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Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/21512

Title: Unsupervised Quality Assessment of Mass Spectrometry Proteomics Experiments by Multivariate Quality Control Metrics
Authors: Bittremieux, Wout
Meysman, Pieter
Martens, Lennart
Valkenborg, Dirk
Laukens, Kris
Issue Date: 2016
Publisher: AMER CHEMICAL SOC
Citation: JOURNAL OF PROTEOME RESEARCH, 15 (4), p. 1300-1307
Abstract: Despite many technological and computational advances, the results of a mass spectrometry proteomics experiment are still subject to a large variability. For the understanding and evaluation of how technical variability affects the results of an experiment, several computationally derived quality control metrics have been introduced. However, despite the availability of these metrics, a systematic approach to quality control is often still lacking because the metrics are not fully understood and are hard to interpret. Here, we present a toolkit of powerful techniques to analyze and interpret multivariate quality control metrics to assess the quality of mass spectrometry proteomics experiments. We show how unsupervised techniques applied to these quality control metrics can provide an initial discrimination between low-quality experiments and high-quality experiments prior to manual investigation. Furthermore, we provide a technique to obtain detailed information on the quality control metrics that are related to the decreased performance, which can be used as actionable information to improve the experimental setup. Our toolkit is released as open-source and can be downloaded from https:// bitbucket.org/proteinspector/qc_analysis/.
Notes: [Bittremieux, Wout; Meysman, Pieter; Laukens, Kris] Univ Antwerp, Dept Math & Comp Sci, B-2020 Antwerp, Belgium. [Bittremieux, Wout; Meysman, Pieter; Laukens, Kris] Univ Antwerp, Biomed Informat Res Ctr Antwerp Biomina, Univ Antwerp Hosp, B-2650 Edegem, Belgium. [Martens, Lennart] VIB, Dept Med Prot Res, B-9000 Ghent, Belgium. [Martens, Lennart] Univ Ghent, Dept Biochem, Fac Med & Hlth Sci, B-9000 Ghent, Belgium. [Martens, Lennart] Univ Ghent, Bioinformat Inst Ghent, B-9000 Ghent, Belgium. [Valkenborg, Dirk] Flemish Inst Technol Res VITO, B-2400 Mol, Belgium. [Valkenborg, Dirk] Univ Antwerp, CFP, B-2020 Antwerp, Belgium. [Valkenborg, Dirk] Hasselt Univ, I BioStat, B-3590 Diepenbeek, Belgium.
URI: http://hdl.handle.net/1942/21512
DOI: 10.1021/acs.jproteome.6b00028
ISI #: 000373519900019
ISSN: 1535-3893
Category: A1
Type: Journal Contribution
Validation: ecoom, 2017
Appears in Collections: Research publications

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