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Determination of Variation Parameters as a Crucial Step in Designing TMT-Based Clinical Proteomics Experiments
- Source :
- PLoS ONE, PLoS ONE, Vol 10, Iss 3, p e0120115 (2015)
- Publication Year :
- 2015
- Publisher :
- Public Library of Science, 2015.
-
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. Evelyne Maes is funded by an Emmanuel Van der Schueren grant of the Vlaamse Liga tegen Kanker (VLK). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
- Subjects :
- Male
Proteomics
Proteome
Science
Pilot Projects
Computational biology
Biology
Bioinformatics
Protein expression
Liquid chromatography–mass spectrometry
Tandem Mass Spectrometry
Cluster Analysis
Humans
Sample preparation
Statistical hypothesis testing
Reproducibility
Multidisciplinary
Middle Aged
Sample size determination
Leukocytes, Mononuclear
Medicine
Female
Peptides
Engineering sciences. Technology
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 10
- Issue :
- 3
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....f444f4b63c6c775bdc1bd47656d9a2a8