@article{Pernas2014, 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.}, author = {Pernas, Lucia Espona and Walzer, Mathias and Nasso, Sara and Bittremieux, Wout and Kelchtermans, Pieter and Nahnsen, Sven and Pichler, Peter and van den Toorn, Henk Wp P. and Staes, An and Vandenbussche, Jonathan and Mazanek, Michael and Taus, Thomas and Scheltema, Richard A. and Kelstrup, Christian D. and Gatto, Laurent and van Breukelen, Bas and Aiche, Stephan and Valkenborg, Dirk and Laukens, Kris and Lilley, Kathryn S. and Olsen, Jesper Velgaard and Heck, Albert J. R. and Mechtler, Karl and Aebersold, Ruedi and Gevaert, Kris and Vizcaino, Juan Antonio and Hermjakob, Henning and Kohlbacher, Oliver and Martens, Lennart}, doi = {10.1074/mcp.m113.035907}, journal = {Molecular and Cellular Proteomics}, month = {apr}, pages = {1905-1913}, title = {qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments}, url = {https://doi.org/10.1074/mcp.m113.035907}, volume = {13}, year = {2014} }