基于鸟枪法蛋白质组学的蛋白质及翻译后修饰检测信息学
Informatics of protein and posttranslational modification detection via shotgun proteomics.
作者信息
Holman Jerry D, Dasari Surendra, Tabb David L
机构信息
Vanderbilt University Medical Center, Nashville, TN, USA.
出版信息
Methods Mol Biol. 2013;1002:167-79. doi: 10.1007/978-1-62703-360-2_14.
Abstract
Frequently, proteomic LC-MS/MS data may contain sets of modifications that evade identification during standard database search. For many laboratories, the standard technique to seek posttranslational modifications (PTMs) adds a short list of specified mass shifts to database search configuration. This technique provides information for only the specified PTMs, takes substantial time to run, and drives false discoveries upward through an exponential expansion of search space. This protocol describes a more structured approach to blind PTM discovery through reducing protein lists, targeting attention to a data-driven list of mass shifts, and seeking the resulting short list of modifications through targeted search.
摘要
蛋白质组液相色谱-串联质谱（LC-MS/MS）数据常常包含在标准数据库搜索过程中无法识别的修饰集。对于许多实验室而言，寻找翻译后修饰（PTM）的标准技术是在数据库搜索配置中添加一小组指定的质量偏移。该技术仅提供指定PTM的信息，运行耗时较长，并且通过搜索空间的指数级扩展导致错误发现率上升。本方案描述了一种更具结构化的方法，用于通过减少蛋白质列表、将注意力集中在数据驱动的质量偏移列表上，并通过靶向搜索寻找由此产生的简短修饰列表来进行盲法PTM发现。
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