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

先前研究指出，经过选择性培育以促进快速生长和增强抗病能力的悉尼岩牡蛎幼虫，相较于未经选择的野生型牡蛎，对海洋酸化的影响具有更强的抵抗力。在本研究中，我们运用蛋白质组学方法，探究成年悉尼岩牡蛎中不同种群之间的分子差异，并旨在确定这些差异是否构成了幼虫观察结果的基础。来自选择性培育系（B2）和非选择性野生型（WT）的成年牡蛎在暴露于增高的二氧化碳浓度（856 μatm）四周后，其蛋白质组与在自然条件下（375 μatm pCO2）培养的牡蛎蛋白质组进行了比较。暴露于增高的二氧化碳浓度导致选择性培育和野生型种群中牡蛎蛋白质组发生显著变化。在赋予生物学功能后，这些差异蛋白质可归类为五种广泛的、可能相互关联的亚细胞功能类别，这两种牡蛎种群均具有。这些功能类别包括能量产生、细胞应激反应、细胞骨架、蛋白质合成和细胞信号传导。在野生型种群中，蛋白质表达量普遍上调。然而，出乎意料的是，这些细胞系统在选择性培育的牡蛎种群中却被下调，表明细胞功能失调。我们认为，这反映了某种权衡，即选择性培育种群中增强的线粒体能量产生能力可能有助于保护幼虫免受高二氧化碳浓度的影响，但同时可能对成年牡蛎产生不利影响。

使用说明
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 211.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 213.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 214.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 306.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 308.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 502.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 1007.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 1404.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 1405.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 1406.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 1407.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 1607.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 1705.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 1706.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 1807.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 2306.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 2707.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 2804.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 3110.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。ET121113_spot 3304.raw
悉尼岩牡蛎差异表达蛋白质的原始质谱文件 - Tryptic肽在QExactive质谱仪（Thermo scientific，CA，美国）上通过反相纳米流液相色谱-串联质谱（LC-MS/MS）进行分析。样品代表在自然和增高的二氧化碳浓度暴露下，来自悉尼岩牡蛎两个种群差异表达蛋白质。

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