Resources

Proteomics Databases



Metabolomics Databases

• • Phosphorylated Protein-Based Biomarker Discovery: From Identification to Validation

  Within the highly orchestrated regulation of biological systems, protein phosphorylation is among the most prevalent post-translational modifications (PTMs) and serves a dual function as a regulatory switch and a signaling relay node. A growing body of evidence indicates that aberrant phosphorylation patterns are tightly associated with diverse diseases, including cancer, metabolic disorders, and neurodegenerative diseases, positioning phosphorylation as a high-value focal point for biomarker discover......

• • Sample Preparation Guide for Phosphorylated Protein Mass Spectrometry Analysis

  Protein phosphorylation is among the most prevalent and biologically important post-translational modifications (Post-Translational Modification, PTM) and is broadly involved in cellular signal transduction, cell-cycle control, metabolic regulation, and other essential biological processes. Systematic identification and quantitative analysis of phosphorylated proteins have become an active area of modern life science research, with significant applications in oncology, neurodegenerative disorders, and......

• • Principles of Phosphorylated Protein Analysis: Unlocking Cellular Signaling Pathways

  The precise transmission of intracellular and extracellular signals depends on a complex network of regulatory mechanisms. Protein phosphorylation, one of the most critical post-translational modifications, functions as a central molecular regulatory language that governs core biological processes ranging from metabolic regulation to cell division, apoptosis, and migration. Protein phosphorylation is catalyzed by protein kinases, which covalently attach a phosphate group (PO₄³⁻) to specific amino acid......

• • Bioinformatic Analysis Of Phosphorylated Proteomes

  Protein phosphorylation is one of the core regulatory mechanisms of cellular signal transduction and is widely involved in key biological processes such as cell growth, differentiation, apoptosis, metabolism, and disease progression. The acquisition of phosphoproteomic data through high-throughput mass spectrometry has become a routine practice in modern life science research; however, truly elucidating its biological significance relies on systematic and precise bioinformatic analysis of phosphorylat......

• • How to Perform Targeted ER Proteomics Using PRM/SRM?

  The endoplasmic reticulum (ER) is a critical membrane-bound organelle responsible for protein folding, post-translational modification, and intracellular transport, and it plays a central role in cellular stress responses, including the unfolded protein response (UPR). Accumulating evidence indicates that ER-associated proteins are of significant biological relevance in neurodegenerative diseases, tumor immunology, and metabolic disorders. However, comprehensive analysis of the ER proteome remains tec......

• • What Is the Workflow of LC-MS/MS-Based Exosome Proteomics?

  With the rapid expansion of exosome research in translational medicine and biomarker discovery, systematic characterization of the exosomal proteome has become a central focus in biomedical research. LC-MS/MS (liquid chromatography-tandem mass spectrometry)-based exosome proteomics enables high-throughput protein identification and quantification, facilitating the evaluation of disease-associated pathways, intercellular communication networks, and potential diagnostic biomarkers. However, obtaining re......

• • What Roles Does DDA Play in Building Spectral Libraries?

  In proteomics and metabolomics research, data-dependent acquisition (DDA) is one of the key approaches for generating high-quality spectral libraries. Such libraries provide a precise reference foundation for subsequent data-independent acquisition (DIA) analyses. Below, we systematically discuss the role of DDA in spectral library construction from the perspectives of underlying principles, practical value, advantages, and limitations. What Is DDA (Data-Dependent Acquisition)? DDA is a mass spectrom......

• • What Are the Advantages and Limitations of DDA Proteomics?

  Data-dependent acquisition (DDA) is among the most widely used mass spectrometry acquisition modes in proteomics and is broadly applicable to protein identification and quantification in complex biological samples. Its core mechanism involves real-time selection of high-intensity precursor ions for fragmentation, thereby generating high-quality MS/MS spectra. This strategy enables strong proteome coverage depth and high specificity in discovery-oriented studies, and it is particularly well suited for ......

• • What Technologies Are Used for Exosome Proteomic Analysis?

  Exosomes are small membrane-bound vesicles (30-150 nm) secreted by diverse cell types. As key mediators of intercellular information transfer, they participate broadly in processes including tumor metastasis, immune regulation, and neurodegenerative disease. With sustained growth in research interest in exosomes, proteomics has become an increasingly important approach for elucidating exosome function and identifying candidate biomarkers. Nevertheless, exosome proteomic analysis remains technically de......

• • How to Optimize DDA Parameters for High-Quality Protein Identification?

  Data-dependent acquisition (DDA) remains one of the most widely used mass spectrometry acquisition strategies in proteomics. Although data-independent acquisition (DIA) has advanced rapidly in recent years, DDA continues to be essential for exploratory studies, spectral library and database construction, and high-resolution identification-focused proteomic analyses. Achieving high-quality protein identification in DDA experiments critically depends on systematic optimization of acquisition parameters.......