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PXD012569 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleCharacterization of Pacific oyster (Crassostrea gigas) proteomic response to natural environmental differences
DescriptionGlobal climate change is rapidly altering coastal marine ecosystems important for food production. A comprehensive understanding of how organisms will respond to these complex environmental changes can come only from observing and studying species within their natural environment. To this end, the effects of environmental drivers — pH, dissolved oxygen content, salinity, and temperature — on Pacific oyster (Crassostrea gigas) physiology were evaluated in an outplant experiment. Sibling juvenile oysters were outplanted to eelgrass and unvegetated habitat at five different estuarine sites within the Acidification Nearshore Monitoring Network in Washington State, USA to evaluate how regional environmental drivers influence molecular physiology. Within each site, we also determined if eelgrass presence that buffered pH conditions changed the oysters’ expressed proteome. A novel, two-step, gel-free proteomic approach was used to identify differences in protein abundance in C. gigas ctenidia tissue after a 29 day outplant by 1) identifying proteins in a data independent acquisition survey step and 2) comparing relative quantities of targeted environmental response proteins using selected reaction monitoring. While there was no difference in protein abundance detected between habitats or among sites within Puget Sound, C. gigas outplanted at Willapa Bay had significantly higher abundances of antioxidant enzymes and molecular chaperones. Environmental factors at Willapa Bay, such as higher average temperature, may have driven this protein abundance pattern. These findings generate a suite of new hypotheses for lab and field experiments to compare the effects of regional conditions on physiological responses of marine invertebrates.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterYaamini Venkataraman
SpeciesList scientific name: Crassostrea gigas; NCBI TaxID: 29159;
ModificationListCarbamidomethyl; Label:13C(6)15N(2); Label:13C(6)15N(4)
InstrumentOrbitrap Fusion Lumos; TSQ Vantage
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-01-30 13:31:57ID requested
12019-08-13 16:09:57announced
Publication List
Venkataraman YR, Timmins-Schiffman E, Horwith MJ, Lowe AT, Nunn B, Vadopalas B, Spencer LH, Roberts SB. Characterization of Pacific oyster Crassostrea gigas proteomic response to natural environmental differences. Marine Ecology Progress Series. 2019 Feb 1;610:65-81. DOI: https://doi.org/10.3354/meps12858
Keyword List
submitter keyword: proteomics, oysters, in situ measurements, estuarine systems, antioxidant enzymes, molecular chaperones
Contact List
Steven Roberts
contact affiliationUniversity of Washington, School of Aquatic and Fishery Sciences
contact emailsr320@uw.edu
lab head
Yaamini Venkataraman
contact affiliationUniversity of Washington School of Aquatic and Fishery Sciences
contact emailyaaminiv@uw.edu
dataset submitter
Full Dataset Link List
Panorama Public dataset URI