title: Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments.
abstract: In MS-based quantitative proteomics, the FDR control (i.e. the limitation of the number of proteins that are wrongly claimed as differentially abundant between several conditions) is a major postanalysis step. It is classically achieved thanks to a specific statistical procedure that computes the adjusted p-values of the putative differentially abundant proteins. Unfortunately, such adjustment is conservative only if the p-values are well-calibrated; the false discovery control being spuriously underestimated otherwise. However, well-calibration is a property that can be violated in some practical cases. To overcome this limitation, we propose a graphical method to straightforwardly and visually assess the p-value well-calibration, as well as the R codes to embed it in any pipeline. All MS data have been deposited in the ProteomeXchange with identifier PXD002370 (http://proteomecentral.proteomexchange.org/dataset/PXD002370).
authors.affiliation: Univ. Grenoble Alpes, iRTSV-BGE, Grenoble, France.|CEA, iRTSV-BGE, Grenoble, France.|INSERM, BGE, Grenoble, France.
authors.forename: Quentin
authors.initials: Q
authors.lastname: Giai Gianetto
authors.affiliation: Univ. Grenoble Alpes, iRTSV-BGE, Grenoble, France.|CEA, iRTSV-BGE, Grenoble, France.|INSERM, BGE, Grenoble, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Combes
authors.affiliation: Univ. Grenoble Alpes, iRTSV-BGE, Grenoble, France.|CNRS, iRTSV-BGE, Grenoble, France.|CEA, iRTSV-BGE, Grenoble, France.|INSERM, BGE, Grenoble, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Ramus
authors.affiliation: Univ. Grenoble Alpes, iRTSV-BGE, Grenoble, France.|CEA, iRTSV-BGE, Grenoble, France.|INSERM, BGE, Grenoble, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Bruley
authors.affiliation: Univ. Grenoble Alpes, iRTSV-BGE, Grenoble, France.|CEA, iRTSV-BGE, Grenoble, France.|INSERM, BGE, Grenoble, France.
authors.forename: Yohann
authors.initials: Y
authors.lastname: Couté
authors.affiliation: Univ. Grenoble Alpes, iRTSV-BGE, Grenoble, France.|CNRS, iRTSV-BGE, Grenoble, France.|CEA, iRTSV-BGE, Grenoble, France.|INSERM, BGE, Grenoble, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Burger
mesh_terms: D002138:Calibration; D003196:Computer Graphics; D013058:Mass Spectrometry / Q000379:methods*; D011506:Proteins / Q000737:chemistry; D040901:Proteomics / Q000379:methods*
chemical_list: D011506:Proteins
keywords: False discovery rate; Relative quantification experiments; Statistical significance