Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting
Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting
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DOI：
10.1093/bioinformatics/bth460
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发表时间：
2004-12-12
期刊：
影响因子：
5.8
通讯作者：
Rögnvaldsson, T
中科院分区：
文献类型：
--
作者：
Samuelsson, J;Dalevi, D;Rögnvaldsson, T
提出了一套新的基于肽质量指纹图谱的蛋白质自动识别算法和软件工具。该软件是自动的，快速的和模块化的，以满足不同的实验室需求，它可以通过Java用户界面操作或从脚本中调用。软件模块进行峰提取、峰过滤和蛋白质数据库匹配，并通过XML进行通信。因此，如果需要，可以很容易地用其他软件替换单个模块，并且用户可以获得所有中间结果。这些算法的设计是在没有人为干预的情况下进行操作，并包含几种新的方法。该软件的性能和能力说明从不同的质谱仪制造商的光谱，并成功识别的影响因素进行了讨论和quantitative.Motivation：蛋白质鉴定与质谱方法是现代蛋白质组学研究的关键步骤。现在有一些工具可用于执行分析中的不同步骤。只有少数商业系统集成的分析中的所有步骤，往往只有一个供应商的硬件，这些系统的细节是不公开的。结果：一个完整的系统做蛋白质鉴定与肽质量指纹，包括一切从峰值采摘匹配数据库蛋白质。不同算法的细节被公开，以便学术研究人员可以完全控制他们的工具。
A set of new algorithms and software tools for automatic protein identification using peptide mass fingerprinting is presented. The software is automatic, fast and modular to suit different laboratory needs, and it can be operated either via a Java user interface or called from within scripts. The software modules do peak extraction, peak filtering and protein database matching, and communicate via XML. Individual modules can therefore easily be replaced with other software if desired, and all intermediate results are available to the user. The algorithms are designed to operate without human intervention and contain several novel approaches. The performance and capabilities of the software is illustrated on spectra from different mass spectrometer manufacturers, and the factors influencing successful identification are discussed and quantified.Motivation: Protein identification with mass spectrometric methods is a key step in modern proteomics studies. Some tools are available today for doing different steps in the analysis. Only a few commercial systems integrate all the steps in the analysis, often for only one vendor's hardware, and the details of these systems are not public.Results: A complete system for doing protein identification with peptide mass fingerprints is presented, including everything from peak picking to matching the database protein. The details of the different algorithms are disclosed so that academic researchers can have full control of their tools.