Metabolomics FAQ

• • How to Identify Differentially Associated Genes for Differential Metabolites?

  After identifying differential metabolites, the following approaches can be used to search for genes associated with them:   Database and Literature Search Search for genes and biological pathways related to the metabolites by using their names or structures in literature databases (such as PubMed) and specialized metabolomics databases (such as HMDB, KEGG, MetaboAnalyst).   Bioinformatics Tools 1. MetaboAnalyst Input differential metabolite data to perform pathway enrichment analysis, identifying ass......

• • How to Construct an S-plot in OPLS-DA?

  S-plot is a widely used visualization tool in OPLS-DA or PLS-DA for identifying variables that contribute most to class separation. By integrating loadings and correlation coefficients, S-plot presents variables in a structured and interpretable manner. The following are the fundamental steps for constructing an S-plot analysis:   Data Preparation A dataset previously analyzed using OPLS-DA is required. This dataset should include measured values of relevant variables, such as metabolite concentration......

• • How Does LC/MS Perform MS1 and MS2 Detection?

  LC-MS is a technique that integrates liquid chromatography with mass spectrometry to achieve qualitative and quantitative analysis of complex samples. In LC-MS, MS1 and MS2 detections correspond to the first- and second-stage mass spectrometry analysis, respectively. Below is an overview of the process for performing MS1 and MS2 detection in LC-MS:   Liquid Chromatography Separation LC-MS begins with liquid chromatography separation, where components in the sample are separated using a stationary phas......

• • 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......