Protein Analysis FAQ

• • What Are the Detection Methods for Direct Interaction Between Two Proteins

  When two proteins directly interact, such interactions can significantly influence their biological functions. In biopharmaceutical research and biotechnology, identifying and characterizing these protein–protein interactions is essential for understanding molecular mechanisms and for drug development. Below are several commonly employed methods for detecting direct protein–protein interactions: 1. Co-Immunoprecipitation (Co-IP) Co-IP is a well-established technique for detecting protein–protein .........

• • Which Instruments Can Visualize Fluorescent Proteins on Native PAGE Without Staining? What Are the Common Markers

  Native PAGE (polyacrylamide gel electrophoresis) is a technique for protein separation that preserves the native structure of proteins, as it does not involve denaturation or staining. In this method, fluorescent proteins can be directly visualized using fluorescence imaging systems. Additionally, several specific proteins are commonly employed as markers for Native PAGE. Instruments Used Fluorescent proteins in Native PAGE can be directly visualized using fluorescence imaging systems. These systems........

• • What Are the Reasons for Mass Spectrometry Failing to Detect Compounds

  Mass spectrometry analysis may fail to obtain valid results due to a variety of reasons. The following are some possible reasons why mass spectrometry may fail to detect compounds: 1. Improper Sample Preparation During the process of sample preparation, problems such as sample loss, non-uniformity, or contamination may occur, leading to a too-low concentration of effective components or making them undetectable. 2. Incompatible Ion Source Different types of ion sources are suitable for different samples....

• • How is Mass Spectrometry Used to Study Proteins

  Mass spectrometry (MS) is a powerful analytical technique widely employed in protein research to investigate mass, structure, post-translational modifications, and molecular interactions. The following are the primary approaches for studying proteins using mass spectrometry: 1. Protein Mass Determination MS enables precise measurement of protein molecular weight, which facilitates assessment of protein purity and molecular consistency. This analysis is typically performed using techniques such as matrix-...

• • How to Determine Protein Phosphorylation Sites

  Determining protein phosphorylation sites requires a combination of biological experiments and bioinformatics analyses. Together, these approaches enable the accurate identification and validation of phosphorylation sites on specific proteins, which is critical for understanding protein functions and for elucidating the regulation of protein–protein interactions. Experimental Methods 1. Mass Spectrometry Analysis Mass spectrometry is one of the most widely used approaches for the identification of protein..

• • What Are Protein Post-Translational Modifications and Their Biological Functions

  Post-translational modifications (PTMs) refer to chemical and functional alterations that occur in proteins following ribosomal synthesis. These modifications are mediated by the addition of chemical groups, cleavage of peptide bonds, conformational changes, or interactions with other biomolecules such as proteins, nucleic acids, or lipids. The major types of PTMs, along with their mechanisms of action and biological functions, are outlined below:

• • How to Use Asp-N or Glu-C Alone or Combined for Protein Digestion? Dosage vs. Trypsin’s 30:1 Ratio

  The following guidelines outline recommended protocols for the usage and dosage of Asp-N and Glu-C in protein digestion experiments: Using Asp-N or Glu-C Alone 1. Asp-N Dosage: A protein-to-enzyme ratio of 50:1 is recommended. Digestion Conditions: Incubate at approximately pH 8.0 and 37°C, typically overnight. 2. Glu-C Dosage: A protein-to-enzyme ratio in the range of 20:1 to 30:1 is recommended. Digestion Conditions: Optimal at pH 7.8, incubated at 37°C overnight. Sequential Digestion with Asp-N and......

• • What’s the Protocol for Detecting O-Glycosylation by WB Antibodies

  The basic steps for O-glycosylation Western Blot (WB) antibody detection are as follows: 1. Sample Preparation Collect and prepare cell or tissue samples containing the target protein. Lyse the samples using an appropriate lysis buffer, followed by centrifugation to remove insoluble debris. 2. Protein Concentration Determination Determine the protein concentration using a BCA protein assay kit or a comparable method. 3. SDS-PAGE Select an appropriate polyacrylamide gel concentration based on the molecular..

• • How Can the Presence of a Specific Receptor Protein on a Cell Be Characterized?

  Characterizing the presence of a specific receptor protein on a cell is essential for verifying and quantifying its expression on the cell surface or within intracellular compartments. Several widely adopted techniques are employed to achieve this, including:   Flow Cytometry Flow cytometry enables the quantitative analysis of receptor expression levels and the proportion of receptor-positive cells. This is achieved by labeling the target receptor with fluorescently tagged, receptor-specific antibodie......

• • How to Use Library Search Results to Identify Compounds in Mass Spectra?

  Library Search Results refer to the output generated by spectral database software when querying compound identities corresponding to peaks in a mass spectrum. To identify the chemical species represented by specific peaks using Library Search Results, the following procedure can be followed:   Acquisition of Mass Spectrometry Data First, analyze the sample using a mass spectrometer (e.g., GC-MS or LC-MS) to acquire the mass spectral data.   Processing of Mass Spectrometry Data Process the acquired da......