Walzer Mathias, Pernas Lucia Espona, Nasso Sara, Bittremieux Wout, Nahnsen Sven, Kelchtermans Pieter, Pichler Peter, van den Toorn Henk W P, Staes An, Vandenbussche Jonathan, Mazanek Michael, Taus Thomas, Scheltema Richard A, Kelstrup Christian D, Gatto Laurent, van Breukelen Bas, Aiche Stephan, Valkenborg Dirk, Laukens Kris, Lilley Kathryn S, Olsen Jesper V, Heck Albert J R, Mechtler Karl, Aebersold Ruedi, Gevaert Kris, Vizcaíno Juan Antonio, Hermjakob Henning, Kohlbacher Oliver, Martens Lennart
From the ‡Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany;
§Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland;
Mol Cell Proteomics. 2014 Aug;13(8):1905-13. doi: 10.1074/mcp.M113.035907. Epub 2014 Apr 23.
Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml.
质量控制日益被视为基于质谱的蛋白质组学的一个关键方面。最近的几篇论文讨论了质量控制的相关参数，并介绍了从仪器原始数据中提取这些参数的应用。然而，一直缺少一种用于报告这些性能指标的标准数据交换格式。因此，我们开发了qcML格式，这是一种基于XML的标准，遵循了HUPO-PSI（蛋白质组学标准倡议）相关的mzML、mzIdentML、mzQuantML和TraML标准的设计原则。除了XML格式，我们还提供了用于计算各种质量指标的工具以及一种数据库格式和相互转换工具，以便现有的实验室信息管理系统（LIMS）能够轻松地将质量控制数据的关系存储添加到其现有模式中。我们在此描述qcML规范，以及可能的用例和后续分析可能性的示例。有关qcML的所有信息可在http://code.google.com/p/qcml上获取。
