RAId_aPS：具有多个评分函数和频谱特定统计信息的MS/MS分析
RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics
摘要：
由于缺乏通用的统计标准，阻碍了对来自各种搜索方法的肽鉴定结果进行统计学上有意义的比较/组合。提供一个E值校准协议，我们之前证明了将任何方法报告的得分或启发式E值转换为教科书定义的E值的可行性，该E值可以作为通用的统计标准。该方案虽然稳健，但可能会丢失光谱特定统计数据，并且在实验设置发生变化时可能需要新的校准。为了缓解这些问题，我们开发了一种新的MS/MS搜索工具RAId_aPS，该工具能够为加性评分函数提供光谱特定的E值。给定从RAId评分、K评分、Hyperscore和XCorr中选择的评分函数，RAId_aPS使用动态编程生成所有可能肽的相应评分直方图。使用这些评分直方图来分配E值，使得无需校准的协议能够为每个评分函数进行准确的显著性分配。RAId_aPS具有四种不同的模式：（i）计算给定分子量范围的可能肽的总数，（ii）生成给定MS/MS谱和评分函数的评分直方图，（iii）重新分配给定MS/MS谱和所选评分函数的候选肽列表的E值，以及（iv）使用所选评分函数执行数据库搜索。在模式（iii）和（iv）中，RAId_aPS还能够使用频谱特定统计来组合来自不同评分函数的结果。网站链接是http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/raid_aps/index.html。Linux、Windows和Mac OS X的相关二进制文件可从同一页面获得。
英文摘要：
Statistically meaningful comparison/combination of peptide identification results from various search methods is impeded by the lack of a universal statistical standard. Providing an E-value calibration protocol, we demonstrated earlier the feasibility of translating either the score or heuristic E-value reported by any method into the textbook-defined E-value, which may serve as the universal statistical standard. This protocol, although robust, may lose spectrum-specific statistics and might require a new calibration when changes in experimental setup occur. To mitigate these issues, we developed a new MS/MS search tool, RAId_aPS, that is able to provide spectrum-specific E-values for additive scoring functions. Given a selection of scoring functions out of RAId score, K-score, Hyperscore and XCorr, RAId_aPS generates the corresponding score histograms of all possible peptides using dynamic programming. Using these score histograms to assign E-values enables a calibration-free protocol for accurate significance assignment for each scoring function. RAId_aPS features four different modes: (i) compute the total number of possible peptides for a given molecular mass range, (ii) generate the score histogram given a MS/MS spectrum and a scoring function, (iii) reassign E-values for a list of candidate peptides given a MS/MS spectrum and the scoring functions chosen, and (iv) perform database searches using selected scoring functions. In modes (iii) and (iv), RAId_aPS is also capable of combining results from different scoring functions using spectrum-specific statistics. The web link is http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/raid_aps/index.html. Relevant binaries for Linux, Windows, and Mac OS X are available from the same page.
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