Journal article Open Access
Walzer, Mathias; Espona Pernas, Lucia; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk W. P.; Staes, An; Vandenbussche, Jonathan; Mazanek, Michael; Taus, Thomas; Scheltema, Richard A.; Kelstrup, Christian D.; Gatto, Laurent; van Breukelen, Bas; Aiche, Stephan; Valkenborg, Dirk; Laukens, Kris; Lilley, Kathryn S.; Olsen, Jesper V.; Heck, Albert J. R.; Mechtler, Karl; Aebersold, Ruedi; Gevaert, Kris; Vizcaíno, Juan Antonio; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart
<?xml version='1.0' encoding='UTF-8'?> <record xmlns="http://www.loc.gov/MARC21/slim"> <leader>00000nam##2200000uu#4500</leader> <controlfield tag="005">20200120152731.0</controlfield> <controlfield tag="001">3551517</controlfield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland</subfield> <subfield code="a">Espona Pernas, Lucia</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland</subfield> <subfield code="a">Nasso, Sara</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium</subfield> <subfield code="a">Bittremieux, Wout</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany</subfield> <subfield code="a">Nahnsen, Sven</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium</subfield> <subfield code="a">Kelchtermans, Pieter</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria</subfield> <subfield code="a">Pichler, Peter</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands</subfield> <subfield code="a">van den Toorn, Henk W. P.</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium</subfield> <subfield code="a">Staes, An</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium</subfield> <subfield code="a">Vandenbussche, Jonathan</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria</subfield> <subfield code="a">Mazanek, Michael</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria</subfield> <subfield code="a">Taus, Thomas</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany</subfield> <subfield code="a">Scheltema, Richard A.</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark</subfield> <subfield code="a">Kelstrup, Christian D.</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom</subfield> <subfield code="a">Gatto, Laurent</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands</subfield> <subfield code="a">van Breukelen, Bas</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Department of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany</subfield> <subfield code="a">Aiche, Stephan</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">I-BioStat, Hasselt University, Belgium</subfield> <subfield code="a">Valkenborg, Dirk</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium</subfield> <subfield code="a">Laukens, Kris</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom</subfield> <subfield code="a">Lilley, Kathryn S.</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark</subfield> <subfield code="a">Olsen, Jesper V.</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands</subfield> <subfield code="a">Heck, Albert J. R.</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria</subfield> <subfield code="a">Mechtler, Karl</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland</subfield> <subfield code="a">Aebersold, Ruedi</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium</subfield> <subfield code="a">Gevaert, Kris</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK</subfield> <subfield code="a">Vizcaíno, Juan Antonio</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK</subfield> <subfield code="a">Hermjakob, Henning</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany</subfield> <subfield code="a">Kohlbacher, Oliver</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium</subfield> <subfield code="a">Martens, Lennart</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">1430645</subfield> <subfield code="z">md5:486ec833e7e4c6e6732469cae44a9522</subfield> <subfield code="u">https://zenodo.org/record/3551517/files/Walzer2014.pdf</subfield> </datafield> <datafield tag="542" ind1=" " ind2=" "> <subfield code="l">open</subfield> </datafield> <datafield tag="260" ind1=" " ind2=" "> <subfield code="c">2014-04-23</subfield> </datafield> <datafield tag="909" ind1="C" ind2="O"> <subfield code="p">openaire</subfield> <subfield code="o">oai:zenodo.org:3551517</subfield> </datafield> <datafield tag="909" ind1="C" ind2="4"> <subfield code="c">1905-1913</subfield> <subfield code="n">8</subfield> <subfield code="p">Molecular & Cellular Proteomics</subfield> <subfield code="v">13</subfield> </datafield> <datafield tag="100" ind1=" " ind2=" "> <subfield code="u">Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany</subfield> <subfield code="a">Walzer, Mathias</subfield> </datafield> <datafield tag="245" ind1=" " ind2=" "> <subfield code="a">qcML: An exchange format for quality control metrics from mass spectrometry experiments</subfield> </datafield> <datafield tag="540" ind1=" " ind2=" "> <subfield code="u">https://creativecommons.org/licenses/by/4.0/legalcode</subfield> <subfield code="a">Creative Commons Attribution 4.0 International</subfield> </datafield> <datafield tag="650" ind1="1" ind2="7"> <subfield code="a">cc-by</subfield> <subfield code="2">opendefinition.org</subfield> </datafield> <datafield tag="520" ind1=" " ind2=" "> <subfield code="a"><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></subfield> </datafield> <datafield tag="024" ind1=" " ind2=" "> <subfield code="a">10.1074/mcp.M113.035907</subfield> <subfield code="2">doi</subfield> </datafield> <datafield tag="980" ind1=" " ind2=" "> <subfield code="a">publication</subfield> <subfield code="b">article</subfield> </datafield> </record>
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