Resources

Proteomics Databases



Metabolomics Databases

• • What Is Label-Free Analysis?

  In multi-omics research areas such as proteomics and metabolomics, quantitative analysis is fundamental to the interpretation of biological variation. With the rapid advancement of mass spectrometry technologies, label-free analysis, commonly referred to as Label-Free Quantification (LFQ), has increasingly been adopted as a primary strategy for quantitative proteomic studies owing to its high throughput, cost efficiency, and streamlined workflow. Label-free analysis enables the relative quantification......

• • What Is Protein-Protein Interaction (PPI) Network Visualization? Recommended Tools and Software

  Protein-protein interaction (PPI) networks represent a fundamental analytical framework for elucidating cellular functions, signaling pathway regulation, and disease mechanisms. Protein-protein interaction visualization involves the graphical representation of complex interaction relationships, enabling researchers to intuitively identify key proteins, functional modules, and network topological features, thereby facilitating biological interpretation and discovery. What Is Protein-Protein Interactio......

• • What Is High-Throughput PPI Screening and What Are the Cutting-Edge Technologies?

  High-throughput protein-protein interaction (PPI) screening refers to a set of methodologies that leverage automation and large-scale experimental platforms to systematically detect and analyze interactions among large numbers of proteins within a limited time frame. This strategy is essential for protein function annotation, signaling pathway elucidation, investigation of disease mechanisms, and drug target discovery, and represents a key enabling tool for deciphering cellular networks and biological......

• • How to Process Shotgun Proteomics Data in Multi-Omics Integration?

  In multi-omics integration analyses, appropriate processing of Shotgun proteomics data is of critical importance. Proteomics data are inherently semi-quantitative, characterized by a high proportion of missing values and substantial variability across samples and analytical platforms. Inadequate data handling can therefore substantially impair integrative analyses with other omics layers, including genomics, transcriptomics, and metabolomics. Shotgun Proteomics: Data Characteristics and Challenges Sh......

• • Disulfide Bonds in Proteins: Formation, Function, and Analytical Methods

  Within the precise architecture of biomolecules, disulfide bonds are often overlooked yet fundamentally important chemical linkages. They are formed through covalent bonding between the sulfur atoms of two cysteine residues and can significantly enhance the structural stability and functional robustness of proteins. In particular, in key biomolecules such as secretory proteins, therapeutic antibodies, and biological enzymes, disulfide bonds frequently serve as molecular locks that ensure correct prote......

• • Membrane Protein–Molecule Interaction Analysis

  Membrane proteins account for nearly 30% of all proteins encoded by the human genome, and they constitute more than 60% of current drug targets. They are not only involved in essential physiological processes such as substance transport, signal transduction, and cell recognition, but also serve as key nodes in a wide range of diseases, including viral invasion, cancer metastasis, and neurodegenerative disorders. The interactions between membrane proteins and ligands, signaling molecules, and other pro......

• • How to Achieve Quantitative Mapping of Protein Localization in Tissues?

  Quantitative mapping of protein localization represents a critical foundation for understanding protein function, regulatory mechanisms, and cellular behavior under pathological conditions. With recent advances in mass spectrometry (MS) technologies, it has become feasible to perform high-throughput and quantitative analyses of protein localization at the subcellular level. Core Significance of Quantitative Mapping of Protein Localization Cellular function critically depends on accurate protein local......

• • Comprehensive Guide to Protein Glycosylation Analysis (LC‑MS/MS Workflow)

  Protein glycosylation is a fundamental post-translational modification (PTM) that is widely distributed in eukaryotic cells. It plays critical roles in regulating protein folding, stability, subcellular localization, and molecular interactions. Glycosylation has become increasingly important in biopharmaceutical development, cancer biomarker discovery, and vaccine research. Compared with other common PTMs such as phosphorylation and acetylation, glycosylation exhibits pronounced structural diversity, ......

• • What Are Targeted Post-Translational Modifications?

  Post-translational modifications (PTMs) are chemical alterations that occur to proteins after translation, including phosphorylation, acetylation, ubiquitination, and others. These modifications not only regulate protein activity, subcellular localization, and stability, but also exert substantial influence on signaling pathways, cellular differentiation, and disease processes. In proteomics, targeted post-translational modifications analysis refers to the selection of specific PTM classes and defined......

• • How to Apply Targeted Mass Spectrometry for PTM Verification?

  Protein post-translational modifications (PTMs) constitute fundamental regulatory mechanisms underlying essential biological processes, including cell fate determination, signal transduction, and metabolic homeostasis. Common PTMs include phosphorylation, acetylation, ubiquitination, and methylation. Although high-throughput mass spectrometry approaches, such as data-dependent acquisition (DDA) and data-independent acquisition (DIA), are widely used for the initial discovery of PTM sites, subsequent v......