Walzer, Mathias3; Pernas, Lucia Espona4; Nasso, Sara4; Bittremieux, Wout4; Nahnsen, Sven4; Kelchtermans, Pieter4; Pichler, Peter4; van den Toorn, Henk W P4; Staes, An4; Vandenbussche, Jonathan4; Mazanek, Michael4; Taus, Thomas4; Scheltema, Richard A4; Kelstrup, Christian D5; Gatto, Laurent4; van Breukelen, Bas4; Aiche, Stephan4; Valkenborg, Dirk4; Laukens, Kris4; Lilley, Kathryn S4; Olsen, Jesper Velgaard5; Heck, Albert J R4; Mechtler, Karl4; Aebersold, Ruedi4; Gevaert, Kris4; Vizcaino, Juan Antonio4; Hermjakob, Henning4; Kohlbacher, Oliver4; Martens, Lennart4
1 Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Københavns Universitet2 Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Københavns Universitet3 University of Tuebingen, Germany;4 unknown5 Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Københavns Universitet
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.
Molecular and Cellular Proteomics, 2014, Vol 13, Issue 8, p. 1905-1913