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Better late than never: Optimising the proteomic analysis of field-collected octopus

Proteomics, the temporal study of proteins expressed by an organism, is a powerful technique that can reveal how organisms respond to biological perturbations, such as disease and environmental stress. Yet, the use of proteomics for addressing ecological questions has been limited, partly due to ina...

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Autores principales: Hua, Qiaz Q. H., Young, Clifford, Pukala, Tara L., Martino, Jasmin C., Hoffmann, Peter, Gillanders, Bronwyn M., Doubleday, Zoe A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10337964/
https://www.ncbi.nlm.nih.gov/pubmed/37437086
http://dx.doi.org/10.1371/journal.pone.0288084
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author Hua, Qiaz Q. H.
Young, Clifford
Pukala, Tara L.
Martino, Jasmin C.
Hoffmann, Peter
Gillanders, Bronwyn M.
Doubleday, Zoe A.
author_facet Hua, Qiaz Q. H.
Young, Clifford
Pukala, Tara L.
Martino, Jasmin C.
Hoffmann, Peter
Gillanders, Bronwyn M.
Doubleday, Zoe A.
author_sort Hua, Qiaz Q. H.
collection PubMed
description Proteomics, the temporal study of proteins expressed by an organism, is a powerful technique that can reveal how organisms respond to biological perturbations, such as disease and environmental stress. Yet, the use of proteomics for addressing ecological questions has been limited, partly due to inadequate protocols for the sampling and preparation of animal tissues from the field. Although RNAlater is an ideal alternative to freezing for tissue preservation in transcriptomics studies, its suitability for the field could be more broadly examined. Moreover, existing protocols require samples to be preserved immediately to maintain protein integrity, yet the effects of delays in preservation on proteomic analyses have not been thoroughly tested. Hence, we optimised a proteomic workflow for wild-caught samples. First, we conducted a preliminary in-lab test using SDS-PAGE analysis on aquaria-reared Octopus berrima confirming that RNAlater can effectively preserve proteins up to 6 h after incubation, supporting its use in the field. Subsequently, we collected arm tips from wild-caught Octopus berrima and preserved them in homemade RNAlater immediately, 3 h, and 6 h after euthanasia. Processed tissue samples were analysed by liquid chromatography tandem mass spectrometry to ascertain protein differences between time delay in tissue preservation, as well as the influence of sex, tissue type, and tissue homogenisation methods. Over 3500 proteins were identified from all tissues, with bioinformatic analysis revealing protein abundances were largely consistent regardless of sample treatment. However, nearly 10% additional proteins were detected from tissues homogenised with metal beads compared to liquid nitrogen methods, indicating the beads were more efficient at extracting proteins. Our optimised workflow demonstrates that sampling non-model organisms from remote field sites is achievable and can facilitate extensive proteomic coverage without compromising protein integrity.
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spelling pubmed-103379642023-07-13 Better late than never: Optimising the proteomic analysis of field-collected octopus Hua, Qiaz Q. H. Young, Clifford Pukala, Tara L. Martino, Jasmin C. Hoffmann, Peter Gillanders, Bronwyn M. Doubleday, Zoe A. PLoS One Research Article Proteomics, the temporal study of proteins expressed by an organism, is a powerful technique that can reveal how organisms respond to biological perturbations, such as disease and environmental stress. Yet, the use of proteomics for addressing ecological questions has been limited, partly due to inadequate protocols for the sampling and preparation of animal tissues from the field. Although RNAlater is an ideal alternative to freezing for tissue preservation in transcriptomics studies, its suitability for the field could be more broadly examined. Moreover, existing protocols require samples to be preserved immediately to maintain protein integrity, yet the effects of delays in preservation on proteomic analyses have not been thoroughly tested. Hence, we optimised a proteomic workflow for wild-caught samples. First, we conducted a preliminary in-lab test using SDS-PAGE analysis on aquaria-reared Octopus berrima confirming that RNAlater can effectively preserve proteins up to 6 h after incubation, supporting its use in the field. Subsequently, we collected arm tips from wild-caught Octopus berrima and preserved them in homemade RNAlater immediately, 3 h, and 6 h after euthanasia. Processed tissue samples were analysed by liquid chromatography tandem mass spectrometry to ascertain protein differences between time delay in tissue preservation, as well as the influence of sex, tissue type, and tissue homogenisation methods. Over 3500 proteins were identified from all tissues, with bioinformatic analysis revealing protein abundances were largely consistent regardless of sample treatment. However, nearly 10% additional proteins were detected from tissues homogenised with metal beads compared to liquid nitrogen methods, indicating the beads were more efficient at extracting proteins. Our optimised workflow demonstrates that sampling non-model organisms from remote field sites is achievable and can facilitate extensive proteomic coverage without compromising protein integrity. Public Library of Science 2023-07-12 /pmc/articles/PMC10337964/ /pubmed/37437086 http://dx.doi.org/10.1371/journal.pone.0288084 Text en © 2023 Hua et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Hua, Qiaz Q. H.
Young, Clifford
Pukala, Tara L.
Martino, Jasmin C.
Hoffmann, Peter
Gillanders, Bronwyn M.
Doubleday, Zoe A.
Better late than never: Optimising the proteomic analysis of field-collected octopus
title Better late than never: Optimising the proteomic analysis of field-collected octopus
title_full Better late than never: Optimising the proteomic analysis of field-collected octopus
title_fullStr Better late than never: Optimising the proteomic analysis of field-collected octopus
title_full_unstemmed Better late than never: Optimising the proteomic analysis of field-collected octopus
title_short Better late than never: Optimising the proteomic analysis of field-collected octopus
title_sort better late than never: optimising the proteomic analysis of field-collected octopus
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10337964/
https://www.ncbi.nlm.nih.gov/pubmed/37437086
http://dx.doi.org/10.1371/journal.pone.0288084
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