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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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An overview of the role of qcML. Experimental data are fed into performance analysis tools, that calculate the values of quality metrics. Those tools output qcML files, which in their turn can be converted to a database format for storage, or managed further with quality control tools. The data in qcML can also be converted to an easily viewable quality report.
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Related In: Results  -  Collection


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Figure 1: An overview of the role of qcML. Experimental data are fed into performance analysis tools, that calculate the values of quality metrics. Those tools output qcML files, which in their turn can be converted to a database format for storage, or managed further with quality control tools. The data in qcML can also be converted to an easily viewable quality report.

Mentions: qcML was designed as a data interchange format for quality control data and thus enables the integration of wide range of software libraries and tools. In parallel with the development of the format, we have been developing these tools to ease the integration of qcML into existing workflows. Fig. 1 gives an overview of the workflows and tools. We will discuss both the format, its contents, and the related tools and libraries in more detail below.


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)

An overview of the role of qcML. Experimental data are fed into performance analysis tools, that calculate the values of quality metrics. Those tools output qcML files, which in their turn can be converted to a database format for storage, or managed further with quality control tools. The data in qcML can also be converted to an easily viewable quality report.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: An overview of the role of qcML. Experimental data are fed into performance analysis tools, that calculate the values of quality metrics. Those tools output qcML files, which in their turn can be converted to a database format for storage, or managed further with quality control tools. The data in qcML can also be converted to an easily viewable quality report.
Mentions: qcML was designed as a data interchange format for quality control data and thus enables the integration of wide range of software libraries and tools. In parallel with the development of the format, we have been developing these tools to ease the integration of qcML into existing workflows. Fig. 1 gives an overview of the workflows and tools. We will discuss both the format, its contents, and the related tools and libraries in more detail below.

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