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Proteomics Databases



Metabolomics Databases

• • What Is Histone Phosphorylation?

  In eukaryotic cells, DNA is not present as naked molecules but is wrapped around histone octamers to form nucleosomes, the fundamental units of chromatin. Histone post-translational modifications (PTMs), including phosphorylation, methylation, and acetylation, represent key regulatory mechanisms governing chromatin structure and function. Histone phosphorylation, characterized by its highly dynamic and signal-dependent nature, plays essential roles in transcriptional activation, DNA damage response, a......

• • How to Analyze Histone Phosphorylation Using Mass Spectrometry?

  Histone phosphorylation is a critical post-translational modification (PTM) in epigenetic research, playing essential roles in regulating chromatin structure, gene expression, DNA damage repair, and the cell cycle. Mass spectrometry (MS) is among the most sensitive and high-throughput techniques for studying histone modifications, enabling precise identification and quantification of phosphorylation sites. Detailed Workflow for Mass Spectrometry Analysis of Histone Phosphorylation 1. Sample Preparati......

• • Protein-Protein Interactions: Analytical Techniques and Biological Significance

  In the cellular microenvironment, proteins rarely act in isolation; instead, they collectively govern a wide range of biological processes through dynamic and intricate interaction networks, termed protein-protein interactions (Protein-Protein Interactions, PPIs). From signal transduction and metabolic regulation to cell-cycle control and disease pathogenesis, PPIs constitute a foundational mode of molecular organization and regulation in living systems. Accordingly, systematic interrogation of PPI ne......

• • What Are Common Pitfalls in Interpreting Acylation Proteomics Data?

  Protein acylation is one of the major areas of post-translational modification (PTM) research in recent years. It encompasses multiple forms, including acetylation, propionylation, and butyrylation, and plays critical roles in regulating chromatin architecture, metabolic pathways, and signal transduction. With advances in high-resolution mass spectrometry, researchers are now able to systematically identify and quantify acylation sites at the proteome-wide level. However, during data interpretation, s......

• • Introduction to TMT Reporter Ions and Mass Spectrometry Analysis

  In large-scale quantitative proteomic analysis, TMT (Tandem Mass Tag) labeling technology has rapidly become a mainstream approach because of its capacity for multiplexed parallel sample analysis and high quantitative precision. Particularly in high-throughput applications such as multi-omics research, disease mechanism studies, and drug target screening, TMT provides researchers with powerful data integration capabilities. What Is TMT? The Technical Core of Integrated Quantitative Tags TMT is a clas......

• • Structure, Functions, and Enzymes in Protein Ubiquitination

  In eukaryotic cells, protein post-translational modifications (PTMs) represent a fundamental mechanism for the precise regulation of cellular processes. Among these modifications, ubiquitination is one of the most important regulatory strategies. By covalently conjugating the small protein ubiquitin to target substrates, ubiquitination enables precise control over protein fate. Beyond regulating protein stability, ubiquitination participates in signal transduction, DNA damage response and repair, immu......

• • Which Factors Affect the Success Rate of Solid-Phase Peptide Synthesis?

  Solid-phase peptide synthesis (SPPS) is a key methodology in modern peptide production and is widely applied in antibody epitope mapping, enzymatic mechanism studies, vaccine development, drug discovery, and protein function analysis. However, in practical laboratory settings, researchers frequently observe that peptide sequences that appear theoretically feasible may encounter various challenges during synthesis, including low coupling efficiency, significant impurity formation, poor product purity, ......

• • One-Stop Immunopeptidomics Service Solution

  In cutting-edge studies such as cancer immunotherapy, personalized vaccine development, and the investigation of autoimmune disease mechanisms, immunopeptidomics serves as a key technology bridging basic immunology research and clinical translation. By analyzing antigenic peptides presented by major histocompatibility complex (MHC) molecules using high-resolution mass spectrometry, immunopeptidomics enables researchers to uncover the molecular mechanisms underlying intracellular antigen processing and......

• • The Role of Data-Dependent Acquisition (DDA) in Shotgun Proteomics

  In proteomics, shotgun proteomics has become a mainstream approach for global proteome identification by leveraging high-throughput mass spectrometric analysis. Among the available acquisition strategies, data-dependent acquisition (DDA) was one of the earliest and most widely adopted modes and continues to play a central role in novel protein identification and exploratory studies. This article systematically examines the working principles, technical advantages, limitations, and experimental optimiz......

• • Applications of Shotgun Proteomics in Biomarker Discovery

  Biomarkers are essential tools for early diagnosis, disease stratification, and personalized therapy. With the rapid advancement of mass spectrometry technologies, proteomics has become an important approach for biomarker discovery. Among the available strategies, shotgun proteomics has demonstrated substantial potential for biomarker screening in complex samples owing to its high throughput, unbiased profiling capability, and broad proteome coverage. Overview of Shotgun Proteomics 1. Technical Princ......