Resources

Proteomics Databases



Metabolomics Databases

• • LC-MS/MS-Based Quantitative Ubiquitinomics

  Ubiquitination is a critical post-translational protein modification involved in cellular regulation and participates in numerous essential physiological processes, including protein degradation, signal transduction, cell cycle control, and DNA damage response. However, the accurate and sensitive quantification of ubiquitinated proteins in complex biological systems remains highly challenging. LC-MS/MS (liquid chromatography–tandem mass spectrometry) has become a core analytical platform for the quant......

• • Role of Protein Ubiquitination in Cellular Signaling Pathways

  Within the highly complex cellular regulatory network, protein ubiquitination is not only a fundamental mechanism for maintaining protein homeostasis but also serves as a precise regulatory system in diverse signaling pathways. By covalently attaching one or more ubiquitin molecules to specific substrate proteins, ubiquitination determines the fate of target proteins, whether they undergo activation, inhibition, subcellular relocalization, or complete proteasomal degradation. Particularly in cellular ......

• • Impact of Ubiquitination on Protein Degradation Pathways

  Proteins within cells are not permanent entities after synthesis. Once they have fulfilled their biological functions, they must be promptly recognized and degraded to maintain protein homeostasis and intracellular equilibrium. Cellular proteins are constantly maintained in a dynamic balance between synthesis and degradation, a process that is essential for sustaining proteostasis and normal cellular function. As a highly conserved post-translational modification, ubiquitination precisely labels prote......

• • Mass Spectrometry-Based Subcellular Proteomics: Advantages, Challenges, and Applications

  Proteomics provides a global overview of protein expression at the whole-cell level; however, it lacks the ability to resolve the precise intracellular localization of proteins. In fact, protein function is tightly associated with its subcellular localization. Organelles such as mitochondria, endoplasmic reticulum, Golgi apparatus, and nucleus each perform distinct biological functions, and protein mislocalization often indicates cellular dysfunction and even disease onset. Subcellular proteomics, par......

• • Why Is Shotgun Proteomics the Preferred Strategy for Comprehensive Proteome Profiling?

  In proteomics research, the efficient characterization of protein composition and dynamic changes in complex biological samples remains a fundamental challenge. Owing to its high throughput, broad proteome coverage, and superior analytical sensitivity, shotgun proteomics has emerged as the most widely adopted strategy for comprehensive proteome profiling. It has been extensively applied in studies of disease mechanisms, biomarker discovery, and integrative multi-omics analyses. What Is Shotgun Proteo......

• • How to Perform Qualitative Shotgun Protein Identification Using DDA Mode?

  In life science research, proteins serve as a central link between genomic information and cellular functions. To systematically identify and characterize the full complement of proteins in biological samples, shotgun protein identification has become one of the most widely adopted strategies in proteomics. This approach involves the direct introduction of enzymatically digested peptide mixtures into a mass spectrometry system, coupled with data-dependent acquisition (DDA) for high-throughput data col......

• • Comprehensive Guide to 4D Label-Free Quantitative Proteomics Workflow

  In the post-genomic era, proteomics has emerged as a pivotal approach for elucidating biological processes, uncovering disease mechanisms, and discovering biomarkers. Specifically, label-free quantitative proteomics (LFQ) has gained widespread application in both basic and translational biomedical research due to its high throughput and the advantage of eliminating the need for costly labeling reagents. With the rapid advancement of mass spectrometry technologies, 4D-based label-free quantification pl......

• • Principles of Top-Down Proteomics

  Top-Down proteomics is a mass spectrometry-based analytical strategy that directly analyzes intact protein molecules. Its core principle is to subject proteins to mass spectrometric fragmentation and sequencing without prior enzymatic digestion, thereby enabling accurate protein identification, detection of post-translational modifications (PTMs), and recognition of protein variants. Compared with Bottom-Up proteomics, the Top-Down approach allows more comprehensive protein identification and structur......

• • How to Integrate Shotgun Proteomics and Targeted Proteomics for Joint Analysis?

  In life science research, proteins are central executors of biological function. Their expression levels, modification states, and interaction networks often directly shape cellular fate and disease progression. To comprehensively characterize these dynamic changes, a range of mass spectrometry–based approaches has been developed. Among the most widely used are Shotgun proteomics (data-dependent acquisition, DDA) and targeted proteomics (e.g., PRM/MRM). Nevertheless, each approach has notable limitati......

• • Histone Modifications in Health and Disease

  The Human Genome Project delineated the human genetic blueprint; however, DNA sequence information alone is insufficient to account for the complexity of cell fate determination. Cells that share an identical genome can nonetheless perform markedly distinct functions across tissues, a divergence that is largely attributable to epigenetic regulation. Within this regulatory framework, histone modifications constitute a central and highly dynamic mechanism that shapes gene expression, chromatin organizat......