-to-protein ratio estimation. RLM can minimize the effect of outliers instead of iteratively removing them which is a common practice in other approaches. Second, the existing algorithms lack applicable implementation. We address this by implementing O18Quant using C# under Microsoft.net framework and R. O18Quant automatically calculates the peptide/protein relative ratio and provides a friendly graphical user interface (GUI) which allows the user to manually validate the quantification results at scan, peptide, and protein levels. The intuitive GUI of O18Quant can greatly enhance the user's visualization and understanding of the data analysis. O18Quant can be downloaded for free as part of the software suite ProteomicsTools.
自从能够均匀标记来自不同蛋白质的所有肽以来，蛋白水解（18）O 标记已被广泛用于定量蛋白质组学。在过去几年中，已经开发出了多种算法和工具来分析高分辨率蛋白水解（16）O/（18）O 标记的质谱。我们开发了一个软件包 O18Quant，它解决了以前开发的算法中的两个主要问题。首先，O18Quant 使用稳健的线性模型（RLM）来估计肽到蛋白质的比率。RLM 可以最小化异常值的影响，而不是像其他方法那样反复删除它们。其次，现有的算法缺乏适用的实现。我们通过在 Microsoft.net 框架下使用 C#和 R 来实现 O18Quant 来解决这个问题。O18Quant 自动计算肽/蛋白质的相对比率，并提供了一个友好的图形用户界面（GUI），允许用户在扫描、肽和蛋白质水平上手动验证定量结果。O18Quant 的直观 GUI 可以大大增强用户对数据分析的可视化和理解。O18Quant 可以作为 ProteomicsTools 软件套件的一部分免费下载。
