title: Computational quality control tools for mass spectrometry proteomics.
abstract: As mass-spectrometry-based proteomics has matured during the past decade, a growing emphasis has been placed on quality control. For this purpose, multiple computational quality control tools have been introduced. These tools generate a set of metrics that can be used to assess the quality of a mass spectrometry experiment. Here we review which types of quality control metrics can be generated, and how they can be used to monitor both intra- and inter-experiment performances. We discuss the principal computational tools for quality control and list their main characteristics and applicability. As most of these tools have specific use cases, it is not straightforward to compare their performances. For this survey, we used different sets of quality control metrics derived from information at various stages in a mass spectrometry process and evaluated their effectiveness at capturing qualitative information about an experiment using a supervised learning approach. Furthermore, we discuss currently available algorithmic solutions that enable the usage of these quality control metrics for decision-making.
authors.affiliation: Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.|Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp, University Hospital, Edegem, Belgium.
authors.forename: Wout
authors.initials: W
authors.lastname: Bittremieux
authors.affiliation: Flemish Institute for Technological Research (VITO), Mol, Belgium.|CFP, University of Antwerp, Antwerp, Belgium.|I-BioStat, Hasselt University, Diepenbeek, Belgium.
authors.forename: Dirk
authors.initials: D
authors.lastname: Valkenborg
authors.affiliation: Medical Biotechnology Center, VIB, Ghent, Belgium.|Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.|Bioinformatics Institute Ghent, Ghent University, Zwijnaarde, Belgium.
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.affiliation: Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.|Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp, University Hospital, Edegem, Belgium.
authors.forename: Kris
authors.initials: K
authors.lastname: Laukens
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods* / Q000592:standards; D040901:Proteomics / Q000379:methods* / Q000592:standards; D011786:Quality Control
keywords: Bioinformatics; Mass spectrometry; Quality control