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Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/17865

Title: qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments
Authors: Walzer, Mathias
Pernas, Lucia Espona
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
Vizcaino, Juan Antonio
Hermjakob, Henning
Kohlbacher, Oliver
Martens, Lennart
Issue Date: 2014
Publisher: AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC
Citation: MOLECULAR & CELLULAR PROTEOMICS, 13 (8), p. 1905-1913
Abstract: 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.
Notes: [Walzer, Mathias; Nahnsen, Sven; Kohlbacher, Oliver] Univ Tubingen, Ctr Bioinformat, Tubingen, Germany. [Walzer, Mathias; Nahnsen, Sven; Kohlbacher, Oliver] Univ Tubingen, Quantitat Biol Ctr, Tubingen, Germany. [Walzer, Mathias; Nahnsen, Sven; Kohlbacher, Oliver] Univ Tubingen, Dept Comp Sci, Tubingen, Germany. [Pernas, Lucia Espona; Nasso, Sara; Aebersold, Ruedi] ETH, Dept Biol, Inst Mol Syst Biol, CH-8092 Zurich, Switzerland. [Nasso, Sara] Univ Zurich, Inst Mol Life Sci, CH-8057 Zurich, Switzerland. [Bittremieux, Wout; Laukens, Kris] Univ Antwerp, Dept Math & Comp Sci, B-2020 Antwerp, Belgium. [Bittremieux, Wout; Laukens, Kris] Univ Antwerp, Univ Antwerp Hosp, Biomed Informat Res Ctr Antwerp Biomina, B-2020 Antwerp, Belgium. [Kelchtermans, Pieter; Staes, An; Vandenbussche, Jonathan; Gevaert, Kris] Univ Ghent VIB, Dept Med Prot Res, B-9000 Ghent, Belgium. [Kelchtermans, Pieter; Staes, An; Vandenbussche, Jonathan; Gevaert, Kris] Univ Ghent, Fac Med & Hlth Sci, Dept Biochem, B-9000 Ghent, Belgium. [Kelchtermans, Pieter; Valkenborg, Dirk] Flemish Inst Technol Res VITO, B-2400 Mol, Belgium. [Pichler, Peter; Mazanek, Michael; Taus, Thomas; Mechtler, Karl] Res Inst Mol Pathol IMP, A-1030 Vienna, Austria. [Pichler, Peter; Laukens, Kris] Austrian Acad Sci IMBA, Inst Mol Biotechnol, A-1030 Vienna, Austria. [van den Toorn, Henk W. P.; van Breukelen, Bas; Heck, Albert J. R.] Univ Utrecht, Bijvoet Ctr Biomol Res, NL-3584 CH Utrecht, Netherlands. [van den Toorn, Henk W. P.; van Breukelen, Bas; Heck, Albert J. R.] Univ Utrecht, Utrecht Inst Pharmaceut Sci, NL-3584 CH Utrecht, Netherlands. [van den Toorn, Henk W. P.; van Breukelen, Bas; Heck, Albert J. R.] Netherlands Prote Ctr, NL-3584 CH Utrecht, Netherlands. [Scheltema, Richard A.] Max Planck Inst Biochem, Dept Prote & Signal Transduct, D-82152 Martinsried, Germany. [Kelstrup, Christian D.] Univ Copenhagen, Novo Nordisk Fdn Ctr Prot Res, Fac Hlth & Med Sci, DK-2200 Copenhagen, Denmark. [Gatto, Laurent; Lilley, Kathryn S.] Univ Cambridge, Dept Biochem, Cambridge Ctr Prote, Cambridge CB2 1GA, England. [Aiche, Stephan] Free Univ Berlin, Dept Math & Comp Sci, D-14195 Berlin, Germany. [Valkenborg, Dirk] Hasselt Univ, I BioStat, Diepenbeek, Belgium. [Valkenborg, Dirk] Univ Antwerp, CFP CeProMa, Antwerp, Belgium. [Aebersold, Ruedi] Univ Zurich, Fac Sci, Zurich, Switzerland. [Vizcaino, Juan Antonio; Hermjakob, Henning] European Mol Biol Lab, European Bioinformat Inst, Cambridge CB10 1SD, England. [Gatto, Laurent] Univ Cambridge, Dept Biochem, Computat Prote Unit, Cambridge CB2 1GA, England.
URI: http://hdl.handle.net/1942/17865
DOI: 10.1074/mcp.M113.035907
ISI #: 000340592400002
ISSN: 1535-9476
Category: A1
Type: Journal Contribution
Validation: ecoom, 2015
Appears in Collections: Research publications

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