DOI: 10.5281/zenodo.16809837
title: Widely Targeted Lipidomics Dataset of SiHa Cells Treated with CeY-B1

description: # 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].