Protein Analysis FAQ

• • Q&A of Protein Glycosylation Analysis

  This FAQ guide provides clear answers to common questions on protein glycosylation analysis. It covers key methods including chromatography, lectin binding assays, enzymatic digestion, and glycan labeling, along with strategies for distinguishing N-linked and O-linked glycosylation, deglycosylation techniques, sample preparation best practices, and troubleshooting tips to optimize glycosylation profiling by mass spectrometry.

• • Q&A of Phosphorylation

  This comprehensive FAQ provides practical guidance for researchers investigating protein phosphorylation. It addresses critical topics such as method selection for phosphorylation site detection, upstream kinase prediction, phosphopeptide enrichment strategies, troubleshooting tips for phospho-Western blotting, and experimental validation approaches. Whether you are performing large-scale phosphoproteomics or focused phosphorylation studies, this resource offers clear, research-based solutions to optimize y

• • What Are the Principles and Comparisons of Common Protein Quantification Methods

  A variety of methods are available for protein quantification; among them, the following are most commonly employed, each based on distinct principles: Bradford Protein Quantification Method 1. Principle: The Coomassie Brilliant Blue G-250 dye exhibits a shift in its absorption maximum from 465 nm to 595 nm upon binding to proteins. The resulting increase in absorbance at 595 nm is proportional to the protein concentration. 2. Advantages: Rapid assay with minimal interference from most common substances.

• • Does GO Analysis Apply to Differential Proteins or the Whole Proteome

  Gene Ontology (GO) analysis is a widely used method for characterizing and interpreting the roles of gene products in terms of their molecular functions, associated cellular components, and involvement in biological processes. It is commonly applied to analyze high-throughput gene or protein datasets generated by techniques such as microarray or mass spectrometry. GO analysis is typically applied in the following contexts: 1. Differential Proteins or Genes When researchers aim to identify proteins or.......

• • Why Is Western Blotting Still Needed to Detect Protein Expression Levels

  This question pertains to two widely used techniques in biological research: gel electrophoresis and Western blotting. Although both are employed for protein detection, they differ significantly in application and advantages. Protein Electrophoresis 1. Purpose Primarily used to analyze the molecular size of proteins and to separate proteins based on size differences. 2. Results Provides a visual representation of protein band patterns, reflecting the distribution and approximate sizes of proteins within....

• • Under What Conditions in Western Blot Can Proteins Be Washed Off the Membrane

  In Western Blot experiments, it is sometimes observed that proteins are washed off the membrane. This phenomenon may result from the following factors: 1. Incorrect Washing Conditions The washing step is critical in Western Blot experiments, serving to eliminate non-specifically bound antibodies and other proteins. If washing conditions are suboptimal—for example, if the buffer concentration is too low or too high, or the washing duration is insufficient or excessive—membrane-bound proteins may be .........

• • What Is the Blue Liquid Added to Protein Samples During Electrophoresis

  In protein electrophoresis experiments, samples are typically prepared using a solution known as protein loading buffer. This buffer is an aqueous mixture that contains denaturing agents, reducing agents, and tracking dyes. The denaturing and reducing agents serve to unfold the protein structures and break disulfide bonds, thereby linearizing the proteins to promote consistent migration through the gel matrix during electrophoresis. The tracking dye is included to provide visual monitoring of the ..........

• • Why Are Peptides Lost After C18 SPE Desalting of Casein Hydrolysate Before LC-MS

  1. Sample Processing Potential complications during sample preparation may contribute to peptide loss. For instance, incomplete binding of peptides to the C18 column or inefficient elution may occur. These issues can arise when sample conditions—such as pH, ionic strength, or organic solvent content—are suboptimal for effective peptide retention and release on the C18 sorbent. 2. Selection of C18 Column C18 columns vary in properties such as particle size, pore diameter, and surface chemistry.

• • Why Does the Observed Protein Run Smaller Than Predicted in Western Blot

  When a protein appears at a lower molecular weight than predicted in a Western blot (WB) experiment, several potential factors may be responsible: 1. Protein Modifications Proteins within cells may undergo various post-translational modifications such as phosphorylation, methylation, or acetylation. These modifications can alter the protein’s charge, conformation, or molecular weight, thereby influencing its electrophoretic mobility. In some cases, such modifications may increase the protein’s migration....

• • Why Can Primary Antibodies Still Recognize SDS-Denatured Proteins on Nitrocellulose in Western Blot

  In Western blotting, primary antibodies are sometimes able to recognize proteins on nitrocellulose membranes even after these proteins have been denatured by SDS. Several possible mechanisms may account for this phenomenon: 1. Structural Properties of Proteins After Membrane Transfer and Binding Upon transfer to the nitrocellulose membrane, proteins bind tightly to the surface. This interaction may induce partial refolding of the proteins, allowing some secondary or tertiary structures to recover to a......