Protein Analysis FAQ

• • How to Analyze Differential Proteins Obtained from Proteomics

  When investigating specific biological processes, diseases, or therapeutic interventions, it is often essential to analyze proteins that are differentially expressed under varying conditions. Once these differential proteins are identified—commonly through techniques such as mass spectrometry or two-dimensional electrophoresis—the subsequent step involves their in-depth analysis and interpretation to elucidate their roles and biological significance: Functional Annotation 1. Utilize databases such as.......

• • What Is the Principle of Tandem Mass Spectrometry

  Tandem mass spectrometry (commonly referred to as MS/MS or MS²) enables the detailed characterization of molecules by sequentially separating and detecting ions through two or more stages of mass spectrometric analysis. This approach is particularly effective for identifying molecular components within complex samples—such as proteins, peptides, and various organic compounds—and is extensively utilized in biochemistry, pharmaceutical research, environmental science, and related fields. The fundamental......

• • Is There a Specific Experimental Method for Cross-Linking Protein Interaction Analysis? How to Select a Cross-Linking Agent

  Cross-linking protein interaction analysis generally consists of three major steps: the cross-linking reaction, protein separation, and detection. For example, in an in vitro cross-linking experiment: 1. Cross-Linking Reaction The target protein solution is mixed with a selected cross-linking agent, allowing the reaction to proceed under appropriate conditions. Cross-linking agents can be broadly classified into chemical cross-linkers and photo-cross-linkers. Commonly used chemical cross-linkers include....

• • How to Convert the Results, Content, and Proportion of Monosaccharide Composition Determination

  Monosaccharides are carbohydrates that cannot be further hydrolyzed into simpler molecules. Many complex polysaccharides, including cellulose and starch, can be hydrolyzed to monosaccharides through acid treatment. By analyzing the hydrolysis products, the types and relative proportions of monosaccharides present in the original polysaccharides can be determined. The conversion process is as follows: 1. Experimental Results First, determine the total concentration of all monosaccharides in the sample.

• • What Should Be Done When SDS-PAGE Bands Contain Multiple Protein Bands in Protein Sequencing?

  When a section of an SDS gel contains more than one protein band, these bands may correspond to distinct proteins or various isoforms, including alternative translation products or forms modified post-translationally. To accurately identify the amino acid sequence of each protein individually, it is necessary to further separate and purify these proteins. The following methods are typically employed to address SDS gels with multiple protein bands:   1. SDS-PAGE Optimization Initially, perform a second......

• • How Are Proteins Smaller than 10 kDa Typically Detected? Is Electrophoresis Applicable?

  Detecting proteins with molecular weights below 10kDa requires specialized methodologies, among which electrophoresis is a notable technique.    1. Electrophoresis Techniques While SDS-PAGE is widely used for protein detection, proteins under 10kDa may migrate rapidly through the gel, potentially exiting from the bottom. Tricine-SDS-PAGE is an adapted electrophoresis method employing Tricine as a buffer, offering improved resolution for proteins in this molecular weight range.    2. Mass Spectrometry ......

• • How Can Motif Representations Be Constructed from Peptide Data Derived from Tandem Mass Spectrometry?

  Peptide data derived from tandem mass spectrometry (MS/MS) can be utilized to generate motif representations, facilitating a deeper understanding of protein sequence features and post-translational modifications (PTMs). The general workflow for constructing such motif profiles includes the following steps:   1. Data Preprocessing Initially, the peptide data obtained from MS/MS should be processed to extract relevant information, such as peptide amino acid sequences, post-translational modification sta......

• • Why Should the Recording Time for the Test Solution Chromatogram Be Twice the Retention Time of the Main Component?

  This guideline pertains to the recommended duration for recording the chromatogram of a test solution during chromatographic analysis. In chromatography, the retention time refers to the amount of time a specific compound takes to pass through the chromatographic system. The main component typically denotes the most abundant or analytically significant compound present in the test solution. Therefore, the retention time of the main component corresponds to the point at which its peak appears on the ch......

• • How to Investigate the Specific Mechanisms of Interactions Between Interacting Proteins?

  Protein-protein interactions underpin numerous biological processes, including signal transduction, immune responses, and DNA repair. Understanding the mechanisms of these interactions is essential for elucidating how these processes function and where they may fail in disease states, which is critical for drug development. Multiple techniques are available for studying protein-protein interactions, and the choice of method often depends on specific research goals and available resources. The followin......

• • What Are the Underlying Principles of Common Protein Separation Techniques?

  Protein separation is a fundamental procedure in biochemistry and molecular biology, and various separation techniques are based on distinct underlying principles:   Precipitation One of the most widely used methods, precipitation relies on the propensity of proteins to aggregate and precipitate under specific solution conditions, such as changes in pH, temperature, or ionic strength. Common precipitants include ammonium sulfate and ethanol.   Chromatography Chromatographic techniques achieve high-res......