The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics.
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics.
复制标题
DOI：
10.1074/mcp.o113.028506
复制
发表时间：
2013-08
期刊：
影响因子：
--
通讯作者：
Jones AR
中科院分区：
文献类型：
--
作者：
Walzer M;Qi D;Mayer G;Uszkoreit J;Eisenacher M;Sachsenberg T;Gonzalez-Galarza FF;Fan J;Bessant C;Deutsch EW;Reisinger F;Vizcaíno JA;Medina-Aunon JA;Albar JP;Kohlbacher O;Jones AR
通过质谱（MS）定量蛋白质丰度的一系列异构方法1导致建模，存档，交换或提交实验数据集作为期刊的补充材料方面的巨大挑战。到目前为止，还没有一种广泛接受的格式来记录软件如何进行定量分析的证据线索，在软件包之间转移数据，或提交给公共数据库。在蛋白质组学标准计划的背景下，我们开发了mzQuantML数据标准。该标准可以表示有关二维保留时间与质量/电荷空间（称为特征）、肽、蛋白质和蛋白质组（其中肽与蛋白质推断存在模糊性）区域的定量数据，并且它为小分子提供了有限的支持（代谢组学）数据。该格式具有用于表示重复MS运行、重复分组（例如，作为研究变量）以及捕获软件包用于获得这些值的参数的结构。该格式能够引用其他标准，如mzML和mzIdentML，因此现在可以描述整个MS工作流程的证据线索。有几个软件实现是可用的，我们鼓励其他生物信息学组使用mzQuantML作为定量软件和构建本地存储库的输入，内部或输出格式。所有项目资源都可以从HUPO蛋白质组学标准倡议http://www.psidev.info/mzquantml获得。
The range of heterogeneous approaches available for quantifying protein abundance via mass spectrometry (MS)1 leads to considerable challenges in modeling, archiving, exchanging, or submitting experimental data sets as supplemental material to journals. To date, there has been no widely accepted format for capturing the evidence trail of how quantitative analysis has been performed by software, for transferring data between software packages, or for submitting to public databases. In the context of the Proteomics Standards Initiative, we have developed the mzQuantML data standard. The standard can represent quantitative data about regions in two-dimensional retention time versus mass/charge space (called features), peptides, and proteins and protein groups (where there is ambiguity regarding peptide-to-protein inference), and it offers limited support for small molecule (metabolomic) data. The format has structures for representing replicate MS runs, grouping of replicates (for example, as study variables), and capturing the parameters used by software packages to arrive at these values. The format has the capability to reference other standards such as mzML and mzIdentML, and thus the evidence trail for the MS workflow as a whole can now be described. Several software implementations are available, and we encourage other bioinformatics groups to use mzQuantML as an input, internal, or output format for quantitative software and for structuring local repositories. All project resources are available in the public domain from the HUPO Proteomics Standards Initiative http://www.psidev.info/mzquantml.