Benchmarking stable isotope labeling based quantitative proteomics
Benchmarking stable isotope labeling based quantitative proteomics
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DOI：
10.1016/j.jprot.2012.10.009
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发表时间：
2013-08-02
影响因子：
3.3
通讯作者：
Mohammed, Shabaz
中科院分区：
文献类型：
--
作者：
Altelaar, A. F. Maarten;Frese, Christian K.;Mohammed, Shabaz
最近，几种基于定量质谱学的技术已经发展起来，以询问蛋白质组的复杂性、互连性和动态性质。目前，最流行的方法是使用代谢或化学同位素标记和MS定量，或者使用等压标记和MS/MS定量的化学标记。在这里，我们通过系统的独立的大规模定量蛋白质组学实验，比较SILAC、二甲基和TMT标记策略，来评估三种最流行的方法的性能。尽管这三种方法都有它们的优缺点，但我们的数据表明，使用经典的(基于MS2的)散弹枪方法，这三种方法都可以达到类似深度的识别蛋白质。仅使用MS2的TMT量化受到共隔离的严重影响，从而导致精密度和准确度的降低。这个问题可以通过使用基于MS3的采集来部分解决；然而，代价是量化的蛋白质数量显著减少。有趣的是，SILAC和基于MS的化学标记定量产生了几乎不可区分的结果，与所使用的数据库搜索算法无关。本文是题为：蛋白质组学的新视野和应用[EuPA 2012]的特刊的一部分。(C)2012爱思唯尔B.V.保留所有权利。
Several quantitative mass spectrometry based technologies have recently evolved to interrogate the complexity, interconnectivity and dynamic nature of proteomes. Currently, the most popular methods use either metabolic or chemical isotope labeling with MS based quantification or chemical labeling using isobaric tags with MS/MS based quantification. Here, we assess the performance of three of the most popular approaches through systematic independent large scale quantitative proteomics experiments, comparing SILAC, dimethyl and TMT labeling strategies. Although all three methods have their strengths and weaknesses, our data indicate that all three can reach a similar depth in number of identified proteins using a classical (MS2 based) shotgun approach. TMT quantification using only MS2 is heavily affected by co-isolation leading to compromised precision and accuracy. This issue may be partly resolved by using an MS3 based acquisition; however, at the cost of a significant reduction in number of proteins quantified. Interestingly, SILAC and chemical labeling with MS based quantification produce almost indistinguishable results, independent of which database search algorithm used. This article is part of a Special Issue entitled:New Horizons and Applications for Proteomics [EuPA 2012]. (C) 2012 Elsevier B.V. All rights reserved.