Title
Determination of variation parameters as a crucial step in designing TMT-based clinical proteomics experiments Determination of variation parameters as a crucial step in designing TMT-based clinical proteomics experiments
Author
Faculty/Department
Faculty of Sciences. Biology
Faculty of Sciences. Chemistry
Faculty of Sciences. Mathematics and Computer Science
Faculty of Medicine and Health Sciences
Publication type
article
Publication
Subject
Biology
Engineering sciences. Technology
Source (journal)
PLoS ONE
Volume/pages
10(2015) :3 , 15 p.
ISSN
1932-6203
1932-6203
Article Reference
e0120115
Carrier
E-only publicatie
Target language
English (eng)
Full text (Publishers DOI)
Affiliation
University of Antwerp
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.
Full text (open access)
https://repository.uantwerpen.be/docman/irua/9219ac/a556542c.pdf
E-info
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