EBprotV2: A Perseus Plugin for Differential Protein Abundance Analysis of Labeling-Based Quantitative Proteomics Data.,Journal of Proteome Research

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EBprotV2: A Perseus Plugin for Differential Protein Abundance Analysis of Labeling-Based Quantitative Proteomics Data.
Journal of Proteome Research ( IF 3.8 ) Pub Date : 2018-11-19 , DOI: 10.1021/acs.jproteome.8b00483
Hiromi W L Koh _{1,

2} , Yunbin Zhang ₃ , Christine Vogel ₃ , Hyungwon Choi _{1,

2,

4}

Affiliation

We present EBprotV2, a Perseus plugin for peptide-ratio-based differential protein abundance analysis in labeling-based proteomics experiments. The original version of EBprot models the distribution of log-transformed peptide-level ratios as a Gaussian mixture of differentially abundant proteins and nondifferentially abundant proteins and computes the probability score of differential abundance for each protein based on the reproducible magnitude of peptide ratios. However, the fully parametric model can be inflexible, and its R implementation is time-consuming for data sets containing a large number of peptides (e.g., >100 000). The new tool built in the C++ language is not only faster in computation time but also equipped with a flexible semiparametric model that handles skewed ratio distributions better. We have also developed a Perseus plugin for EBprotV2 for easy access to the tool. In addition, the tool now offers a new submodule (MakeGrpData) to transform label-free peptide intensity data into peptide ratio data for group comparisons and performs differential abundance analysis using mixture modeling. This approach is especially useful when the label-free data have many missing peptide intensity data points.

中文翻译：

EBprotV2：用于基于标记的定量蛋白质组学数据差异蛋白质丰度分析的Perseus插件。

我们介绍了EBprotV2，这是一个Perseus插件，用于在基于标记的蛋白质组学实验中基于肽比率的差异蛋白质丰度分析。EBprot的原始版本以差异丰富的蛋白质和非差异丰富的蛋白质的高斯混合物为模型，对数转换后的肽水平比率的分布进行了建模，并基于可重复的肽比率的大小来计算每种蛋白质的差异丰度的概率得分。然而，完全参数化模型可能是不灵活的，并且它的R实现对于包含大量肽段（例如> 100 000）的数据集来说是耗时的。用C ++语言构建的新工具不仅计算速度更快，而且还配备了灵活的半参数模型，可以更好地处理偏斜比分布。我们还为EBprotV2开发了一个Perseus插件，以方便使用该工具。此外，该工具现在提供了一个新的子模块（MakeGrpData），可将无标签的肽段强度数据转换为肽段比例数据以进行组比较，并使用混合物建模执行差异丰度分析。当无标记数据缺少许多肽强度数据点时，此方法特别有用。

更新日期：2018-11-20

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