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Proteomes 2015, 3(4), 440-453; doi:10.3390/proteomes3040440

Proteomics Is Analytical Chemistry: Fitness-for-Purpose in the Application of Top-Down and Bottom-Up Analyses

1
Molecular Physiology and the Molecular Medicine Research Group, School of Medicine, Western Sydney University, Office 30.2.15, Campbelltown Campus, Locked Bag 1797, Penrith 2570, NSW, Australia
2
National Institute of Child Health and Human Development, NIH, Building 10, Room 9D 52, Bethesda, MD 20892, USA
*
Authors to whom correspondence should be addressed.
Academic Editor: Jacek R. Wisniewski
Received: 23 October 2015 / Revised: 21 November 2015 / Accepted: 26 November 2015 / Published: 3 December 2015
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Abstract

Molecular mechanisms underlying health and disease function at least in part based on the flexibility and fine-tuning afforded by protein isoforms and post-translational modifications. The ability to effectively and consistently resolve these protein species or proteoforms, as well as assess quantitative changes is therefore central to proteomic analyses. Here we discuss the pros and cons of currently available and developing analytical techniques from the perspective of the full spectrum of available tools and their current applications, emphasizing the concept of fitness-for-purpose in experimental design based on consideration of sample size and complexity; this necessarily also addresses analytical reproducibility and its variance. Data quality is considered the primary criterion, and we thus emphasize that the standards of Analytical Chemistry must apply throughout any proteomic analysis. View Full-Text
Keywords: 2DE; Bottom-up; Discovery proteomics; LC/MS/MS; protein species; proteoforms; shotgun; Top-down; two-dimensional gel electrophoresis 2DE; Bottom-up; Discovery proteomics; LC/MS/MS; protein species; proteoforms; shotgun; Top-down; two-dimensional gel electrophoresis
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Coorssen, J.R.; Yergey, A.L. Proteomics Is Analytical Chemistry: Fitness-for-Purpose in the Application of Top-Down and Bottom-Up Analyses. Proteomes 2015, 3, 440-453.

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