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American Chemical Society, Journal of Proteome Research, 7(13), p. 3484-3487

DOI: 10.1021/pr401274z

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

This paper is available in a repository.
This paper is available in a repository.

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Abstract

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. ; This work was supported by SBO grant "InSPECtor" (120025) of the Flemish agency for Innovation by Science and Technology (IWT). ; mass spectrometry; proteomics; quality control; qcML; Java; API; open source; XML; qcDB; database