Broad-based proteomic strategies: a practical guide to proteomics and functional screening

• Published in: The Journal of physiology Vol. 563; no. 1; pp. 1 - 9
• Main Authors: Graham, David R. M., Elliott, Steven T., Van Eyk, Jennifer E.
• Format: Journal Article
• Language: English
• Published: 9600 Garsington Road , Oxford , OX4 2DQ , UK The Physiological Society 15-02-2005; Blackwell Science Ltd; Blackwell Science Inc
• Subjects: Animals; Chromatography - methods; Computer Simulation; Electrophoresis; Gene Expression Profiling - methods; Humans; Mass Spectrometry - methods; Models, Biological; Protein Array Analysis - methods; Proteome - analysis; Proteome - chemistry; Proteome - metabolism; Proteomics - methods; Research Design; Special Proteomics Papers
• ISSN: 0022-3751; 1469-7793
• DOI: 10.1113/jphysiol.2004.080341

Proteomics, the study of the proteome (the collection of all the proteins expressed from the genome in all isoforms, polymorphisms
and post-translational modifications), is a rapidly developing field in which there are numerous new and often expensive technologies,
making it imperative to use the most appropriate technology for the biological system and hypothesis being addressed. This
review provides some guidelines on approaching a broad-based proteomics project, including strategies on refining hypotheses,
choosing models and proteomic approaches with an emphasis on aspects of sample complexity (including abundance and protein
characteristics), and separation technologies and their respective strengths and weaknesses. Finally, issues related to quantification,
mass spectrometry and informatics strategies are discussed. The goal of this review is therefore twofold: the first section
provides a brief outline of proteomic technologies, specifically with respect to their applications to broad-based proteomic
approaches, and the second part provides more details about the application of these technologies in typical scenarios dealing
with physiological and pathological processes. Proteomics at its best is the integration of carefully planned research and
complementary techniques with the advantages of powerful discovery technologies that has the potential to make substantial
contributions to the understanding of disease and disease processes.