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 Velgaard Olsen; Albert J R Heck; Karl Mechtler; Ruedi Aebersold; Kris Gevaert; Juan Antonio Vizcaino; Henning Hermjakob; Oliver Kohlbacher; Lennart Martens

doi:10.1074/mcp.M113.035907

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 LilleyJesper Velgaard Olsen, Albert J R Heck, Karl Mechtler, Ruedi Aebersold, Kris Gevaert, Juan Antonio Vizcaino, Henning Hermjakob, Oliver Kohlbacher, Lennart Martens

Novo Nordisk Foundation Center for Protein Research

38 Citations (Scopus)

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.

Original language	English
Journal	Molecular & Cellular Proteomics
Volume	13
Issue number	8
Pages (from-to)	1905-1913
Number of pages	9
ISSN	1535-9484
DOIs	https://doi.org/10.1074/mcp.M113.035907
Publication status	Published - Aug 2014

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Walzer, M., Pernas, L. E., Nasso, S., Bittremieux, W., Nahnsen, S., Kelchtermans, P., Pichler, P., van den Toorn, H. W. P., Staes, A., Vandenbussche, J., Mazanek, M., Taus, T., Scheltema, R. A., Kelstrup, C. D., Gatto, L., van Breukelen, B., Aiche, S., Valkenborg, D., Laukens, K., ... Martens, L. (2014). qcML: an exchange format for quality control metrics from mass spectrometry experiments. Molecular & Cellular Proteomics, 13(8), 1905-1913. https://doi.org/10.1074/mcp.M113.035907

Walzer, M, Pernas, LE, Nasso, S, Bittremieux, W, Nahnsen, S, Kelchtermans, P, Pichler, P, van den Toorn, HWP, 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, AJR, Mechtler, K, Aebersold, R, Gevaert, K, Vizcaino, JA, Hermjakob, H, Kohlbacher, O & Martens, L 2014, 'qcML: an exchange format for quality control metrics from mass spectrometry experiments', Molecular & Cellular Proteomics, vol. 13, no. 8, pp. 1905-1913. https://doi.org/10.1074/mcp.M113.035907

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title = "qcML: an exchange format for quality control metrics from mass spectrometry experiments",

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.",

author = "Mathias Walzer and Pernas, {Lucia Espona} and Sara Nasso and Wout Bittremieux and Sven Nahnsen and Pieter Kelchtermans and Peter Pichler and {van den Toorn}, {Henk W P} and An Staes and Jonathan Vandenbussche and Michael Mazanek and Thomas Taus and Scheltema, {Richard A} and Kelstrup, {Christian D} and Laurent Gatto and {van Breukelen}, Bas and Stephan Aiche and Dirk Valkenborg and Kris Laukens and Lilley, {Kathryn S} and Olsen, {Jesper Velgaard} and Heck, {Albert J R} and Karl Mechtler and Ruedi Aebersold and Kris Gevaert and Vizcaino, {Juan Antonio} and Henning Hermjakob and Oliver Kohlbacher and Lennart Martens",

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AU - Walzer, Mathias

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AU - Nahnsen, Sven

AU - Kelchtermans, Pieter

AU - Pichler, Peter

AU - van den Toorn, Henk W P

AU - Staes, An

AU - Vandenbussche, Jonathan

AU - Mazanek, Michael

AU - Taus, Thomas

AU - Scheltema, Richard A

AU - Kelstrup, Christian D

AU - Gatto, Laurent

AU - van Breukelen, Bas

AU - Aiche, Stephan

AU - Valkenborg, Dirk

AU - Laukens, Kris

AU - Lilley, Kathryn S

AU - Olsen, Jesper Velgaard

AU - Heck, Albert J R

AU - Mechtler, Karl

AU - Aebersold, Ruedi

AU - Gevaert, Kris

AU - Vizcaino, Juan Antonio

AU - Hermjakob, Henning

AU - Kohlbacher, Oliver

AU - Martens, Lennart

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AB - 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.

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

Abstract

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