Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/18756
Title: jqcML: An Open-Source Java API for Mass Spectrometry Quality Control Data in the qcML Format
Authors: Bittremieux, Wout
Kelchtermans, Pieter
Valkenborg, Dirk 
Martens, Lennart
Laukens, Kris
Issue Date: 2014
Publisher: AMER CHEMICAL SOC
Source: JOURNAL OF PROTEOME RESEARCH, 13 (7), p. 3484-3487
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.
Notes: [Bittremieux, Wout; Laukens, Kris] Univ Antwerp, Dept Math & Comp Sci, B-2020 Antwerp, Belgium. [Bittremieux, Wout; Laukens, Kris] Univ Antwerp, Biomed Informat Res Ctr Antwerp Biomina, Univ Antwerp Hosp, B-2650 Antwerp, Belgium. [Kelchtermans, Pieter; Martens, Lennart] VIB, Dept Med Prot Res, B-9000 Ghent, Belgium. [Kelchtermans, Pieter; Martens, Lennart] Univ Ghent, Dept Biochem, Fac Med & Hlth Sci, B-9000 Ghent, Belgium. [Kelchtermans, Pieter; Vakenborg, Dirk] Flemish Inst Technol Res VITO, B-2400 Mol, Belgium. [Vakenborg, Dirk] Univ Antwerp, CFP CeProMa, B-2020 Antwerp, Belgium. [Vakenborg, Dirk] Hasselt Univ, I BioStat, B-3590 Diepenbeek, Belgium.
Keywords: mass spectrometry; proteomics; quality control; qcML; Java; API; open source; XML; qcDB; database;mass spectrometry; proteomics; quality control; qcML; Java; API; open source; XML; qcDB; database
Document URI: http://hdl.handle.net/1942/18756
ISSN: 1535-3893
e-ISSN: 1535-3907
DOI: 10.1021/pr401274z
ISI #: 000338693400032
Rights: © 2014 American Chemical Society.
Category: A1
Type: Journal Contribution
Validations: ecoom 2015
Appears in Collections:Research publications

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