Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon (Salmo salar)

Nuez Ortín, Waldo G., Carter, Chris G., Nichols, Peter D., and Wilson, Richard (2016) Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon (Salmo salar). Proteomics, 16 (14). pp. 2043-2047.

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Abstract

Understanding diet- and environmentally induced physiological changes in fish larvae is a major goal for the aquaculture industry. Proteomic analysis of whole fish larvae comprising multiple tissues offers considerable potential but is challenging due to the very large dynamic range of protein abundance. To extend the coverage of the larval phase of the Atlantic salmon (Salmo salar) proteome, we applied a two-step sequential extraction (SE) method, based on differential protein solubility, using a nondenaturing buffer containing 150 mM NaCl followed by a denaturing buffer containing 7 M urea and 2 M thiourea. Extracts prepared using SE and one-step direct extraction were characterized via label-free shotgun proteomics using nanoLC-MS/MS (LTQ-Orbitrap). SE partitioned the proteins into two fractions of approximately equal amounts, but with very distinct protein composition, leading to identification of approximate to 40% more proteins than direct extraction. This fractionation strategy enabled the most detailed characterization of the salmon larval proteome to date and provides a platform for greater understanding of physiological changes in whole fish larvae.

Item ID: 45983
Item Type: Article (Research - C1)
ISSN: 1615-9861
Keywords: animal proteomic, fish larvae, protein fractionation, proteome coverage
Funders: Australian Research Council (ARC), CSIRO Food Futures Flagship, Nuseed Global
Projects and Grants: ARC LE0775570
Date Deposited: 10 Oct 2016 03:09
FoR Codes: 11 MEDICAL AND HEALTH SCIENCES > 1101 Medical Biochemistry and Metabolomics > 110199 Medical Biochemistry and Metabolomics not elsewhere classified @ 100%
SEO Codes: 83 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 8301 Fisheries - Aquaculture > 830199 Fisheries - Aquaculture not elsewhere classified @ 100%
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