Metabolomics FAQ

• • What Reagents and Their Names Are Required in Metabolomics?

  In metabolomics, the reagents commonly employed are typically associated with sample preparation, metabolite extraction, derivatization, and analysis. Below are some widely used reagents at each stage of metabolomics research:   Sample Preparation and Extraction 1. Methanol Frequently used in sample pretreatment and extraction.   2. Acetonitrile Utilized for metabolite extraction and protein precipitation.   3. Chloroform Commonly employed for extracting lipid metabolites.   Derivatization Reagents 1.......

• • How Should One Interpret an OPLS-DA Plot in MetaboAnalyst?

  An OPLS-DA plot typically comprises a score plot and a loading plot. The score plot illustrates how samples are projected onto the principal components of the model and is commonly utilized to depict the separation between different groups, such as disease and control groups. The loading plot, on the other hand, indicates the contribution of individual variables (e.g., metabolites) in distinguishing between these groups.   Interpretation of the Score Plot 1. Sample Clustering Assess whether samples fr......

• • How to Perform WGCNA on a Pathway of Interest and Identify Hub Genes?

  1. Data Preparation To begin, a high-quality gene expression dataset is required, typically derived from RNA-seq or microarray experiments.   2. Data Preprocessing Standardize the dataset, eliminate batch effects (if applicable), and filter out genes with minimal expression levels to reduce noise.   3. Selection of Pathways of Interest Based on the research objectives, select one or more relevant pathways from well-established biological databases such as KEGG and Reactome.   4. Construction of the Ex......

• • Which Software Is Commonly Used for Generating PLS-DA/OPLS-DA 2D Plots?

  PLS-DA/OPLS-DA 2D plots are typically generated using specialized statistical and data analysis software. Commonly used tools include:   R Language R is a powerful statistical computing and visualization tool. By utilizing packages such as mixOmics or ropls, users can conduct PLS-DA and OPLS-DA analyses and generate corresponding 2D plots.   MetaboAnalyst MetaboAnalyst is a web-based platform that provides a comprehensive suite of tools specifically designed for metabolomics data analysis. It includes......

• • Is an OPLS-DA Model with a Q2Y Value of Around 0.2 Considered Reliable in the Case of a Small Sample Size?

  Q2Y Value as a Critical Metric for Evaluating the Predictive Performance of OPLS-DA Models 1. Understanding the Q2Y Value The Q2Y value is widely used in OPLS-DA to assess the predictive performance of a model. A higher Q2Y value (close to 1) indicates strong predictive reliability, whereas a lower Q2Y value suggests poor predictive performance. Typically, a Q2Y value above 0.5 is deemed acceptable for model validation.   2. Impact of Small Sample Sizes on Q2Y Values When working with small sample siz......

• • How to Calculate Polysaccharide Purity?

  The purity of polysaccharides is typically determined using analytical techniques such as high-performance liquid chromatography (HPLC) or gel permeation chromatography (GPC). Different analytical methods may employ distinct calculation approaches. Here, we describe a purity calculation method based on chromatographic analysis:   Sample Preparation and Analysis The polysaccharide sample is subjected to analysis using an appropriate chromatographic system.   Peak Area Calculation In the chromatogram, p......

• • What Is the Optimal Concentration Method for High-Volume Solutions in Polysaccharide Extraction and Purification?

  During the extraction and purification of polysaccharides, if the solution volume is large, the following concentration methods can be considered:   Filtration-Based Concentration An appropriate filter membrane or filter paper can be used to remove macromolecules and impurities from the polysaccharide solution, yielding a relatively pure filtrate. The filtrate is then subjected to reduced temperature or vacuum conditions to facilitate solvent evaporation, thereby achieving concentration.   Membrane Se......

• • How to Purify Polysaccharides Using a Sephadex Gel Column After Impurities Remain Following Fibrous Column Chromatography?

  Polysaccharide purification is a multistep process that often requires optimization to achieve high purity. If impurities persist after processing with a fibrous column, further purification using a Sephadex gel filtration column may be necessary. The following steps outline the procedure for gel filtration purification of polysaccharides:   1. Selection of an Appropriate Sephadex Gel Choose a Sephadex gel suitable for the molecular weight range of the polysaccharide to be separated, such as Sepharose......

• • What Are the Common Methods for Polysaccharide Degradation?

  Polysaccharides are biopolymers composed of multiple monosaccharide units linked by glycosidic bonds, including starch, cellulose, and glycogen. Various methods exist for polysaccharide degradation, and the choice of method depends on the polysaccharide type, the intended purpose of degradation, and specific application requirements. Below are some commonly employed degradation strategies:   Enzymatic Hydrolysis Polysaccharides can be hydrolyzed by specific enzymes that catalyze the cleavage of glycos......

• • What Are the Targeted Methods for Detecting Short-Chain Fatty Acids in Fecal Samples?

  Targeted detection of short-chain fatty acids (SCFAs) in fecal samples is commonly conducted using gas chromatography-mass spectrometry (GC-MS), owing to its high suitability for analyzing volatile organic compounds, a category to which SCFAs belong. This technique allows for highly specific and quantitative analysis of SCFAs, including acetic acid, propionic acid, and butyric acid. The overall analytical workflow typically involves the following steps:   Sample Collection and Preparation 1. Collectio......