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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

qcML : an exchange format for quality control metrics from mass spectrometry experiments. / Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk W P; Staes, An; Vandenbussche, Jonathan; Mazanek, Michael; Taus, Thomas; Scheltema, Richard A; Kelstrup, Christian D; Gatto, Laurent; van Breukelen, Bas; Aiche, Stephan; Valkenborg, Dirk; Laukens, Kris; Lilley, Kathryn S; Olsen, Jesper Velgaard; Heck, Albert J R; Mechtler, Karl; Aebersold, Ruedi; Gevaert, Kris; Vizcaino, Juan Antonio; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart.

In: Molecular & Cellular Proteomics, Vol. 13, No. 8, 23.04.2014, p. 1905-1913.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

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

APA

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

Vancouver

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 Apr 23;13(8):1905-1913. https://doi.org/10.1074/mcp.M113.035907

Author

Walzer, Mathias ; Pernas, Lucia Espona ; Nasso, Sara ; Bittremieux, Wout ; Nahnsen, Sven ; Kelchtermans, Pieter ; Pichler, Peter ; van den Toorn, Henk W P ; Staes, An ; Vandenbussche, Jonathan ; Mazanek, Michael ; Taus, Thomas ; Scheltema, Richard A ; Kelstrup, Christian D ; Gatto, Laurent ; van Breukelen, Bas ; Aiche, Stephan ; Valkenborg, Dirk ; Laukens, Kris ; Lilley, Kathryn S ; Olsen, Jesper Velgaard ; Heck, Albert J R ; Mechtler, Karl ; Aebersold, Ruedi ; Gevaert, Kris ; Vizcaino, Juan Antonio ; Hermjakob, Henning ; Kohlbacher, Oliver ; Martens, Lennart. / qcML : an exchange format for quality control metrics from mass spectrometry experiments. In: Molecular & Cellular Proteomics. 2014 ; Vol. 13, No. 8. pp. 1905-1913.

Bibtex

@article{098e34b578db4c218223d6d9e78b5ce3,
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. All information about qcML is available at http://code.google.com/p/qcml.",
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",
year = "2014",
month = apr,
day = "23",
doi = "10.1074/mcp.M113.035907",
language = "English",
volume = "13",
pages = "1905--1913",
journal = "Molecular and Cellular Proteomics",
issn = "1535-9476",
publisher = "American Society for Biochemistry and Molecular Biology",
number = "8",

}

RIS

TY - JOUR

T1 - qcML

T2 - an exchange format for quality control metrics from mass spectrometry experiments

AU - Walzer, Mathias

AU - Pernas, Lucia Espona

AU - Nasso, Sara

AU - Bittremieux, Wout

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

PY - 2014/4/23

Y1 - 2014/4/23

N2 - 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.

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. All information about qcML is available at http://code.google.com/p/qcml.

U2 - 10.1074/mcp.M113.035907

DO - 10.1074/mcp.M113.035907

M3 - Journal article

C2 - 24760958

VL - 13

SP - 1905

EP - 1913

JO - Molecular and Cellular Proteomics

JF - Molecular and Cellular Proteomics

SN - 1535-9476

IS - 8

ER -

ID: 110600165