RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database
RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database
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DOI：
10.1002/1615-9861(200201)2:1
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发表时间：
2002-01-01
期刊：
影响因子：
3.4
通讯作者：
Beavis, RC
中科院分区：
文献类型：
--
作者：
Field, HI;Fenyö, D;Beavis, RC
RADARS是一个快速、自动化的数据存档和检索软件系统，用于高通量蛋白质组学质谱数据的处理和存储。大多数质谱仪数据文件都与RADARS兼容，以便进行一致的处理。该系统自动获取未处理的数据文件，通过计算机数据库搜索识别蛋白质，然后将处理后的数据和搜索结果存储在适合定制报告的关系数据库中。该系统是强大的，在24/7操作中使用，通过Web浏览器可供内联网的多个用户访问，可由虚拟专用网络监控，并且是安全的。RADARS可以扩展到一台或多台计算机上使用，并且适合于多处理器系统。它可以以FASTA格式合并任何本地数据库，并可以在线搜索蛋白质和DNA数据库。一个关键功能是一套可视化工具（许多免费提供），允许轻松操作光谱，手动注释，重新分析，并访问所有程序。我们还描述了Sonar MS/MS的使用，这是一种新型的快速搜索引擎，每个过程需要40 MB RAM，用于搜索所有六个阅读框架中翻译的基因组或EST数据库。RADARS通过其高效的算法降低了分析成本：Sonar MS/MS可以识别蛋白质，而无需准确了解母离子质量和蛋白质标签。统计评分方法提供了接近专家的准确性，并为非专家用户带来了强大的数据分析。
RADARS, a rapid, automated, data archiving and retrieval software system for high-throughput proteomic mass spectral data processing and storage, is described. The majority of mass spectrometer data files are compatible with RADARS, for consistent processing. The system automatically takes unprocessed data files, identifies proteins via in silico database searching, then stores the processed data and search results in a relational database suitable for customized reporting. The system is robust, used in 24/7 operation, accessible to multiple users of an intranet through a web browser, may be monitored by Virtual Private Network, and is secure. RADARS is scalable for use on one or many computers, and is suited to multiple processor systems. It can incorporate any local database in FASTA format, and can search protein and DNA databases online. A key feature is a suite of visualisation tools (many available gratis), allowing facile manipulation of spectra, by hand annotation, reanalysis, and access to all procedures. We also described the use of Sonar MS/MS, a novel, rapid search engine requiring similar to40 MB RAM per process for searches against a genomic or EST database translated in all six reading frames. RADARS reduces the cost of analysis by its efficient algorithms: Sonar MS/MS can identifiy proteins without accurate knowledge of the parent ion mass and without protein tags. Statistical scoring methods provide close-to-expert accuracy and brings robust data analysis to the non-expert user.