Review of software tools for design and analysis of large scale MRM proteomic datasets.
Review of software tools for design and analysis of large scale MRM proteomic datasets.
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DOI：
10.1016/j.ymeth.2013.05.004
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发表时间：
2013-06-15
期刊：
影响因子：
4.8
通讯作者：
Cheung, Kei-Hoi
中科院分区：
文献类型：
--
作者：
Colangelo, Christopher M.;Chung, Lisa;Bruce, Can;Cheung, Kei-Hoi
选择性或多反应监测（SRM/MRM）是一种液相色谱（LC）/串联质谱（MS/MS）方法，通过分析其选定胰蛋白酶肽的前体离子和碎片离子，可以定量样品中的特定蛋白质。仪器软件已经发展到可以在耦合到LC的三重四极杆仪器中通过精心设计的m/z窗口的调度和选择来测量数千个跃迁（初级和次级m/z值对）的程度。良好的MRM检测的设计依赖于先前发现阶段LC-MS/MS研究中肽谱的可用性。手动开发和处理涉及数千次转换的MRM测定的繁琐方面已经刺激了软件工具的开发以使该过程自动化。已经开发了用于项目管理、测定开发、测定验证、数据导出、峰积分、质量评估和生物统计分析的软件包。没有一个单一的工具提供了一个完整的端到端的解决方案，因此，本文回顾了目前的状态，并讨论了这些软件工具的未来发展方向，以使研究人员能够联合收割机这些工具，一个全面的有针对性的蛋白质组学工作流程。
Selective or Multiple Reaction monitoring (SRM/MRM) is a liquid-chromatography (LC)/tandem-mass spectrometry (MS/MS) method that enables the quantitation of specific proteins in a sample by analyzing precursor ions and the fragment ions of their selected tryptic peptides. Instrumentation software has advanced to the point that thousands of transitions (pairs of primary and secondary m/z values) can be measured in a triple quadrupole instrument coupled to an LC, by a well-designed scheduling and selection of m/z windows. The design of a good MRM assay relies on the availability of peptide spectra from previous discovery-phase LC-MS/MS studies. The tedious aspect of manually developing and processing MRM assays involving thousands of transitions has spurred to development of software tools to automate this process. Software packages have been developed for project management, assay development, assay validation, data export, peak integration, quality assessment, and biostatistical analysis. No single tool provides a complete end-to-end solution, thus this article reviews the current state and discusses future directions of these software tools in order to enable researchers to combine these tools for a comprehensive targeted proteomics workflow.
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