Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon ( Salmo salar )
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 abund...
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Online Access: | https://doi.org/10.1002/pmic.201600051 http://www.ncbi.nlm.nih.gov/pubmed/27272914 http://ecite.utas.edu.au/109648 |
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ftunivtasecite:oai:ecite.utas.edu.au:109648 2023-05-15T15:31:25+02:00 Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon ( Salmo salar ) Nuez-Ortin, W Carter, CG Nichols, PD Wilson, R 2016 https://doi.org/10.1002/pmic.201600051 http://www.ncbi.nlm.nih.gov/pubmed/27272914 http://ecite.utas.edu.au/109648 en eng WILEY-VCH Verlag GmbH & Co. KGaA http://dx.doi.org/10.1002/pmic.201600051 Nuez-Ortin, W and Carter, CG and Nichols, PD and Wilson, R, Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon ( Salmo salar ), Proteomics, 16, (14) pp. 2043-2047. ISSN 1615-9861 (2016) [Refereed Article] http://www.ncbi.nlm.nih.gov/pubmed/27272914 http://ecite.utas.edu.au/109648 Biological Sciences Biochemistry and Cell Biology Proteomics and Intermolecular Interactions (excl. Medical Proteomics) Refereed Article PeerReviewed 2016 ftunivtasecite https://doi.org/10.1002/pmic.201600051 2019-12-13T22:10:19Z 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 ∼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. The MS data are available via the ProteomeXchange Consortium PRIDE partner repository, dataset PXD003366. Article in Journal/Newspaper Atlantic salmon Salmo salar eCite UTAS (University of Tasmania) PROTEOMICS 16 14 2043 2047 |
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eCite UTAS (University of Tasmania) |
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ftunivtasecite |
language |
English |
topic |
Biological Sciences Biochemistry and Cell Biology Proteomics and Intermolecular Interactions (excl. Medical Proteomics) |
spellingShingle |
Biological Sciences Biochemistry and Cell Biology Proteomics and Intermolecular Interactions (excl. Medical Proteomics) Nuez-Ortin, W Carter, CG Nichols, PD Wilson, R Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon ( Salmo salar ) |
topic_facet |
Biological Sciences Biochemistry and Cell Biology Proteomics and Intermolecular Interactions (excl. Medical Proteomics) |
description |
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 ∼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. The MS data are available via the ProteomeXchange Consortium PRIDE partner repository, dataset PXD003366. |
format |
Article in Journal/Newspaper |
author |
Nuez-Ortin, W Carter, CG Nichols, PD Wilson, R |
author_facet |
Nuez-Ortin, W Carter, CG Nichols, PD Wilson, R |
author_sort |
Nuez-Ortin, W |
title |
Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon ( Salmo salar ) |
title_short |
Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon ( Salmo salar ) |
title_full |
Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon ( Salmo salar ) |
title_fullStr |
Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon ( Salmo salar ) |
title_full_unstemmed |
Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon ( Salmo salar ) |
title_sort |
sequential protein extraction as an efficient method for improved proteome coverage in larvae of atlantic salmon ( salmo salar ) |
publisher |
WILEY-VCH Verlag GmbH & Co. KGaA |
publishDate |
2016 |
url |
https://doi.org/10.1002/pmic.201600051 http://www.ncbi.nlm.nih.gov/pubmed/27272914 http://ecite.utas.edu.au/109648 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
http://dx.doi.org/10.1002/pmic.201600051 Nuez-Ortin, W and Carter, CG and Nichols, PD and Wilson, R, Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon ( Salmo salar ), Proteomics, 16, (14) pp. 2043-2047. ISSN 1615-9861 (2016) [Refereed Article] http://www.ncbi.nlm.nih.gov/pubmed/27272914 http://ecite.utas.edu.au/109648 |
op_doi |
https://doi.org/10.1002/pmic.201600051 |
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PROTEOMICS |
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16 |
container_issue |
14 |
container_start_page |
2043 |
op_container_end_page |
2047 |
_version_ |
1766361921949270016 |