title: Exploring the Arabidopsis proteome: influence of protein solubilization buffers on proteome coverage.
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.
authors.affiliation: 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.
authors.forename: Claudius
authors.initials: C
authors.lastname: Marondedze
authors.affiliation: 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.
authors.forename: Aloysius
authors.initials: A
authors.lastname: Wong
authors.affiliation: Cambridge Centre for Proteomics, Cambridge System Biology, University of Cambridge, Department of Biochemistry, Tennis Court Road, Cambridge CB2 1QR, UK. ajg86@cam.ac.uk.
authors.forename: Arnoud
authors.initials: A
authors.lastname: Groen
authors.affiliation: 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.
authors.forename: Natalia
authors.initials: N
authors.lastname: Serrano
authors.affiliation: 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.
authors.forename: Boris
authors.initials: B
authors.lastname: Jankovic
authors.affiliation: Cambridge Centre for Proteomics, Cambridge System Biology, University of Cambridge, Department of Biochemistry, Tennis Court Road, Cambridge CB2 1QR, UK. ksl23@cam.ac.uk.
authors.forename: Kathryn
authors.initials: K
authors.lastname: Lilley
authors.affiliation: 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.
authors.forename: Christoph
authors.initials: C
authors.lastname: Gehring
authors.affiliation: 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.
authors.forename: Ludivine
authors.initials: L
authors.lastname: Thomas
mesh_terms: D017360:Arabidopsis / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000378:metabolism; D002021:Buffers; D003902:Detergents / Q000737:chemistry; D015180:Electrophoresis, Gel, Two-Dimensional; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000032:analysis*; D012995:Solubility; D053719:Tandem Mass Spectrometry
chemical_list: D029681:Arabidopsis Proteins; D002021:Buffers; D003902:Detergents; D020543:Proteome