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Title: Determination of Variation Parameters as a Crucial Step in Designing TMT-Based Clinical Proteomics Experiments
Authors: Maes, Evelyne
Baggerman, Geert
Willems, Hanny
Landuyt, Bart
Schoofs, Liliane
Mertens, Inge
Issue Date: 2015
Source: PLOS ONE, 10 (3)
Abstract: In quantitative shotgun proteomic analyses by liquid chromatography and mass spectrometry, a rigid study design is necessary in order to obtain statistically relevant results. Hypothesis testing, sample size calculation and power estimation are fundamental concepts that require consideration upon designing an experiment. For this reason, the reproducibility and variability of the proteomic platform needs to be assessed. In this study, we evaluate the technical (sample preparation), labeling (isobaric labels), and total (biological + technical + labeling + experimental) variability and reproducibility of a workflow that employs a shotgun LC-MS/MS approach in combination with TMT peptide labeling for the quantification of peripheral blood mononuclear cell (PBMC) proteome. We illustrate that the variability induced by TMT labeling is small when compared to the technical variation. The latter is also responsible for a substantial part of the total variation. Prior knowledge about the experimental variability allows for a correct design, a prerequisite for the detection of biologically significant disease-specific differential proteins in clinical proteomics experiments.
Notes: [Maes, Evelyne; Valkenborg, Dirk; Baggerman, Geert; Willems, Hanny; Mertens, Inge] Flemish Inst Technol Res VITO, Mol, Belgium. [Maes, Evelyne; Valkenborg, Dirk; Baggerman, Geert; Willems, Hanny; Mertens, Inge] Univ Antwerp, CFP CeProMa, B-2020 Antwerp, Belgium. [Maes, Evelyne; Landuyt, Bart; Schoofs, Liliane] Katholieke Univ Leuven, Res Grp Funct Genom & Prote, Leuven, Belgium. [Valkenborg, Dirk] Hasselt Univ, Interuniv Inst Biostat & Stat Bioinformat, Diepenbeek, Belgium.
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ISSN: 1932-6203
e-ISSN: 1932-6203
DOI: 10.1371/journal.pone.0120115
ISI #: 000351183500151
Rights: Copyright: © 2015 Maes et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Category: A1
Type: Journal Contribution
Validations: ecoom 2016
Appears in Collections:Research publications

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