The MaxQuant computational platform for mass spectrometry-based shotgun proteomics
The MaxQuant computational platform for mass spectrometry-based shotgun proteomics
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DOI：
10.1038/nprot.2016.136
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发表时间：
2016-12-01
期刊：
影响因子：
14.8
通讯作者：
Cox, Juergen
中科院分区：
文献类型：
--
作者：
Tyanova, Stefka;Temu, Tikira;Cox, Juergen
MaxQuant是基于质谱（MS）的蛋白质组学数据分析最常用的平台之一。自2008年首次发布以来，它在功能上有了大幅增长，可以与更多的MS平台结合使用。在这里，我们提出了一个更新的协议，涵盖了最重要的基本计算工作流程，包括那些设计用于定量无标记蛋白质组学，MS1水平标记和同量异位素标记技术。该协议提供了MaxQuant中使用的参数的完整描述，以及其集成搜索引擎Andromeda的配置选项。本协议更新描述了对现有协议的改编，该协议对该技术进行了实质性修改。简要介绍了鸟枪法蛋白质组学的重要概念及其在MaxQuant中的实现，包括不同的定量策略和错误发现率（FDR）的控制，以及翻译后修饰（PTM）的分析。详细解释了MaxQuant输出表，其中包含有关蛋白质和PTM定量的信息。此外，我们提供了一个简短的版本的工作流程，适用于简单和标准的实验设计的数据集。MaxQuant算法可在多个处理器上高效并行化，并可从台式计算机扩展到具有多个核心的服务器。该软件是用C#编写的，可以在http://www.maxquant.org上免费获得。
MaxQuant is one of the most frequently used platforms for mass-spectrometry (MS)-based proteomics data analysis. Since its first release in 2008, it has grown substantially in functionality and can be used in conjunction with more MS platforms. Here we present an updated protocol covering the most important basic computational workflows, including those designed for quantitative label-free proteomics, MS1-level labeling and isobaric labeling techniques. This protocol presents a complete description of the parameters used in MaxQuant, as well as of the configuration options of its integrated search engine, Andromeda. This protocol update describes an adaptation of an existing protocol that substantially modifies the technique. Important concepts of shotgun proteomics and their implementation in MaxQuant are briefly reviewed, including different quantification strategies and the control of false-discovery rates (FDRs), as well as the analysis of post-translational modifications (PTMs). The MaxQuant output tables, which contain information about quantification of proteins and PTMs, are explained in detail. Furthermore, we provide a short version of the workflow that is applicable to data sets with simple and standard experimental designs. The MaxQuant algorithms are efficiently parallelized on multiple processors and scale well from desktop computers to servers with many cores. The software is written in C# and is freely available at http://www.maxquant.org.