title: Unsupervised Quality Assessment of Mass Spectrometry Proteomics Experiments by Multivariate Quality Control Metrics.
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/ .
authors.affiliation: Department of Mathematics and Computer Science, University of Antwerp , 2020 Antwerp, Belgium.|Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital , 2650 Edegem, Belgium.
authors.forename: Wout
authors.initials: W
authors.lastname: Bittremieux
authors.affiliation: Department of Mathematics and Computer Science, University of Antwerp , 2020 Antwerp, Belgium.|Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital , 2650 Edegem, Belgium.
authors.forename: Pieter
authors.initials: P
authors.lastname: Meysman
authors.affiliation: Department of Medical Protein Research, VIB , 9000 Ghent, Belgium.|Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University , 9000 Ghent, Belgium.|Bioinformatics Institute Ghent, Ghent University , 9000 Ghent, Belgium.
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.affiliation: Flemish Institute for Technological Research (VITO) , 2400 Mol, Belgium.|CFP, University of Antwerp , 2020 Antwerp, Belgium.|I-BioStat, Hasselt University , 3590 Diepenbeek, Belgium.
authors.forename: Dirk
authors.initials: D
authors.lastname: Valkenborg
authors.affiliation: Department of Mathematics and Computer Science, University of Antwerp , 2020 Antwerp, Belgium.|Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital , 2650 Edegem, Belgium.
authors.forename: Kris
authors.initials: K
authors.lastname: Laukens
mesh_terms: D019540:Area Under Curve; D001426:Bacterial Proteins / Q000737:chemistry / Q000302:isolation & purification*; D002853:Chromatography, Liquid / Q000592:standards*; D015179:Colorectal Neoplasms / Q000737:chemistry; D006801:Humans; D013058:Mass Spectrometry / Q000592:standards*; D009363:Neoplasm Proteins / Q000737:chemistry / Q000302:isolation & purification*; D010446:Peptide Fragments / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods / Q000592:standards*; D011786:Quality Control; D012372:ROC Curve; D020592:Shewanella / Q000737:chemistry; D012984:Software
chemical_list: D001426:Bacterial Proteins; D009363:Neoplasm Proteins; D010446:Peptide Fragments
keywords: mass spectrometry; outlier detection; outlier interpretation; proteomics; quality assessment; quality control