Resources

Proteomics Databases



Metabolomics Databases

• • Protein MS1 and MS2 Spectra

  Protein MS1 and MS2 spectra are essential components of protein mass spectrometry, a powerful analytical technique employed for the identification and quantification of proteins and their post-translational modifications. This process typically involves multiple levels of analysis, with the most commonly utilized being the MS1 (first-stage mass spectrum) and MS2 (second-stage mass spectrum) spectra. MS1 Spectrum The MS1 spectrum, also referred to as the precursor ion spectrum, represents the initial stage..

• • Antibody-Drug Conjugates Analysis

  Antibody-Drug Conjugates (ADCs) are an innovative class of targeted cancer therapeutics composed of monoclonal antibodies chemically linked to cytotoxic small molecule drugs via specialized linkers. Designed to selectively deliver potent drugs to malignant cells, ADCs minimize toxicity to healthy tissues. Accurate characterization of ADC composition, drug release mechanisms, and molecular stability is essential for assessing their therapeutic efficacy and safety. Composition of ADC 1. Antibody Monoclonal...

• • Prediction of Lysine Acetylation Sites in Proteins

  Sequence-Based Prediction Methods 1. Feature Extraction (1) Sequence-based features: The identification of lysine acetylation sites based on primary amino acid sequences relies on extracting residues flanking the lysine site. Features such as physicochemical properties of amino acids and secondary structure propensities are employed for prediction. (2) Conservation analysis: Multiple sequence alignment is used to assess the evolutionary conservation of the target lysine residue. Sites with high .........

• • Phosphorylated Protein Western Blot Result Analysis

  Phosphorylated protein western blot result analysis is a multi-step procedure designed to detect and quantify the presence and relative abundance of specific proteins and their phosphorylated forms. Sample Preparation 1. Cell Lysis and Protein Extraction Cells are lysed using a buffer supplemented with phosphatase inhibitors to preserve the phosphorylation state of proteins. 2. Protein Concentration Determination Protein concentration is measured using BCA or Bradford assays to ensure equal protein ........

• • Sugar Structures

  Monosaccharides Monosaccharides represent the most fundamental form of carbohydrates in sugar structures and cannot be further hydrolyzed into simpler sugar units. Common examples include glucose and fructose. 1. Glucose (1) Molecular formula: C₆H₁₂O₆ (2) Structural characteristics: A six-carbon sugar (hexose) that typically exists in a cyclic form, most often as a six-membered ring (pyranose structure). The configuration of the hydroxyl group (-OH) attached to the first carbon atom determines whether the..

• • In Vitro Ubiquitination Assay

  Key Steps of In Vitro Ubiquitination Assay An in vitro ubiquitination assay is a reconstituted system that allows precise dissection of ubiquitination events under controlled biochemical conditions. 1. Preparation of the Ubiquitination Reaction Mixture This mixture consists of purified ubiquitin, E1 ubiquitin-activating enzyme, E2 ubiquitin-conjugating enzyme, E3 ubiquitin ligase, and ATP. These components are combined in an appropriate buffer to mimic the intracellular ubiquitination process. 2. Addition..

• • Antibody Sequence Analysis Tools

  A wide range of computational tools have been developed for antibody sequence analysis, enabling comprehensive interpretation of amino acid sequences alongside structural and functional insights. These tools are extensively applied in bioinformatics and immunological research. The following summarizes several widely used antibody sequence analysis tools: 1. IMGT/HighV-QUEST IMGT/HighV-QUEST is a high-throughput sequence analysis platform provided by the international ImMunoGeneTics information system.......

• • Method for Inferring Nucleotide Sequence from Amino Acid Sequence

  If the amino acid sequence is known, the corresponding nucleotide sequence can be inferred through the following approaches: 1. Database Query Databases such as the NCBI Protein database allow users to search by amino acid sequence to identify the corresponding protein. Once the correct protein entry is located, associated nucleotide information—such as the mRNA or genomic DNA sequence—can typically be retrieved via linked annotations or related records. 2. Reverse Translation Online tools or specialized...

• • Fast Protein Liquid Chromatography

  Liquid Chromatography (LC) is an essential analytical technique for the separation of complex mixtures, widely utilized in biochemical and molecular biology research. Fast protein liquid chromatography (FPLC) is a specialized form of LC tailored for the purification of proteins with high efficiency and resolution. Working Principle Fast protein liquid chromatography operates on the principle of adsorption chromatography. Samples are introduced into a chromatography column packed with a stationary phase.....

• • SDS-PAGE Gel Electrophoresis for Protein Molecular Weight Determination

  SDS-PAGE gel electrophoresis for protein molecular weight determination is a widely used technique based on the principle that proteins, when treated with SDS, migrate through a polyacrylamide gel at rates inversely proportional to their molecular weights. SDS, or sodium dodecyl sulfate, is an anionic surfactant that binds uniformly to polypeptide chains, linearizing the protein structure and imparting a consistent negative charge. This enables size-based separation of proteins under an applied electric....