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Proteomics Databases



Metabolomics Databases

• • How Does Mass Spectrometry Reveal the Amino Acid Sequence of Proteins

  Introduction: The Core Pathway of Protein Structure Analysis Protein function is determined by its structure, with the linear sequence of amino acids—known as the primary structure—forming the first hierarchical level. Mass spectrometry, particularly liquid chromatography-tandem mass spectrometry (LC-MS/MS), has emerged as a central technique for elucidating protein structure. Compared to traditional Edman degradation, mass spectrometry offers advantages such as high throughput, automation, and the ........

• • Understanding and Analyzing Protein Primary Structure

  Introduction: The Starting Point of Protein Structure Research The primary structure of a protein refers to the linear sequence of amino acids, which determines its higher-order spatial arrangements—including secondary, tertiary, and quaternary structures—and ultimately its biological functions. This sequence not only represents the expression of the genetic information encoded by the protein but also forms the foundation for its functional realization. Accurately deciphering the primary structure of ......

• • Preparing Samples for Protein Sequencing

  In proteomics, mass spectrometry (MS) serves as the central analytical technique, with its results heavily dependent on sample quality. Regardless of the analytical approach—whether comprehensive proteome analysis, modification-focused studies, or targeted protein quantification—high-quality sample preparation is a prerequisite. This paper systematically examines the sample preparation workflow for protein sequencing, encompassing pretreatment strategies for various sample types, protein extraction.......

• • Principle and Steps of Protein Sequencing

  Proteins play direct and essential roles in biological processes, and their types, abundances, and post-translational modification states directly determine cellular function. In contrast to DNA sequencing, which focuses on the “potential coding information,” protein sequencing aims to uncover the “actual expression and functional states” of proteins. By precisely identifying protein sequences and their modification patterns, researchers can gain comprehensive insights into cellular behavior, disease ......

• • What Software Tools Are Available for Single-Cell Sequencing Analysis?

  Various software tools and algorithms have been developed for the analysis of single-cell sequencing data. These tools enable comprehensive examination of gene expression in individual cells, facilitating the identification of cell types, functional characteristics, and cellular interactions. Below are several commonly used single-cell sequencing analysis tools and their respective functionalities: Seurat Seurat is a widely adopted software suite for single-cell RNA sequencing analysis, offering.......

• • Is 10X Single-Cell Sequencing Limited to Capturing the 3'UTR Region?

  The 10X single-cell sequencing technology is based on GEM (Gel Bead in EMulsion) technology, where individual cells are co-encapsulated with barcoded gel beads in an oil-water emulsion. Each gel bead carries a unique barcode for labeling RNA molecules derived from the same cell. Upon cell lysis within the droplets, the released RNA hybridizes with the barcodes on the beads, forming RNA-barcode complexes. These complexes are subsequently reverse transcribed and amplified to generate cDNA, which is then......

• • How Can T Cell Subpopulations Be Classified from Single-Cell Sequencing Data?

  The classification of T cell subpopulations from single-cell sequencing data can be conducted through the following steps: 1. First, apply quality control to the raw single-cell sequencing data by filtering out low-quality cells and genes, and by correcting for potential noise and batch effects. 2. Next, normalize gene expression levels across cells to minimize technical variability. 3. Subsequently, perform clustering analysis to group cells based on similarities in gene expression profiles. Feature ......

• • What Are the Applications of Single-Cell Sequencing and How Does It Differ from Conventional Gene Sequencing?

  Single-cell sequencing is a recently developed high-throughput technique that enables comprehensive profiling of the genome, transcriptome, or epigenome at the level of individual cells. Its principal applications include the following: Identification and Classification of Cell Types Single-cell sequencing allows for the classification and identification of individual cells within tissues or organs, thereby uncovering the diversity and functional characteristics of distinct cell types. Elucidation of.......

• • How Can Cell Type Annotation Be Performed in Single-Cell Sequencing Without Analyzing Each Cluster Individually?

  When conducting cell type annotation in single-cell sequencing without performing individual analysis for each cluster, the following steps can be followed: Prior to single-cell sequencing, there are typically well-characterized marker genes available for identifying cell types. If such marker genes are not known, they can be identified through literature reviews or database searches.In the absence of individual cluster analysis, differential gene expression analysis can be applied to infer cell types......

• • What Is GEM and What Role Does It Play in 10x Genomics Single-Cell Sequencing?

  In 10x Genomics single-cell sequencing, GEM (Gel Bead-in-Emulsion) is a critical component, consisting of gel beads encapsulated within microdroplets (emulsions). This technology represents a core step in the workflow, enabling the isolation of individual cells and the capture of their mRNA. Each gel bead is preloaded with synthetic oligonucleotide probes, which contain a unique cell barcode, a UMI (Unique Molecular Identifier), and a poly-A tail. When a single cell and a gel bead are co-encapsulated ......