Protein Analysis FAQ

• • Why Are Differentially Expressed Proteins Identified by Proteomics Undetectable by Western Blot

  Proteomics, particularly when employing techniques such as mass spectrometry, can identify differentially expressed proteins that are sometimes undetectable by Western blot. This discrepancy may arise due to several factors: 1. Differences in Detection Sensitivity Proteomic techniques, such as mass spectrometry, typically offer higher sensitivity compared to Western blot, enabling the detection of low-abundance proteins that may fall below the detection threshold of Western blot. 2. Target Protein .........

• • What Factors Should Be Considered During Protein Separation and Purification

  Protein separation and purification is a complex procedure that necessitates the careful consideration of various factors to ensure both efficiency and specificity. The following are several critical considerations: 1. Selection of Buffer Solution An appropriate buffer system should be employed to preserve the native conformation and biological activity of the protein. 2. Salt Concentration and pH Value Adjusting the ionic strength and pH of the buffer is essential for optimizing the solubility and ........

• • Should Positive Ion Mode or Negative Ion Mode Be Used for Amino Acid Mass Spectrometry Detection

  Amino acid mass spectrometry detection is typically performed in positive ion mode. This preference arises from the propensity of amino acids to form cationic species in solution, particularly under acidic conditions. In mass spectrometric analysis, the positive ion mode allows for more efficient detection and characterization of these positively charged amino acid species. Nevertheless, under certain conditions, negative ion mode may be employed—particularly when specific amino acids or their ..........

• • What Is the Structural Composition of the Fc Region of IgG Antibody

  The Fc region of the IgG antibody refers to the constant region at the carboxyl-terminal end of the antibody molecule, which bears carbohydrate moieties and is primarily formed by the constant regions of two associated heavy chains. This region comprises two main domains, CH2 and CH3, connected by a flexible hinge region. The hinge, enriched in cysteine residues, confers structural flexibility that facilitates effective engagement with Fc receptors. The CH2 domain contains one or more attached .........

• • Difference Between Sequencing and Mass Spectrometry: Is Mass Spec More Limited

  Sequencing and mass spectrometry are distinct biomolecular analysis techniques, each with unique applications and advantages. Sequencing Primarily used for analyzing nucleic acid sequences (DNA or RNA), sequencing provides detailed genomic or transcriptomic information. It enables the identification of complete gene sequences, mutations, and gene expression differences, making it essential in genomics, genetics, and molecular biology research. Mass Spectrometry Mainly used to analyze proteins, metabolites..

• • How Is Ubiquitinated Protein Generally Detected

  Ubiquitination is a post-translational modification process in which ubiquitin is attached to proteins, regulating their degradation, signaling, and other functions. Common methods for detecting ubiquitinated proteins include: 1. Western Blot (WB) Protein extraction is performed on cell or tissue samples, followed by SDS-PAGE separation. The separated proteins are transferred to a membrane and incubated with an anti-ubiquitin antibody. If ubiquitination occurs, higher molecular weight ubiquitinated ........

• • What Are the Advantages of Gas Chromatography-Mass Spectrometry

  Gas Chromatography-Mass Spectrometry (GC-MS) combines the strengths of both gas chromatography (GC) and mass spectrometry (MS), offering several key advantages: 1. Strong Separation Capability GC effectively separates complex mixtures into individual compounds. By adjusting column properties and operating conditions, GC-MS achieves high-precision separation, enhancing analytical accuracy and reliability. 2. High Sensitivity MS provides ultra-high sensitivity, detecting trace-level compounds. In GC-MS, GC...

• • How to Predict Its Glycosylation Sites If Only an Amino Acid Sequence Is Known

  Protein site modifications can indeed cause molecular weight changes, especially upward shifts. Predicting glycosylation sites in a protein typically involves identifying which amino acid residues might be modified by carbohydrate molecules. The most common types of glycosylation are N-linked glycosylation and O-linked glycosylation. Given a known partial amino acid sequence, glycosylation sites can be predicted using the following methods: Sequence-Based Rules 1. For N-linked glycosylation, a typical......

• • Does Modification of Protein Sites Cause an Increase in Molecular Weight

  Protein site modifications can indeed alter molecular weight, often leading to an upward shift (increase). Protein modifications are common biological phenomena that regulate various functions, including protein activity, stability, and localization. These modifications typically involve the addition of small molecular groups, such as phosphorylation, ubiquitination, glycosylation, and lipid anchoring. Since these added molecules have their own molecular weight, modified proteins usually exhibit an ........

• • How to Remove the Solvent Peak in Gas Chromatography So That It Does Not Display in the Chromatogram

  In gas chromatography (GC) analysis, the presence of a solvent peak may interfere with the detection of target compounds. Several strategies can be employed to mitigate or eliminate solvent peak interference: 1. Extending Retention Time Modifying chromatographic conditions, such as reducing the column temperature or utilizing a longer chromatographic column, can increase the retention time of target compounds. This facilitates better separation between target compound peaks and the solvent peak ......