Preview: A Program for Surveying Shotgun Proteomics Tandem Mass Spectrometry Data
Preview: A Program for Surveying Shotgun Proteomics Tandem Mass Spectrometry Data
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DOI：
10.1021/ac200609a
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发表时间：
2011-07-01
影响因子：
7.4
通讯作者：
Bern, Marshall
中科院分区：
文献类型：
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作者：
Kil, Yong J.;Becker, Christopher;Bern, Marshall
用于通过串联质谱法进行肽鉴定的数据库搜索程序要求其用户设置各种参数，包括前体和片段质量公差、消化特异性和允许的修饰类型。即使是对样本有详细了解的蛋白质组学专家也可能发现，在没有进行大量调查的情况下，很难做出这些选择，而糟糕的选择可能会导致错过鉴定和误导性结果。在这里，我们描述了一个程序称为预览，分析了一组质谱的质量误差，消化特异性，已知和未知的修改，从而促进参数选择。此外，Preview还可以选择重新校准电荷质量测量，从而进一步改善识别结果。在一项对布鲁顿酪氨酸激酶的研究中，我们发现使用Preview可以提高质谱和磷酸化位点的数量约50%。
Database search programs for peptide identification by tandem mass spectrometry ask their users to set various parameters, including precursor and fragment mass tolerances, digestion specificity, and allowed types of modifications. Even proteomics experts with detailed knowledge of their samples may find it difficult to make these choices without significant investigation, and poor choices can lead to missed identifications and misleading results. Here we describe a program called Preview that analyzes a set of mass spectra for mass errors, digestion specificity, and known and unknown modifications, thereby facilitating parameter selection. Moreover, Preview optionally recalibrates mass over charge measurements, leading to further improvement in identification results. In a study of Bruton's tyrosine kinase, we find that the use of Preview improved the number of confidently identified mass spectra and phosphorylation sites by about 50%.