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Reference Library Searching Strategies in Proteomics

机译：参考文库搜索蛋白质组学中的策略

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For mass spectrometry-based proteomics applications, assigning tandem mass spectra to peptide sequences is fundamental to extrapolating biological information from an experiment. This is commonly achieved by comparing experimental spectra to a database of spectra simulated from peptide sequences; however, current knowledge of collision-induced dissociation of peptides in a mass spectrometer is far from complete and often simulated spectra may not accurately represent experimental spectra, thus hindering identification. Searching spectra against a reference library of tandem mass spectra circumvents this issue, as peptide fragmentation events are inherently modeled in real spectra. We present a novel method combining sequence database and reference library searching approaches to identify tandem mass spectra, applying a linear discriminant approach to minimize false positives, increase sensitivity, and increase the confidence of peptide identifications compared with those obtained using sequence database searching approaches alone. In addition, we present a comparative method applying reference library searching to generate a hierarchical tree of tandem mass spectra and subsequently identify clusters of similar spectra significantly contributing to a particular biological state or condition. Comparing analyses of untreated and TNF-treated HeLa cells, spectra significantly more abundant in one analysis over another were identified. This approach did not require spectra to be assigned to peptide sequences and was able to identify significant spectra that could not be identified by standard sequence database searching methods.
机译：对于基于质谱的蛋白质组学应用，将串联质谱分配给肽序列是从实验中推断生物信息的基础。通过将实验光谱比较到从肽序列模拟的光谱数据库中，通常实现这一点。然而，目前对质谱仪中肽的碰撞诱导的解离的目前的知识远非完全，并且通常模拟光谱可能无法精确地代表实验光谱，从而阻碍识别。根据肽片段发生事件在真实光谱中固有地建模，搜索串联质谱库的参考文库促进串联质谱库。我们提出了一种组合序列数据库和参考库搜索方法的新方法来识别串联质谱，应用线性判别方法以最小化误报，增加灵敏度，并增加肽鉴定的置信度，与使用序列数据库搜索方法获得的那些。另外，我们提出了一种应用参考文库搜索的比较方法，用于生成串联质谱的分层树，随后识别显着促进特定生物状态或条件的类似光谱的簇。比较未处理和TNF处理的HeLa细胞的分析，鉴定了一个分析中的一个分析的光谱在另一个分析中明显更加丰富。该方法不需要将光谱分配给肽序列，并且能够识别无法通过标准序列数据库搜索方法识别的重要光谱。

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