Metabolomics FAQ

• • How to Collect and Process Blood Samples for Metabolomics Testing

  Blood Sample Collection 1. Collection Time It is best to collect blood samples at the same time point (e.g., in the morning on an empty stomach) to minimize the impact of biological rhythms. 2. Collection Method Venipuncture is typically used with sterile collection tubes, which may contain or lack anticoagulants depending on the subsequent processing and analysis requirements. 3. Sample Volume Usually, 1-2 mL of blood is required. Blood Sample Processing 1. Centrifugation Centrifuge the blood samples at...

• • What Is the Appropriate Range for R2 and Q2 Intercepts in PLS-DA

  In Partial Least Squares Discriminant Analysis (PLS-DA), R2 is used to measure how well the model fits the data, whereas Q2 assesses the model's predictive capability. Ideally, R2 should approach 1, and Q2 should also be a positive value, with values closer to 1 indicating better performance. During cross-validation, examining the intercepts of the regression lines for R2 and Q2 can provide insights into potential overfitting tendencies of the model.

• • Purification and Detection Methods of Polysaccharides

  Polysaccharides are macromolecules composed of multiple glycosyl units, which play significant roles in biological functions and have varied applications. Purification and detection of polysaccharides often require a combination of sophisticated techniques. Purification Techniques for Polysaccharides: 1. Gel Chromatography: This method includes Gel Permeation Chromatography (GPC) and Gel Affinity Chromatography (GAC), which separate polysaccharides based on size and affinity differences for effective.......

• • In Untargeted Metabolomics, What Is the Difference Between Performing PLS-DA Analysis and OPLS-DA Analysis

  PLS-DA (Partial Least Squares Discriminant Analysis) and OPLS-DA (Orthogonal Partial Least Squares Discriminant Analysis) are widely used multivariate statistical techniques in metabolomics for identifying metabolites that differ significantly between groups. While both methods are employed for classification and prediction tasks, they differ in their modeling approaches and interpretability.

• • How Can the OPLS-DA Permutation Test Plot Be Considered Not Overfitted

  When applying the OPLS-DA (Orthogonal Partial Least Squares Discriminant Analysis) model for permutation testing, it is crucial to evaluate the model's predictive accuracy, particularly the Q2 statistic, in relation to the distribution of Q2 values obtained from the permutations. Specifically: The Q2 statistic of the original model should exceed the distribution of Q2 values derived from the permuted datasets. This indicates that the model's performance with the original dataset is substantially better.....

• • How to Purify Polysaccharides Using a DEAE Column in Ion Exchange Chromatography?

  Polysaccharide purification methods vary based on the polysaccharide characteristics, desired purity, and experimental requirements. Common methods include gel filtration chromatography, ion exchange chromatography, affinity chromatography, thin-layer chromatography, and ultrafiltration. The DEAE (diethylaminoethyl) column, an anion exchange column, is commonly used in ion exchange chromatography to separate positively charged biological macromolecules from mixtures.   In ion exchange chromatography, ......

• • 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......