IDENTIFYING DIFFERENCES IN PROTEIN EXPRESSION LEVELS BY SPECTRAL COUNTING AND FE

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 光谱计数是一种定量分析预先消化的蛋白质混合物中的相对蛋白质浓度的策略，可通过串联质谱仪在线进行分析。在本研究中，我们使用归一化和统计(特征选择)相结合的方法对光谱计数数据进行验证，以验证当比较复杂的蛋白质混合物时，我们是否可以准确地确定哪些和多少蛋白质有差异表达。这些组合是在真实但受控的实验(酵母裂解产物中添加了不同浓度的蛋白质标记以模拟差异)上进行评估的，因此这些实验是可以验证的。采用了以下归一化方法：全信号归一化、Z归一化、混合归一化和测井预处理。特征选择方法有：Golub指数、学生t检验、前向支持向量机模型中基于权重的策略和支持向量机递归特征消除。结果表明，Z归一化与支持向量机F相结合，正确地识别了在所有不同浓度的酵母裂解产物中添加了哪些以及多少个蛋白质标记。我们使用的软件在http://pcarvalho.com/patternlab.上有售

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Spectral counting is a strategy to quantify relative protein concentrations in pre-digested protein mixtures analyzed by liquid chromatography online with tandem mass spectrometry. In the present study, we used combinations of normalization and statistical (feature selection) methods on spectral counting data to verify whether we could pinpoint which and how many proteins were differentially expressed when comparing complex protein mixtures. These combinations were evaluated on real, but controlled, experiments (yeast lysates were spiked with protein markers at different concentrations to simulate differences), which were therefore verifiable. The following normalization methods were applied: total signal, Z-normalization, hybrid normalization, and log preprocessing. The feature selection methods were: the Golub index, the Student t-test, a strategy based on the weighting used in a forward-support vector machine (SVM-F) model, and SVM recursive feature elimination. The results showed that Z-normalization combined with SVM-F correctly identified which and how many protein markers were added to the yeast lysates for all different concentrations. The software we used is available at http://pcarvalho.com/patternlab.