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

Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L - Mol. Cell Proteomics (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: From the ‡Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany;

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The backbone of the XML schema. This schema specifies the encapsulation of data in a qcML file. The full XML schema and ER schema of qcDB are available in the Supplementary Information.
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Figure 2: The backbone of the XML schema. This schema specifies the encapsulation of data in a qcML file. The full XML schema and ER schema of qcDB are available in the Supplementary Information.

Mentions: Fig. 2 shows the backbone of the XML schema used to represent the information stored in qcML. Furthermore, see the Supplementary Information for a graphical representation of the detailed structure of the XML schema, as discussed in this section. The qcML format is built around a basic element containing the information about one metric or metadatum, namely the qualityParameter element. This element represents a parameter and includes a name and a reference to a controlled vocabulary in order to describe the content of the parameter. Furthermore, it contains the value of the parameter, along with the unit in which this value is expressed, again with a reference to a controlled vocabulary in which the unit is described. Optionally, a threshold and flag can be supplied to indicate whether the metric has exceeded a specified threshold.


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

Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L - Mol. Cell Proteomics (2014)

The backbone of the XML schema. This schema specifies the encapsulation of data in a qcML file. The full XML schema and ER schema of qcDB are available in the Supplementary Information.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4125725&req=5

Figure 2: The backbone of the XML schema. This schema specifies the encapsulation of data in a qcML file. The full XML schema and ER schema of qcDB are available in the Supplementary Information.
Mentions: Fig. 2 shows the backbone of the XML schema used to represent the information stored in qcML. Furthermore, see the Supplementary Information for a graphical representation of the detailed structure of the XML schema, as discussed in this section. The qcML format is built around a basic element containing the information about one metric or metadatum, namely the qualityParameter element. This element represents a parameter and includes a name and a reference to a controlled vocabulary in order to describe the content of the parameter. Furthermore, it contains the value of the parameter, along with the unit in which this value is expressed, again with a reference to a controlled vocabulary in which the unit is described. Optionally, a threshold and flag can be supplied to indicate whether the metric has exceeded a specified threshold.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: From the ‡Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Dept. of Computer Science, University of Tuebingen, Germany;

Show MeSH