qcML: an exchange format for quality control metrics from mass spectrometry experiments.
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.
From the ‡Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany;
Mathias
M
Walzer
§Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland;
Lucia Espona
LE
Pernas
¶Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland; §Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland;
Sara
S
Nasso
‖Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; **Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Antwerp, Belgium;
Wout
W
Bittremieux
From the ‡Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany;
Sven
S
Nahnsen
‡‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §§Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; ¶¶Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol Belgium;
Pieter
P
Kelchtermans
‖‖Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, A-1030 Vienna, Austria;
Peter
P
Pichler
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands;
Henk W P
HW
van den Toorn
‡‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §§Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium;
An
A
Staes
‡‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §§Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium;
Jonathan
J
Vandenbussche
‖‖Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, A-1030 Vienna, Austria;
Michael
M
Mazanek
‖‖Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, A-1030 Vienna, Austria;
Thomas
T
Taus
Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany;
Richard A
RA
Scheltema
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark;
Christian D
CD
Kelstrup
Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom; Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
Laurent
L
Gatto
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands;
Bas
B
van Breukelen
Department of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany;
Stephan
S
Aiche
¶¶Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol Belgium; I-BioStat, Hasselt University, Belgium; CFP-CeProMa, University of Antwerp, Belgium;
Dirk
D
Valkenborg
‖Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; **Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Antwerp, Belgium;
Kris
K
Laukens
Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom;
Kathryn S
KS
Lilley
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark;
Jesper V
JV
Olsen
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands;
Albert J R
AJ
Heck
‖‖Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, A-1030 Vienna, Austria;
Karl
K
Mechtler
§Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland;
Ruedi
R
Aebersold
‡‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §§Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium;
Kris
K
Gevaert
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK;
Juan Antonio
JA
Vizcaíno
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK;
Henning
H
Hermjakob
From the ‡Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany;
Oliver
O
Kohlbacher
‡‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §§Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; lennart.martens@vib-ugent.be.
Lennart
L
Martens
D030562:Databases, Protein; D013058:Mass Spectrometry / Q000592:standards*; D011381:Programming Languages; D040901:Proteomics / Q000592:standards; D011786:Quality Control; D012984:Software