jqcML: an open-source java API for mass spectrometry quality control data in the qcML format

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 dis...

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Bibliographic Details
Published in:Journal of proteome research Vol. 13; no. 7; p. 3484
Main Authors: Bittremieux, Wout, Kelchtermans, Pieter, Valkenborg, Dirk, Martens, Lennart, Laukens, Kris
Format: Journal Article
Language:English
Published: United States 03.07.2014
Subjects:
Data Interpretation, Statistical
Humans
Mass Spectrometry - standards
Programming Languages
Proteomics
Quality Control
Software
ISSN:1535-3907, 1535-3907
Online Access:Get more information
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Summary: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 .
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ISSN:1535-3907
1535-3907
DOI:10.1021/pr401274z