Resources

Proteomics Databases



Metabolomics Databases

• • 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.......

• • What Is Exosome Proteomics?

  Exosomal proteomics has emerged in recent years as an active area of life science research, with growing importance in research frontiers such as cancer biomarker discovery, studies of neurological disorders, and elucidation of immune regulatory mechanisms. Exosomes are membrane-bound extracellular vesicles released into the extracellular space upon fusion of multivesicular bodies with the plasma membrane, typically ranging from 30 to 150 nm in diameter. Nearly all cell types can secrete exosomes, whi......

• • Phosphoproteomics Analysis in Cancer Research

  Protein phosphorylation is among the most prevalent post-translational modifications and plays essential roles in regulating the cell cycle, apoptosis, metabolic reprogramming, and tumor metastasis. Systematic interrogation of the phosphoproteome enables researchers to capture a global view of dysregulated kinase activity and signaling-network rewiring in cancer cells. Phosphorylation occurs primarily on serine (Ser), threonine (Thr), and tyrosine (Tyr) residues, with kinases catalyzing phosphate addi......

• • From Discovery to Biomarkers: Translating Phosphoproteomics into Clinical Applications

  Protein phosphorylation represents a central regulatory mechanism in cellular signal transduction, governing fundamental biological processes including cell proliferation, differentiation, and apoptosis. Aberrant phosphorylation events have been extensively implicated in cancer, autoimmune disorders, neurodegenerative diseases, and other pathological conditions. Accordingly, systematic characterization of the dynamic landscape of phosphorylation modifications not only advances our understanding of dis......

• • SILAC vs. TMT: Comparative Analysis in Quantitative Subcellular Proteomics

  Cells are highly compartmentalized systems in which distinct subcellular organelles, such as the nucleus, mitochondria, endoplasmic reticulum, and Golgi apparatus, perform specialized biological functions. Subcellular proteomics focuses on elucidating the spatial distribution and dynamic behavior of proteins within the cellular environment and plays a critical role in advancing our understanding of signal transduction, metabolic reprogramming, disease pathogenesis, and drug target discovery. Achieving......

• • Step-by-Step LC-MS/MS Workflow for Immunopeptidomics Analysis

  As immunotherapy has become a major focus for intervention research in cancer, viral infection, and autoimmune disease, our understanding of antigen presentation has continued to deepen. In this context, immunopeptidomics has emerged as a critical bridge between molecular omics and immunology. The overarching aim of this approach is to comprehensively characterize the repertoire of peptides presented by major histocompatibility complex (MHC) molecules at the cell surface, peptides that can be directly......

• • The Role of Immunopeptidomics in Cancer Vaccine Development

  In cancer immunotherapy, cancer vaccines represent an important strategy for mobilizing a patient’s own immune system to eliminate tumor cells, and the field is experiencing renewed momentum. The central task in cancer vaccine development is to identify and deliver tumor-specific antigens capable of activating cytotoxic T lymphocytes (CTLs), thereby enabling precise cytotoxic killing of malignant cells. A major bottleneck, however, is the prioritization of antigens that are truly immunogenic and are a......