Resources

Proteomics Databases



Metabolomics Databases

• • False Discovery Rate Proteomics

  False Discovery Rate Proteomics refers to the proportion of incorrectly identified proteins among all identifications that are deemed statistically significant during protein identification, typically performed using mass spectrometry. As a statistical measure, False Discovery Rate Proteomics is used to assess the reliability of protein identification results and aims to mitigate the impact of false positives on scientific conclusions. Given the vast amount of data and the intrinsic noise associated with...

• • Methods for C-Terminal Sequence Analysis in the Proteomic Era

  With the advancement of proteomics, the analysis of C-terminal sequences has become increasingly critical. The C-terminus plays a pivotal role in determining protein function, stability, subcellular localization, and interactions, and is frequently regulated by post-translational modifications (PTMs) or specific proteolytic cleavage. However, C-terminal sequencing poses greater technical challenges compared to N-terminal sequencing, primarily due to the absence of a stepwise chemical degradation approach...

• • Data-Dependent Acquisition

  Data-Dependent Acquisition (DDA) is one of the most established and widely adopted data acquisition strategies in proteomics mass spectrometry analysis. In this approach, a full scan (MS1) of all ions present in the sample is first performed, followed by the selection of several precursor ions with the highest intensities for fragmentation scanning (MS2), enabling the derivation of their peptide sequence information for subsequent protein identification and quantification. Data-Dependent Acquisition .......

• • Edman Sequencing: Principles, Methods, and Key Technologies

  Edman degradation is a classical method for sequencing the N-terminus of proteins and is widely utilized in the analysis of primary protein structure. Although mass spectrometry has become the dominant technology in proteomics in recent years, Edman degradation retains unique advantages for the precise determination of N-terminal amino acid sequences. This paper introduces the basic principles and experimental methods of Edman degradation and discusses key strategies for its optimization.

• • Macromolecular Proteomics

  Macromolecular proteomics refers to the comprehensive investigation of macromolecular proteins and their complexes within organisms, particularly large protein assemblies involved in essential biological processes and functions. This field of macromolecular proteomics focuses on identifying, quantifying, and elucidating the interaction networks formed by these macromolecular proteins, how such interactions contribute to their biological functions, and how these proteins participate in a range of cellular...

• • Proteomics Analysis Workflow

  Proteomics is the scientific study of the structure and function of all proteins within a biological system. Proteomics analysis serves as a comprehensive approach to understanding these proteins in both qualitative and quantitative dimensions. The objective of proteomics analysis is to elucidate how protein expression, function, and interactions influence the state and dynamic changes of biological systems. A typical proteomics analysis workflow consists of the following key steps:

• • Proteomics Sequencing Analysis

  Proteomics sequencing analysis is a comprehensive technique used to investigate the expression, function, and interactions of the complete set of proteins within a biological sample. As a core methodology in modern molecular biology, proteomics sequencing analysis enables researchers to gain deeper insights into the proteomic composition of cells and the biological processes in which these proteins participate. This process involves the extraction, separation, identification, and quantitative measurement...

• • Determination of Protein Hydrophobicity

  The determination of protein hydrophobicity is an experimental approach used to analyze and quantify hydrophobic regions within protein molecules. Hydrophobicity refers to the tendency of certain amino acid residues in proteins to avoid interaction with water molecules. This property plays a critical role in protein structure formation and biological function, as it facilitates correct protein folding in aqueous environments and influences protein–protein interactions. Importance of Hydrophobicity..........

• • Analysis of Protein Secondary Structure

  Secondary structure analysis of proteins refers to the local spatial arrangement of amino acid residues within the protein chain. It consists of structural motifs such as α-helices, β-sheets, β-turns, and random coils. Techniques for Analyzing Protein Secondary Structure 1. Circular Dichroism (CD) Circular dichroism is a widely used technique for secondary structure analysis of proteins. It is based on the characteristic differential absorption of circularly polarized light by various secondary structural..

• • Introduction to Amino Acid Sequence Homology Alignment Analysis

  Amino acid sequence homology alignment analysis is a widely used approach in molecular biology for comparing the amino acid sequences of two or more proteins. This analysis provides insights into the structural, functional, and evolutionary relationships among members of a protein family. The fundamental steps involved in conducting amino acid sequence homology alignment analysis are as follows: Tool Selection Widely used tools for amino acid sequence alignment include BLAST (particularly BLASTP), .........