Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
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DOI：
10.1021/pr101065j
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发表时间：
2011-04-01
影响因子：
4.4
通讯作者：
Mann, Matthias
中科院分区：
文献类型：
--
作者：
Cox, Juergen;Neuhauser, Nadin;Mann, Matthias
基于质谱（MS）的蛋白质组学的关键步骤是通过其碎片光谱识别序列数据库中的肽。在这里，我们描述仙女座，一种新的肽搜索引擎使用概率评分模型。在蛋白质组数据上，根据基于目标诱饵搜索的灵敏度和特异性分析，仙女座菌株的表现与Mascot（一种广泛使用的商业搜索引擎）一样好。此外，它可以处理具有任意高的片段质量准确度的数据，能够分配和评分复杂的翻译后修饰模式，如高度磷酸化的肽，并容纳非常大的数据库。给出了Andromeda的算法。Andromeda可以独立运行，也可以作为广泛使用的MaxQuant计算蛋白质组学平台的集成搜索引擎，两者都可以在www.maxquantorg上免费获得。该组合使得能够在台式计算机上以简单的分析工作流程分析大型数据集。搜索个别光谱仙女座菌株也可以通过网络服务器访问。我们证明了该系统的灵活性，通过实施的能力，以确定共片段肽，显着提高识别肽的总数。
A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel peptide search engine using a probabilistic scoring model. On proteome data, Andromeda performs as well as Mascot, a widely used commercial search engine, as judged by sensitivity and specificity analysis based on target decoy searches. Furthermore, it can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, such as highly phosphorylated peptides, and accommodates extremely large databases. The algorithms of Andromeda are provided. Andromeda can function independently or as an integrated search engine of the widely used MaxQuant computational proteomics platform and both are freely available at www.maxquantorg. The combination enables analysis of large data sets in a simple analysis workflow on a desktop computer. For searching individual spectra Andromeda is also accessible via a web server. We demonstrate the flexibility of the system by implementing the capability to identify cofragmented peptides, significantly improving the total number of identified peptides.