PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis
PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis
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DOI：
10.1021/ac2000994
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发表时间：
2011-04-01
影响因子：
7.4
通讯作者：
Breitling, Rainer
中科院分区：
文献类型：
--
作者：
Scheltema, Richard A.;Jankevics, Andris;Breitling, Rainer
最近高分辨率质谱仪的普及产生了大量新的数据分析方法。然而，将这些方法灵活地集成到最适合研究问题的配置中，受到异构文件格式和单一软件开发的阻碍。mzXML、mzData和mzML文件格式支持对未处理的原始数据的统一访问。在本文中，我们介绍了我们的努力，以产生一个同样简单和强大的格式，PeakML，以统一地交换处理过的中介和结果数据。为了展示PeakML的多功能性，我们开发了一个开源的Java工具包，用于在可定制的管道（mzMatch）中处理、过滤和注释质谱，以及一个用户友好的数据可视化环境（PeakML Viewer）。PeakML格式特别支持在由不同组或公司创建的软件之间灵活地交换处理过的数据，正如我们通过将广泛使用的XCMS包与mzMatch数据处理工具提供基于PeakML的集成来说明的那样。作为一个额外的优势，下游分析可以从直接访问汇总质谱结果的完整质量痕量信息中受益，为用户提供快速验证结果的手段。PeakML/mzMatch软件可以在http://mzmatchsourceforge.net上免费获得，有文档、教程和社区论坛。
The recent proliferation of high-resolution mass spectrometers has generated a wealth of new data analysis methods. However, flexible integration of these methods into configurations best suited to the research question is hampered by heterogeneous file formats and monolithic software development. The mzXML, mzData, and mzML file formats have enabled uniform access to unprocessed raw data. in this paper we present our efforts to produce an equally simple and powerful format, PeakML, to uniformly exchange processed intermediary and result data. To demonstrate the versatility of PeakML, we have developed an open source Java toolkit for processing, filtering, and annotating mass spectra in a customizable pipeline (mzMatch), as well as a user-friendly data visualization environment (PeakML Viewer). The PeakML format in particular enables the flexible exchange of processed data between software created by different groups or companies, as we illustrate by providing a PeakML-based integration of the widely used XCMS package with mzMatch data processing tools. As an added advantage, downstream analysis can benefit from direct access to the full mass trace information underlying summarized mass spectrometry results, providing the user with the means to rapidly verify results. The PeakML/mzMatch software is freely available at http://mzmatchsourceforge.net, with documentation, tutorials, and a community forum.