Metabolomics FAQ

• • How Are Highly Enriched Pathways Identified in KEGG Analysis?

  The purpose of KEGG pathway analysis is to identify which biological pathways are significantly enriched under your experimental conditions and, consequently, may play a critical role in the biological processes being studied. The following approaches can be used to identify the most highly enriched pathways from the KEGG analysis results:   P-value and Adjusted P-value (e.g., False Discovery Rate - FDR) The KEGG analysis results generally provide a P-value, which indicates the statistical significanc......

• • How to Extract Intracellular Lipids in Lipidomics Research?

  The process of extracting intracellular lipids typically involves the following steps:   Cell Collection The cultured cells are collected by washing and centrifugation.   Cell Lysis A lysis buffer (e.g., a salt solution containing a detergent) is used to disrupt the cell membrane and release the cellular contents, ensuring the release of lipids.   Lipid Extraction The most commonly used methods are the Bligh and Dyer method and the Folch method. Both methods involve the use of organic solvents (such a......

• • Why Is Q2 Negative in the PLS-DA/OPLS-DA 2D Plot?

  The Q2 value is a statistical metric used in PLS-DA/OPLS-DA to assess the model's predictive capability. Specifically, Q2 represents the squared correlation coefficient for prediction. During modeling, Q2 is obtained through cross-validation. A positive Q2 indicates that the model has some predictive capability for the test dataset, whereas a negative Q2 usually signifies poor predictive performance or overfitting of the model.   Several factors may contribute to a negative Q2 value, including:   1. M......

• • What Does the VIP Score Represent in the OPLS-DA Model

  Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) is a multivariate statistical method widely used for pattern recognition and classification. In the OPLS-DA model, the Variable Importance in the Projection (VIP) score serves as a key metric for assessing the relative importance of each variable in the model.   Interpretation of the VIP Score 1. The VIP score quantifies the contribution of a variable to the model’s predictive performance and classification accuracy.   2. A higher VIP sc......

• • How to Collect Mouse Serum Samples

  The procedures for collecting mouse serum samples: 1. Blood Collection: Blood samples are collected from the mouse's tail vein or jugular vein. 2. Coagulation: The collected blood is allowed to clot at room temperature for approximately 15-30 minutes. 3. Centrifugation: The clotted blood is centrifuged at 3000-5000 g for 10-15 minutes to separate the serum from the clot. 4. Serum Collection: The serum is transferred to a clean centrifuge tube and stored at -20°C or -80°C for subsequent analyses.