mz5: Space- and Time-efficient Storage of Mass Spectrometry Data Sets
mz5: Space- and Time-efficient Storage of Mass Spectrometry Data Sets
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DOI：
10.1074/mcp.o111.011379
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发表时间：
2012-01-01
影响因子：
7
通讯作者：
Steen, Hanno
中科院分区：
文献类型：
--
作者：
Wilhelm, Mathias;Kirchner, Marc;Steen, Hanno
在许多MS驱动的组学领域，研究人员目睹了越来越多的高通量MS数据的获取，并面临着对其紧凑但可有效访问的存储的需求。为了满足对开放数据交换格式的需求，系统生物学研究所的蛋白质组学标准计划和西雅图蛋白质组中心分别独立开发了mzData和mzXML格式。在随后的共同努力中，他们定义了一个本体和相关的受控词汇表，用于指定MS数据文件的内容，并以较新的mzML格式实现。所有这三种格式都基于XML，因此在存储空间需求或读/写速度方面都不是特别有效。本文介绍了mz 5，这是一个完整的mzML本体的重新实现，它基于高效的工业级存储后端HDF 5。与当前的mzML标准相比，该策略产生的平均文件大小减少了约54%，线性读写速度提高了约3-4倍。该格式作为ProteoWizard项目的一部分实现，并在许可的Apache许可证下可用。其他信息和下载链接可从http://software.steenlab.org/mz5获得。Molecular & Cellular Proteomics 11：10.1074/mcp. O111.011379，1-5，2012.
Across a host of MS-driven-omics fields, researchers witness the acquisition of ever increasing amounts of high throughput MS data and face the need for their compact yet efficiently accessible storage. Addressing the need for an open data exchange format, the Proteomics Standards Initiative and the Seattle Proteome Center at the Institute for Systems Biology independently developed the mzData and mzXML formats, respectively. In a subsequent joint effort, they defined an ontology and associated controlled vocabulary that specifies the contents of MS data files, implemented as the newer mzML format. All three formats are based on XML and are thus not particularly efficient in either storage space requirements or read/write speed. This contribution introduces mz5, a complete reimplementation of the mzML ontology that is based on the efficient, industrial strength storage backend HDF5. Compared with the current mzML standard, this strategy yields an average file size reduction to similar to 54% and increases linear read and write speeds similar to 3-4-fold. The format is implemented as part of the ProteoWizard project and is available under a permissive Apache license. Additional information and download links are available from http://software.steenlab.org/mz5. Molecular & Cellular Proteomics 11: 10.1074/mcp.O111.011379, 1-5, 2012.