qcML: an exchange format for quality control metrics from mass spectrometry experiments

Mathias Walzer, Lucia Espona Pernas, Sara Nasso, Wout Bittremieux, Sven Nahnsen, Pieter Kelchtermans, Peter Pichler, Henk W P van den Toorn, An Staes, Jonathan Vandenbussche, Michael Mazanek, Thomas Taus, Richard A Scheltema, Christian D Kelstrup, Laurent Gatto, Bas van Breukelen, Stephan Aiche, Dirk Valkenborg, Kris Laukens, Kathryn S Lilley, Jesper V Olsen, Albert J R Heck, Karl Mechtler, Ruedi Aebersold, Kris Gevaert, Juan Antonio Vizcaíno, Henning Hermjakob, Oliver Kohlbacher, Lennart Martens
Molecular & Cellular Proteomics: MCP 2014, 13 (8): 1905-13
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

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