3551517
doi
10.1074/mcp.M113.035907
oai:zenodo.org:3551517
Espona Pernas, Lucia
Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland
Nasso, Sara
Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
Bittremieux, Wout
Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
Nahnsen, Sven
Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany
Kelchtermans, Pieter
Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
Pichler, Peter
Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria
van den Toorn, Henk W. P.
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
Staes, An
Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
Vandenbussche, Jonathan
Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
Mazanek, Michael
Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria
Taus, Thomas
Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria
Scheltema, Richard A.
Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
Kelstrup, Christian D.
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
Gatto, Laurent
Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom
van Breukelen, Bas
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
Aiche, Stephan
Department of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany
Valkenborg, Dirk
I-BioStat, Hasselt University, Belgium
Laukens, Kris
Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
Lilley, Kathryn S.
Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom
Olsen, Jesper V.
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
Heck, Albert J. R.
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
Mechtler, Karl
Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria
Aebersold, Ruedi
Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland
Gevaert, Kris
Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
Vizcaíno, Juan Antonio
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Hermjakob, Henning
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Kohlbacher, Oliver
Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany
Martens, Lennart
Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
qcML: An exchange format for quality control metrics from mass spectrometry experiments
Walzer, Mathias
Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
<p>Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml.</p>
Zenodo
2014-04-23
info:eu-repo/semantics/article
3551516
1579534051.430064
1430645
md5:486ec833e7e4c6e6732469cae44a9522
https://zenodo.org/records/3551517/files/Walzer2014.pdf
public
Molecular & Cellular Proteomics
13
8
1905-1913
2014-04-23