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United States Department of Agriculture

Agricultural Research Service

Research Project: MODIFICATION OF SOYBEAN SEED COMPOSITION FOR FOOD, FEED, AND OTHER INDUSTRIAL USES Title: The proteomic future: where mass spectrometry should be taking us

Authors
item Thelen, Jay -
item Miernyk, Jan

Submitted to: Biochemical Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 22, 2012
Publication Date: April 11, 2012
Repository URL: http://handle.nal.usda.gov/10113/54154
Citation: Thelen, J.J., Miernyk, J.A. 2012. The proteomic future: where mass spectrometry should be taking us. Biochemical Journal. 444/169-181.

Interpretive Summary: Mass spectrometry is a method of chemical analysis that is increasingly being applied to biological systems. When used to study proteins, the method is referred to as proteomics. Unfortunately, in many instances proteomics studies are improberly designed. Strategies to avoid the most common problems, incompleteness and lack of quantification, are described. Additionally, biological problems that are amenable to study using mass spectrometry are described, including analysis of protein interactions and chemical modifications of proteins pointed out. Finally, there is speculation as to which aspects of proteomics will become areas of focus in the future. This information will be useful to scientists in their efforts to improve agricultural crop production through both classical breeding and application of biotechnology strategies.

Technical Abstract: A newcomer to the -omics era, proteomics is a broad, instrument-intensive research area that has advanced rapidly since its inception less than twenty years ago. Although the “wet-bench” aspects of proteomics have undergone a renaissance with the improvement in protein and peptide separation techniques, including various improvements in two-dimensional gel electrophoresis and gel-free or off-gel protein focusing, it has been the seminal advances in mass spectrometry that have led to the ascension of this field. Recent improvements in sensitivity, mass accuracy, and fragmentation have led to achievements previously only dreamed of, including whole proteome identification and quantitation and extensive mapping of specific post-translational modifications (PTMs). With such capabilities in the present, one might conclude that proteomics has already reached its zenith. However, “capability” indicates that the envisioned goals have not yet been achieved. Herein we focus on what we perceive as the areas requiring more attention to achieve the improvements in work flow and instrumentation that will bridge the gap between capability and achievement for at least most proteomes and PTMs. Additionally, it is essential that we extend our ability to understand protein structures, interactions, and localizations. Towards these ends, we briefly focus on selected methods and research areas where we anticipate the next wave of proteomic advances.

Last Modified: 10/25/2014
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