Metabolomics FAQ

• • How Can Significant Differential Metabolites Be Identified in Untargeted Metabolomics, and What Are Their Three Categories?

  In untargeted metabolomics data analysis, differential metabolites are defined as those exhibiting significant differences between distinct sample groups (e.g., control and experimental groups). Identifying these differential metabolites enables a deeper understanding of biological differences between sample groups, the discovery of potential biomarkers, and the investigation of alterations in metabolic pathways. Differential metabolites are generally categorized into three types: upregulated metaboli......

• • How Should a PLS-DA Plot Be Interpreted?

  PLS-DA (Partial Least Squares Discriminant Analysis) is widely used to visualize and interpret class separation in high-dimensional datasets. PLS-DA results are typically represented through various types of plots, each offering distinct insights. The following are common PLS-DA plots and their interpretations:   Score Plot The score plot illustrates the distribution of samples within the PLS-DA model. Each point represents an individual sample, with different colors or shapes denoting different categ......

• • Does FDR in KEGG Pathway Analysis Indicate Enrichment Level or Simply Reflect a Smaller P-value?

  False Discovery Rate (FDR) is a statistical method used in multiple hypothesis testing to control the occurrence of false positives. When performing a large number of hypothesis tests (e.g., analyzing thousands of genes for associations with a disease), some statistically significant results may arise purely due to random chance. To mitigate such false positives, FDR correction is applied. The FDR value ranges from 0 to 1, with a lower FDR indicating greater confidence that the observed pathway enrich......

• • What Are the Major Pathways of Lipid Metabolism?

  Lipid metabolism consists of biochemical reactions and enzyme-catalyzed processes responsible for lipid synthesis, degradation, and regulation in the human body. The following are key lipid metabolic pathways:   Triacylglycerol Synthesis Pathway Triacylglycerol is a major energy storage molecule synthesized in adipose tissue. This pathway involves several key enzymes, including glycerol-3-phosphate dehydrogenase, glycerol-3-phosphatase, and glycerol-3-phosphate acyltransferase.   Cholesterol Synthesis......

• • What Are the Methods for Processing Serum Samples?

  The standard methods for processing serum samples are as follows:   Blood Collection Blood should be collected from the subject’s vein using aseptic techniques and placed into a tube without anticoagulants.   Coagulation Incubate the blood sample at room temperature for 30 minutes to 1 hour to allow for coagulation.   Centrifugation Centrifuge the blood sample containing the clot at approximately 1000 to 2000 g for 15 to 20 minutes.   Serum Collection Carefully aspirate the serum (upper liquid) using ......

• • 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.