An Optimized Comparative Proteomic Approach as a Tool in Neurodegenerative Disease Research
Abstract
:1. Introduction
2. Proteomics as Applied to Neurodegenerative Disease Research
3. Considerations, Not Limitations
- Sample collection and preparation of in vitro cells, in vivo tissue from animal models of disease, or post mortem tissue from end-stage patients or age-matched controls.
- Protein identification and absolute or relative quantitation within sample(s) including appropriate statistical analysis and multi-database searches, generally conducted within one of several commonly used proteomics software (Figure 1: Raw Output).
- Post-mass spectrometry filtering, if appropriate (Figure 1: “Meaningful Data Cleanup”) and:
3.1. Sample Collection
3.2. Mass Spectrometry Experiment and Proteomic Data Analysis
3.2.1. Quantitative Proteomic Profiling via Mass Spectrometry
3.2.2. Pre-Processing Analysis and Normalisation
3.2.3. Post-Processing Analysis
3.2.4. Data Deposition
3.3. Downstream Data Analysis
3.3.1. Enrichment Analysis: As a Whole vs. for Individual Trends
3.3.2. Network and Pathway Analysis
4. Comparative Proteomics May Uncover Common Regulators of Neuronal Stability within and between Distinct Models of Disease
4.1. Comparative Approaches for Complex or Unknown Aetiologies
4.2. Incorporation of Human Proteome Analysis
5. Concluding Commentary
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Appendix A
Appendix A.1. Methods
Appendix A.1.1. Source Datasets
Appendix A.1.2. Standardisation for Alignment
Appendix A.1.3. BioLayout Express3D
Appendix A.1.4. DAVID
Appendix A.1.5. Ingenuity Pathway Analysis
Appendix A.2. Example Results
References
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Kline, R.A.; Lößlein, L.; Kurian, D.; Aguilar Martí, J.; Eaton, S.L.; Court, F.A.; Gillingwater, T.H.; Wishart, T.M. An Optimized Comparative Proteomic Approach as a Tool in Neurodegenerative Disease Research. Cells 2022, 11, 2653. https://doi.org/10.3390/cells11172653
Kline RA, Lößlein L, Kurian D, Aguilar Martí J, Eaton SL, Court FA, Gillingwater TH, Wishart TM. An Optimized Comparative Proteomic Approach as a Tool in Neurodegenerative Disease Research. Cells. 2022; 11(17):2653. https://doi.org/10.3390/cells11172653
Chicago/Turabian StyleKline, Rachel A., Lena Lößlein, Dominic Kurian, Judit Aguilar Martí, Samantha L. Eaton, Felipe A. Court, Thomas H. Gillingwater, and Thomas M. Wishart. 2022. "An Optimized Comparative Proteomic Approach as a Tool in Neurodegenerative Disease Research" Cells 11, no. 17: 2653. https://doi.org/10.3390/cells11172653
APA StyleKline, R. A., Lößlein, L., Kurian, D., Aguilar Martí, J., Eaton, S. L., Court, F. A., Gillingwater, T. H., & Wishart, T. M. (2022). An Optimized Comparative Proteomic Approach as a Tool in Neurodegenerative Disease Research. Cells, 11(17), 2653. https://doi.org/10.3390/cells11172653