Representation of selected-reaction monitoring data in the mzQuantML data standard.
Representation of selected-reaction monitoring data in the mzQuantML data standard.
复制标题
DOI：
10.1002/pmic.201400281
复制
发表时间：
2015-08
期刊：
影响因子：
3.4
通讯作者：
Jones AR
中科院分区：
文献类型：
--
作者：
Qi D;Lawless C;Teleman J;Levander F;Holman SW;Hubbard S;Jones AR
mzQuantML数据标准旨在捕获蛋白质组学中定量软件的输出，以支持提交到公共存储库，可视化软件和管道/模块化方法的开发。该标准是围绕一个公共核心设计的，该核心可以通过发布由验证软件检查的语义规则来扩展，以支持特定类型的技术。mzQuantML的第一个版本通过四套语义规则支持四种定量蛋白质组学技术：(i)基于强度的（MS1）无标签，（ii）基于MS1标签的（如SILAC或N15）， （iii）基于MS2标签的（iTRAQ或串联质量标签），以及（iv）光谱计数。我们对mzQuantML进行了更新，以支持SRM技术。该更新包括表示SRM转换的定量测量和相关元数据，推断肽水平或蛋白质水平定量值的机制，以及通过创建语义规则和受控词汇表术语来支持基于标签或无标签的SRM协议。我们已经更新了mzQuantML（版本1.0.1）和mzQuantML验证器的规范文档，以确保由不同的导出器生成一致的文件。我们还报告了从流行的SRM软件包（如Skyline和Anubis）中生成mzQuantML文件的能力。
The mzQuantML data standard was designed to capture the output of quantitative software in proteomics, to support submissions to public repositories, development of visualization software and pipeline/modular approaches. The standard is designed around a common core that can be extended to support particular types of technique through the release of semantic rules that are checked by validation software. The first release of mzQuantML supported four quantitative proteomics techniques via four sets of semantic rules: (i) intensity-based (MS1) label free, (ii) MS1 label-based (such as SILAC or N15), (iii) MS2 tag-based (iTRAQ or tandem mass tags), and (iv) spectral counting. We present an update to mzQuantML for supporting SRM techniques. The update includes representing the quantitative measurements, and associated meta-data, for SRM transitions, the mechanism for inferring peptide-level or protein-level quantitative values, and support for both label-based or label-free SRM protocols, through the creation of semantic rules and controlled vocabulary terms. We have updated the specification document for mzQuantML (version 1.0.1) and the mzQuantML validator to ensure that consistent files are produced by different exporters. We also report the capabilities for production of mzQuantML files from popular SRM software packages, such as Skyline and Anubis.