Please use this identifier to cite or link to this item:
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
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
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:
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

Files in This Item:
File Description SizeFormat 
bittremieux 1.pdf
  Restricted Access
published version288.17 kBAdobe PDFView/Open    Request a copy
Show full item record


checked on Sep 3, 2020


checked on May 13, 2022

Page view(s)

checked on May 18, 2022


checked on May 18, 2022

Google ScholarTM



Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.