Resources

Proteomics Databases



Metabolomics Databases

• • iTRAQ/TMT Quantitative Proteomics Steps

  Sample Preparation 1. Protein Extraction: Total proteins are extracted from various biological samples. 2. Protein Quantification: Protein concentrations are determined using methods such as BCA or Bradford assays. Protein Digestion: Proteins are enzymatically digested using trypsin or other enzymes, cleaving at specific residues like lysine or arginine, to generate peptides.

• • Can the Binding of Small Molecules to Proteins Be Detected by LC-MS/MS

  LC-MS/MS is a powerful analytical technique widely used for the qualitative and quantitative analysis of small molecules, peptides, proteins, and other biomacromolecules. In the study of small molecule-protein interactions, LC-MS/MS is an essential and irreplaceable technology.

• • How Many Proteins Can Label-Free Detect

  Label-free technology is extensively applied in proteomics research for the identification and quantification of proteins within samples. Unlike methods that utilize fluorescent or radioactive labels, this approach employs mass spectrometry (MS) for the direct analysis of proteins. The number of detectable proteins is contingent upon several factors, such as the performance of the mass spectrometer, sample complexity, experimental design, and data processing and analysis techniques. Modern MS technologies..

• • Tobacco Co-Immunoprecipitation Experiment

  Co-Immunoprecipitation (Co-IP) experiments in Nicotiana tabacum are employed to investigate protein-protein interactions. This method facilitates the identification and verification of interactions between specific proteins and their potential partners. Below are the detailed steps to perform a tobacco Co-IP experiment:

• • Mass Spectrometry Detects Molecular Weight

  Mass spectrometry is an analytical technique that can accurately measure the masses of molecules and atoms. This is primarily done by measuring the mass-to-charge ratio (m/z) of ions. Mass spectrometry is also employed for the structural determination of compounds, for example, by measuring the masses of molecular ions and fragment ions.

• • Discovery of New Antigens

  Since antigens were first successfully used to stimulate the immune system to produce antibodies, scientists have achieved significant breakthroughs in antigen research. Recently, a novel discovery of antigens has not only deepened our understanding of antigens and immune responses but also holds promising implications for vaccine development and immunotherapy.

• • Immunopeptides Analysis

  Immunopeptides are a distinct category of peptides that play a crucial role in immune system function. Composed of short chains of amino acids, these molecules are recognized and presented by immune cells, thereby initiating specific immune responses. Within the human immune system, the generation, processing, and presentation of immunopeptides are essential steps in T-cell-mediated immunity. The following is a detailed introduction to the relevant knowledge of immune peptides:

• • Use MaxQuant for Proteomics Data Identification and Quantification

  Steps for Identification and Quantification of Proteomics Data Using MaxQuant:1. Data Preparation（1）Collect raw mass spectrometry data files (.raw format).（2）Prepare a protein database (e.g., Uniprot). 2. Parameter Setting（1）Open the MaxQuant software and create a new project.（2）Import raw data files and the protein database.（3）Set search parameters (e.g., enzymatic digestion rules, modification types, mass error tolerance, etc.).

• • Microbial Proteomics

  Microbial proteomics is a scientific discipline focused on understanding the composition, structure, function, and interactions of proteins within microorganisms. Advances in genomics and proteomics technologies allow researchers to gain a more comprehensive understanding of microbial protein characteristics and functions. Key research areas in microbial proteomics include the following:

• • Spatial Proteomics in Plant Research

  Application of spatial proteomics in plant research mainly includes the following aspects:1. Cellular Localization: Examining protein distributions across various organelles or tissues to elucidate mechanisms of cellular function differentiation and signal transduction. 2. Growth and Development: Analyzing the dynamic changes in protein expression throughout plant growth and development processes to comprehend underlying regulatory mechanisms.