Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25362893", "kind": "science-record", "revision": 7, "content_hash": "sha256:26992de76cc0e69bf985e466ad2fbbce9b32a736db7bb874ed57cd1a5e7fa5ad", "created_at": "2026-11-01T15:40:06Z", "updated_at": "2026-11-01T21:58:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas.", "doi": "10.1186/1471-2164-15-951", "pmid": "25362893", "authors": ["Emma Timmins-Schiffman", "William D Coffey", "Wilber Hua", "Brook L Nunn", "Gary H Dickinson", "Steven B Roberts"], "journal": "BMC genomics", "year": 2014, "abstract": "BACKGROUND: Ocean acidification as a result of increased anthropogenic CO2 emissions is occurring in marine and estuarine environments worldwide. The coastal ocean experiences additional daily and seasonal fluctuations in pH that can be lower than projected end-of-century open ocean pH reductions. In order to assess the impact of ocean acidification on marine invertebrates, Pacific oysters (Crassostrea gigas) were exposed to one of four different p CO2 levels for four weeks: 400 μatm (pH 8.0), 800 μatm (pH 7.7), 1000 μatm (pH 7.6), or 2800 μatm (pH 7.3).\nRESULTS: At the end of the four week exposure period, oysters in all four p CO2 environments deposited new shell, but growth rate was not different among the treatments. However, micromechanical properties of the new shell were compromised by elevated p CO2. Elevated p CO2 affected neither whole body fatty acid composition, nor glycogen content, nor mortality rate associated with acute heat shock. Shotgun proteomics revealed that several physiological pathways were significantly affected by ocean acidification, including antioxidant response, carbohydrate metabolism, and transcription and translation. Additionally, the proteomic response to a second stress differed with p CO2, with numerous processes significantly affected by mechanical stimulation at high versus low p CO2 (all proteomics data are available in the ProteomeXchange under the identifier PXD000835).\nCONCLUSIONS: Oyster physiology is significantly altered by exposure to elevated p CO2, indicating changes in energy resource use. This is especially apparent in the assessment of the effects of p CO2 on the proteomic response to a second stress. The altered stress response illustrates that ocean acidification may impact how oysters respond to other changes in their environment. These data contribute to an integrative view of the effects of ocean acidification on oysters as well as physiological trade-offs during environmental stress.", "claims": [{"id": "claim-method", "statement": "In order to statistically test for significant abundance differences, treatments were compared in a pairwise fashion (400 vs. 2800 μatm, 400 μatm vs. 400 + mechanical stress, and 2800 μatm vs. 2800 + mechanical stress) using the qvalue package in R [73, 90] with a q-value cut-off of 0.10.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25362893", "locator": "sections[25] \"Protein informatics analysis\" paragraph 5", "quote": "In order to statistically test for significant abundance differences, treatments were compared in a pairwise fashion (400 vs. 2800 μatm, 400 μatm vs. 400 + mechanical stress, and 2800 μatm vs. 2800 + mechanical stress) using the qvalue package in R [73, 90] with a q-value cut-off of 0.10."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All raw data accompanying this manuscript is also available through the data compilation on the biological response to ocean acidification through Ocean Acidification International Coordination Centre (http://doi.pangaea.de/10.1594/PANGAEA.837671). The data set supporting the results of this article is available in the ProteomeExchange repository, [PXD000835 http://proteomecentral.proteomexchange.org].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25362893", "locator": "sections[26] \"Availability of supporting data\" paragraph 2", "quote": "All raw data accompanying this manuscript is also available through the data compilation on the biological response to ocean acidification through Ocean Acidification International Coordination Centre (http://doi.pangaea.de/10.1594/PANGAEA.837671). The data set supporting the results of this article is available in the ProteomeExchange repository, [PXD000835 http://proteomecentral.proteomexchange.org]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used shotgun proteomics with pairwise differential-abundance testing based on the q-value package in R (q-value cut-off <0.10), supplemented by a twofold abundance-change criterion. Proteomics data are available through ProteomeXchange under PXD000835, and raw supporting data are available through PANGAEA under DOI 10.1594/PANGAEA.837671. The headline result is that elevated pCO2 significantly altered oyster physiology, indicating changes in energy-resource use.", "kind": "quantitative", "target": {"value": 2.0, "unit": "fold change", "tolerance": null, "source": "Proteins were considered differentially abundant if either there was 1) a 2-fold difference in abundance between treatment groups or 2) a q-value <0.10."}, "evidence": [{"asset": "source:pmid:25362893", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Oyster physiology is significantly altered by exposure to elevated p CO2, indicating changes in energy resource use."}, {"asset": "source:pmid:25362893", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Shotgun proteomics revealed that several physiological pathways were significantly affected by ocean acidification, including antioxidant response, carbohydrate metabolism, and transcription and translation."}, {"asset": "source:pmid:25362893", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Additionally, the proteomic response to a second stress differed with p CO2, with numerous processes significantly affected by mechanical stimulation at high versus low p CO2 (all proteomics data are available in the ProteomeXchange under the identifier PXD000835)."}, {"asset": "source:pmid:25362893", "locator": "sections[25] \"Protein informatics analysis\" paragraph 5", "quote": "In order to statistically test for significant abundance differences, treatments were compared in a pairwise fashion (400 vs. 2800 μatm, 400 μatm vs. 400 + mechanical stress, and 2800 μatm vs. 2800 + mechanical stress) using the qvalue package in R [73, 90] with a q-value cut-off of 0.10."}, {"asset": "source:pmid:25362893", "locator": "sections[26] \"Availability of supporting data\" paragraph 2", "quote": "All raw data accompanying this manuscript is also available through the data compilation on the biological response to ocean acidification through Ocean Acidification International Coordination Centre (http://doi.pangaea.de/10.1594/PANGAEA.837671)."}, {"asset": "source:pmid:25362893", "locator": "sections[26] \"Availability of supporting data\" paragraph 2", "quote": "The data set supporting the results of this article is available in the ProteomeExchange repository, [PXD000835 http://proteomecentral.proteomexchange.org]."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used shotgun proteomics with pairwise differential-abundance testing based on the q-value package in R (q-value cut-off <0.10), supplemented by a twofold abundance-change criterion. Proteomics data are available through ProteomeXchange under PXD000835, and raw supporting data are available through PANGAEA under DOI 10.1594/PANGAEA.837671. The headline result is that elevated pCO2 significantly altered oyster physiology, indicating changes in energy-resource use.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:25362893"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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