Metabolomics FAQ

• • Where to Find the Specific Functions of Metabolites, Such as Their Impact on Plasma Membrane Integrity

  To investigate the specific functions of metabolites, including their potential influence on cellular processes such as plasma membrane integrity, the following databases are valuable resources: 1. KEGG Pathway Database (KEGG) A comprehensive database that provides detailed information on genes, chemical compounds, enzymatic reactions, and biological pathways. The KEGG pathway module is particularly useful for elucidating the roles of metabolites within cellular metabolism and biochemical networks.

• • Is It Better for Each R²X and R²Y to Exceed 0.5 or for Their Cumulative Values? How to Interpret the Q² Intercept

  For the two-dimensional plots of PLS-DA or OPLS-DA, it is generally considered more favorable when the cumulative values of R²X and R²Y across all principal components exceed 0.5, indicating that the model explains more than half of the total variance. Specifically, R²X quantifies the proportion of variance in the predictor variables (X) that is explained by the model, while R²Y quantifies the model’s ability to account for variance in the response variables (Y). A cumulative value above 0.5 suggests that..

• • What Is the Best Method for Metabolite Detection

  Metabolite detection is commonly performed using the following methods: 1. Mass Spectrometry (MS) Mass spectrometry enables accurate determination of both the mass and structural features of metabolites. Commonly used techniques include Gas Chromatography-Mass Spectrometry (GC-MS) and Liquid Chromatography-Mass Spectrometry (LC-MS). 2. Nuclear Magnetic Resonance (NMR) NMR provides detailed structural information about metabolites and is particularly suitable for analyzing complex biological samples ........

• • How is the Molecular Weight of Polysaccharides Calculated? How is the Standard Curve for Dextran Standards Prepared?

  Calculation of Polysaccharide Molecular Weight 1.  Gel Permeation Chromatography (GPC) or High-Performance Liquid Chromatography (HPLC) These are common methods for determining the molecular weight of polysaccharides. The molecular weight is calculated by comparing the sample to standards of known molecular weight, using the sample's retention volume in the chromatographic column.   2. Light Scattering Method This method utilizes the scattering of laser light by proteins or polysaccharides in solution......

• • Is Secondary Identification Required in Untargeted Metabolomics? Why Use m/z Ratios for Metabolite Identification?

  Untargeted metabolomics typically requires secondary identification, as primary mass spectrometry data (such as m/z ratios) usually only provide information on the ion's mass-to-charge ratio and potential molecular formulas, but cannot accurately determine the compound's structure. Secondary identification, through tandem mass spectrometry analysis, provides additional structural information about metabolites, which helps ensure the accuracy of compound identification.   However, in certain cases, res......

• • How Much Internal Standard Should Be Added in Targeted Metabolomics?

  The amount of internal standard added in targeted metabolomics analysis depends on several factors, including sample type, analytical method, instrument sensitivity, and the concentration range of the target metabolites. Below are some general guidelines:   Selection of the Appropriate Internal Standard 1. Isotopically Labeled Internal Standards These are internal standards labeled with isotopes that have a similar structure to the target metabolites but differ in mass.   2. Structurally Similar Inter......

• • How to Address Compaction and Slowing Flow Rate During Gel Filtration Column Equilibration?

  Compaction of the packing material and a reduction in flow rate are common issues during gel filtration chromatography. These problems can be caused by various factors, and addressing them requires targeted solutions:   Improper Packing Process The packing process of the chromatography column requires careful attention. If not done correctly, it may lead to tightly compacted packing material, reducing the available flow space within the column and, consequently, slowing down the flow rate.   Solution ......

• • What Do the Percentages on the X and Y Axes of a PLAS-DA Score Plot Represent?

  The percentages on the X and Y axes of a PLAS-DA score plot typically represent the proportion of total variance explained by the corresponding components (principal components). For example, if the percentage on the X-axis is 30%, it indicates that the first principal component explains 30% of the total variance.   MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider. Related Services PLS-DA/OPLS-DA Two-Dimensional Diagrams Analysis Service

• • What Molecular Weight Cut-Off Should Be Chosen for Dialysis Bags in Bacterial Polysaccharide Purification?

  When performing dialysis purification of bacterial polysaccharides, the molecular weight cut-off (MWCO) of the dialysis bag should be smaller than the polysaccharide’s molecular weight. It is generally recommended to select a MWCO that is one-third to one-half of the polysaccharide's molecular weight. For instance, if the molecular weight of the bacterial polysaccharide is approximately 300,000 Da, the MWCO of the dialysis bag should be between 100,000 and 150,000 Da. This ensures that small molecular......

• • Identification Methods of Sugars in Glycosides

  Glycosides are compounds consisting of a sugar moiety and a non-carbohydrate moiety (commonly an aromatic or aliphatic compound). Identifying the sugar component is a critical step in elucidating the structure and function of glycosides. The following methods are commonly employed for the identification of sugars in glycosides: 1. Chromatographic Methods High-performance liquid chromatography (HPLC) and gas chromatography (GC) are frequently used techniques. These methods enable the separation and ........