PXD043096-2

PXD043096 is an original dataset announced via ProteomeXchange.

Title	Better late than never: optimising the proteomic analysis of field-collected octopus
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.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:12:41.703.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Qiaz Hua
SpeciesList	scientific name: Octopus berrima; NCBI TaxID: 264561;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-06-19 04:34:19	ID requested
1	2023-10-24 18:19:29	announced
⏵ 2	2023-11-14 09:12:42	announced	2023-11-14: Updated project metadata.
3	2024-10-22 06:13:18	announced	2024-10-22: Updated project metadata.

Hua QQH, Young C, Pukala TL, Martino JC, Hoffmann P, Gillanders BM, Doubleday ZA, Better late than never: Optimising the proteomic analysis of field-collected octopus. PLoS One, 18(7):e0288084(2023) [pubmed]

submitter keyword: liquid chromatography, octopus, proteomics methods,cephalopod, mass spectrometry, ecological proteomics, differential protein abundance, wild specimen

Qiaz Hua
contact affiliation	Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
contact email	qiaz.qh.hua@gmail.com
lab head
Qiaz Hua
contact affiliation	University of Adelaide
contact email	qiaz.qh.hua@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD043096
     1. Label: PRIDE project
     2. Name: Better late than never: optimising the proteomic analysis of field-collected octopus