The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.
The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.
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DOI：
10.1074/mcp.o113.036681
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发表时间：
2014-10
期刊：
影响因子：
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通讯作者：
Hermjakob H
中科院分区：
文献类型：
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作者：
Griss J;Jones AR;Sachsenberg T;Walzer M;Gatto L;Hartler J;Thallinger GG;Salek RM;Steinbeck C;Neuhauser N;Cox J;Neumann S;Fan J;Reisinger F;Xu QW;Del Toro N;Pérez-Riverol Y;Ghali F;Bandeira N;Xenarios I;Kohlbacher O;Vizcaíno JA;Hermjakob H
HUPO蛋白质组学标准计划开发了几种标准化数据格式，以促进基于质谱（MS）的蛋白质组学的数据共享。这使得研究人员能够以统一的方式报告他们的完整结果。然而，目前还没有一种格式可以用简单的表格形式来描述蛋白质组学和代谢组学实验的最终定性和定量结果。许多下游分析用例只关注实验的最终结果，需要易于访问的格式，与Microsoft Excel或r等工具兼容。我们为基于ms的蛋白质组学和代谢组学结果开发了mzTab文件格式，以满足这一需求。mzTab旨在作为现有的基于xml的标准文件格式（mzML、mzIdentML、mzQuantML）的轻量级补充，提供全面的摘要，在概念上类似于科学出版物的补充材料。mzTab文件可以包含蛋白质、肽、小分子鉴定以及实验元数据和基本定量信息。该格式不是为了存储完整的实验证据，而是提供了在不同细节级别报告结果的机制。这些范围从最终结果的简单总结到结果的表示，包括实验设计。这种格式非常适合将基于ms的蛋白质组学和代谢组学结果提供给ms领域之外的更广泛的生物群落。一些蛋白质组学和代谢组学的软件工具已经将这种格式作为输出格式。全面的mzTab规范文档和大量的附加文档可以在网上找到。
The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools such as Microsoft Excel or R. We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. These range from a simple summary of the final results to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found online.