Spreadsheet of chromatogram areas for all dairy cows.

The hypothesis of this study is that volatile organic compounds (VOCs) present in bovine cerumen reflect systemic metabolic changes occurring during the transition from late gestation to early lactation and can serve as non-invasive indicators of energy balance and metabolic health in dairy cows. To evaluate this hypothesis, cerumen samples were collected longitudinally from the same animals at different physiological stages and analyzed using headspace gas chromatography–mass spectrometry (HS/GC–MS). The dataset consists of raw and processed HS/GC–MS chromatograms from which 97 unique VOCs were identified after spectral deconvolution and removal of contaminants, including siloxanes. The detected compounds belong to several chemical classes, such as aldehydes, ketones, alcohols, amides, carboxylic acids, esters, lactones, heterocyclic compounds, and hydrocarbons. Each chromatogram corresponds to a single biological sample, allowing both cross-sectional comparisons between breeds and longitudinal evaluation within individual animals across time. Data acquisition was performed under standardized HS/GC–MS conditions to ensure analytical reproducibility. Peak detection, alignment, and normalization were applied prior to statistical analysis. An untargeted metabolomics approach was used, meaning that no metabolites were predefined before analysis. Instead, statistical tools including fold-change analysis, non-parametric tests, volcano plots, hierarchical clustering, and heatmap visualization were applied to identify relevant metabolic differences between breeds and physiological stages. The data reveal clear metabolic differentiation between Jersey and Girolando cows, as well as between pre-partum and early lactation periods. Notable differences were observed in metabolites related to lipid metabolism, oxidative stress, and energy balance, including fatty acids, aldehydes, ketone-related compounds, and alcohols. These patterns are consistent with known physiological adaptations to negative energy balance during the transition period. Overall, the chromatographic profiles represent metabolic fingerprints that integrate breed-specific characteristics and temporal physiological changes. This dataset can be reused for biomarker discovery, comparative metabolomic studies, validation of alternative statistical approaches, or the development of non-invasive monitoring tools to support health management and decision-making in dairy production systems.本研究提出的核心假设为：牛耳垢（bovine cerumen）中含有的挥发性有机化合物（volatile organic compounds, VOCs）可反映奶牛从妊娠晚期向泌乳早期过渡阶段的全身代谢变化，能够作为奶牛能量平衡与代谢健康的非侵入性检测指标。为验证该假设，研究人员从同批受试奶牛的不同生理阶段纵向采集耳垢样本，并采用顶空气相色谱-质谱联用法（headspace gas chromatography–mass spectrometry, HS/GC–MS）开展分析。 本数据集包含原始与预处理后的HS/GC–MS色谱图，经光谱去卷积与污染物（包括硅氧烷）去除流程后，共鉴定得到97种独特的挥发性有机化合物。所检出的化合物涵盖多个化学类别，包括醛类、酮类、醇类、酰胺类、羧酸类、酯类、内酯类、杂环化合物与烃类。每张色谱图对应单个生物样本，既可支持不同品种间的横向比较，也可实现单只奶牛随时间推移的纵向生理状态评估。 数据采集严格遵循标准化的HS/GC–MS实验条件，以保障分析结果的可重复性。统计分析前已完成峰识别、峰对齐与峰归一化处理。本研究采用非靶向代谢组学方法，即分析前未预先设定代谢物范围。研究通过包括倍数变化分析、非参数检验、火山图、层次聚类及热图可视化在内的多种统计工具，识别不同品种与生理阶段间的显著代谢差异。 数据分析结果清晰显示，娟姗牛（Jersey）与吉罗兰多牛（Girolando）之间，以及产前与泌乳早期之间均存在明显的代谢分化。在与脂质代谢、氧化应激及能量平衡相关的代谢物中观察到显著差异，涵盖脂肪酸、醛类、酮类相关化合物与醇类。上述变化模式与奶牛过渡期应对能量负平衡的已知生理适应性特征一致。 总体而言，该色谱图谱可视为整合了品种特异性特征与时序生理变化的代谢指纹。本数据集可重复应用于生物标志物发掘、比较代谢组学研究、替代统计方法验证，或开发用于辅助乳制品生产系统健康管理与决策的非侵入式监测工具。