Resources

Proteomics Databases



Metabolomics Databases

• • Introduction to De Novo Sequencing: Principles, Workflow, and Applications

  What Is De Novo Sequencing? De Novo sequencing refers to a method that infers the sequences of biological macromolecules (such as proteins, DNA, or RNA) directly from experimental data, without relying on any known reference sequences or databases. In the field of proteomics, it specifically denotes the process of acquiring MS/MS fragment data of enzymatically digested peptides using high-resolution mass spectrometry, followed by algorithmic analysis of the fragment ions to reconstruct the amino acid.......

• • De Novo Monoclonal Antibody Sequencing: Technical Analysis, Advantages, and Applications

  What Is De Novo Monoclonal Antibody Sequencing? De Novo antibody sequencing is a technique that reconstructs complete monoclonal antibody sequences directly from protein samples, without relying on any reference gene or sequence databases. Using high-resolution liquid chromatography–tandem mass spectrometry (LC-MS/MS), enzymatically digested antibody peptides are analyzed, and algorithms are applied to interpret MS/MS fragment spectra and progressively deduce the corresponding amino acid sequences.

• • Protein Sequence Analysis for Drug Discovery

  What Is Protein Sequence Analysis? Protein sequence analysis involves the systematic comparison, annotation, structural modeling, and functional prediction of amino acid sequences and their characteristic features, such as signal peptides, transmembrane domains, and functional sites. This process typically incorporates several categories of analytical approaches: Sequence alignment (e.g., BLAST, Clustal Omega): used to identify sequences homologous to known proteins, enabling inference of potential ........

• • Amino Acid Sequence Analysis: Techniques and Challenges

  The amino acid sequence forms the foundation of protein function and serves as a crucial entry point for understanding regulatory mechanisms in organisms, disease progression, and the action of molecular drugs. With the rapid advances in proteomics, amino acid sequence analysis has evolved from traditional chemical determination methods to high-throughput, modifiable, and multidimensional data integration approaches, establishing itself as a vital link between genomics and phenotypic function. This paper...

• • 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......