An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology.
An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology.
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DOI：
10.1002/pmic.201100571
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发表时间：
2012-04
期刊：
影响因子：
3.4
通讯作者：
Moritz, Robert L.
中科院分区：
文献类型：
--
作者：
Brusniak, Mi-Youn K.;Chu, Caroline S.;Kusebauch, Ulrike;Sartain, Mark J.;Watts, Julian D.;Moritz, Robert L.
选择反应监测（SRM）是一种精确的定量技术，通常用于小分子质谱（MS）。SRM已成为一种重要的技术，有针对性的和假设驱动的蛋白质组学研究，并正在成为复杂的生物样品中的蛋白质定量的参考方法。与传统的基于鸟枪的串联质谱（LC-MS/MS）方法相比，SRM具有高选择性、较低的检测限和更高的重现性。与LC-MS/MS需要计算密集型信息后分析不同，SRM需要采集前生物信息分析来确定蛋白质型肽和最佳转换，以唯一识别和准确定量目标蛋白质。大量基于网络和独立的生物信息学软件工具已经出版，以帮助研究人员确定最佳肽和过渡集。通常基于优选的前体电荷状态、肽分子量、疏水性、在给定碰撞能量（CE）下的片段化模式和所选择的仪器来选择跃迁。对每种肽的选定转换进行验证至关重要，因为肽的性能取决于所用的质谱仪。在这篇综述中，我们提供了一个开源和商业生物信息学工具的概述，用于分析SRM获得的LC-MS数据。
Selected reaction monitoring (SRM) is an accurate quantitative technique, typically used for small-molecule mass spectrometry (MS). SRM has emerged as an important technique for targeted and hypothesis-driven proteomic research, and is becoming the reference method for protein quantification in complex biological samples. SRM offers high selectivity, a lower limit of detection and improved reproducibility, compared to conventional shot-gun based tandem MS (LC-MS/MS) methods. Unlike LC-MS/MS, which requires computationally intensive informatic post-analysis, SRM requires pre-acquisition bioinformatic analysis to determine proteotypic peptides and optimal transitions to uniquely identify and to accurately quantitate proteins of interest. Extensive arrays of bioinformatics software tools, both web-based and stand-alone, have been published to assist researchers to determine optimal peptides and transition sets. The transitions are oftentimes selected based on preferred precursor charge state, peptide molecular weight, hydrophobicity, fragmentation pattern at a given collision energy (CE), and instrumentation chosen. Validation of the selected transitions for each peptide is critical since peptide performance varies depending on the mass spectrometer used. In this review, we provide an overview of open source and commercial bioinformatic tools for analyzing LC-MS data acquired by SRM.
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通过选择反应监测质谱法估计未标记样品的绝对蛋白质含量。
DOI：
10.1074/mcp.m111.013987
发表时间：
2012-03
期刊：
Molecular & cellular proteomics : MCP
影响因子：
--
作者：
Ludwig C;Claassen M;Schmidt A;Aebersold R
通讯作者：
Aebersold R
影响因子：
2.9
作者：
Lame, Mary E.;Chambers, Erin E.;Blatnik, Matthew
通讯作者：
Blatnik, Matthew
影响因子：
9.3
作者：
Abbatiello SE;Mani DR;Keshishian H;Carr SA
通讯作者：
Carr SA
影响因子：
9.9
作者：
Lange, Vinzenz;Picotti, Paola;Domon, Bruno;Aebersold, Ruedi
通讯作者：
Aebersold, Ruedi
影响因子：
6.1
作者：
Christin, Christin;Bischoff, Rainer;Horvatovich, Peter
通讯作者：
Horvatovich, Peter