Metabolomics FAQ

• • Which Sample Is Better for Metabolomics Analysis Serum or Plasma?

  Plasma and serum are widely used in metabolomics research, each offering distinct advantages and applications. The selection should be based on specific research objectives and experimental requirements. Below is an overview of their respective applications.   Plasma Applications 1. Investigation of Dynamic Metabolic Processes Plasma is obtained by centrifugation of anticoagulated blood and retains nearly all blood metabolites, including those involved in coagulation pathways. It is particularly suita......

• • How to Interpret the Loading Plot in OPLS-DA Analysis?

  Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) is a multivariate statistical method designed to extract meaningful patterns from high-dimensional datasets. It is widely applied in high-throughput analyses such as metabolomics and proteomics.   In OPLS-DA, the loading plot is a key visualization tool that facilitates the interpretation of variable contributions within the model. Each point in the loading plot represents a variable, with its position indicating its relative contributio......

• • Is the Insolubility of Polysaccharides in Water After Alcohol Precipitation a Normal Phenomenon?

  Alcohol precipitation involves increasing the concentration of alcohol (e.g., ethanol) to induce polysaccharide precipitation. This method is widely used to efficiently separate polysaccharides from complex biological mixtures.   The solubility of polysaccharides is influenced by their chemical structure and environmental factors, such as temperature, pH, and ionic strength. While some polysaccharides are highly soluble in water, others exhibit limited solubility. Alcohol precipitation can induce stru......

• • How Should Visualization Plots Be Interpreted in Metabolomics Data Analysis?

  Following bioinformatics analysis of metabolomics data, various types of visualization plots are typically generated, each providing distinct insights into the dataset. Proper interpretation of these plots enables a multi-dimensional understanding of metabolomic patterns:   Principal Component Analysis (PCA) Plot PCA is an unsupervised dimensionality reduction technique used to visualize the overall structure and distribution of the data. In a PCA plot, each point represents a sample, with closer poin......

• • What Are the Methods for Deproteinizing Polysaccharides? Is Drying Necessary After Deproteinization?

  Extracting polysaccharides from protein-rich biological samples presents a significant challenge in biological and biochemical research. Two commonly used methods for polysaccharide deproteinization are as follows:   Trichloroacetic Acid (TCA)/Acetone Precipitation Method Proteins can be precipitated using TCA or a cold acetic acid-acetone mixture, allowing polysaccharides to remain in the supernatant. The precipitated proteins are then washed with cold acetone to remove residual polysaccharides.   Ch......

• • How Should the Issue of Unmatched Metabolites in KEGG Pathway Enrichment Analysis Be Addressed?

  When performing pathway enrichment analysis, some metabolites may not have corresponding KEGG IDs, leading to the failure of certain pathways to be enriched. To address this issue, the following approaches can be considered:   Database Updates and Alternative Resources Ensure that the KEGG database in use is up to date. Additionally, consider exploring alternative bioinformatics databases such as MetaCyc or Reactome, which may contain more comprehensive and recently updated metabolite information.   C......

• • 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......