Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries
Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries
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DOI：
10.1021/ac060279n
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发表时间：
2006-08-15
影响因子：
7.4
通讯作者：
MacCoss, Michael J.
中科院分区：
文献类型：
--
作者：
Frewen, Barbara E.;Merrihew, Gennifer E.;MacCoss, Michael J.
用于表征复杂蛋白质混合物的广泛蛋白质组学程序将串联质谱法和数据库搜索软件结合起来，产生具有鉴定肽序列的质谱。相同的多肽通常在多个实验中被检测到，一旦它们被确定，各自的光谱可以用于未来的鉴定。我们提出了一种方法，收集以前确定串联质谱到一个参考库，用于识别新的光谱。将查询谱与库中的引用进行比较，以找到最相似的查询谱。点积度量是用来度量相似度的。在我们最大的数据库中，搜索查询集可以找到91%的光谱鉴定和93.7%的蛋白质鉴定，这些鉴定可以通过SEQUEST数据库搜索得到。第二个实验表明，LCQ离子阱质谱仪上获得的查询可以用LTQ离子阱质谱仪上获得的参考文献库进行识别。点积相似度评分可以很好地区分正确和错误的识别。
A widespread proteomics procedure for characterizing a complex mixture of proteins combines tandem mass spectrometry and database search software to yield mass spectra with identified peptide sequences. The same peptides are often detected in multiple experiments, and once they have been identified, the respective spectra can be used for future identifications. We present a method for collecting previously identified tandem mass spectra into a reference library that is used to identify new spectra. Query spectra are compared to references in the library to find the ones that are most similar. A dot product metric is used to measure the degree of similarity. With our largest library, the search of a query set finds 91% of the spectrum identifications and 93.7% of the protein identifications that could be made with a SEQUEST database search. A second experiment demonstrates that queries acquired on an LCQ ion trap mass spectrometer can be identified with a library of references acquired on an LTQ ion trap mass spectrometer. The dot product similarity score provides good separation of correct and incorrect identifications.