Resources

Proteomics Databases



Metabolomics Databases

• • Untargeted Metabolomics Analysis: Principles, Applications, and Workflow

  In the context of the continuous evolution of systems biology, metabolomics has emerged as a key discipline for interpreting dynamic changes in biological processes. Among its subfields, untargeted metabolomics plays a central role in both basic research and translational medicine due to its capability to perform global, unbiased profiling of metabolites without predefined targets. Compared with targeted approaches, untargeted strategies emphasize discovery and enable the capture of potentially critic......

• • How to Isolate and Enrich Exosomes for Proteomics Analysis?

  In life science research, exosomes serve as important mediators of intercellular communication and have attracted considerable attention as sources of disease biomarkers, drug delivery vehicles, and tools for basic biological research due to their cargo of proteins, nucleic acids, and lipids. For proteomics analysis, the isolation of exosomes with high purity and effective enrichment is a critical prerequisite. Overview of Exosomes and Their Proteomic Value Exosomes are nanoscale vesicles with diamet......

• • How to Perform Golgi Quantitative Proteomics Analysis?

  The Golgi apparatus is a key membranous organelle responsible for protein modification, sorting, and trafficking, serving as an indispensable central hub for maintaining normal cellular functions. With the rapid advancement of proteomics technologies, researchers can not only identify the protein composition of the Golgi apparatus but also quantitatively characterize its dynamic alterations under different physiological or pathological conditions. Golgi quantitative proteomics provides a systematic fr......

• • 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......

• • 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......

• • 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......

• • 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......

• • 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......

• • 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......

• • 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......