Resources

Proteomics Databases



Metabolomics Databases

• • Troubleshooting Common Issues in iTRAQ Proteomics Experiments

  iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) is widely employed in quantitative proteomics and enables the relative quantification of up to 8 or 16 samples within a single mass spectrometry run. This capability makes it particularly suitable for comparative analyses involving multiple samples, such as clinical cohorts, disease models, and studies of drug mechanisms of action. Nevertheless, the high throughput and sensitivity of iTRAQ-based workflows place stringent demands on experimen......

• • What Is PPI Prediction?

  Proteins serve as the primary functional units within cells. However, individual proteins rarely operate in isolation; instead, most biological processes are executed through coordinated protein-protein interactions (PPIs). These interactions are fundamental to diverse biological processes, including signal transduction, metabolic regulation, and immune responses, and they also play pivotal roles in the initiation and progression of diseases. Comprehensive experimental identification of all possible P......

• • Principles of iTRAQ-Based Quantitative Proteomics and Reporter Ion Analysis

  Accurate and high-throughput protein quantification across multiple samples is a fundamental requirement in modern proteomics for elucidating biological variability. Since its introduction in 2004, iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) has become a widely adopted strategy for multiplexed quantitative proteomic analysis. By combining isobaric isotope labeling with mass spectrometry, iTRAQ enables the simultaneous quantification of up to eight samples (iTRAQ 8-plex), offering subs......

• • How to Build and Analyze Protein-Protein Interaction Networks?

  Within cells, protein-protein interactions (PPIs) function as central hubs that coordinate diverse biological processes. Proteins rarely act in isolation; instead, through binding, assembly, and regulatory interactions with other proteins, they form highly complex biological networks. A protein-protein interaction network represents these molecular relationships in a systematic and graphical manner, in which nodes correspond to proteins and edges denote their interactions. Such networks not only facil......

• • Membrane Proteomics in Cell Communication

  In multicellular organisms, intercellular communication gives rise to complex signaling networks that regulate essential biological processes, including proliferation, differentiation, and immune responses. Membrane proteins residing on the plasma membrane serve as central nodes within these networks by mediating extracellular signal reception, ligand recognition, and activation of downstream signaling pathways. Membrane proteins encompass a wide range of functional classes, such as G protein-coupled ......

• • What Are Protein-Protein Interactions？

  Protein-protein interactions (PPIs) refer to the processes by which two or more protein molecules associate to form functional complexes or regulate one another through non-covalent forces, including hydrogen bonding, hydrophobic interactions, and electrostatic forces. PPIs are ubiquitous within cells and underpin a wide range of essential biological processes. From signal transduction and cell cycle control to metabolic pathways and immune responses, virtually all cellular activities rely on precisel......

• • How to Analyze Protein–Protein Interactions?

  Protein-protein interactions (PPIs) represent fundamental mechanisms underlying cellular function and biological processes. They play essential roles in signal transduction, metabolic regulation, and gene expression. Investigating PPIs facilitates the elucidation of disease mechanisms, the identification of therapeutic targets, and the construction of regulatory networks. With advances in mass spectrometry technologies, PPI detection has progressed from conventional validation approaches to high-throu......

• • What Is Label-Free Quantification in Proteomics?

  Quantitative analysis is a fundamental approach in proteomics research for elucidating dynamic biological processes, identifying differentially expressed proteins, and investigating disease mechanisms. Compared with labeling-based quantification strategies, such as SILAC, iTRAQ, and TMT, label-free quantification (LFQ) has been increasingly adopted in recent years owing to its operational simplicity, broad applicability, and relatively low cost. In particular, LFQ offers distinct advantages for the an......

• • The Role of Phosphoproteomics in Multi-Omics Integration

  In the post-genomic era, life science research is transitioning from isolated, single-layer investigations toward comprehensive systems-level integration. Technologies such as transcriptomics, proteomics, metabolomics, epigenomics, and single-cell omics each provide snapshots of biological systems at distinct molecular layers. However, only through multi-omics integration can the dynamic and coordinated nature of biological processes be fully reconstructed. Within this integrative framework, phosphopr......

• • Common Pitfalls in Phosphoproteomics Experiments And How to Avoid Them

  Phosphoproteomics is a critical research field dedicated to the systematic investigation of protein phosphorylation and its functional roles in cellular biology. Phosphorylation, dynamically regulated by protein kinases and phosphatases, modulates protein activity, subcellular localization, stability, and molecular interactions. This post-translational modification plays a central role in a wide range of biological processes, including signal transduction, cell cycle control, metabolic regulation, gen......