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Proteomics Databases



Metabolomics Databases

• • 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 ......

• • How Can The Content And Structure Of Plant Polysaccharides Be Determined Directly By Mass Spectrometry?

  Content Determination: The quantification of polysaccharides was performed using liquid chromatography-mass spectrometry (LC-MS). First, polysaccharides in the sample were separated by liquid chromatography (LC). Subsequently, the separated polysaccharides entered the mass spectrometer, where the molecules were ionized to form ions. By measuring the mass-to-charge ratios (m/z) of the polysaccharide ions, the concentration of polysaccharides was quantified. This quantification generally requires comparison..

• • Why Do Samples Form a Continuous Line During Protein Electrophoresis in WB

  During WB experiments, the appearance of a continuous line of the sample on the membrane is due to the accumulation of proteins during electrophoresis separation and transfer, as well as the continuous distribution of proteins. This phenomenon may affect the interpretation of experimental results, so it is essential to optimize the sample loading and electrophoresis conditions to achieve optimal protein separation and transfer efficiency on both the gel and the membrane. 1. Accumulation Effect During ......