Protein Analysis FAQ

• • How to Interpret Glycosylation Site Results

  The identification of glycosylation sites is typically accomplished using mass spectrometry (MS). These data allow researchers to gain a detailed understanding of protein function, its roles within biological systems, and the changes that may occur in response to genetic variations or under pathological conditions. For result interpretation, we recommend focusing on the following key aspects: 1. Location of Glycosylation Sites MS data can be used to pinpoint specific amino acid residues on the protein......

• • CDPro and BESTSEL Yield 0% α-Helix and Low β-Content: Why Results Deviate from Literature and Can Dilution Improve Accuracy

  Using CDPro and BESTSEL to analyze circular dichroism (CD) spectra yielded an α-helix content of 0% and a markedly low β-sheet content, which significantly deviates from values reported in the literature. What recommendations can be made to improve the reliability of the experimental results? Could lowering the protein concentration (currently at 1 mg/mL) enhance measurement accuracy? When employing CD spectroscopy to assess protein secondary structure, discrepancies between calculated results and .........

• • How to Choose a Protein Database in Proteomics

  Selecting an appropriate protein database is a crucial decision in proteomics research, as it directly influences the accuracy of mass spectrometry-based data analysis and protein identification. Below are some commonly used protein databases along with their typical applications: 1. UniProt (Universal Protein Resource) One of the most comprehensive protein databases, UniProt provides protein sequences from a wide range of species. It is suitable for proteomic studies across various organisms..........

• • Consultation on Protein Mass Spectrometry Identification Data Analysis

  Protein mass spectrometry analysis yields various types of data, which primarily include: 1. Peptide Mass-to-Charge Ratio (m/z) Data This fundamental output of mass spectrometry reflects the mass-to-charge ratios of peptide ions. These values allow inference of the molecular weights of the peptides. 2. Peptide Fragment Ion Data In tandem mass spectrometry (MS/MS), peptides are further fragmented into smaller ions, producing characteristic fragmentation spectra. These spectra serve as the basis for peptide..

• • How to Fix Severe Clogging and Extremely Slow Flow Rate in Sephadex G-100 Protein Purification Columns

  When using Sephadex G-100 for protein purification, issues such as severe column clogging and significantly reduced flow rate may occur. The following approaches can be considered to address these problems: 1. Examine Column Packing Ensure that the Sephadex G-100 medium is packed uniformly and free of air bubbles. The presence of air pockets or uneven packing can impair column flow and compromise separation efficiency. 2. Adjust Sample Volume and Concentration Excessive sample volume or overly .........

• • How to Determine Which Amino Acids Are Present from a Mass Spectrum? How to Determine the Position of Modification

  Analysis of Mass Spectrum 1. Examination of Mass Spectral Peaks Peaks in the mass spectrum correspond to ions with distinct mass-to-charge (m/z) ratios. The masses of amino acid residues inferred from these peaks can provide insight into the specific amino acids present in the protein. 2. Calculation of Mass Differences By analyzing the mass differences between adjacent peaks, it is possible to identify individual amino acid residues, as each has a characteristic mass increment. 3. Reference to Amino Acid..

• • How Should Endogenous SUMO Co-IP Be Performed

  Endogenous Co-Immunoprecipitation (Co-IP) of SUMO (Small Ubiquitin-like Modifier)–modified proteins is typically conducted according to the following steps: 1. Cell Collection Begin by harvesting cells. For studies of SUMOylation, transiently transfected cells or cells subjected to specific treatments are commonly used to enhance the levels of SUMOylated proteins. 2. Preparation of Lysis Buffer Prepare a lysis buffer containing protease inhibitors and deSUMOylation inhibitors, such as N-ethylmaleimide (NEM)

• • What Is Protein Glycosylation (Protein Glycosylation Modification)

  Protein glycosylation is a common form of post-translational modification in cells, wherein one or more sugar moieties are covalently attached to specific amino acid residues of a target protein. This process primarily takes place in the endoplasmic reticulum and Golgi apparatus. Glycosylation is generally categorized into two major types: N-glycosylation, in which glycans are linked to the amide group of asparagine residues, and O-glycosylation, where sugars are attached to the hydroxyl groups of serine...

• • What Is the Principle of Determining Amino Acids by Mass Spectrometry

  The principle of amino acid determination by mass spectrometry is based on measuring the mass-to-charge ratio (m/z) of intact amino acid molecules or their fragments. The procedure typically involves the following steps: 1. Ionization The amino acid sample is first ionized to facilitate detection by mass spectrometry. Common ionization techniques include Electrospray Ionization (ESI) and Matrix-Assisted Laser Desorption/Ionization (MALDI). 2. Mass Analysis The resulting ions are introduced into the mass....

• • What Is Protein Glycation

  Protein glycation is a non-enzymatic biochemical reaction in which sugar molecules—typically reducing sugars like glucose or fructose—undergo spontaneous chemical reactions with proteins. This process results in the formation of compounds known as advanced glycation end-products (AGEs). Glycation can occur naturally over time, or it can be accelerated under certain physiological conditions, such as elevated blood glucose levels in diabetes.