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Int. J. Mol. Sci. 2015, 16(1), 857-870; doi:10.3390/ijms16010857

Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

1
Biological and Environmental Sciences and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
2
Cambridge Centre for Proteomics, Cambridge System Biology, University of Cambridge, Department of Biochemistry, Tennis Court Road, Cambridge CB2 1QR, UK
*
Author to whom correspondence should be addressed.
Academic Editor: David Sheehan
Received: 5 November 2014 / Accepted: 23 December 2014 / Published: 31 December 2014
(This article belongs to the Collection Advances in Proteomic Research)
View Full-Text   |   Download PDF [1228 KB, uploaded 31 December 2014]   |  

Abstract

The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins. View Full-Text
Keywords: two-dimensional gel electrophoresis (2DE); Arabidopsis thaliana; detergent; mass spectrometry (MS); OFFGEL fractionation two-dimensional gel electrophoresis (2DE); Arabidopsis thaliana; detergent; mass spectrometry (MS); OFFGEL fractionation
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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Marondedze, C.; Wong, A.; Groen, A.; Serrano, N.; Jankovic, B.; Lilley, K.; Gehring, C.; Thomas, L. Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage. Int. J. Mol. Sci. 2015, 16, 857-870.

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Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
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