Metabolomics FAQ

• • How Should Upregulation and Downregulation Be Interpreted in KEGG Bubble Plots?

  KEGG bubble plots are a visualization tool used to represent changes in gene expression data within KEGG pathways. Each bubble in the plot corresponds to a specific pathway, with the color and size of the bubble reflecting the changes in gene/protein/metabolite expression within that pathway. This approach aids in understanding the differential roles of genes/proteins/metabolites in biological pathways under varying conditions.   In KEGG bubble plots, upregulation and downregulation of gene expression......

• • Does a Q2 of 0.2 and an R2 of 0.9 in the OPLS-DA Model Indicate Poor Model Performance?

  When evaluating the performance of an OPLS-DA (Orthogonal Partial Least Squares Discriminant Analysis) model, R2 quantifies the model's ability to explain the variance in the data, while Q2 serves as an indicator of its predictive capability.   An R2 of 0.9 suggests that the model accounts for 90% of the variance in the dataset, which is generally considered a strong fit. However, this may also indicate potential overfitting. Specifically, in the case you described:   A Q2 of 0.2 indicates limited pre......

• • Should Glucose be Detected Using Positive or Negative Ion Mode in Liquid Chromatography-Mass Spectrometry?

  When glucose is detected using liquid chromatography-mass spectrometry (LC-MS), positive ion mode is generally preferred. This is because carbohydrates, such as glucose, are more likely to ionize in positive ion mode and typically exhibit higher signal intensity and sensitivity.   In positive ion mode of LC-MS, glucose molecules can acquire a positive charge by forming adducts with metal ions (such as sodium or potassium) or through other ionization mechanisms. This enhances their detectability in the......

• • What Are the Polysaccharide Extraction Steps? Does Skipping Acetone Washing Affect Subsequent Experiments?

  Polysaccharide extraction typically follows a systematic approach to isolate and purify polysaccharides from biological sources. The following outlines a standard extraction protocol:   Sample Preparation 1. Select an appropriate biological source (e.g., plant roots, leaves, stems, fruits, animal tissues, or microbial cells). 2. Homogenize or pulverize the sample to enhance extraction efficiency.   Protein Removal 1. The raw material is typically treated with a chloroform-n-butanol mixture (1:4 v/v) t......

• • Which Software is Used for Metabolite Identification, and How Can the Accuracy of Identification Results Be Ensured?

  Software for Metabolite Identification Several software tools are available for metabolite identification, including MZmine, XCMS, MetaboAnalyst, and Compound Discoverer. A brief overview of their functions is provided below:   1. MZmine MZmine is a versatile software platform for processing mass spectrometry (MS) data, including essential tasks such as data cleaning, peak detection, alignment, and normalization. It also interfaces with online compound databases, such as PubChem and ChemSpider, enabli......

• • What Are the Methods for Identifying Polysaccharide Structures?

  Polysaccharides are composed of monosaccharide units linked by glycosidic bonds. Their structures are highly complex and diverse, encompassing aspects such as monosaccharide composition, linkage types, branching patterns, and molecular weight. The identification of polysaccharide structures is a challenging process that typically requires the integration of multiple analytical techniques. The following are some commonly employed methods for polysaccharide structural analysis:   Mass Spectrometry (MS) ......

• • What is the Minimum Sample Size Required for Metabolomics Analysis?

  There is no universally established sample size for metabolomics studies. However, by considering factors such as the research objectives, sample heterogeneity, technology platforms, statistical methods, and the expected effect size, the required sample size for metabolomics analysis can be more accurately determined through appropriate experimental design and pilot studies.   Research Design To obtain statistically significant results, it is recommended to perform a power analysis based on preliminar......

• • What are the Analytical Methods for Polysaccharides?

  Polysaccharide analysis typically involves the processes of separation, identification, and quantification. Several analytical techniques are commonly employed, each with its own advantages depending on the application. These methods include:   High-Performance Liquid Chromatography (HPLC) HPLC is widely used for the separation and quantification of polysaccharides. Different types of chromatographic columns (e.g., reverse-phase, ion-exchange, or gel permeation) can be selected to separate polysacchar......

• • Are Five Biological Replicates Standard in Animal Metabolomics? Is Three Sufficient?

  In metabolomics research, biological replicates are essential for assessing experimental reproducibility and minimizing errors, thereby improving the reliability of the resulting data. To ensure accuracy and reproducibility, researchers typically perform multiple independent experiments.   In scientific research, three biological replicates are commonly used and widely accepted. However, if experimental conditions permit, increasing the number of replicates enhances statistical power and strengthens t......

• • How Can Metabolomics Results Be Further Validated?

  Following the acquisition of metabolomics data, a series of validation approaches are necessary to ensure result accuracy and reliability. The following methods are commonly employed:   1. Replication Experiments Experimental replication is fundamental for confirming metabolomics findings. Conducting multiple independent experiments allows assessment of result reproducibility and stability. At least three independent replicates are generally recommended for validation.   2. Standard Compound Validatio......