Data from: Differential proteomic responses of selectively bred and wild Sydney rock oyster populations exposed to elevated CO2

Previous work suggests that larvae from Sydney rock oysters that have been selectively bred for fast growth and disease resistance are more resilient to the impacts of ocean acidification than nonselected, wild-type oysters. In this study, we used proteomics to investigate the molecular differences between oyster populations in adult Sydney rock oysters and to identify whether these form the basis for observations seen in larvae. Adult oysters from a selective breeding line (B2) and nonselected wild types (WT) were exposed for 4 weeks to elevated pCO2 (856 μatm) before their proteomes were compared to those of oysters held under ambient conditions (375 μatm pCO2). Exposure to elevated pCO2 resulted in substantial changes in the proteomes of oysters from both the selectively bred and wild-type populations. When biological functions were assigned, these differential proteins fell into five broad, potentially interrelated categories of subcellular functions, in both oyster populations. These functional categories were energy production, cellular stress responses, the cytoskeleton, protein synthesis and cell signalling. In the wild-type population, proteins were predominantly upregulated. However, unexpectedly, these cellular systems were downregulated in the selectively bred oyster population, indicating cellular dysfunction. We argue that this reflects a trade-off, whereby an adaptive capacity for enhanced mitochondrial energy production in the selectively bred population may help to protect larvae from the effects of elevated CO2, whilst being deleterious to adult oysters.

Usage Notes
Raw mass spec files from differentially expressed proteins of Sydney rock oysters - spot 211Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 211.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 213Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 213.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 214Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 214.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 306Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 306.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 308Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 308.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 502Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 502.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1007Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 1007.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1404Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 1404.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1405Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 1405.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1406Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 1406.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1407Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 1407.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1607Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 1607.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1705Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 1705.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1706Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 1706.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1807Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 1807.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 2306Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 2306.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 2707Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 2707.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 2804Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 2804.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 3110Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA). Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.ET121113_spot 3110.rawRaw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 3304Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mas....see Dryad link for full text

既往研究表明，经快速生长与抗病性选育的悉尼岩牡蛎（Sydney rock oyster）幼虫，相较于未选育的野生型牡蛎，对海洋酸化胁迫的耐受性更强。本研究采用蛋白质组学（proteomics）方法，探究成年悉尼岩牡蛎不同种群间的分子差异，并验证这些差异是否为幼虫阶段观测结果的分子基础。
本研究将选育系（B2）与未选育的野生型（WT）成年悉尼岩牡蛎暴露于升高的二氧化碳分压（pCO2，856 μatm）环境中4周，随后将其蛋白质组与处于环境二氧化碳分压（375 μatm pCO2）条件下的牡蛎蛋白质组进行比较。结果显示，升高的pCO2胁迫可使选育种群与野生种群牡蛎的蛋白质组均发生显著改变。对差异表达蛋白进行功能注释后发现，两个种群的差异蛋白均可归为五大类潜在相互关联的亚细胞功能范畴，分别为能量产生、细胞应激反应、细胞骨架、蛋白质合成以及细胞信号转导。
野生型种群的差异蛋白整体呈现上调表达趋势；但出乎意料的是，选育种群的上述细胞系统均出现下调表达，提示细胞功能异常。本研究认为这一现象反映了一种权衡机制：选育种群中增强的线粒体能量生产适应能力，可帮助幼虫抵御升高的CO₂胁迫，却会对成年牡蛎产生有害影响。

### 使用说明
本数据集包含悉尼岩牡蛎差异表达蛋白的原始质谱文件：
1. 斑点211：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 211.raw
2. 斑点213：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 213.raw
3. 斑点214：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 214.raw
4. 斑点306：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 306.raw
5. 斑点308：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 308.raw
6. 斑点502：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 502.raw
7. 斑点1007：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 1007.raw
8. 斑点1404：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 1404.raw
9. 斑点1405：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 1405.raw
10. 斑点1406：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 1406.raw
11. 斑点1407：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 1407.raw
12. 斑点1607：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 1607.raw
13. 斑点1705：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 1705.raw
14. 斑点1706：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 1706.raw
15. 斑点1807：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 1807.raw
16. 斑点2306：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 2306.raw
17. 斑点2707：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 2707.raw
18. 斑点2804：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 2804.raw
19. 斑点3110：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪（赛默飞世尔科技，美国加利福尼亚州）上完成分析，样本取自两种悉尼岩牡蛎种群在环境CO₂与升高CO₂暴露条件下的差异表达蛋白，对应原始文件为ET121113_spot 3110.raw
20. 斑点3304：胰蛋白酶肽段经反相纳流液相色谱-串联质谱（LC-MS/MS）在QExactive质谱仪上完成分析，完整数据集详见Dryad链接。