Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
J Proteome Res. 2011 Apr 1;10(4):1794-805. doi: 10.1021/pr101065j. Epub 2011 Feb 22.
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.maxquant.org. 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.
基于质谱（MS）的蛋白质组学的一个关键步骤是通过其碎片谱在序列数据库中鉴定肽。在这里，我们描述了一种新的肽搜索引擎 Andromeda，它使用概率评分模型。在蛋白质组数据上，Andromeda 的性能与广泛使用的商业搜索引擎 Mascot 一样好，这可以通过基于目标诱饵搜索的灵敏度和特异性分析来判断。此外，它可以处理具有任意高碎片质量精度的数据，能够分配和评分复杂的翻译后修饰模式，如高度磷酸化肽，并适应非常大的数据库。提供了 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，两者均可在 www.maxquant.org 上免费获得。该组合能够在台式计算机上的简单分析工作流程中分析大型数据集。对于单个光谱的搜索，也可以通过网络服务器访问 Andromeda。我们通过实现识别共碎片肽的功能来展示该系统的灵活性，这显著提高了鉴定的肽的总数。
