Protein Analysis FAQ

• • Q&A of Label-Free Quantification Proteomics

  Q1: What are the key features of Label-Free Quantification (LFQ)? A1: 1. No chemical or isotopic labeling required Quantitation is derived directly from MS signal intensity, avoiding the extra steps and cost introduced by labels.

• • In WB, Should the Sample With the Lowest Gray Value Be Diluted for Equal Loading and Mixed With the Calculated Diluent?

  The meaning of the dilution ratio calculated from the sample gray value is how many times the original sample needs to be diluted, rather than directly adding a volume of diluent equal to the ratio. Below is a procedure for diluting the sample according to the calculated dilution ratio: Steps 1. Determine the target gray value: Select a target gray value, which is usually the one with the lowest gray value among the samples as the reference. 2. Calculate the dilution ratio: For each sample, calculate the...

• • What Preparations Are Required for Conducting a Western Blot Experiment?

  Prior to conducting a Western Blot (WB) experiment, a series of essential preparations should be carried out to ensure the reliability and reproducibility of the results: Experimental Design 1. Identify the target protein and select appropriate primary and secondary antibodies. 2. Choose a suitable internal loading control (e.g., GAPDH or β-actin). 3. Define the sample type (e.g., cell lysates, tissue extracts). Sample Preparation 1. Collect and process biological samples (e.g., cultured cells, tissues).

• • Does the Presence of Ice During WB Protein Extraction Influence Experimental Outcomes?

  If ice from the storage container is inadvertently introduced into the protein extraction process, it may alter both the concentration and the purity of the protein sample: Dilution Effect Upon melting, the ice increases the total liquid volume, thereby diluting the sample and potentially reducing the protein concentration. Sample Contamination Although uncommon, ice produced under non-sterile conditions may serve as a source of microbial or other extraneous contaminants. For most Western Blot (WB) .......

• • Is Reuse of Electrophoresis Buffer in Western Blotting Acceptable?

  In most cases, reusing electrophoresis buffer in Western blot experiments is not recommended. The buffer components—such as Tris, SDS, and other ionic species—may become depleted or accumulate contaminants, including residual proteins, cellular debris, and other impurities introduced during electrophoresis. These changes can compromise the consistency and accuracy of protein migration and ultimately affect the reliability of experimental outcomes. Furthermore, previously used running buffer carries a risk..

• • What Is the Purpose of Keeping Tissue Homogenate on Ice During Total Protein Extraction in Western Blot?

  In Western blot experiments, briefly placing the tissue homogenate on ice following homogenization serves a critical role in preserving protein integrity. This step primarily aims to prevent thermal denaturation of proteins caused by heat generated during mechanical disruption. Maintaining the homogenate at low temperatures helps stabilize the native conformation of proteins and minimizes the activity of endogenous proteases and phosphatases, thereby improving the accuracy and reproducibility of downstream

• • Is Yellow Coloration of Intestinal Tissue Lysate Supernatant Normal During Western Blot Sample Preparation?

  In the context of Western blotting, it is common for the supernatant obtained from intestinal tissue protein extraction to exhibit a yellow coloration. This is typically due to the presence of bile pigments naturally found in intestinal tissue, which can impart a yellow hue to the lysate. Importantly, the color of the lysate does not directly influence Western Blot outcomes. Instead, the reliability of the experiment primarily depends on the efficiency of protein extraction and the accuracy of concentration

• • Does Setting the Shaker to 130 rpm During the Blocking Step in Western Blot Compromise Experimental Outcomes?

  In Western blotting, an unintended setting of 130 rpm for orbital shaking during the blocking step is generally not expected to compromise the quality or interpretability of the results. The primary aim of blocking is to reduce nonspecific binding of antibodies, which largely depends on the choice and concentration of the blocking reagent, as well as the blocking duration. Shaking during this step serves to facilitate uniform distribution of the blocking buffer across the membrane surface, thereby .......

• • What Are the Possible Causes and Solutions When Proteins Fail to Migrate During Western Blot Electrophoresis?

  When a Western blot yields no observable bands or fails to produce detectable results, several technical issues may underlie the problem: Power Supply Configuration 1. Verify that the electrophoresis power supply is properly connected and operational. 2. Ensure that voltage and current settings are appropriate for the gel type and expected run time. Electrode Polarity Orientation 1. Confirm that the electrode connections are correctly polarized. Reversed polarity may prevent proteins from migrating toward.

• • Why Is the Target Band Missing in WB When GAPDH and Positive Control Are Both Normal?

  If such a situation occurs, several possible causes should be considered: Low Expression Level of the Target Protein The target protein may be expressed at a level too low to be detected. This could result from the intrinsic properties of the sample or from protein loss during sample preparation. Insufficient Antibody Specificity or Affinity The primary or secondary antibody used may not adequately recognize the target protein. It is essential to verify the specificity and activity of the antibodies .......