Resources

Proteomics Databases



Metabolomics Databases

• • Protein-Protein Interaction Network Analysis and Strategic Approaches

  Within the highly organized molecular environment of the cell, proteins do not function in isolation. Instead, they coordinate a wide range of biological processes through protein-protein interactions (PPIs), including signal transduction, metabolic regulation, cell cycle control, and immune responses. Comprehensive analysis of protein-protein interaction networks not only enhances our understanding of the systemic organization and complexity of biological systems, but also provides a robust foundatio......

• • How to Optimize Sample Preparation and Digestion in Shotgun Proteomics?

  In shotgun proteomics, while mass spectrometer performance is essential, upstream sample preparation and proteolytic digestion strategies are often the primary determinants of overall experimental quality. This is particularly critical when handling complex and highly heterogeneous biological samples (e.g., tissues, biofluids, and clinical specimens), where appropriate pretreatment directly impacts protein extraction efficiency, peptide coverage, and the total number of protein identifications. Sampl......

• • In Which Biological Samples Can Acylation Proteomics Be Applied?

  Acylation proteomics, an important branch of epigenetics and protein post-translational modification (PTM) research, has rapidly advanced with the development of mass spectrometry technologies. It enables the systematic characterization of diverse acyl modifications on proteins, including acetylation, propionylation, butyrylation, and succinylation. Investigation of these modifications provides critical insights into cellular metabolic states, signaling pathway regulation, and disease mechanisms. Howe......

• • LC-MS vs GC-MS for Untargeted Metabolomics: Which to Choose?

  In metabolomics research, untargeted metabolomics has emerged as a powerful approach for biomarker discovery, metabolic pathway elucidation, and the investigation of disease mechanisms. Among the available analytical platforms, mass spectrometry-based techniques are central, with LC-MS (liquid chromatography-mass spectrometry) and GC-MS (gas chromatography-mass spectrometry) representing the two most widely used strategies. A key practical question faced by researchers is how to select between LC-MS a......

• • MS-Based Quantitative Acetylproteomics: Workflow and Data Interpretation Guide

  Protein acetylation is among the most prevalent post-translational modifications (PTMs) and regulates key biological processes, including gene expression, metabolic pathways, and the cell cycle. In recent years, acetylation research has progressed from the "discovery stage" of modification sites to the "quantitative stage" focused on mechanistic understanding. Mass spectrometry (MS)-based quantitative acetylproteomics has become a central tool for elucidating the dynamic regulation of acetylation. Com......

• • Top 5 Phosphopeptide Enrichment Strategies Compared: IMAC, TiO₂, and More

  Protein phosphorylation is one of the most prevalent post-translational modifications and plays a central role in biological processes such as signal transduction, cell cycle regulation, and apoptosis. Due to the extremely low abundance of phosphopeptides in complex proteomes (typically <1%), comprehensive coverage is difficult to achieve by direct LC-MS/MS analysis. Therefore, effective phosphopeptide enrichment prior to mass spectrometry is a critical step for elucidating phosphorylation-mediated re......

• • New Trends in Target Validation: Decoding Competitive ABPP

  In drug discovery and development, target screening does not equate to target confirmation. Even if a candidate protein is repeatedly identified through differential expression analysis or pathway enrichment analysis, this does not necessarily mean that it is a direct drug target. The key questions are: Is this protein a direct target of the drug? Does covalent binding occur? Is the inhibition selective? Are there potential off-target effects? These questions are difficult to address directly using c......

• • How Does Untargeted Metabolomics Contribute to Biomarker Discovery?

  In the context of the continuous advancement of disease research and precision medicine, biomarkers have emerged as a central focus in life sciences. They are indispensable for early tumor diagnosis, evaluation of drug efficacy, as well as disease classification and prognostic assessment. However, biomarker discovery has traditionally relied on single biomarkers or hypothesis-driven approaches, which often fail to comprehensively capture the complexity of physiological and pathological processes. In r......

• • Advantages and Disadvantages of Targeted Metabolomics

  Targeted metabolomics, as a core strategy in metabolomics research, has been widely applied in life sciences, biomedical research, and clinical translation owing to its high sensitivity, specificity, and reproducibility. Nevertheless, like any analytical approach, it possesses inherent strengths as well as certain limitations. Major Advantages of Targeted Metabolomics 1. High Sensitivity and Specificity Targeted metabolomics typically utilizes multiple reaction monitoring (MRM) or selected reaction m......

• • Targeted Metabolomics Workflow Using LC-MS/MS

  With the continuous advancement of life sciences, metabolomics has emerged as a critical tool for elucidating dynamic changes in biological systems and underlying disease mechanisms. Among various approaches, targeted metabolomics based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) is widely applied in disease research, drug development, and nutritional metabolism studies due to its high sensitivity, high specificity, and robust quantitative capability. This article systematically outli......