Widely Targeted Lipidomics Dataset of SiHa Cells Treated with CeY-B1

# README - Extensively Targeted Lipidomics Dataset of SiHa Cells Treated with CeY-B1 ## 1. Dataset DescriptionSiHa cells were treated with CeY-B1 in the experimental group and DMSO in the control group. Untargeted lipidomics sequencing (LC-MS/MS) was performed 48 hours later.This dataset is primarily used to compare lipid profiles before and after CeY-B1 treatment. Data File: 'ALL_sample_data_raw.xlsx'Contents: Lipid information table for all samples (data before missing value filling and CV filtering) ---## 2. Sample Grouping Table- Total number of samples: 13- Control group (DMSO-treated): DMSO-1 to DMSO-5- Experimental group (CeY-B1-treated): Cer-B1-1 to Cer-B1-5- Quality control (QC): QC01 to QC03 ---## 3. Column Description|Column Name | Meaning ||------|------||Home | Sequential number or unique identifier of the compound in the dataset ||Compound | English name of the compound (usually the lipid name) ||Substance | Chinese name of the compound ||Class I | Major lipid class (e.g., CE, ST, FA, SP, etc.) ||Substance Class I | Chinese name of the first-level class (corresponding to the Chinese description of Class I) ||Secondary |Lipid secondary classification (e.g., BA, CAR, Cer-NS, etc.) ||Substance secondary classification | Secondary classification name in Chinese (corresponding to the Chinese description of Class II) ||Q1 (Da) | Mass-to-charge ratio (m/z), unit: Da ||Molecular weight (Da) | Molecular weight, unit: Da ||Ionization model | Ionization mode (e.g., [M+H]+, [M+NH4]+, [M-H]-, etc.) ||Formula | Chemical formula (e.g., C27H46O) ||DMSO-1 to DMSO-5 | Peak area or relative abundance of five biological replicates of the control group (DMSO treatment) ||Cer-B1-1 to Cer-B1-5 | Peak area or relative abundance of five biological replicates of the experimental group (CeY-B1 treatment) ||QC01 to QC03 | Quality control sample test value ||cpd_ID | Internal database ID of the compound ||HMDB | Human Metabolome Database ID ||PubChem Customer Identification Information |PubChem Compound Database CID ||Lipid Map ID |LIPID MAPS Lipid Database ID ||CAS Company |Compound CAS Registry Number ||ChEBI |Chemical Entity of Biological Significance ID ||Metlin |Metlin Metabolite Database ID | ---## 4. Experimental Methods**Sample Extraction:**1. Remove sample from -80°C freezer and thaw on ice;2. Add 1 mL of extraction solvent (MTBE:MeOH = 3:1, v/v, containing internal standard mixture) and vortex for 15 minutes;3. Add 200 μL of ultrapure water, vortex for 1 minute, and centrifuge at 12,000 rpm for 10 minutes;4. Take 500 μL of the supernatant organic phase and concentrate to dryness under vacuum;5. Dissolve in 200 μL of reconstitution solution (ACN:IPA = 1:1, v/v) and perform LC-MS/MS analysis. **LC-MS/MS Conditions:**- Instrument: UPLC, ExionLC AD; Mass Spectrometer: QTRAP® 6500+ (Sciex)- Column: Thermo Accucore™ C30 (2.6 μm, 2.1 × 100 mm)- Mobile Phase: A: ACN/Water (60/40, 0.1% Formic Acid, 10 mmol/L Ammonium Formate) B: ACN/IPA (10/90, 0.1% Formic Acid, 10 mmol/L Ammonium