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- Title
Determination of Variation Parameters as a Crucial Step in Designing TMT-Based Clinical Proteomics Experiments.
- Authors
Maes, Evelyne; Valkenborg, Dirk; Baggerman, Geert; Willems, Hanny; Landuyt, Bart; Schoofs, Liliane; Mertens, Inge
- 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.
- Subjects
PROTEOMICS; LIQUID chromatography-mass spectrometry; CHEMICAL sample preparation; MONONUCLEAR leukocytes; COMPARATIVE studies; SAMPLE size (Statistics)
- Publication
PLoS ONE, 2015, Vol 10, Issue 3, p1
- ISSN
1932-6203
- Publication type
Article
- DOI
10.1371/journal.pone.0120115