Protein Analysis FAQ

• • Do "Self-MHC Molecules," Recognized by T Cells, Belong to the T Cells Themselves or to the Host Organism?

  The term "self-MHC molecules" refers specifically to the MHC molecules of the host organism. T cells recognize antigenic peptides presented by MHC molecules through the T-cell receptors (TCRs) located on their surface, a critical immunological process known as antigen presentation. Certain specialized cells within the immune system, including dendritic cells, macrophages, and B cells, are responsible for antigen capture, processing, and presentation; these cells are collectively termed professional an......

• • What Causes Proteins to Migrate into the Marker Lane in Western Blot?

  In a Western Blot experiment, proteins are separated during electrophoresis and transferred onto a membrane, where they bind to target proteins through specific antibodies, forming distinct protein bands. However, sometimes proteins may migrate out of the intended lane or multiple bands may appear during the process. Below are some possible causes of this issue:   1. Improper Electrophoresis Conditions If the electrophoresis voltage or current is too high, it may cause the proteins to migrate too quic......

• • How to Calculate Sample Load and Binding Capacity for Biomolecular Chromatography Columns (Affinity, Ion Exchange)?

  In biomolecular chromatography, Affinity Chromatography and Ion Exchange Chromatography are widely used techniques for separation. To achieve optimal separation, it is essential to accurately calculate both the sample load and the binding capacity of the chromatography column.   Sample Load The sample load refers to the total amount of sample that can be applied to the chromatography column. It is calculated based on the column's volume and the concentration of the sample. To ensure efficient separati......

• • Possible Causes for Target Bands Merging into One in WB, While Internal Control is Normal?

  If your Western Blot (WB) target bands merge into a single band, but the internal control is normal, the possible causes could include:   Sample Overloading If too much of the target protein sample is loaded, the bands may merge into one. Make sure to load an appropriate amount of sample to avoid overloading.   High Antibody Concentration or Affinity If the primary or secondary antibody has too high an affinity or concentration, it may lead to over-staining and cause the bands to merge.   Excessive Mi......

• • What is the Operational Principle for Calculating Protein Sample Concentration in Western Blot (WB)?

  When using Western Blot (WB) technology to detect protein expression levels, determining the protein sample concentration is essential. This is because, in WB experiments, it is important to load the same amount of protein sample onto the gel to ensure the comparability and accuracy of results. The operational principle for calculating the protein sample concentration in WB is as follows:   Theoretical Basis The principle behind calculating protein sample concentration in WB relies on colorimetric ass......

• • What Are the Optimal Transfer Conditions for a 160 kDa Protein in WB?

  When performing Western blot (WB) analysis for a 160 kDa target protein, several key transfer conditions must be optimized to ensure efficient protein transfer onto the membrane.   1. Choice of Membrane For high molecular weight proteins such as 160 kDa, PVDF (polyvinylidene fluoride) membranes are preferred due to their superior protein-binding affinity compared to nitrocellulose membranes.   2. Transfer Buffer Composition The transfer buffer should contain methanol at a concentration of 10–20%. Meth......

• • How to Address Inconsistencies in Trends in Western Blot (WB) Experiments?

  In Western Blot (WB) experiments, inconsistencies in trends often indicate significant variability between repeated trials. To resolve this issue, the primary strategy is to thoroughly review each step of the experiment to ensure accuracy and reproducibility. Recommended measures include:   1. Sample Preparation Ensure that the protein concentrations are uniform across all samples. Use protease inhibitors to prevent protein degradation. Standardize the handling of samples during the experiment to avoi......

• • How Can MS/MS Fragmentation Information Be Utilized?

  MS/MS (Tandem Mass Spectrometry) is a powerful analytical technique that enables structural elucidation of compounds by generating secondary fragment ions through sequential fragmentation of precursor ions. By analyzing the mass-to-charge ratio (m/z) and intensity of these fragment ions, critical insights into molecular structures can be obtained. The primary applications of MS/MS fragmentation data include:   1. Structural Elucidation and Characterization By examining the m/z values and relative inte......

• • What Is the Experimental Procedure for Isoelectric Focusing?

  Isoelectric focusing (IEF) is a high-resolution electrophoretic technique that separates proteins based on their isoelectric points (pI) within a pH gradient by applying an electric field. IEF utilizes the principle that biomolecules have a net charge of zero at their pI, causing them to focus at specific locations within the pH gradient. The general protocol for IEF is as follows:   1. Sample Preparation Protein samples may require purification or processing based on experimental needs. The prepared ......

• • How Is the N-Terminal Amino Acid Position Determined? Can It Be Defined Arbitrarily?

  To accurately determine the specific amino acid sequence position of a protein's N-terminus (amino terminus), the following steps should be considered:   Identifying the N-Terminal Sequence Position The N-terminal sequence refers to the initial region of a protein or polypeptide chain, typically starting with the first amino acid residue in the sequence.   Defining the N-Terminus in Functional Domains or Signal Peptides In certain contexts, such as studies on functional domains or signal peptides, the......