ArticlePloS one2015
Determination of variation parameters as a crucial step in designing TMT-based clinical proteomics experiments.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 38 citations in OpenAlex.
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- An enzymatic cascade enables sensitive and specific proximity labeling proteomics in challenging biological systems.Nature communications · 2025Article
- A curated tissue-specific proteome, phosphoproteome, and kinome map of Drosophila melanogaster with an integrated outlook in circadian physiology.Functional & integrative genomics · 2025Article
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- Identification of lipidomic profiles associated with drug-resistant prostate cancer cells.Lipids in health and disease · 2021Article
- Chronic exposure of humans to high level natural background radiation leads to robust expression of protective stress response proteins.Scientific reports · 2021Article
- Determination of variability due to biological and technical variation in urinary extracellular vesicles as a crucial step in biomarker discovery studies.Journal of extracellular vesicles · 2019Article
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- Proteome Profiling of Developing Murine Lens Through Mass Spectrometry.Investigative ophthalmology & visual science · 2018Article
- Molecular detection of infection homogeneity and impact of miltefosine treatment in a Syrian golden hamster model of Leishmania donovani and L. infantum visceral leishmaniasis.Parasitology research · 2016Article
- CONSTANd : A Normalization Method for Isobaric Labeled Spectra by Constrained Optimization.Molecular & cellular proteomics : MCP · 2016Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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