通过经验优化，开发针对蛋白质组学的选定反应监测方法。
The development of selected reaction monitoring methods for targeted proteomics via empirical refinement.
机构信息
Department of Genome Sciences, University of Washington, Seattle, WA, USA.
出版信息
Proteomics. 2012 Apr;12(8):1134-41. doi: 10.1002/pmic.201200042.
Abstract
Software advancements in the last several years have had a significant impact on proteomics from method development to data analysis. Herein, we detail a method, which uses our in-house developed software tool termed Skyline, for empirical refinement of candidate peptides from targeted proteins. The method consists of four main steps from generation of a testable hypothesis, method development, peptide refinement, to peptide validation. The ultimate goal is to identify the best performing peptide in terms of ionization efficiency, reproducibility, specificity, and chromatographic characteristics to monitor as a proxy for protein abundance. It is important to emphasize that this method allows the user to perform this refinement procedure in the sample matrix and organism of interest with the instrumentation available. Finally, the method is demonstrated in a case study to determine the best peptide to monitor the abundance of surfactant protein B in lung aspirates.
摘要
在过去的几年中，软件的进步对蛋白质组学产生了重大影响，从方法开发到数据分析。在这里，我们详细介绍了一种方法，该方法使用我们内部开发的软件工具 Skyline，从靶向蛋白质中对候选肽进行经验性优化。该方法主要包括四个步骤，从生成可测试假设、方法开发、肽优化到肽验证。最终目标是根据离子化效率、重现性、特异性和色谱特性来识别性能最佳的肽，以作为监测蛋白质丰度的替代物。重要的是要强调的是，该方法允许用户在感兴趣的样本基质和生物体中使用可用的仪器进行此优化过程。最后，该方法通过一个案例研究进行了演示，以确定监测肺抽吸物中表面活性剂蛋白 B 丰度的最佳肽。
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本文引用的文献
1
Ion formation from charged droplets: Roles of geometry, energy, and time.带电液滴的离子形成：几何形状、能量和时间的作用。
J Am Soc Mass Spectrom. 1993 Jul;4(7):524-35. doi: 10.1016/1044-0305(93)85014-O.
2
Using iRT, a normalized retention time for more targeted measurement of peptides.使用 iRT，对肽进行更有针对性的测量的归一化保留时间。
Proteomics. 2012 Apr;12(8):1111-21. doi: 10.1002/pmic.201100463.
3
mProphet: automated data processing and statistical validation for large-scale SRM experiments.mProphet：用于大规模 SRM 实验的自动化数据处理和统计验证。
Nat Methods. 2011 May;8(5):430-5. doi: 10.1038/nmeth.1584. Epub 2011 Mar 20.
4
ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry.ATAQS：一种用于高通量过渡优化和验证的计算软件工具，适用于选定反应监测质谱法。
BMC Bioinformatics. 2011 Mar 18;12:78. doi: 10.1186/1471-2105-12-78.
5
More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS.在单次鸟枪法蛋白质组学运行中可洗脱超过 100,000 种可检测肽，但大多数肽是无法通过基于数据的 LC-MS/MS 获得的。
J Proteome Res. 2011 Apr 1;10(4):1785-93. doi: 10.1021/pr101060v. Epub 2011 Feb 28.
6
Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry.碰撞能量优化对选择反应监测（SRM）质谱法测定肽的影响。
Anal Chem. 2010 Dec 15;82(24):10116-24. doi: 10.1021/ac102179j. Epub 2010 Nov 19.
7
Collision energy optimization of b- and y-ions for multiple reaction monitoring mass spectrometry.用于多重反应监测质谱法的 b-和 y-离子的碰撞能量优化。
J Proteome Res. 2011 Jan 7;10(1):231-40. doi: 10.1021/pr1004289. Epub 2010 Nov 22.
8
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9
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.Skyline：用于创建和分析靶向蛋白质组学实验的开源文档编辑器。
Bioinformatics. 2010 Apr 1;26(7):966-8. doi: 10.1093/bioinformatics/btq054. Epub 2010 Feb 9.
10
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Proteomics. 2010 Mar;10(6):1106-26. doi: 10.1002/pmic.200900396.
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