Pepitome: Evaluating Improved Spectral Library Search for Identification Complementarity and Quality Assessment
Pepitome: Evaluating Improved Spectral Library Search for Identification Complementarity and Quality Assessment
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DOI：
10.1021/pr200874e
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发表时间：
2012-03-01
影响因子：
4.4
通讯作者：
Tabb, David L.
中科院分区：
文献类型：
--
作者：
Dasari, Surendra;Chambers, Matthew C.;Tabb, David L.
光谱库已经成为蛋白质序列数据库用于多肽鉴定的一种可行的替代方案。这些文库包含先前检测到的肽序列及其对应的串联质谱图(MS/MS)。然后，搜索引擎可以通过将实验中的MS/MS扫描与图书馆中的扫描进行比较来识别多肽。其中许多算法使用点积分数来衡量光谱-光谱匹配(SSM)的质量。该评分系统没有提供明确的统计解释，并且忽略了评分中的碎片离子m/z差异。我们开发了一个新的光谱库搜索引擎Pepitome，它使用统计系统来给SSM评分。在分析在三个不同的质谱学平台上获得的数据集时，Pepitome的表现优于领先的文库搜索工具spectraST。我们通过通过RNA-Seq数据确认鸟枪式蛋白质组学鉴定来表征谱库搜索的可靠性。对同一样品进行光谱库和数据库搜索，揭示了它们的互补性。百事可乐的鉴定使鸟枪式蛋白质组学数据采集管道的质量分析和质量控制(QA/QC)自动化。
Spectral libraries have emerged as a viable alternative to protein sequence databases for peptide identification. These libraries contain previously detected peptide sequences and their corresponding tandem mass spectra (MS/MS). Search engines can then identify peptides by comparing experimental MS/MS scans to those in the library. Many of these algorithms employ the dot product score for measuring the quality of a spectrum-spectrum match (SSM). This scoring system does not offer a clear statistical interpretation and ignores fragment ion m/z discrepancies in the scoring. We developed a new spectral library search engine, Pepitome, which employs statistical systems for scoring SSMs. Pepitome outperformed the leading library search tool, SpectraST, when analyzing data sets acquired on three different mass spectrometry platforms. We characterized the reliability of spectral library searches by confirming shotgun proteomics identifications through RNA-Seq data. Applying spectral library and database searches on the same sample revealed their complementary nature. Pepitome identifications enabled the automation of quality analysis and quality control (QA/QC) for shotgun proteomics data acquisition pipelines.