Formate)- Gradient Elution: 0–20 min Multi-step Gradient- ESI Dual Mode (Positive and Negative Ion), Spray Voltage +5500 V/-4500 V, Temperature 500°C **Qualitative and Quantitative:**- Data Acquisition: MRM (Multiple Reaction Monitoring)- Data Processing: Metware Database (MWDB)- Missing value imputation method: KNN (k-nearest neighbors)- Quality control criteria: QC sample CV ≤ 0.3 ---## 5. Data processing and analysis- Missing value imputation: R package 'impute' (KNN)- Normalization: Unit variance (UV scaling)- Statistical analysis:- PCA ('prcomp')- HCA ('ComplexHeatmap')- OPLS-DA ('MetaboAnalystR', VIP>1)- Differential screening criteria: VIP>1 and p<0.05- Enrichment analysis:- KEGG & HMDB annotations- Metabolic pathway enrichment (Hypergeometric test) ---## 6. CitationLi, J.C., et al. (2025). Targeting cell membrane sphingolipids: A novel ceramide analog, CeY-B1, inhibits migration and invasion of cervical cancer cells. Zenodo. DOI: [DOI assigned at the time of upload].# 说明文档——经CeY-B1处理的SiHa细胞广靶向脂质组学数据集 ## 1. 数据集概况 实验组采用CeY-B1处理SiHa细胞，对照组采用二甲基亚砜（DMSO）处理。培养48小时后进行非靶向脂质组学测序（液相色谱-串联质谱，LC-MS/MS）。本数据集主要用于对比CeY-B1处理前后的脂质谱特征。 数据文件：'ALL_sample_data_raw.xlsx' 内容：所有样本的脂质信息表（缺失值填充与变异系数过滤前的原始数据） ---## 2. 样本分组表 - 总样本数：13份 - 对照组（DMSO处理）：DMSO-1至DMSO-5 - 实验组（CeY-B1处理）：Cer-B1-1至Cer-B1-5 - 质量控制（QC）样本：QC01至QC03 ---## 3. 列属性说明 |列名|含义| |------|------| |Home|数据集内化合物的序号或唯一标识符| |Compound|化合物英文名称（通常为脂质名称）| |Substance|化合物中文名称| |Class I|脂质一级大类（如CE、ST、FA、SP等）| |Substance Class I|一级类别的中文名称（对应Class I的中文描述）| |Secondary|脂质二级分类（如BA、CAR、Cer-NS等）| |Substance secondary classification|二级分类的中文名称（对应Class II的中文描述）| |Q1 (Da)|质荷比（m/z），单位：道尔顿（Da）| |Molecular weight (Da)|分子量，单位：道尔顿（Da）| |Ionization model|离子化模式（如[M+H]+、[M+NH4]+、[M-H]-等）| |Formula|化学分子式（如C27H46O）| |DMSO-1至DMSO-5|对照组（DMSO处理）5个生物学重复的峰面积或相对丰度| |Cer-B1-1至Cer-B1-5|实验组（CeY-B1处理）5个生物学重复的峰面积或相对丰度| |QC01至QC03|质量控制样本检测值| |cpd_ID|化合物内部数据库ID| |HMDB|人类代谢组数据库（HMDB）ID| |PubChem Customer Identification Information|PubChem化合物数据库CID| |Lipid Map ID|LIPID MAPS脂质数据库ID| |CAS Company|化合物CAS登记号| |ChEBI|生物意义化学实体（ChEBI，Chemical Entity of Biological Significance）ID| |Metlin|Metlin代谢物数据库ID| ---## 4. 实验方法 **样本前处理：** 1. 从-80℃冰箱取出样本，置于冰上解冻； 2. 加入1mL萃取溶剂（甲基叔丁基醚:甲醇=3:1，体积比，含内标混合物），涡旋振荡15分钟； 3. 加入200μL超纯水，涡旋1分钟，12000 rpm离心10分钟； 4. 取500μL上层有机相，真空浓缩至干； 5. 用200μL复溶溶剂（乙腈:异丙醇=1:1，体积比）复溶，随后进行LC-MS/MS分析。 **LC-MS/MS分析条件：** - 仪器：超高效液相色谱（UPLC）ExionLC AD；质谱仪：QTRAP® 6500+（Sciex公司） - 色谱柱：Thermo Accucore™ C30（2.6 μm，2.1 × 100 mm） - 流动相： A相：乙腈/水（60/40，含0.1%甲酸、10 mmol/L甲酸铵） B相：乙腈/异丙醇（10/90，含0.1%甲酸、10 mmol/L甲酸铵） - 梯度洗脱：0–20 min 多步梯度洗脱 - 电喷雾离子化双模式（正、负离子模式），喷雾电压+5500 V/-4500 V，离子源温度500℃ **定性与定量分析：** - 数据采集：多反应监测（MRM，Multiple Reaction Monitoring） - 数据处理：Metware数据库（MWDB） - 缺失值填充方法：K近邻法（KNN，k-nearest neighbors） - 质量控制标准：QC样本变异系数（CV）≤0.3 ---## 5. 数据处理与分析 - 缺失值填充：使用R包'impute'（KNN算法） - 归一化：单位方差归一化（UV scaling） - 统计分析： 主成分分析（PCA，采用'prcomp'函数）、层次聚类分析（HCA，采用'ComplexHeatmap'包）、正交偏最小二乘判别分析（OPLS-DA，采用'MetaboAnalystR'包，变量重要性投影（VIP）>1） - 差异筛选标准：VIP>1且p<0.05 - 富集分析： KEGG与HMDB注释、代谢通路富集分析（采用超几何检验） ---## 6. 参考文献 Li, J.C. 等（2025）. 靶向细胞膜鞘脂：新型酰胺类似物CeY-B1抑制宫颈癌细胞迁移与侵袭. Zenodo. DOI：[上传时分配的DOI]