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

(2014) MOLECULAR & CELLULAR PROTEOMICS. 13(8). p.1905-1913
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Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
SYSTEMS, TANDEM, WORKFLOW, STANDARDS, PROTEOMICS DATA, PERFORMANCE METRICS

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Citation

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Chicago
Walzer, Mathias, Lucia Espona Pernas, Sara Nasso, Wout Bittremieux, Sven Nahnsen, Pieter Kelchtermans, Peter Pichler, et al. 2014. “qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments.” Molecular & Cellular Proteomics 13 (8): 1905–1913.
APA
Walzer, M., Pernas, L. E., Nasso, S., Bittremieux, W., Nahnsen, S., Kelchtermans, P., Pichler, P., et al. (2014). qcML: an exchange format for quality control metrics from mass spectrometry experiments. MOLECULAR & CELLULAR PROTEOMICS, 13(8), 1905–1913.
Vancouver
1.
Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, et al. qcML: an exchange format for quality control metrics from mass spectrometry experiments. MOLECULAR & CELLULAR PROTEOMICS. 2014;13(8):1905–13.
MLA
Walzer, Mathias, Lucia Espona Pernas, Sara Nasso, et al. “qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments.” MOLECULAR & CELLULAR PROTEOMICS 13.8 (2014): 1905–1913. Print.
@article{5716171,
  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       = {Walzer, Mathias and Pernas, Lucia Espona and Nasso, Sara and Bittremieux, Wout and Nahnsen, Sven and Kelchtermans, Pieter and Pichler, Peter and van den Toorn, Henk WP 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 V and Heck, Albert JR and Mechtler, Karl and Aebersold, Ruedi and Gevaert, Kris and Vizca{\'i}no, Juan Antonio and Hermjakob, Henning and Kohlbacher, Oliver and Martens, Lennart},
  issn         = {1535-9476},
  journal      = {MOLECULAR \& CELLULAR PROTEOMICS},
  keyword      = {SYSTEMS,TANDEM,WORKFLOW,STANDARDS,PROTEOMICS DATA,PERFORMANCE METRICS},
  language     = {eng},
  number       = {8},
  pages        = {1905--1913},
  title        = {qcML: an exchange format for quality control metrics from mass spectrometry experiments},
  url          = {http://dx.doi.org/10.1074/mcp.M113.035907},
  volume       = {13},
  year         = {2014},
}

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