jqcML: An Open-Source Java API for Mass Spectrometry Quality Control Data in the qcML Format

• Published in: Journal of proteome research Vol. 13; no. 7; pp. 3484 - 3487
• Main Authors: Bittremieux, Wout, Kelchtermans, Pieter, Valkenborg, Dirk, Martens, Lennart, Laukens, Kris
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 03.07.2014
• Subjects: computer software; Data Interpretation, Statistical; Humans; mass spectrometry; Mass Spectrometry - standards; Programming Languages; proteome; Proteomics; Quality Control; Software; Java; open source; database; proteomics; quality control; qcDB; qcML; XML; mass spectrometry; API
• ISSN: 1535-3893; 1535-3907; 1535-3907
• DOI: 10.1021/pr401274z

The awareness that systematic quality control is an essential factor to enable the growth of proteomics into a mature analytical discipline has increased over the past few years. To this aim, a controlled vocabulary and document structure have recently been proposed by Walzer et al. to store and disseminate quality-control metrics for mass-spectrometry-based proteomics experiments, called qcML. To facilitate the adoption of this standardized quality control routine, we introduce jqcML, a Java application programming interface (API) for the qcML data format. First, jqcML provides a complete object model to represent qcML data. Second, jqcML provides the ability to read, write, and work in a uniform manner with qcML data from different sources, including the XML-based qcML file format and the relational database qcDB. Interaction with the XML-based file format is obtained through the Java Architecture for XML Binding (JAXB), while generic database functionality is obtained by the Java Persistence API (JPA). jqcML is released as open-source software under the permissive Apache 2.0 license and can be downloaded from https://bitbucket.org/proteinspector/jqcml.