PXD016570

PXD016570 is an original dataset announced via ProteomeXchange.

Title	Plasma proteome profiling of freshwater and seawater life stages of rainbow trout (Oncorhynchus mykiss)
Description	The sea-run phenotype of rainbow trout (Oncorhynchus mykiss), like other anadromous salmonids, present a juvenile stage fully adapted to life in freshwater known as parr. Development in freshwater is followed by the smolt stage, where preadaptations needed for seawater life are developed making fish ready to migrate to the ocean, after which event they become post-smolts. While these three life stages have been studied using a variety of approaches, proteomics has never been used for such purpose. The present study characterised the blood plasma proteome of parr, smolt and post-smolt rainbow trout using a gel electrophoresis liquid chromatography tandem mass spectrometry approach alone or in combination with low-abundant protein enrichment technology (combinatorial peptide ligand library). In total, 1,822 proteins were quantified, 17.95% of them being detected only in plasma post enrichment. Across all life stages, the most abundant proteins were ankyrin-2, DNA primase large subunit, actin, serum albumin, apolipoproteins, hemoglobin subunits, hemopexin-like proteins and complement C3. When comparing the different life stages, 17 proteins involved in mechanisms to cope with hyperosmotic stress and retinal changes, as well as the downregulation of nonessential processes in smolts, were significantly different between parr and smolt samples. On the other hand, 11 proteins related to increased growth in post-smolts, and also related to coping with hyperosmotic stress and to retinal changes, were significantly different between smolt and post-smolt samples. Overall, this study presents a series of proteins with the potential to complement current seawater-readiness assessment tests in rainbow trout, which can be measured non-lethally in an easily accessible biofluid. Furthermore, this study represents a first in-depth characterisation of the rainbow trout blood plasma proteome, having considered three life stages of the fish and used both fractionation alone or in combination with enrichment methods to increase protein detection.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:59:14.457.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Bernat Morro
SpeciesList	scientific name: Oncorhynchus mykiss (Rainbow trout) (Salmo gairdneri); NCBI TaxID: 8022;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2019-12-04 03:27:11	ID requested
1	2020-01-07 08:27:56	announced
⏵ 2	2024-10-22 04:59:20	announced	2024-10-22: Updated project metadata.

10.1371/journal.pone.0227003;

Morro B, Doherty MK, Balseiro P, Handeland SO, MacKenzie S, Sveier H, Albalat A, Plasma proteome profiling of freshwater and seawater life stages of rainbow trout (Oncorhynchus mykiss). PLoS One, 15(1):e0227003(2020) [pubmed]

submitter keyword: freshwater, seawater, adaptation,Rainbow trout, smoltification, salmonid, fish

Amaya Albalat
contact affiliation	Institute of Aquaculture, University of Stirling
contact email	amaya.albalat@stir.ac.uk
lab head
Bernat Morro
contact affiliation	Institute of Aquaculture, Stirling
contact email	bernat.morro@stir.ac.uk
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD016570

PRIDE project URI

• PRIDE
  1. PXD016570
     1. Label: PRIDE project
     2. Name: Plasma proteome profiling of freshwater and seawater life stages of rainbow trout (Oncorhynchus mykiss)