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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 | Source: | 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. | Keywords: | mass spectrometry; proteomics; quality control; quality assessment; outlier detection; outlier interpretation;mass spectrometry; proteomics; quality control; quality assessment; outlier detection; outlier interpretation | Document URI: | http://hdl.handle.net/1942/21512 | ISSN: | 1535-3893 | e-ISSN: | 1535-3907 | DOI: | 10.1021/acs.jproteome.6b00028 | ISI #: | 000373519900019 | Rights: | © 2016 American Chemical Society | Category: | A1 | Type: | Journal Contribution | Validations: | ecoom 2017 |
Appears in Collections: | Research publications |
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