A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study.
A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study.
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DOI：
10.1186/1477-5956-9-30
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发表时间：
2011-06-11
期刊：
影响因子：
2
通讯作者：
Nattkemper TW
中科院分区：
文献类型：
--
作者：
Albaum SP;Hahne H;Otto A;Haußmann U;Becher D;Poetsch A;Goesmann A;Nattkemper TW
基于质谱的蛋白质组学已经达到可以在一次实验中全面分析细胞的整个蛋白质组的阶段。在这里，稳定同位素的使用已成为产生蛋白质相对丰度值的标准技术。近年来，越来越多的实验不仅描绘了不同时间点上调或下调蛋白质的静态图像，而且还比较了生物体的发育阶段或不同的实验条件。尽管这些实验背后的科学问题当然是多方面的，但仍然经常出现两个问题：1）哪些蛋白质在选定的实验条件下受到差异性调节，2）是否有一组蛋白质显示出相似的丰度比，表明它们具有相似的周转率？我们就如何回答这两个问题提供建议，并全面比较各种常用的计算方法及其结果。这项工作提供了通过计算方法丛林来分析基于质谱的同位素标记数据集的指导，并推荐了一种有效且易于使用的评估策略。我们用三个最近发布的枯草芽孢杆菌和谷氨酸棒杆菌数据集展示了我们的方法。特别关注聚类分析方法的应用和验证。所有应用的方法均在富互联网应用程序 QuPE 中实施。结果可以在 http://qupe.cebitec.uni-bielefeld.de 上找到。
Mass spectrometry-based proteomics has reached a stage where it is possible to comprehensively analyze the whole proteome of a cell in one experiment. Here, the employment of stable isotopes has become a standard technique to yield relative abundance values of proteins. In recent times, more and more experiments are conducted that depict not only a static image of the up- or down-regulated proteins at a distinct time point but instead compare developmental stages of an organism or varying experimental conditions. Although the scientific questions behind these experiments are of course manifold, there are, nevertheless, two questions that commonly arise: 1) which proteins are differentially regulated regarding the selected experimental conditions, and 2) are there groups of proteins that show similar abundance ratios, indicating that they have a similar turnover? We give advice on how these two questions can be answered and comprehensively compare a variety of commonly applied computational methods and their outcomes. This work provides guidance through the jungle of computational methods to analyze mass spectrometry-based isotope-labeled datasets and recommends an effective and easy-to-use evaluation strategy. We demonstrate our approach with three recently published datasets on Bacillus subtilis and Corynebacterium glutamicum . Special focus is placed on the application and validation of cluster analysis methods. All applied methods were implemented within the rich internet application QuPE. Results can be found at http://qupe.cebitec.uni-bielefeld.de.
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影响因子：
11.2
作者：
GLASS, GV;PECKHAM, PD;SANDERS, JR
通讯作者：
SANDERS, JR
影响因子：
3.4
作者：
Haussmann, Ute;Qi, Su-Wei;Poetsch, Ansgar
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DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
3.2
作者：
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通讯作者：
Becher, Doerte
影响因子：
3
作者：
Giancarlo R;Scaturro D;Utro F
通讯作者：
Utro F