Resources

Proteomics Databases



Metabolomics Databases

• • Protein Motif Analysis

  Protein motif analysis is an important task in bioinformatics, aiming to identify short sequence patterns in protein sequences that have specific functional or structural significance. These short sequences, often referred to as motifs or functional sites, are crucial for understanding the biological functions of proteins, protein-protein interactions, and regulatory mechanisms.

• • Methods and Applications for Protein Sequence Determination

  Protein sequencing is the process of determining the exact order of amino acids in a protein. It can analyze amino acid sequences, confirm protein structure and function, identify new protein biomarkers and drug targets, construct phylogenetic trees to understand evolutionary relationships, and identify orthologous and paralogous proteins.

• • How to Analyze Protein Multiple Sequence Alignment Results

  Multiple Sequence Alignment (MSA) is a technique to arrange three or more protein sequences in order to identify their similarities and differences to the maximum extent. Analyzing the results of protein MSA can reveal evolutionary relationships, structural domains, functional sites, and other important biological information among protein family members.

• • Overview of Single-Cell Protein Sequencing

  Single-cell proteomics is a method for studying the protein expression and regulation of individual cells. This technique is crucial for understanding cellular heterogeneity, revealing how different proteins interact within cells, and how they respond to external stimuli. Single-cell proteomics provides more detailed and accurate information because it directly measures the functional unit of cells - proteins.

• • De Novo Protein Sequencing: Basic Concepts and Applications

  De novo protein sequencing refers to determining the amino acid sequence of a protein without relying on known protein databases. Unlike other analysis methods that depend on known protein sequences or mass spectrometry databases, de novo sequencing directly analyzes peptide fragments using tandem mass spectrometry. Therefore, peptides that are not included in protein databases, protein sequences from new species, and protein sequences that have not been sequenced in the genome can all be analyzed.

• • N-Terminal Sequencing: Methods and Applications

  N-terminal sequencing is a technique used to determine the amino acid sequence of the N-terminal (amino-terminal) of a protein or peptide. This technique is useful in the field of biochemistry and molecular biology, particularly when researchers want to confirm the starting position of a protein or determine if a specific protein has undergone a particular modification.

• • Using Mass Spectrometry to Determine Unknown Protein Sequences

  Unknown proteins refer to those that exist in organisms but whose functions, structures, or affiliations have not been clearly identified. The identification of unknown proteins faces challenges due to the lack of corresponding data support. The emergence of mass spectrometry technology provides a powerful means for the identification of unknown proteins. De novo sequencing based on mass spectrometry is different from database-dependent searching.

• • Using Tandem Mass Spectrometry for Amino Acid Sequence Analysis

  Tandem Mass Spectrometry (MS/MS) is the main technique used for protein and peptide amino acid sequence analysis. This method allows researchers to determine the amino acid composition of small peptides and further identify the identity of proteins. The basic process of determining amino acid sequences using MS/MS is as follows.

• • Edman Degradation: Identifying Amino Acid Sequences for Peptides

  Edman degradation is a chemical method used to determine the N-terminal amino acid sequence of peptides, such as proteins and peptide segments, in a sequential manner. This method was developed by Pehr Edman in the 1950s.

• • Amino Acid Sequence Analysis and Its Applications

  Amino acid sequence analysis is a fundamental field in protein research that involves the identification and interpretation of the linear sequence of amino acids in proteins. The amino acid sequence of a protein can provide important information about its structure, function, and evolution. Here are the applications of amino acid sequence analysis in protein research.