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Designing biomedical proteomics experiments : state-of-the-art and future perspectives

(2016) EXPERT REVIEW OF PROTEOMICS. 13(5). p.495-511
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Abstract
With the current expanded technical capabilities to perform mass spectrometry-based biomedical proteomics experiments, an improved focus on the design of experiments is crucial. As it is clear that ignoring the importance of a good design leads to an unprecedented rate of false discoveries which would poison our results, more and more tools are developed to help researchers designing proteomic experiments. In this review, we apply statistical thinking to go through the entire proteomics workflow for biomarker discovery and validation and relate the considerations that should be made at the level of hypothesis building, technology selection, experimental design and the optimization of the experimental parameters.
Keywords
Design of experiments, proteomics, mass spectrometry, bioinformatics, computer-aided optimization of LC-MS, DATA-INDEPENDENT ACQUISITION, SPECTROMETRY-BASED PROTEOMICS, RETENTION TIME PREDICTION, MASS-SPECTROMETRY, QUANTITATIVE PROTEOMICS, LIQUID-CHROMATOGRAPHY, PROTEIN IDENTIFICATION, ABSOLUTE QUANTIFICATION, PEPTIDE IDENTIFICATION, SAMPLES

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Chicago
Maes, Evelyne, Pieter Kelchtermans, Wout Bittremieux, Kurt De Grave, Sven Degroeve, Jef Hooyberghs, Inge Mertens, et al. 2016. “Designing Biomedical Proteomics Experiments : State-of-the-art and Future Perspectives.” Expert Review of Proteomics 13 (5): 495–511.
APA
Maes, Evelyne, Kelchtermans, P., Bittremieux, W., De Grave, K., Degroeve, S., Hooyberghs, J., Mertens, I., et al. (2016). Designing biomedical proteomics experiments : state-of-the-art and future perspectives. EXPERT REVIEW OF PROTEOMICS, 13(5), 495–511.
Vancouver
1.
Maes E, Kelchtermans P, Bittremieux W, De Grave K, Degroeve S, Hooyberghs J, et al. Designing biomedical proteomics experiments : state-of-the-art and future perspectives. EXPERT REVIEW OF PROTEOMICS. 2016;13(5):495–511.
MLA
Maes, Evelyne, Pieter Kelchtermans, Wout Bittremieux, et al. “Designing Biomedical Proteomics Experiments : State-of-the-art and Future Perspectives.” EXPERT REVIEW OF PROTEOMICS 13.5 (2016): 495–511. Print.
@article{8572804,
  abstract     = {With the current expanded technical capabilities to perform mass spectrometry-based biomedical proteomics experiments, an improved focus on the design of experiments is crucial. As it is clear that ignoring the importance of a good design leads to an unprecedented rate of false discoveries which would poison our results, more and more tools are developed to help researchers designing proteomic experiments. In this review, we apply statistical thinking to go through the entire proteomics workflow for biomarker discovery and validation and relate the considerations that should be made at the level of hypothesis building, technology selection, experimental design and the optimization of the experimental parameters.},
  author       = {Maes, Evelyne and Kelchtermans, Pieter and Bittremieux, Wout and De Grave, Kurt and Degroeve, Sven and Hooyberghs, Jef and Mertens, Inge and Baggerman, Geert and Ramon, Jan and Laukens, Kris and Martens, Lennart and Valkenborg, Dirk},
  issn         = {1478-9450},
  journal      = {EXPERT REVIEW OF PROTEOMICS},
  language     = {eng},
  number       = {5},
  pages        = {495--511},
  title        = {Designing biomedical proteomics experiments : state-of-the-art and future perspectives},
  url          = {http://dx.doi.org/10.1586/14789450.2016.1172967},
  volume       = {13},
  year         = {2016},
}

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