Multi-region proteomics maps mitochondrial and proteostatic networks recovery by subthreshold magnetic stimulation in Alzheimer mice

This dataset accompanies the manuscript "Multi-region proteomics maps mitochondrial and proteostatic networks recovery by subthreshold magnetic stimulation in Alzheimer mice." The study uses quantitative proteomics across multiple brain regions to map mitochondrial and proteostatic network changes in a mouse model of Alzheimer's disease, and to characterise their recovery following subthreshold magnetic stimulation.
This Mendeley Data record contains the processed proteomics outputs and supporting materials for the manuscript: protein and peptide quantification matrices, search parameter files, sample metadata describing the experimental design (brain region, genotype, and treatment group), and analysis outputs supporting the figures and statistics in the manuscript.
Raw spectra were searched with SequestHT (Proteome Discoverer) against the UniProt Mus musculus database (SwissProt + TrEMBL with isoforms, TaxID 10090, version 2024-01-24). Tryptic digestion was used with up to 2 missed cleavages and a minimum peptide length of 6 amino acids. Precursor mass tolerance was set to 10 ppm and fragment mass tolerance to 0.02 Da. Carbamidomethylation of cysteine was set as a static modification; oxidation of methionine and N-terminal acetylation were set as dynamic modifications. Peptide-spectrum matches were validated with Percolator using a concatenated target/decoy strategy with FDR thresholds of 1% (strict) and 5% (relaxed). Detailed search parameters are provided in the 02_search_parameters/ folder.
The raw mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository under the dataset identifier PXD077354. This Mendeley Data record should be cited together with the PRIDE deposit and the associated manuscript.

本数据集配套于论文《阿尔茨海默病小鼠经阈下磁刺激后，多区域蛋白质组学揭示线粒体与蛋白稳态网络的恢复过程》。
本研究通过多脑区域定量蛋白质组学，绘制阿尔茨海默病小鼠模型中线粒体与蛋白稳态网络的变化特征，并解析其经阈下磁刺激后的恢复过程。
本孟德雷数据（Mendeley Data）记录包含配套于该论文的已处理蛋白质组学输出结果与辅助材料：包括蛋白质与肽段定量矩阵、检索参数文件、描述实验设计（脑区域、基因型与处理组）的样本元数据，以及支撑论文中图表与统计分析的结果文件。
原始质谱光谱数据通过SequestHT（Proteome Discoverer）软件，针对小家鼠（Mus musculus）通用蛋白质知识库（UniProt）数据库（SwissProt + TrEMBL 含同工型，分类学标识符（TaxID）10090，版本2024-01-24）进行检索。本实验采用胰蛋白酶酶解，允许最多2个漏切位点，肽段最小长度为6个氨基酸。前体质量容差设为10 ppm，碎片质量容差设为0.02 Da。将半胱氨酸的氨基甲酰甲基化设为固定修饰；将甲硫氨酸氧化与N端乙酰化设为可变修饰。肽谱匹配结果通过Percolator软件，采用串联靶标-诱饵策略进行验证，错误发现率（FDR，False Discovery Rate）严格阈值为1%、宽松阈值为5%。详细检索参数存放在02_search_parameters/文件夹中。
原始质谱数据已通过PRIDE合作库提交至ProteomeXchange联盟，数据集标识符为PXD077354。引用本孟德雷数据记录时，需同时标注PRIDE提交条目与相关论文。