Protein Analysis FAQ

• • Does the Protein Degrade if Mixed with Loading Buffer for WB and Frozen at -80°C Without Prior Boiling for Denaturation?

  In Western blot (WB) experiments, when protein is mixed with loading buffer but not boiled for denaturation, and is subsequently frozen at -80°C, protein degradation generally does not occur.   The loading buffer typically contains reducing agents (e.g., β-mercaptoethanol) and SDS (sodium dodecyl sulfate), which facilitate protein denaturation and dissociation. During WB experiments, protein samples are typically mixed with loading buffer and then boiled to denature the proteins and dissociate them in......

• • Does the Appearance of Two Bands in a Western Blot Suggest Protein Degradation?

  The presence of two bands in a Western blot may indicate protein degradation. However, other factors could also account for this phenomenon, including:   1. Protein Degradation Protein degradation may occur during sample handling, storage, or experimental procedures, leading to the formation of multiple bands. To minimize degradation, protease inhibitors should be used, and repeated freeze-thaw cycles should be avoided.   2. Post-Translational Modifications Post-translational modifications (e.g., phos......

• • How Can Glycosylation Sites and the Molecular Weight After Glycosylation Be Analyzed, and Which Prediction Tools Are Available?

  Methods for Analyzing Glycosylation Sites 1. Experimental Approaches (1) Mass Spectrometry (MS) Analysis: Mass spectrometry (MS) is the gold standard for identifying glycosylation sites in proteins. MS/MS analysis of specific peptide fragments enables precise localization of glycosylation sites. (2) Immunoblotting: Detection of glycosylated proteins can be achieved using antibodies specific to glycosylation sites.   2. Bioinformatics-Based Prediction (1) Prediction Tools: Computational tools such as N......

• • Which Amino Acids Can Be Ubiquitinated?

  Ubiquitination is a post-translational modification in which ubiquitin, a small regulatory protein, is covalently attached to substrate proteins. This modification predominantly occurs on specific amino acid residues:   1. Lysine (K) The ε-amino group of lysine is the primary site for ubiquitination. Ubiquitin’s C-terminal glycine forms a covalent isopeptide bond with the lysine residue of the substrate protein.   2. Cysteine (C) Although less common, cysteine residues can also undergo ubiquitination.......

• • What Buffer Should Be Used to Dilute Boiled Protein Lysate for Western Blotting?

  For Western blotting, boiled protein lysate can be diluted using one of the following buffers:   Protein Extraction Buffer The extraction buffer used for initial protein isolation (e.g., RIPA buffer, PBS, or Tris buffer) can also be used for dilution, helping to maintain protein stability.   1X Loading Buffer A 1X SDS-PAGE loading buffer, typically composed of SDS, β-mercaptoethanol, glycerol, bromophenol blue, and Tris-HCl, ensures proper protein migration during electrophoresis.   Dilution Procedure......

• • Why Is the Recommended Protein Load for Western Blot 20–30 μg? How Does Loading Affect Results? Does It Depend on the Purpose?

  In Western Blot (WB) experiments, the recommended protein loading amount typically ranges from 20 μg to 30 μg. This range is generally sufficient to produce well-defined bands while preventing overloading, which may cause signal saturation or band smearing. Excessive protein loading can lead to overly intense signals, blurred bands, or even band aggregation. Conversely, insufficient protein loading may result in weak signals, making it challenging to detect the target protein.   Moreover, the optimal ......

• • What is the SEC-HPLC Method for Determining Protein Purity?

  When determining the purity of a protein sample, a commonly employed method involves combining Size Exclusion Chromatography (SEC) with High-Performance Liquid Chromatography (HPLC). The following provides a detailed explanation of the procedure for SEC-HPLC protein purity assessment:   SEC-HPLC is a separation technique based on protein molecular size. It uses a porous gel column where larger protein molecules, unable to enter the gel, flow through the column more quickly, while smaller impurity mole......

• • Why Does the Rightmost Mass Spectrum Peak Reflect a Molecule’s Relative Molecular Mass, Irrespective of Its Intensity?

  Mass spectrometry (MS) is a technique employed to determine the mass, structure, and composition of molecules. In a mass spectrum, the horizontal axis represents the mass-to-charge ratio (m/z), while the vertical axis represents signal intensity. Each peak corresponds to a specific ion or molecular fragment, with the peak intensity reflecting its relative abundance.   The rightmost peak in a mass spectrum is generally identified as the molecular ion peak (M⁺), which corresponds to the intact ion of th......

• • How Can Relative Abundance Be Calculated?

  In mass spectrometry, relative abundance typically refers to the natural abundance of isotopes-that is, the proportion of a given isotope present in a sample. This parameter can be measured using a mass spectrometer. The general procedure for calculating relative abundance is as follows:   1. Sample Collection Collect samples that contain the isotopes of interest.   2. Ionization Convert the molecules in the sample into ions using the ion source of the mass spectrometer.   3. Mass Spectrometric Analys......

• • How Can the Differences Between Protein and mRNA Levels Be Explained?

  Differences between protein levels and mRNA levels are a well-documented phenomenon in biological research, arising from regulation at multiple stages of gene expression. Key factors contributing to these differences include:   1. Post-Transcriptional Regulation A variety of regulatory mechanisms operate between mRNA synthesis (transcription) and protein synthesis (translation). Factors such as mRNA stability, transport, and subcellular localization determine the pool of mRNA available for translation......