title: Designing biomedical proteomics experiments: state-of-the-art and future perspectives.
abstract: With the current expanded technical capabilities to perform mass spectrometry-based biomedical proteomics experiments, an improved focus on the design of experiments is crucial. As it is clear that ignoring the importance of a good design leads to an unprecedented rate of false discoveries which would poison our results, more and more tools are developed to help researchers designing proteomic experiments. In this review, we apply statistical thinking to go through the entire proteomics workflow for biomarker discovery and validation and relate the considerations that should be made at the level of hypothesis building, technology selection, experimental design and the optimization of the experimental parameters.
authors.affiliation: a Applied Bio & molecular systems , VITO , Mol , Belgium.|b CFP , University of Antwerp , Antwerp , Belgium.
authors.forename: Evelyne
authors.initials: E
authors.lastname: Maes
authors.affiliation: b CFP , University of Antwerp , Antwerp , Belgium.|c Medical Biotechnology Center , VIB , Ghent , Belgium.|d Department of Biochemistry , Ghent University , Ghent , Belgium.|e Bioinformatics Institute Ghent , Ghent University , Ghent , Belgium.
authors.forename: Pieter
authors.initials: P
authors.lastname: Kelchtermans
authors.affiliation: f Department of Mathematics and Computer Science , University of Antwerp , Antwerp , Belgium.|g Biomedical Informatics Research Center Antwerp (biomina) , University of Antwerp/Antwerp University Hospital , Antwerp , Belgium.
authors.forename: Wout
authors.initials: W
authors.lastname: Bittremieux
authors.affiliation: h Department of Computer Science , KU Leuven , Leuven , Belgium.
authors.forename: Kurt
authors.initials: K
authors.lastname: De Grave
authors.affiliation: c Medical Biotechnology Center , VIB , Ghent , Belgium.|d Department of Biochemistry , Ghent University , Ghent , Belgium.|e Bioinformatics Institute Ghent , Ghent University , Ghent , Belgium.
authors.forename: Sven
authors.initials: S
authors.lastname: Degroeve
authors.affiliation: a Applied Bio & molecular systems , VITO , Mol , Belgium.
authors.forename: Jef
authors.initials: J
authors.lastname: Hooyberghs
authors.affiliation: a Applied Bio & molecular systems , VITO , Mol , Belgium.|b CFP , University of Antwerp , Antwerp , Belgium.
authors.forename: Inge
authors.initials: I
authors.lastname: Mertens
authors.affiliation: a Applied Bio & molecular systems , VITO , Mol , Belgium.|b CFP , University of Antwerp , Antwerp , Belgium.
authors.forename: Geert
authors.initials: G
authors.lastname: Baggerman
authors.affiliation: h Department of Computer Science , KU Leuven , Leuven , Belgium.|i INRIA , Lille , France.
authors.forename: Jan
authors.initials: J
authors.lastname: Ramon
authors.affiliation: f Department of Mathematics and Computer Science , University of Antwerp , Antwerp , Belgium.|g Biomedical Informatics Research Center Antwerp (biomina) , University of Antwerp/Antwerp University Hospital , Antwerp , Belgium.
authors.forename: Kris
authors.initials: K
authors.lastname: Laukens
authors.affiliation: c Medical Biotechnology Center , VIB , Ghent , Belgium.|d Department of Biochemistry , Ghent University , Ghent , Belgium.|e Bioinformatics Institute Ghent , Ghent University , Ghent , Belgium.
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.affiliation: a Applied Bio & molecular systems , VITO , Mol , Belgium.|b CFP , University of Antwerp , Antwerp , Belgium.|j Interuniversity Institute for Biostatistics and statistical Bioinformatics , Hasselt University , Hasselt , Belgium.
authors.forename: Dirk
authors.initials: D
authors.lastname: Valkenborg
mesh_terms: D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D040901:Proteomics / Q000379:methods* / Q000706:statistics & numerical data / Q000639:trends; D012107:Research Design
keywords: Design of experiments; bioinformatics; computer-aided optimization of LC-MS; mass spectrometry; proteomics