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Int J Mol Sci. 2014 Dec 31;16(1):857-70. doi: 10.3390/ijms16010857.

Exploring the Arabidopsis proteome: influence of protein solubilization buffers on proteome coverage.

Author information

1
Biological and Environmental Sciences and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia. claudius.marondedze@kaust.edu.sa.
2
Biological and Environmental Sciences and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia. aloysius.wong@kaust.edu.sa.
3
Cambridge Centre for Proteomics, Cambridge System Biology, University of Cambridge, Department of Biochemistry, Tennis Court Road, Cambridge CB2 1QR, UK. ajg86@cam.ac.uk.
4
Biological and Environmental Sciences and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia. natalia.serrano@kaust.edu.sa.
5
Biological and Environmental Sciences and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia. boris.jankovic@kaust.edu.sa.
6
Cambridge Centre for Proteomics, Cambridge System Biology, University of Cambridge, Department of Biochemistry, Tennis Court Road, Cambridge CB2 1QR, UK. ksl23@cam.ac.uk.
7
Biological and Environmental Sciences and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia. christoph.gehring@kaust.edu.sa.
8
Biological and Environmental Sciences and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia. ludivine.thomas@kaust.edu.sa.

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.

PMID:
25561235
PMCID:
PMC4307279
DOI:
10.3390/ijms16010857
[Indexed for MEDLINE]
Free PMC Article

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