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

Citation

Nuez Ortin, W and Carter, CG and Nichols, PD and Wilson, RR, Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon (Salmo salar), Proteomics, 16, (14) pp. 2043-7. ISSN 1615-9861 (2016) [Refereed Article]

Copyright Statement

Copyright 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

DOI: doi:10.1002/pmic.201600051

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 non-denaturing 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 (DE) 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 ~40% more proteins than DE. 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. The mass spectrometry data are available via the ProteomeXchange Consortium PRIDE partner repository, dataset PXD003366.

Item Details

Item Type:Refereed Article
Keywords:Animal proteomics; Fish larvae; Protein fractionation; Proteome coverage
Research Division:Biological Sciences
Research Group:Biochemistry and Cell Biology
Research Field:Proteomics and Intermolecular Interactions (excl. Medical Proteomics)
Objective Division:Animal Production and Animal Primary Products
Objective Group:Fisheries - Aquaculture
Objective Field:Fisheries - Aquaculture not elsewhere classified
Author:Nuez Ortin, W (Mr Waldo Nuez Ortin)
Author:Carter, CG (Professor Chris Carter)
Author:Wilson, RR (Dr Richard Wilson)
ID Code:109648
Year Published:2016
Deposited By:Central Science Laboratory
Deposited On:2016-06-24
Last Modified:2016-10-12
Downloads:0

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