mzMLb: a future-proof raw mass spectrometry data format based on standards-compliant mzML and optimized for speed and storage requirements
mzMLb: a future-proof raw mass spectrometry data format based on standards-compliant mzML and optimized for speed and storage requirements
复制标题
mzMLb：一种面向未来的原始质谱数据格式，基于符合标准的 mzML，并针对速度和存储要求进行了优化
DOI：
10.1101/2020.02.13.947218
复制
发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Bhamber R
中科院分区：
文献类型：
--
作者：
Bhamber R
随着质谱 (MS) 蛋白质组学和代谢组学产生的数据量不断增加，以及现在分析的样本量巨大，对同时具有文件大小效率和更快的读/写速度的通用开放格式的需求已成为推动下一代数据分析流程的最重要因素。蛋白质组学标准倡议 (PSI) 为数据交换建立了清晰、精确的可扩展标记语言 (XML) 表示形式 mzML，并得到广泛采用；然而，存储和文件访问效率并不是主要关注点。我们提出了一种 HDF5 文件格式“mzMLb”，该格式针对读/写速度和原始质谱数据的存储进行了优化。我们对写入速度、随机读取速度和存储大小进行了广泛的验证，展示了一种灵活的格式，无论是否压缩，在几乎所有情况下都比所有现有方法更快，而压缩后的大小与专有供应商文件格式相当。由于我们的方法独特地保留了元数据的 XML 编码，因此该格式隐式支持 mzML 的未来版本并且易于实现：mzMLb 的设计遵循 HDF5 和 NetCDF4 标准实现，由于第三方广泛的编程语言支持，因此可以轻松地被第三方使用。提供了已建立的 ProteoWizard 工具包中的参考实现。
With ever-increasing amounts of data produced by mass spectrometry (MS) proteomics and metabolomics, and the sheer volume of samples now analyzed, the need for a common open format possessing both file size efficiency and faster read/write speeds has become paramount to drive the next generation of data analysis pipelines. The Proteomics Standards Initiative (PSI) has established a clear and precise extensible markup language (XML) representation for data interchange, mzML, receiving substantial uptake; nevertheless, storage and file access efficiency has not been the main focus. We propose an HDF5 file format “mzMLb” that is optimized for both read/write speed and storage of the raw mass spectrometry data. We provide an extensive validation of the write speed, random read speed, and storage size, demonstrating a flexible format that with or without compression is faster than all existing approaches in virtually all cases, while with compression is comparable in size to proprietary vendor file formats. Since our approach uniquely preserves the XML encoding of the metadata, the format implicitly supports future versions of mzML and is straightforward to implement: mzMLb’s design adheres to both HDF5 and NetCDF4 standard implementations, which allows it to be easily utilized by third parties due to their widespread programming language support. A reference implementation within the established ProteoWizard toolkit is provided.